TY  - JOUR
AB  - Comparative studies of microbial communities occupying different body sites in wild vertebrates are scarce, but they are crucial for advancing our understanding of the ecological and evolutionary factors shaping animal microbiomes. We therefore used a natural experiment comprising mother-offspring pairs from two adjacent Antarctic fur seal breeding colonies that differ in social density to investigate differences between skin and gut microbial communities in relation to host-specific and environmental factors. Using 16S rRNA amplicon sequencing, we uncovered a strong influence of colony on the diversity and composition of skin but not gut microbial communities. Specifically, we observed a suppressive effect of high social density on skin microbial alpha diversity as well as an overabundance of phyla associated with diseases and bite wounds in the high-density colony. Our findings suggest that skin microbial communities may be more sensitive to external factors, whereas gut communities are more tightly regulated by the host. Overall, this study highlights the importance of considering multiple body sites and their distinct microbial communities to develop a more comprehensive understanding of the factors shaping microbial diversity and composition in marine mammals.
AU  - Botsidou, P.
AU  - Schloter, M.
AU  - Maraci, Ö.*
AU  - Gschwendtner, S.
AU  - Nagel, R.*
AU  - Forcada, J.*
AU  - Hoffman, J.I.*
C1  - 75159
C2  - 57812
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Skin, but not gut, microbial communities vary with social density in Antarctic fur seals.
JO  - Front. Microbiol.
VL  - 16
PB  - Frontiers Media Sa
PY  - 2025
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - INTRODUCTION: The global decline in biodiversity and insect populations highlights the urgent need to conserve ecosystem functions, such as plant pollination by solitary bees. Human activities, particularly agricultural intensification, pose significant threats to these essential services. Changes in land use alter resource and nest site availability, pesticide exposure and other factors impacting the richness, diversity, and health of solitary bee species. In this study, we investigated yet another facet currently less well investigated in such context: Microbial communities associated with wild bees play crucial roles in larval development, metabolism, immunity and overall bee health. However, the drivers and dynamics of healthy microbiome in solitary bees are still poorly understood, especially regarding the direct and indirect effects of land use on the diversity and composition of these microbial communities. METHODS: We examined bacterial communities in the offspring and nest materials of the Megachilid trap-nesting solitary bee, Osmia bicornis, along a gradient of land use intensification by 16S rRNA gene metabarcoding. Given that landscape composition, climatic conditions, and food resources are known to influence microbial compositions in solitary bee species, we hypothesized that land use changes would alter resources available for food and nest material collection and thereby affecting the microbiomes in offspring and their nest environments. We anticipated reduced microbial diversity and altered composition with increased land use intensification, which is known to decrease the number and diversity of resources, including the pool of floral and soil bacteria in the surrounding environment. RESULTS: As expected, we observed significant shifts in the bacterial composition and diversity of bees and their nests across varying degrees of land use intensity, differing in management types and the availability of flowers. The Shannon diversity of bacteria in nest materials (larval pollen provision, soil nest enclosure) and larval guts decreased with increasing land use intensity. However, the pupae microbiome remained unaffected, indicating a reorganization of the microbiome during metamorphosis, which is not significantly influenced by land use and available resources. DISCUSSION: Our findings provide new insights into the factors shaping environmental transmission and changes in solitary bee microbiomes. This understanding is crucial for comprehending the impacts of intensive land use on wild bee health and developing strategies to mitigate these effects.
AU  - Peters, B.*
AU  - Leonhardt, S.D.*
AU  - Schloter, M.
AU  - Keller, A.*
C1  - 73151
C2  - 56932
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Direct and indirect effects of land use on microbiomes of trap-nesting solitary bee larvae and nests.
JO  - Front. Microbiol.
VL  - 15
PB  - Frontiers Media Sa
PY  - 2025
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53–79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.
AU  - Hyams, Y.*
AU  - Rubin-Blum, M.*
AU  - Rosner, A.*
AU  - Brodsky, L.*
AU  - Rinkevich, Y.
AU  - Rinkevich, B.*
C1  - 68520
C2  - 54687
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii.
JO  - Front. Microbiol.
VL  - 14
PB  - Frontiers Media Sa
PY  - 2023
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - INTRODUCTION: Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes. METHODS: We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality. RESULTS AND DISCUSSION: Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.
AU  - Kurth, J.
AU  - Albrecht, M.*
AU  - Gläser, K.*
AU  - Karsten, U.*
AU  - Vestergaard, G.*
AU  - Armbruster, M.*
AU  - Kublik, S.
AU  - Schmid, C.
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 68047
C2  - 54525
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention.
JO  - Front. Microbiol.
VL  - 14
PB  - Frontiers Media Sa
PY  - 2023
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - BACKGROUND: Chronic obstructive pulmonary disease (COPD) collectively refers to chronic and progressive lung diseases that cause irreversible limitations in airflow. Patients with COPD are at high risk for severe respiratory symptoms upon influenza virus infection. Airway epithelial cells provide the first-line antiviral defense, but whether or not their susceptibility and response to influenza virus infection changes in COPD have not been elucidated. Therefore, this study aimed to compare the susceptibility of COPD- and control-derived airway epithelium to the influenza virus and assess protein changes during influenza virus infection by quantitative proteomics. MATERIALS AND METHODS: The presence of human- and avian-type influenza A virus receptor was assessed in control and COPD lung sections as well as in fully differentiated primary human bronchial epithelial cells (phBECs) by lectin- or antibody-based histochemical staining. PhBECs were from COPD lungs, including cells from moderate- and severe-stage diseases, and from age-, sex-, smoking, and history-matched control lung specimens. Protein profiles pre- and post-influenza virus infection in vitro were directly compared using quantitative proteomics, and selected findings were validated by qRT-PCR and immunoblotting. RESULTS: The human-type influenza receptor was more abundant in human airways than the avian-type influenza receptor, a property that was retained in vitro when differentiating phBECs at the air-liquid interface. Proteomics of phBECs pre- and post-influenza A virus infection with A/Puerto Rico/8/34 (PR8) revealed no significant differences between COPD and control phBECs in terms of flu receptor expression, cell type composition, virus replication, or protein profile pre- and post-infection. Independent of health state, a robust antiviral response to influenza virus infection was observed, as well as upregulation of several novel influenza virus-regulated proteins, including PLSCR1, HLA-F, CMTR1, DTX3L, and SHFL. CONCLUSION: COPD- and control-derived phBECs did not differ in cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Finally, we identified novel influenza A virus-regulated proteins in bronchial epithelial cells that might serve as potential targets to modulate the pathogenicity of infection and acute exacerbations.
AU  - Nakayama, M.
AU  - Marchi, H.
AU  - Dmitrieva, A.
AU  - Chakraborty, A.
AU  - Merl-Pham, J.
AU  - Hennen, E.
AU  - Le Gleut, R.
AU  - Ruppert, C.*
AU  - Guenther, A.*
AU  - Kahnert, K.*
AU  - Behr, J.*
AU  - Hilgendorff, A.
AU  - Hauck, S.M.
AU  - Adler, H.
AU  - Staab-Weijnitz, C.A.
C1  - 67337
C2  - 54177
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection.
JO  - Front. Microbiol.
VL  - 13
PB  - Frontiers Media Sa
PY  - 2023
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Epstein-Barr virus (EBV) is a double-stranded DNA virus of the Herpesviridae family. This virus preferentially infects human primary B cells and persists in the human B cell compartment for a lifetime. Latent EBV infection can lead to the development of different types of lymphomas as well as carcinomas such as nasopharyngeal and gastric carcinoma in immunocompetent and immunocompromised patients. The early phase of viral infection is crucial for EBV to establish latency, but different viral components are sensed by cellular sensors called pattern recognition receptors (PRRs) as the first line of host defense. The efficacy of innate immunity, in particular the interferon-mediated response, is critical to control viral infection initially and to trigger a broad spectrum of specific adaptive immune responses against EBV later. Despite these restrictions, the virus has developed various strategies to evade the immune reaction of its host and to establish its lifelong latency. In its different phases of infection, EBV expresses up to 44 different viral miRNAs. Some act as viral immunoevasins because they have been shown to counteract innate as well as adaptive immune responses. Similarly, certain virally encoded proteins also control antiviral immunity. In this review, we discuss how the virus governs innate immune responses of its host and exploits them to its advantage.
AU  - Albanese, M.
AU  - Tagawa, T.
AU  - Hammerschmidt, W.
C1  - 65859
C2  - 52946
TI  - Strategies of Epstein-Barr virus to evade innate antiviral immunity of its human host.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. Despite recent advances in understanding microbial sources in infants, the relative contribution of various microbial sources to the colonization of the gut microbiota in pigs remains unclear. Here, we longitudinally sampled the microbiota of 20 sow-piglet pairs (three piglets per sow) reared under identical conditions from multiple body sites and the surrounding weaning environment from birth to 28 days postpartum (1,119 samples in total). Source-tracking analysis revealed that the contribution of various microbial sources to the piglet gut microbiome gradually changed over time. The neonatal microbiota was initially sparsely populated, and the predominant contribution was from the maternal vaginal microbiota that increased gradually from 69.0% at day 0 to 89.3% at day 3 and dropped to 0.28% at day 28. As the piglets aged, the major microbial community patterns were most strongly associated with the sow feces and slatted floor, with contributions increasing from 0.52 and 9.6% at day 0 to 62.1 and 33.8% at day 28, respectively. The intestinal microbial diversity, composition, and function significantly changed as the piglets aged, and 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent shifts in their relative abundance, which likely reflected the effect of the maternal and environmental microbial sources on the selection and adaptation of the piglet gut microbiota. Overall, these data demonstrate that the vaginal microbiota is the primary source of the gut microbiota in piglets within 3 days after birth and are gradually replaced by the sow fecal and slatted floor microbiota over time. These findings may offer novel strategies to promote the establishment of exogenous symbiotic microbes to improve piglet gut health.
AU  - Chen, W.*
AU  - Ma, J.*
AU  - Jiang, Y.
AU  - Deng, L.
AU  - Lv, N.*
AU  - Gao, J.*
AU  - Cheng, J.*
AU  - Liang, J.B.*
AU  - Wang, Y.*
AU  - Lan, T.*
AU  - Liao, X.*
AU  - Mi, J.*
C1  - 65007
C2  - 52613
TI  - Selective maternal seeding and rearing environment from birth to weaning shape the developing piglet gut microbiome.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.
AU  - Elbehery, A.H.A.*
AU  - Deng, L.
C1  - 66440
C2  - 53180
TI  - Insights into the global freshwater virome.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7–4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4–5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3–6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1–3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.
AU  - Entfellner, E.*
AU  - Li, R.
AU  - Jiang, Y.
AU  - Ru, J.
AU  - Blom, J.*
AU  - Deng, L.
AU  - Kurmayer, R.*
C1  - 65921
C2  - 52990
TI  - Toxic/bioactive peptide synthesis genes rearranged by insertion sequence elements among the bloom-forming cyanobacteria Planktothrix.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AU  - Huber, K.J.*
AU  - Pester, M.*
AU  - Eichorst, S.A.*
AU  - Navarrete, A.A.*
AU  - Fösel, B.
C1  - 65644
C2  - 52846
TI  - Editorial: Acidobacteria - Towards unraveling the secrets of a widespread, though enigmatic, phylum.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.
AU  - Kuhl-Nagel, T.
AU  - Rodriguez, P.A.
AU  - Gantner, I.
AU  - Chowdhury, S.P.
AU  - Schwehn, P.
AU  - Rosenkranz, M.
AU  - Schnitzler, J.-P.
AU  - Kublik, S.
AU  - Schloter, M.
AU  - Rothballer, M.
AU  - Falter-Braun, P.
C1  - 65751
C2  - 52893
TI  - Novel Pseudomonas sp. SCA7 promotes plant growth in two plant families and induces systemic resistance in Arabidopsis thaliana.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
AU  - Mahnkopp-Dirks, F.*
AU  - Radl, V.
AU  - Kublik, S.
AU  - Gschwendtner, S.
AU  - Schloter, M.
AU  - Winkelmann, T.*
C1  - 64800
C2  - 52499
TI  - Dynamics of bacterial root endophytes of Malus domestica plants grown in field soils affected by apple replant disease.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.
AU  - Muster, C.*
AU  - Leiva, D.*
AU  - Morales, C.*
AU  - Grafe, M.
AU  - Schloter, M.
AU  - Carú, M.*
AU  - Orlando, J.*
C1  - 65690
C2  - 52404
TI  - Peltigera frigida lichens and their Substrates reduce the influence of forest cover change on phosphate solubilizing bacteria.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.
AU  - Olmo, R.*
AU  - Wetzels, S.U.*
AU  - Armanhi, J.S.L.*
AU  - Arruda, P.*
AU  - Berg, G.*
AU  - Cernava, T.*
AU  - Cotter, P.D.*
AU  - Araujo, S.C.*
AU  - de Souza, R.S.C.*
AU  - Ferrocino, I.*
AU  - Frisvad, J.C.*
AU  - Georgalaki, M.*
AU  - Hansen, H.H.*
AU  - Kazou, M.*
AU  - Kiran, G.S.*
AU  - Kostic, T.*
AU  - Krauss-Etschmann, S.*
AU  - Kriaa, A.*
AU  - Lange, L.*
AU  - Maguin, E.*
AU  - Mitter, B.*
AU  - Nielsen, M.O.*
AU  - Olivares, M.*
AU  - Quijada, N.M.*
AU  - Romaní-Pérez, M.*
AU  - Sanz, Y.*
AU  - Schloter, M.
AU  - Schmitt-Kopplin, P.
AU  - Seaton, S.C.*
AU  - Selvin, J.*
AU  - Sessitsch, A.*
AU  - Wang, M.*
AU  - Zwirzitz, B.*
AU  - Selberherr, E.*
AU  - Wagner, M.*
C1  - 65820
C2  - 52921
TI  - Microbiome research as an effective driver of success stories in agrifood systems – a selection of case studies.
JO  - Front. Microbiol.
VL  - 13
PY  - 2022
SN  - 1664-302X
ER  - 

TY  - JOUR
AU  - Chowdhury, S.P.
AU  - Kredics, L.*
AU  - Asiegbu, F.O.*
AU  - Lagunas, B.*
AU  - Schikora, A.*
C1  - 63873
C2  - 51633
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Editorial: Multilateral interactions in the rhizosphere.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Bioremediation of polluted groundwater is one of the most difficult actions in environmental science. Nonetheless, the clean-up of nitrate polluted groundwater may become increasingly important as nitrate concentrations frequently exceed the EU drinking water limit of 50 mg L , largely due to intensification of agriculture and food production. Denitrifiers are natural catalysts that can reduce increasing nitrogen loading of aquatic ecosystems. Porous aquifers with high nitrate loading are largely electron donor limited and additionally, high dissolved oxygen concentrations are known to reduce the efficiency of denitrification. Therefore, denitrification lag times (time prior to commencement of microbial nitrate reduction) up to decades were determined for such groundwater systems. The stimulation of autotrophic denitrifiers by the injection of hydrogen into nitrate polluted regional groundwater systems may represent a promising remediation strategy for such environments. However, besides high costs other drawbacks, such as the transient or lasting accumulation of the cytotoxic intermediate nitrite or the formation of the potent greenhouse gas nitrous oxide, have been described. In this article, we detect causes of incomplete denitrification, which include environmental factors and physiological characteristics of the underlying bacteria and provide possible mitigation approaches. –1
AU  - Duffner, C.
AU  - Wunderlich, A.*
AU  - Schloter, M.
AU  - Schulz, S.
AU  - Einsiedl, F.*
C1  - 61665
C2  - 50375
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Strategies to overcome intermediate accumulation during in situ nitrate remediation in groundwater by hydrogenotrophic denitrification.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.
AU  - Fillinger, L.*
AU  - Hürkamp, K.
AU  - Stumpp, C.
AU  - Weber, N.
AU  - Forster, D.
AU  - Hausmann, B.*
AU  - Schultz, L.*
AU  - Griebler, C.
C1  - 63841
C2  - 51682
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Spatial and annual variation in microbial abundance, community composition, and diversity associated with alpine surface snow.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - A very common way to classify bacteria is through microscopic images. Microscopic cell counting is a widely used technique to measure microbial growth. To date, fully automated methodologies are available for accurate and fast measurements; yet for bacteria dividing longitudinally, as in the case of Candidatus Thiosymbion oneisti, its cell count mainly remains manual. The identification of this type of cell division is important because it helps to detect undergoing cellular division from those which are not dividing once the sample is fixed. Our solution automates the classification of longitudinal division by using a machine learning method called residual network. Using transfer learning, we train a binary classification model in fewer epochs compared to the model trained without it. This potentially eliminates most of the manual labor of classifying the type of bacteria cell division. The approach is useful in automatically labeling a certain bacteria division after detecting and segmenting (extracting) individual bacteria images from microscopic images of colonies.
AU  - Garcia Perez, C.
AU  - Ito, K.
AU  - Geijo, J.*
AU  - Feldbauer, R.*
AU  - Schreiber, N.
AU  - zu Castell, W.
C1  - 62370
C2  - 50805
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Efficient detection of longitudinal bacteria fission using transfer learning in deep neural networks.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The atmosphere plays an important role in transporting microorganisms on a global scale, yet the processes affecting the composition of the airborne microbiome, the aerobiome, are not fully outlined. Here we present the community compositions of bacteria and fungi obtained by DNA amplicon-sequencing of aerosol samples collected in a size-resolved manner during nine consecutive days in central Israel. The campaign captured dust events originating from the Sahara and the Arabian deserts, as well as days without dust ("clear days"). We found that the source of the aerosol was the main variable contributing to the composition of both fungal and bacterial communities. Significant differences were also observed between communities representing particles of different sizes. We show evidence for the significant transport of bacteria as cell-aggregates and/or via bacterial attachment to particles during dust events. Our findings further point to the mixing of local and transported bacterial communities, observed mostly in particles smaller than 0.6 μm in diameter, representing bacterial single cells. Fungal communities showed the highest dependence on the source of the aerosols, along with significant daily variability, and without significant mixing between sources, possibly due to their larger aerodynamic size and shorter atmospheric residence times. These results, obtained under highly varied atmospheric conditions, provide significant assurances to previously raised hypotheses and could set the course for future studies on aerobiome composition.
AU  - Gat, D.
AU  - Reicher, N.*
AU  - Schechter, S.*
AU  - Alayof, M.*
AU  - Tarn, M.D.*
AU  - Wyld, B.V.*
AU  - Zimmermann, R.
AU  - Rudich, Y.*
C1  - 63726
C2  - 51751
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Size-resolved community structure of bacteria and fungi transported by dust in the middle east.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.
AU  - Kuhl-Nagel, T.
AU  - Chowdhury, S.P.
AU  - Uhl, J.
AU  - Rothballer, M.
C1  - 62951
C2  - 51201
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Genome-based characterization of plant-associated Rhodococcus 
      qingshengii RL1 reveals stress tolerance and plant-microbe interaction 
      traits.
JO  - Front. Microbiol.
VL  - 12
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76–90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87–97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61–74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
AU  - Windisch, S.*
AU  - Sommermann, L.*
AU  - Babin, D.*
AU  - Chowdhury, S.P.
AU  - Grosch, R.*
AU  - Moradtalab, N.*
AU  - Walker, F.*
AU  - Höglinger, B.*
AU  - El-Hasan, A.*
AU  - Armbruster, W.*
AU  - Nesme, J.*
AU  - Sørensen, S.J.*
AU  - Schellenberg, I.*
AU  - Geistlinger, J.*
AU  - Smalla, K.*
AU  - Rothballer, M.
AU  - Ludewig, U.*
AU  - Neumann, G.*
C1  - 61167
C2  - 50084
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Impact of long-term organic and mineral fertilization on rhizosphere metabolites, root-microbial interactions and plant health of lettuce.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2021
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Pseudomonas sp. BGI-2 is a psychrotrophic bacterium isolated from the ice sample collected from Batura glacier, Pakistan. This strain produces highly viscous colonies on agar media supplemented with glucose. In this study, we have optimized growth and production of exopolysaccharide (EPS) by the cold-adapted Pseudomonas sp. BGI-2 using different nutritional and environmental conditions. Pseudomonas sp. BGI-2 is able to grow in a wide range of temperatures (4–35°C), pH (5–11), and salt concentrations (1–5%). Carbon utilization for growth and EPS production was extensively studied and we found that glucose, galactose, mannose, mannitol, and glycerol are the preferable carbon sources. The strain is also able to use sugar waste molasses as a growth substrate, an alternative for the relatively expensive sugars for large scale EPS production. Maximum EPS production was observed at 15°C, pH 6, NaCl (10 g L–1), glucose as carbon source (100 g L–1), yeast extract as nitrogen source (10 g L–1), and glucose/yeast extract ratio (10/1). Under optimized conditions, EPS production was 2.01 g L–1, which is relatively high for a Pseudomonas species compared to previous studies using the same method for quantification. High-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) analysis of EPS revealed glucose, galactose, and glucosamine as the main sugar monomers. Membrane protection assay using human RBCs revealed significant reduction in cell lysis (∼50%) in the presence of EPS, suggesting its role in membrane protection. The EPS (5%) also conferred significant cryoprotection for a mesophilic Escherichia coli k12 which was comparable to glycerol (20%). Also, improvement in lipid peroxidation inhibition (in vitro) resulted when lipids from the E. coli was pretreated with EPS. Increased EPS production at low temperatures, freeze thaw tolerance of the EPS producing strain, and increased survivability of E. coli in the presence of EPS as cryoprotective agent supports the hypothesis that EPS production is a strategy for survival in extremely cold environments such as the glacier ice.
AU  - Ali, P.*
AU  - Shah, A.A.*
AU  - Hasan, F.*
AU  - Hertkorn, N.
AU  - Gonsior, M.*
AU  - Sajjad, W.*
AU  - Chen, F.*
C1  - 58630
C2  - 48243
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - A glacier bacterium produces high yield of cryoprotective exopolysaccharide.
JO  - Front. Microbiol.
VL  - 10
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Agro-ecosystems experience huge losses of land every year due to soil erosion induced by poor agricultural practices such as intensive tillage. Erosion can be minimized by the presence of stable soil aggregates, the formation of which can be promoted by bacteria. Some of these microorganisms have the ability to produce exopolysaccharides and lipopolysaccharides that "glue" soil particles together. However, little is known about the influence of tillage intensity on the bacterial potential to produce these polysaccharides, even though more stable soil aggregates are usually observed under less intense tillage. As the effects of tillage intensity on soil aggregate stability may vary between sites, we hypothesized that the response of polysaccharide-producing bacteria to tillage intensity is also determined by site-specific conditions. To investigate this, we performed a high-throughput shotgun sequencing of DNA extracted from conventionally and reduced tilled soils from three tillage system field trials characterized by different soil parameters. While we confirmed that the impact of tillage intensity on soil aggregates is site-specific, we could connect improved aggregate stability with increased absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides. The potential to produce polysaccharides was generally promoted under reduced tillage due to the increased microbial biomass. We also found that the response of most potential producers of polysaccharides to tillage was site-specific, e.g., Oxalobacteraceae had higher potential to produce polysaccharides under reduced tillage at one site, and showed the opposite response at another site. However, the response of some potential producers of polysaccharides to tillage did not depend on site characteristics, but rather on their taxonomic affiliation, i.e., all members of Actinobacteria that responded to tillage intensity had higher potential for exopolysaccharide and lipopolysaccharide production specifically under reduced tillage. This could be especially crucial for aggregate stability, as polysaccharides produced by different taxa have different "gluing" efficiency. Overall, our data indicate that tillage intensity could affect aggregate stability by both influencing the absolute abundance of genes involved in the production of exopolysaccharides and lipopolysaccharides, as well as by inducing shifts in the community of potential polysaccharide producers. The effects of tillage intensity depend mostly on site-specific conditions.
AU  - Cania, B.
AU  - Vestergaard, G.
AU  - Suhadolc, M.*
AU  - Mihelič, R.*
AU  - Krauss, M.*
AU  - Fliessbach, A.*
AU  - Mäder, P.*
AU  - Szumełda, A.*
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 58899
C2  - 48561
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Site-specific conditions change the response of bacterial producers of 
      soil structure-stabilizing agents such as exopolysaccharides and 
      lipopolysaccharides to tillage intensity.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the "beneficial" nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the "plant beneficial and environmental" (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.
AU  - Herpell, J.B.*
AU  - Schindler, F.*
AU  - Bejtović, M.*
AU  - Fragner, L.*
AU  - Diallo, B.*
AU  - Bellaire, A.*
AU  - Kublik, S.
AU  - Fösel, B.
AU  - Gschwendtner, S.
AU  - Kerou, M.*
AU  - Schloter, M.
AU  - Weckwerth, W.*
C1  - 59090
C2  - 48612
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - The potato yam phyllosphere ectosymbiont Paraburkholderia sp. Msb3 is a potent growth promotor in tomato.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L−1sed d−1, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L−1sed d−1]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L−1sed d−1 and 14.3(±3.5) μgC L−1sed d−1, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.
AU  - Hofmann, R.
AU  - Uhl, J.
AU  - Hertkorn, N.
AU  - Griebler, C.
C1  - 60582
C2  - 49398
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Linkage between dissolved organic matter transformation, bacterial carbon production, and diversity in a shallow oligotrophic aquifer: Results from flow-through sediment microcosm experiments.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - There are two main strategies known how microorganisms regulate substrate utilization: specialization on one preferred substrate at high concentrations in batch cultures or simultaneous utilization of many substrates at low concentrations in chemostats. However, it remains unclear how microorganisms utilize substrates at low concentrations in the subsurface: do they focus on a single substrate and exhibit catabolite repression or do they de-repress regulation of all catabolic pathways? Here, we investigated the readiness ofGeobacter metallireducensto degrade organic substrates under sessile growth in sediment columns in the presence of a mixed community as a model for aquifers. Three parallel columns were filled with sand and flushed with anoxic medium at a constant inflow (18 ml h(-1)) of the substrate benzoate (1 mM) with non-limiting nitrate concentrations (30 mM) as electron acceptor. Columns were inoculated with the anaerobic benzoate degraderG. metallireducens. Microbial degradation produced concentration gradients of benzoate toward the column outlet. Metagenomics and label-free metaproteomics were used to detect and quantify the protein expression ofG. metallireducens. Bulk benzoate concentrations below 0.2 mM led to increased abundance of catabolic proteins involved in utilization of fermentation products and aromatic compounds including the complete upregulation of the toluene-degrading pathway although toluene was not added to the medium. We propose that under sessile conditions and low substrate concentrationsG. metallireducensexpresses a specific set of catabolic pathways for preferred substrates, even when these substrates are not present.
AU  - Marozava, S.
AU  - Merl-Pham, J.
AU  - Müller, H.*
AU  - Meckenstock, R.U.*
C1  - 59632
C2  - 48937
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Adaptation of carbon source utilization patterns of Geobacter metallireducens during sessile growth.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interactions among them. In this study, we investigated how SRMs compete with the established methanogenic communities in sediment from a long-term, electron acceptor-depleted, asphalt-exposed ecosystem and how they affect the composition of the organic material. We hypothesized that, upon addition of sulfate, SRMs (i) outcompete the methanogenic communities and (ii) markedly contribute to transformations of the organic material. We sampled sediments from the test and proximate control sites under anoxic conditions and incubated them in seawater medium with or without sulfate. Abundance and activity pattern of SRMs and methanogens, as well as the total prokaryotic community, were followed for 6 weeks by using qPCR targeting selected marker genes. Some of these genes were also subjected to amplicon sequencing to assess potential shifts in diversity patterns. Alterations of the organic material in the microcosms were determined by mass spectrometry. Our results indicate that the competition of SRMs with methanogens upon sulfate addition strongly depends on the environment studied and the starting microbiome composition. In the asphalt-free sediments (control), the availability of easily degradable organic material (mainly plant-derived) allows SRMs to use a larger variety of substrates, reducing interspecies competition with methanogens. In contrast, the abundant presence of recalcitrant compounds in the asphalt-exposed sediment was associated with a strong competition between SRMs and methanogens, ultimately detrimental for the latter. Our data underpin the importance of the quality of bioavailable organic materials in anoxic environments as a driver for microbial community structure and function.
AU  - Michas, A.
AU  - Harir, M.
AU  - Lucio, M.
AU  - Vestergaard, G.*
AU  - Himmelberg, A.M.
AU  - Schmitt-Kopplin, P.
AU  - Lueders, T.*
AU  - Hatzinikolaou, D.G.*
AU  - Schöler, A.*
AU  - Rabus, R.*
AU  - Schloter, M.
C1  - 60322
C2  - 49257
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Sulfate alters the competition among microbiome members of sediments chronically exposed to asphalt.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - In wine, one method of limiting the addition of sulphites, a harmful and allergenic agent, is bio-protection. This practice consists of the early addition of microorganisms on grape must before fermentation. Non-Saccharomycesyeasts have been proposed as an interesting alternative to sulphite addition. However, scientific data proving the effectiveness of bio-protection remains sparse. This study provides the first analysis of the chemical and microbiological effects of aMetschnikowia pulcherrimastrain inoculated at the beginning of the red winemaking process in three wineries as an alternative to sulphiting. Like sulphiting, bio-protection effectively limited the growth of spoilage microbiota and had no influence on the phenolic compounds protecting musts and wine from oxidation. The bio-protection had no effect on the volatile compounds and the sensory differences were dependent on the experimental sites. However, a non-targeted metabolomic analysis by FTICR-MS highlighted a bio-protection signature.
AU  - Simonin, S.*
AU  - Roullier-Gall, C.*
AU  - Ballester, J.*
AU  - Schmitt-Kopplin, P.
AU  - Quintanilla-Casas, B.*
AU  - Vichi, S.*
AU  - Peyron, D.*
AU  - Alexandre, H.*
AU  - Tourdot-Maréchal, R.*
C1  - 59576
C2  - 48850
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Bio-protection as an alternative to sulphites: Impact on chemical and microbial characteristics of red wines.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularlyPinus sylvestris,Picea abies, andPopulus x wettsteinii, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
AU  - Tedersoo, L.*
AU  - Anslan, S.*
AU  - Bahram, M.*
AU  - Drenkhan, R.*
AU  - Pritsch, K.
AU  - Buegger, F.
AU  - Padari, A.*
AU  - Hagh-Doust, N.*
AU  - Mikryukov, V.*
AU  - Gohar, D.*
AU  - Amiri, R.*
AU  - Hiiesalu, I.*
AU  - Lutter, R.*
AU  - Rosenvald, R.*
AU  - Rahn, E.*
AU  - Adamson, K.*
AU  - Drenkhan, T.*
AU  - Tullus, H.*
AU  - Jurimaa, K.*
AU  - Sibul, I.*
AU  - Otsing, E.*
AU  - Polme, S.*
AU  - Metslaid, M.*
AU  - Loit, K.*
AU  - Agan, A.*
AU  - Puusepp, R.*
AU  - Varik, I.*
AU  - Koljalg, U.*
AU  - Abarenkov, K.*
C1  - 60300
C2  - 49373
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Regional-scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe.
JO  - Front. Microbiol.
VL  - 11
PB  - Frontiers Media Sa
PY  - 2020
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Fungi of the genus Trichoderma are economically important due to their plant growth- and performance-promoting effects, such as improved nutrient supply, mycoparasitism of plant-pathogens and priming of plant defense. Due to their mycotrophic lifestyle, however, they might also be antagonistic to other plant-beneficial fungi, such as mycorrhiza-forming species. Trichoderma spp. release a high diversity of volatile organic compounds (VOCs), which likely play a decisive role in the inter-species communication. It has been shown that Trichoderma VOCs can inhibit growth of some plant pathogens, but their inhibition potentials during early interactions with mutualistic fungi remain unknown. Laccaria bicolor is a common ectomycorrhizal fungus which in symbiotic relationship is well known to facilitate plant performance. Here, we investigated the VOC profiles of three strains of Trichoderma species, Trichoderma harzianum, Trichoderma Hamatum, and Trichoderma velutinum, as well as L. bicolor by stir bar sorptive extraction and gas chromatography - mass spectrometry (SBSE-GC-MS). We further examined the fungal performance and the VOC emission profiles during confrontation of the Trichoderma species with L. bicolor in different co-cultivation scenarios. The VOC profiles of the three Trichoderma species were highly species-dependent. T. harzianum was the strongest VOC emitter with the most diverse compound pattern, followed by T. hamatum and T. velutinum. Co-cultivation of Trichoderma spp. and L. bicolor altered the VOC emission patterns dramatically in some scenarios. The co-cultivations also revealed contact degree-dependent inhibition of one of the fungal partners. Trichoderma growth was at least partially inhibited when sharing the same headspace with L. bicolor. In direct contact between both mycelia, however, L. bicolor growth was impaired, indicating that Trichoderma and L. bicolor apply different effectors when defending their territory. Multivariate analysis demonstrated that all examined individual fungal species in axenic cultures, as well as their co-cultivations were characterized by a distinct VOC emission pattern. The results underline the importance of VOCs in fungal interactions and reveal unexpected adjustability of the VOC emissions according to the specific biotic environments.
AU  - Guo, Y.
AU  - Ghirardo, A.
AU  - Weber, B.
AU  - Schnitzler, J.-P.
AU  - Benz, J.P.*
AU  - Rosenkranz, M.
C1  - 56054
C2  - 46764
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Trichoderma species differ in their volatile profiles and in antagonism towards ectomycorrhiza Laccaria bicolor.
JO  - Front. Microbiol.
VL  - 10
PB  - Frontiers Media Sa
PY  - 2019
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Alpine lakes are considered pristine freshwater ecosystems and sensitive to direct and indirect changes in water temperature as induced by climate change. The bacterial plankton constitutes a key component in the water column and bacterial metabolic activity has direct consequences for water quality. In order to understand bacterial response to global temperature rise in five alpine lakes located in the Austrian Alps (1700–2188 m a.S.L.) water temperature was compared within a decadal period. Depth-integrated samples were characterized in community composition by 16S rDNA deep-amplicon sequencing early (56 ± 16 (SD) days after ice break up) and later (88 ± 16 days) in the growing season. Within the ten years period, temperature rise was observed through reduced ice cover duration and increased average water temperature. During the early growing season, the average water temperature recorded between circulation in spring until sampling date (WAS), and the day of autumn circulation, as well as chemical composition including dissolved organic carbon influenced bacterial community composition. In contrast, only nutrients (such as nitrate) were found influential later in the growing season. Metabolic theory of ecology (MTE) was applied to explain the dependence of taxonomic richness on WAS in mathematical terms. The calculated activation energy exceeded the frequently reported prediction emphasizing the role of WAS during early growing season. Accordingly, the relative abundance of predicted metabolism related genes increased with WAS. Thus, the dominant influence of temperature after ice break up could be explained by overall climate change effects, such as a more intense warming in spring and an overall higher amplitude of temperature variation.
AU  - Jiang, Y.
AU  - Huang, H.
AU  - Ma, T.
AU  - Ru, J.
AU  - Blank, S.*
AU  - Kurmayer, R.*
AU  - Deng, L.
C1  - 56603
C2  - 47094
TI  - Temperature response of planktonic microbiota in remote alpine lakes.
JO  - Front. Microbiol.
VL  - 10
PY  - 2019
SN  - 1664-302X
ER  - 

TY  - JOUR
AU  - Kaderali, L.*
AU  - Theis, F.J.
AU  - Ganusov, V.V.*
AU  - Ciupe, S.M.*
AU  - Mehr, R.*
AU  - Ribeiro, R.M.*
AU  - Hernandez-Vargas, E.A.*
C1  - 55440
C2  - 46209
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Editorial: Integrative computational systems biology approaches in immunology and medicine.
JO  - Front. Microbiol.
VL  - 9
PB  - Frontiers Media Sa
PY  - 2019
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - © 2019 Stoeger and Adler. After primary infection, herpesviruses persist for life in their hosts in a latent stage (Adler et al., 2017). Different subfamilies of herpesviruses establish latency in specific and different sets of cells (Pellett and Roizman, 2013; Lieberman, 2016). The latent stage can be interrupted by periods of lytic replication, termed reactivation. Reactivation is important for viral spread to new hosts or for the maintenance of the viral reservoir in the host. Usually, reactivation is not associated with disease but under certain circumstances, it may be accompanied by clinical symptoms. The stimuli and the precise molecular mechanisms that lead to reactivation from the latent state are not fully understood and can differ from one herpesvirus to another.
AU  - Stöger, T.
AU  - Adler, H.
C1  - 55204
C2  - 46243
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - "Novel" triggers of herpesvirus reactivation and their potential health relevance.
JO  - Front. Microbiol.
VL  - 9
PB  - Frontiers Media Sa
PY  - 2019
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N2O to N2, NO is proposed to be directly disproportionated into N2 and O2 in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.
AU  - Zhu, B.
AU  - Wang, J.*
AU  - Bradford, L.
AU  - Ettwig, K.*
AU  - Hu, B.*
AU  - Lueders, T.
C1  - 56626
C2  - 47119
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Nitric oxide dismutase (NOD) genes as a functional marker for the diversity and phylogeny of methane-driven oxygenic denitrifiers.
JO  - Front. Microbiol.
VL  - 10
PB  - Frontiers Media Sa
PY  - 2019
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental "omics." Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio. reads per density-resolved RNA fraction), an average of 1.2% of reads per sample were identified as non-rRNA, including mRNA. Members of the (including those related to spp.) were most abundant and enriched in C-rRNA, while well-known aerobic degraders such as spp. remained unlabeled. Transcripts related to cell motility, secondary metabolite formation and xenobiotics degradation were highly labeled with C. mRNA of phenol hydroxylase genes were highly labeled and abundant, while other transcripts of toluene-activation were not detected. Clear labeling of catechol 2,3-dioxygenase transcripts supported previous findings that some of these extradiol dioxygenases were adapted to low oxygen concentrations. We introduce a novel combination of total RNA-SIP with calculation of transcript-specific enrichment factors (EFs) in C-RNA, enabling a targeted approach to process-relevant gene expression in complex microbiomes.
AU  - Bradford, L.
AU  - Vestergaard, G.
AU  - Táncsics, A.*
AU  - Zhu, B.
AU  - Schloter, M.*
AU  - Lueders, T.
C1  - 54785
C2  - 45868
CY  - Avenue Du Tribunal Federal 34, Lausanne, Ch-1015, Switzerland
TI  - Transcriptome-stable isotope probing provides targeted functional and taxonomic insights into microaerobic pollutant-degrading aquifer microbiota.
JO  - Front. Microbiol.
VL  - 9
PB  - Frontiers Media Sa
PY  - 2018
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Quorum sensing (QS) in Pseudomonas aeruginosa coordinates the expression of virulence factors, such as exoproteases and siderophores, that are public goods utilized by the whole population of bacteria, regardless of whether they invested or not in their production. These public goods can be used by QS defective mutants for growth, and since these mutants do not contribute to public goods production, they are considered social cheaters. Pyocyanin is a phenazine that is a toxic, QS-controlled metabolite produced by P. aeruginosa. It is a redox-active compound and promotes the generation of reactive oxygen species; it also possesses antibacterial properties and increases fitness in competition with other bacterial species. Since QS-deficient individuals are less able to tolerate oxidative stress, we hypothesized that the pyocyanin produced by the wild-type population could promote selection of functional QS systems in this bacterium. Here, we demonstrate, using competition experiments and mathematical models, that, indeed, pyocyanin increases the fitness of the cooperative QS-proficient individuals and restricts the appearance of social cheaters. In addition, we also show that pyocyanin is able to select QS in other bacteria such as Acinetobacter baumannii.
AU  - Castañeda-Tamez, P.*
AU  - Ramírez-Peris, J.*
AU  - Pérez-Velázquez, J.
AU  - Kuttler, C.*
AU  - Jalalimanesh, A.*
AU  - Saucedo-Mora, M.A.*
AU  - Jiménez-Cortés, J.G.*
AU  - Maeda, T.*
AU  - González, Y.*
AU  - Tomás, M.*
AU  - Wood, T.K.*
AU  - García-Contreras, R.*
C1  - 53869
C2  - 45018
CY  - Po Box 211, 1000 Ae Amsterdam, Netherlands
TI  - Pyocyanin restricts social cheating in Pseudomonas aeruginosa.
JO  - Front. Microbiol.
VL  - 9
PB  - Elsevier Science Bv
PY  - 2018
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
AU  - Elbehery, A.H.A.
AU  - Feichtmayer, J.
AU  - Singh, D.*
AU  - Griebler, C.
AU  - Deng, L.
C1  - 53641
C2  - 44803
TI  - The human virome protein cluster database (HVPC): A human viral metagenomic database for diversity and function annotation.
JO  - Front. Microbiol.
VL  - 9
IS  - MAY
PY  - 2018
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.
AU  - Pérez-de-Mora, A.
AU  - Lacourt, A.*
AU  - McMaster, M.L.*
AU  - Liang, X.M.*
AU  - Dworatzek, S.M.*
AU  - Edwards, E.A.*
C1  - 53583
C2  - 44703
TI  - Chlorinated electron acceptor abundance drives selection of Dehalococcoides mccartyi (D. mccartyi) strains in dechlorinating enrichment cultures and groundwater environments.
JO  - Front. Microbiol.
VL  - 9
IS  - MAY
PY  - 2018
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (apnA-E) through comparing 125 strains of the bloom-forming cyanobacterium Planktothrix spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire apnA-E gene cluster. In order to quantify apn gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire apn gene cluster without interruption. Within the 11 strains assigned to P. pseudagardhii, P. mougeotii, or P. tepida (Lineage 3), neither apnA-E genes nor remnants were observed. Within the P. agardhii/P. rubescens strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking apn genes occurred, while among the strains lacking the apnA-E genes, the presence of the 5'end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), apnA-E genes were always present. A high similarity of apn genes of the genus Planktothrix when compared with strains of the genus Microcystis suggested its horizontal gene transfer during the speciation of P. agardhii/P. rubescens. Genetic analysis of the first (A1-) domain of the apnA gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of apnA A1 genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.
AU  - Entfellner, E.*
AU  - Frei, M.*
AU  - Christiansen, G.*
AU  - Deng, L.
AU  - Blom, J.*
AU  - Kurmayer, R.*
C1  - 50616
C2  - 42530
CY  - Lausanne
TI  - Evolution of anabaenopeptin peptide structural variability in the cyanobacterium planktothrix.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Despite the active and intense treatment of wastewater, pathogenic microorganisms and viruses are frequently introduced into the aquatic environment. For most human pathogens, however, this is a rather hostile place, where starvation, continuous inactivation, and decay generally occur, rather than successful reproduction. Nevertheless, a great diversity of the pathogenic microorganisms can be detected, in particular, in the surface waters receiving wastewater. Pathogen survival depends majorly on abiotic factors such as irradiation, changes in water ionic strength, temperature, and redox state. In addition, inactivation is enhanced by the biotic interactions in the environment. Although knowledge of the antagonistic biotic interactions has been available since a long time, certain underlying processes and mechanisms still remain unclear. Others are well-appreciated and increasingly are applied to the present research. Our review compiles and discusses the presently known biotic interactions between autochthonous microbes and pathogens introduced into the aquatic environment, including protozoan grazing, virus-induced bacterial cell lysis, antimicrobial substances, and predatory bacteria. An overview is provided on the present knowledge, as well as on the obvious research gaps. Individual processes that appear promising for future applications in the aquatic environment are presented and discussed.
AU  - Feichtmayer, J.
AU  - Deng, L.
AU  - Griebler, C.
C1  - 52389
C2  - 43942
CY  - Lausanne
SP  - 2192
TI  - Antagonistic microbial interactions: Contributions and potential applications for controlling pathogens in the aquatic systems.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - GATA-type transcription factors (TFs) such as the nitrogen regulators AreA and AreB, or the light-responsive TFs WC-1 and WC-2, play global roles in fungal growth and development. The conserved GATA TF NsdD is known as an activator of sexual development and key repressor of conidiation in Aspergillus nidulans, and as light-regulated repressor of macroconidia formation in Botrytis cinerea. In the present study, we functionally characterized the NsdD ortholog in Fusarium fujikuroi, named Csm1. Deletion of this gene resulted in elevated microconidia formation in the wild-type (WT) and restoration of conidiation in the non-sporulating velvet mutant Δvel1 demonstrating that Csm1 also plays a role as repressor of conidiation in F. fujikuroi. Furthermore, biosynthesis of the PKS-derived red pigments, bikaverin and fusarubins, is de-regulated under otherwise repressing conditions. Cross-species complementation of the Δcsm1 mutant with the B. cinerea ortholog LTF1 led to full restoration of WT-like growth, conidiation and pigment formation. In contrast, the F. fujikuroi CSM1 rescued only the defects in growth, the tolerance to H2O2 and virulence, but did not restore the light-dependent differentiation when expressed in the B. cinerea Δltf1 mutant. Microarray analysis comparing the expression profiles of the F. fujikuroi WT and the Δcsm1 mutant under different nitrogen conditions revealed a strong impact of this GATA TF on 19 of the 47 gene clusters in the genome of F. fujikuroi. One of the up-regulated silent gene clusters is the one containing the sesquiterpene cyclase-encoding key gene STC1. Heterologous expression of STC1 in Escherichia coli enabled us to identify the product as the volatile bioactive compound (-)-germacrene D.
AU  - Niehaus, E.M.*
AU  - Schumacher, J.*
AU  - Burkhardt, I.*
AU  - Rabe, P.*
AU  - Spitzer, E.*
AU  - Münsterkötter, M.
AU  - Güldener, U.*
AU  - Sieber, C.M.K.*
AU  - Dickschat, J.S.*
AU  - Tudzynski, B.*
C1  - 51452
C2  - 43235
CY  - Lausanne
TI  - The GATA-type transcription factor Csm1 regulates conidiation and secondary metabolism in Fusarium fujikuroi.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Quorum sensing (QS) in Pseudomonas aeruginosa coordinates the expression of virulence factors, some of which are used as public goods. Since their production is a cooperative behavior, it is susceptible to social cheating in which non-cooperative QS deficient mutants use the resources without investing in their production. Nevertheless, functional QS systems are abundant; hence, mechanisms regulating the amount of cheating should exist. Evidence that demonstrates a tight relationship between QS and the susceptibility of bacteria against the attack of lytic phages is increasing; nevertheless, the relationship between temperate phages and QS has been much less explored. Therefore, in this work, we studied the effects of having a functional QS system on the susceptibility to temperate bacteriophages and how this affects the bacterial and phage dynamics. We find that both experimentally and using mathematical models, that the lysogenic bacteriophages D3112 and JBD30 select QS-proficient P. aeruginosa phenotypes as compared to the QS-deficient mutants during competition experiments with mixed strain populations in vitro and in vivo in Galleria mellonella, in spite of the fact that both phages replicate better in the wild-type background. We show that this phenomenon restricts social cheating, and we propose that temperate phages may constitute an important selective pressure toward the conservation of bacterial QS.
AU  - Saucedo-Mora, M.A.*
AU  - Castaneda-Tamez, P.*
AU  - Cazares, A.*
AU  - Pérez-Velázquez, J.
AU  - Hense, B.A.
AU  - Cazares, D.*
AU  - Figueroa, W.*
AU  - Carballo, M.*
AU  - Guarneros, G.*
AU  - Perez-Eretza, B.*
AU  - Cruz, N.*
AU  - Nishiyama, Y.*
AU  - Maeda, T.*
AU  - Belmont-Diaz, J.A.*
AU  - Wood, T.K.*
AU  - García-Contreras, R.*
C1  - 51865
C2  - 43541
CY  - Lausanne
TI  - Selection of functional quorum sensing systems by lysogenic bacteriophages in Pseudomonas aeruginosa.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Cell-cell communication, also termed quorum sensing (QS), is a widespread process that coordinates gene expression in bacterial populations. The generally accepted view is that QS optimizes the cell density-dependent benefit attained from cooperative behaviors, often in the form of secreted products referred to as "public goods." This view is challenged by an increasing number of cell-associated products or "private goods" reported to be under QS-control for which a collective benefit is not apparent. A prominent example is nucleoside hydrolase from Pseudomonas aeruginosa, a periplasmic enzyme that catabolizes adenosine. Several recent studies have shown that private goods can function to stabilize cooperation by co-regulated public goods, seemingly explaining their control by QS. Here we argue that this property is a by-product of selection for other benefits rather than an adaptation. Emphasizing ecophysiological context, we propose alternative explanations for the QS control of private goods. We suggest that the benefit attained from private goods is associated with high cell density, either because a relevant ecological condition correlates with density, or because the private good is, directly or indirectly, involved in cooperative behavior. Our analysis helps guide a systems approach to QS, with implications for antivirulence drug design and synthetic biology.
AU  - Schuster, M.*
AU  - Sexton, D.J.*
AU  - Hense, B.A.
C1  - 51254
C2  - 42971
TI  - Why quorum sensing controls private goods.
JO  - Front. Microbiol.
VL  - 8
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Here we intend to clarify the function of rbsD, a conserved gene involved in bacterial ribose utilization. As stated in the original article, rbsD is absent in P. aeruginosa, which is the likely cause for its slow growth rate on adenosine as a carbon source. Adenosine is cleaved into ribose and adenine by a periplasmic, quorum sensing-dependent nucleoside hydrolase (Nuh). In the section "The case of Nuh," we suggested that rbsD contributes to ribose uptake, based on the original characterization of an rbsD mutant in E. coli (Oh et al., 1999). However, subsequent biochemical studies have revealed a more specific function. E. coli rbsD encodes a ribose mutarotase that catalyzes the conversion between the pyranose and furanose forms of D-ribose immediately after cytoplasmic uptake by the ribose transporter RbsABC (Kim et al., 2003; Ryu et al., 2004). While ribose primarily exists as a pyranose in solution, the furanose is the preferred substrate in the ensuing phosphorylation by the ribokinase RbsK (Sigrell et al., 1998). Thus, the intracellular level of the furanose as a substrate for RbsK may be the growth-limiting factor in rbsD-deficient P. aeruginosa. Irrespective of these biochemical details, however, our main conclusions drawn in the original article remain the same: Adenosine is a relevant nitrogen but not carbon source in the ecology of P. aeruginosa. As a carbon source, adenosine does not constrain cheating in native P. aeruginosa but rather promotes non-social adaptation during long-term cultivation.
AU  - Schuster, M.*
AU  - Sexton, D.J.*
AU  - Hense, B.A.
C1  - 51630
C2  - 43401
CY  - Lausanne
TI  - Corrigendum: Why quorum sensing controls private goods [Front. Microbiol, 8, (2017) (885)] doi: 10.3389/fmicb.2017.00885.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Aiming to comprehensively survey the potential pollution of an alpine cryoconite (Jamtalferner glacier, Austria), and its bacterial community structure along with its biodegrading potential, first chemical analyses of persistent organic pollutants, explicitly polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) as well as polycyclic aromatic hydrocarbons (PAHs), revealed a significant contamination. In total, 18 PCB congeners were detected by high resolution gas chromatography/mass spectrometry with a mean concentration of 0.8 ng/g dry weight; 16 PAHs with an average concentration of 1,400 ng/g; and 26 out of 29 OCPs with a mean concentration of 2.4 ng/g. Second, the microbial composition was studied using 16S amplicon sequencing. The analysis revealed high abundances of Proteobacteria (66%), the majority representing a-Proteobacteria (87%); as well as Cyanobacteria (32%), however high diversity was due to 11 low abundant phyla comprising 75 genera. Biodegrading potential of cryoconite bacteria was further analyzed using enrichment cultures (microcosms) with PCB mixture Aroclor 1242. 16S rDNA analysis taxonomically classified 37 different biofilm-forming and PCB-degrading bacteria, represented by Pseudomonas, Shigella, Subtercola, Chitinophaga, and Janthinobacterium species. Overall, the combination of culture-dependent and culture-independent methods identified degrading bacteria that can be potential candidates to develop novel bioremediation strategies.
AU  - Weiland-Bräuer, N.*
AU  - Fischer, M.A.*
AU  - Schramm, K.-W.
AU  - Schmitz, R.A.*
C1  - 51401
C2  - 43042
CY  - Lausanne
TI  - Polychlorinated biphenyl (PCB)-degrading potential of microbes present in a cryoconite of Jamtalferner glacier.
JO  - Front. Microbiol.
VL  - 8
PB  - Frontiers Media Sa
PY  - 2017
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Fusarium graminearum is an opportunistic pathogen of cereals where it causes severe yield losses and concomitant mycotoxin contamination of the grains. The pathogen has mixed biotrophic and necrotrophic (saprophytic) growth phases during infection and the regulatory networks associated with these phases have so far always been analyzed together. In this study we compared the transcriptomes of fungal cells infecting a living, actively defending plant representing the mixed live style (pathogenic growth on living flowering wheat heads) to the response of the fungus infecting identical, but dead plant tissues (cold-killed flowering wheat heads) representing strictly saprophytic conditions. We found that the living plant actively suppressed fungal growth and promoted much higher toxin production in comparison to the identical plant tissue without metabolism suggesting that molecules signaling secondary metabolite induction are not pre-existing or not stable in the plant in sufficient amounts before infection. Differential gene expression analysis was used to define gene sets responding to the active or the passive plant as main impact factor and driver for gene expression. We correlated our results to the published F. graminearum transcriptomes, proteomes, and secretomes and found that only a limited number of in planta- expressed genes require the living plant for induction but the majority uses simply the plant tissue as signal. Many secondary metabolite (SM) gene clusters show a heterogeneous expression pattern within the cluster indicating that different genetic or epigenetic signals govern the expression of individual genes within a physically linked cluster. Our bioinformatic approach also identified fungal genes which were actively repressed by signals derived from the active plant and may thus represent direct targets of the plant defense against the invading pathogen.
AU  - Boedi, S.*
AU  - Berger, H.*
AU  - Sieber, C.M.K.*
AU  - Münsterkötter, M.
AU  - Maloku, I.*
AU  - Warth, B.*
AU  - Sulyok, M.*
AU  - Lemmens, M.*
AU  - Schuhmacher, R.*
AU  - Güldener, U.*
AU  - Strauss, J.*
C1  - 49254
C2  - 41779
CY  - Lausanne
TI  - Comparison of Fusarium graminearum transcriptomes on living or dead wheat differentiates substrate-responsive and defense-responsive genes.
JO  - Front. Microbiol.
VL  - 7
PB  - Frontiers Media Sa
PY  - 2016
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
AU  - Kramer, S.*
AU  - Dibbern, D.
AU  - Moll, J.*
AU  - Huenninghaus, M.*
AU  - Koller, R.*
AU  - Krueger, D.*
AU  - Marhan, S.*
AU  - Urich, T.*
AU  - Wubet, T.*
AU  - Bonkowski, M.*
AU  - Buscot, F.*
AU  - Lueders, T.
AU  - Kandeler, E.*
C1  - 49708
C2  - 40881
CY  - Lausanne
TI  - Resource partitioning between bacteria, fungi, and protists in the detritusphere of an agricultural soil.
JO  - Front. Microbiol.
VL  - 7
PB  - Frontiers Media Sa
PY  - 2016
SN  - 1664-302X
ER  - 

TY  - JOUR
AU  - Nesme, J.
AU  - Achouak, W.*
AU  - Agathos, S.N.*
AU  - Bailey, M.*
AU  - Baldrian, P.*
AU  - Brunel, D.*
AU  - Frostegård,*
AU  - Heulin, T.*
AU  - Jansson, J.K.*
AU  - Jurkevitch, E.*
AU  - Kruus, K.L.*
AU  - Kowalchuk, G.A.*
AU  - Lagares, A.*
AU  - Lappin-Scott, H.M.*
AU  - Lemanceau, P.*
AU  - Le Paslier, D.*
AU  - Mandic-Mulec, I.*
AU  - Murrell, J.C.*
AU  - Myrold, D.D.*
AU  - Nalin, R.*
AU  - Nannipieri, P.*
AU  - Neufeld, J.D.*
AU  - O'Gara, F.*
AU  - Parnell, J.J.*
AU  - Pühler, A.*
AU  - Pylro, V.*
AU  - Ramos, J.L.*
AU  - Roesch, L.F.*
AU  - Schloter, M.
AU  - Schleper, C.*
AU  - Sczyrba, A.*
AU  - Sessitsch, A.*
AU  - Sjöling, S.*
AU  - Sørensen, J.*
AU  - Sørensen, S.J.*
AU  - Tebbe, C.C.*
AU  - Topp, E.M.*
AU  - Tsiamis, G.*
AU  - van Elsas, J.D.*
AU  - van Keulen, G.*
AU  - Widmer, F.*
AU  - Wagner, M.*
AU  - Zhang, T.*
AU  - Zhang, X.*
AU  - Zhao, L.*
AU  - Zhu, Y.G.*
AU  - Vogel, T.M.*
AU  - Simonet, P.*
C1  - 47949
C2  - 39771
CY  - Lausanne
TI  - Back to the future of soil metagenomics.
JO  - Front. Microbiol.
VL  - 7
PB  - Frontiers Media Sa
PY  - 2016
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation.
AU  - Stempfhuber, B.
AU  - Richter-Heitmann, T.*
AU  - Regan, K.M.*
AU  - Kölbl, A.*
AU  - Kaul, P.*
AU  - Marhan, S.*
AU  - Sikorski, J.*
AU  - Overmann, J.*
AU  - Friedrich, M.W.*
AU  - Kandeler, E.*
AU  - Schloter, M.
C1  - 47629
C2  - 39426
TI  - Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil.
JO  - Front. Microbiol.
VL  - 6
PY  - 2016
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Household washing machines (WMs) launder soiled clothes and textiles, but do not sterilize them. We investigated the microbial exchange occurring in five household WMs. Samples from a new cotton T-shirt were laundered together with a normal laundry load. Analyses were performed on the influent water and the ingoing cotton samples, as well as the greywater and the washed cotton samples. The number of living bacteria was generally not lower in the WM effluent water as compared to the influent water. The laundering process caused a microbial exchange of influent water bacteria, skin-, and clothes-related bacteria and biofilm-related bacteria in the WM. A variety of biofilm-producing bacteria were enriched in the effluent after laundering, although their presence in the cotton sample was low. Nearly all bacterial genera detected on the initial cotton sample were still present in the washed cotton samples. A selection for typical skin- and clothes-related microbial species occurred in the cotton samples after laundering. Accordingly, malodour-causing microbial species might be further distributed to other clothes. The bacteria on the ingoing textiles contributed for a large part to the microbiome found in the textiles after laundering.
AU  - Callewaert, C.*
AU  - van Nevel, S.*
AU  - Kerckhof, F.M.*
AU  - Granitsiotis, M.S.
AU  - Boon, N.*
C1  - 47577
C2  - 39323
TI  - Bacterial exchange in household washing machines.
JO  - Front. Microbiol.
VL  - 6
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Bacillus amyloliquefaciens subsp. plantarum FZB42 is a Gram-positive model bacterium for unraveling plant-microbe interactions in Bacilli. In addition, FZB42 is used commercially as biofertilizer and biocontrol agent in agriculture. Genome analysis of FZB42 revealed that nearly 10% of the FZB42 genome is devoted to synthesizing antimicrobial metabolites and their corresponding immunity genes. However, recent investigations in planta demonstrated that - except surfactin - the amount of such compounds found in vicinity of plant roots is relatively low, making doubtful a direct function in suppressing competing microflora including plant pathogens. These metabolites have been also suspected to induce changes within the rhizosphere microbial community, which might affect environment and plant health. However, sequence analysis of rhizosphere samples revealed only marginal changes in the root microbiome, suggesting that secondary metabolites are not the key factor in protecting plants from pathogenic microorganisms. On the other hand, adding FZB42 to plants compensate, at least in part, changes in the community structure caused by the pathogen, indicating an interesting mechanism of plant protection by beneficial Bacilli. Sub-lethal concentrations of cyclic lipopeptides and volatiles produced by plant-associated Bacilli trigger pathways of induced systemic resistance (ISR), which protect plants against attacks of pathogenic microbes, viruses, and nematodes. Stimulation of ISR by bacterial metabolites is likely the main mechanism responsible for biocontrol action of FZB42.
AU  - Chowdhury, S.P.
AU  - Hartmann, A.
AU  - Gao, X.*
AU  - Borriss, R.*
C1  - 46583
C2  - 37700
CY  - Lausanne
TI  - Biocontrol mechanism by root-associated Bacillus amyloliquefaciens FZB42 - a review.
JO  - Front. Microbiol.
VL  - 6
PB  - Frontiers Media Sa
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.
AU  - Gründger, F.*
AU  - Jimenez, N.*
AU  - Thielemann, T.*
AU  - Straaten, N.*
AU  - Lüders, T.
AU  - Richnow, H.-H.*
AU  - Krüger, M.*
C1  - 44047
C2  - 36724
CY  - Lausanne
TI  - Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany.
JO  - Front. Microbiol.
VL  - 6
PB  - Frontiers Research Foundation
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.
AU  - Uksa, M.
AU  - Schloter, M.
AU  - Endesfelder, D.
AU  - Kublik, S.
AU  - Engel, M.
AU  - Kautz, T.*
AU  - Köpke, U.*
AU  - Fischer, D.
C1  - 47383
C2  - 39275
TI  - Prokaryotes in subsoil - evidence for a strong spatial separation of different phyla by analysing co-occurrence networks.
JO  - Front. Microbiol.
VL  - 6
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - In recent years, cases of botulism in cattle and other farm animals and also in farmers increased dramatically. It was proposed, that these cases could be affiliated with the spreading of compost or other organic manures contaminated with Clostridium botulinum spores on farm land. Thus, soils and fodder plants and finally farm animals could be contaminated. Therefore, the colonization behavior and interaction of the botulinum neurotoxin (BoNT D) producing C. botulinum strain 2301 and the non-toxin producing Clostridium sporogenes strain 1739 were investigated on clover (Trifolium repens) in a field experiment as well as in phytochamber experiments applying axenic and additionally soil based systems under controlled conditions. Plants were harvested and divided into root and shoot parts for further DNA isolation and polymerase chain reaction (PCR) assays; subsamples were fixed for fluorescence in situ hybridization analysis in combination with confocal laser scanning microscopy. In addition, we observed significant differences in the growth behavior of clover plants when inoculated with clostridial spores, indicating a plant growth promoting effect. Inoculated plants showed an increased growth index (shoot size, wet and dry weight) and an enlarged root system induced by the systemic colonization of clover by C. botulinum strain 2301. To target C. botulinum and C. sporogenes, 16S rDNA directed primers were used and to specifically detect C. botulinum, BoNT D toxin genes targeted primers, using a multiplex PCR approach, were applied. Our results demonstrate an effective colonization of roots and shoots of clover by C. botulinum strain 2301 and C. sporogenes strain 1739. Detailed analysis of colonization behavior showed that C. botulinum can occur as individual cells, in cell clusters and in microcolonies within the rhizosphere, lateral roots and within the roots tissue of clover.
AU  - Zeiller, M.
AU  - Rothballer, M.
AU  - Iwobi, A.*
AU  - Böhnel, H.*
AU  - Gessler, F.*
AU  - Hartmann, A.
AU  - Schmid, M.
C1  - 47157
C2  - 39122
TI  - Systemic colonization of clover (Trifolium repens) by Clostridium botulinum strain 2301.
JO  - Front. Microbiol.
VL  - 6
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of "everything is everywhere, but the environment selects." Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches.
AU  - Zwirglmaier, K.*
AU  - Keiz, K.*
AU  - Engel, M.
AU  - Geist, J.*
AU  - Raeder, U.*
C1  - 47135
C2  - 39165
TI  - Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria.
JO  - Front. Microbiol.
VL  - 6
PY  - 2015
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant’s second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.
AU  - Berg, G.*
AU  - Grube, M.*
AU  - Schloter, M.
AU  - Smalla, K.*
C1  - 31564
C2  - 34551
CY  - Lausanne
TI  - Unraveling the plant microbiome: Looking back and future perspectives.
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The study of plant-microbe associations by new techniques has significantly improved our understanding of the structure and specificity of the plant microbiome. Yet, microbiome function and the importance of the plant’s microbiome in the context of human and plant health are largely unexplored. Comparable with our human microbiome, millions of microbes inhabit plants, forming complex ecological communities that influence plant growth and health through its collective metabolic activities and host interactions. Viewing the microbiota from an ecological perspective can provide insight into how to promote plant health and stress tolerance of their hosts or how to adapt to a changing climate by targeting this microbial community. Moreover, the plant microbiome has a substantial impact on human health by influencing our gut microbiome by eating raw plants such as lettuce and herbs and but also by influencing the microbiome of our environment through airflow. This research topic will highlight the current knowledge regarding plant microbiomes, their specificity, diversity and function. Especially welcome are articles focused on the microbiomes of fresh edible plants and their impact on human health. Furthermore all applied aspects studying the management of plant microbiomes to enhance plant growth, health quality and stress tolerance are encouraged.
AU  - Berg, G.*
AU  - Grube, M.*
AU  - Schloter, M.
AU  - Smalla, K.*
C1  - 32185
C2  - 34984
CY  - Lausanne
TI  - The plant microbiome and its importance for plant and human health.
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Many bacteria belonging to the phylum of Actinobacteria are known as antagonists against phytpathogenic microbes. This study aimed to analyze the effect of ozone on the actinobacterial community of the rhizosphere of four years old European beech (Fagus sylvatica L.) trees during different time points of the vegetation period. Effects of ozone on the total community structure of Actinobacteria were studied based on the analysis of 16S rRNA gene amplicons. In addition effects of the ozone treatment on the diversity of potential biocontrol active Actionobacteria being able to produce antibiotics were characterized by using the type II polyketide synthases (PKS) genes as marker. Season as well as ozone treatments had a significant effect on parts of the actinobacterial rhizosphere community of European beech. However on the basis of the performed analysis, the diversity of Actinobacteria possessing type II PKS genes is neither affected by seasonal changes nor by the ozone treatments, indicating no influence of the investigated treatments on the biocontrol active part of the actinobacterial community.
AU  - Haesler, F.
AU  - Hagn, A.
AU  - Engel, M.
AU  - Schloter, M.
C1  - 30668
C2  - 36326
CY  - Lausanne
TI  - Impact of elevated atmospheric O3 on the actinobacterial community structure and function in the rhizosphere of European beech (Fagus sylvatica L.).
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - In recent years, increasing numbers of outbreaks caused by the consumption of vegetables contaminated with human pathogenic bacteria were reported. The application of organic fertilizers during vegetable production is one of the possible reasons for contamination with those pathogens. In this study laboratory experiments in axenic and soil systems following common practices in organic farming were conducted to identify the minimal dose needed for bacterial colonization of plants and to identify possible factors like bacterial species or serovariation, plant species or organic fertilizer types used, influencing the success of plant colonization by human pathogenic bacteria. Spinach and corn salad were chosen as model plants and were inoculated with different concentrations of Salmonella enterica sv. Weltevreden, Listeria monocytogenes sv. 4b and EGD-E sv. 1/2a either directly (axenic system) or via agricultural soil amended with spiked organic fertilizers (soil system). In addition to PCR- and culture-based detection methods, fluorescence in situ hybridization (FISH) was applied in order to localize bacteria on or in plant tissues. Our results demonstrate that shoots were colonized by the pathogenic bacteria at inoculation doses as low as 4 × 10 CFU/ml in the axenic system or 4 × 10(5) CFU/g in the soil system. In addition, plant species dependent effects were observed. Spinach was colonized more often and at lower inoculation doses compared to corn salad. Differential colonization sites on roots, depending on the plant species could be detected using FISH-CLSM analysis. Furthermore, the transfer of pathogenic bacteria to plants via organic fertilizers was observed more often and at lower initial inoculation doses when fertilization was performed with inoculated slurry compared to inoculated manure. Finally, it could be shown that by introducing a simple washing step, the bacterial contamination was reduced in most cases or even was removed completely in some cases.
AU  - Hofmann, A.
AU  - Fischer, D.
AU  - Hartmann, A.
AU  - Schmid, M.
C1  - 31282
C2  - 34406
CY  - Lausanne
TI  - Colonization of plants by human pathogenic bacteria in the course of organic vegetable production.
JO  - Front. Microbiol.
VL  - 5
IS  - MAY
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Application of the plant associated bacterium Bacillus amyloliquefaciens FZB42 on lettuce (Lactuca sativa) confirmed its capability to promote plant growth and health by reducing disease severity (DS) caused by the phytopathogenic fungus Rhizoctonia solani. Therefore this strain is commercially applied as an eco-friendly plant protective agent. It is able to produce cyclic lipopeptides (CLP) and polyketides featuring antifungal and antibacterial properties. Production of these secondary metabolites led to the question of a possible impact of strain FZB42 on the composition of microbial rhizosphere communities after its application. Rating of DS and lettuce growth during a field trial confirmed the positive impact of strain FZB42 on the health of the host plant. To verify B. amyloliquefaciens as an environmentally compatible plant protective agent, its effect on the indigenous rhizosphere community was analyzed by metagenome sequencing. Rhizosphere microbial communities of lettuce treated with B. amyloliquefaciens FZB42 and non-treated plants were profiled by high-throughput metagenome sequencing of whole community DNA. Fragment recruitments of metagenome sequence reads on the genome sequence of B. amyloliquefaciens FZB42 proved the presence of the strain in the rhizosphere over 5 weeks of the field trial. Comparison of taxonomic community profiles only revealed marginal changes after application of strain FZB42. The orders Burkholderiales, Actinomycetales and Rhizobiales were most abundant in all samples. Depending on plant age a general shift within the composition of the microbial communities that was independent of the application of strain FZB42 was observed. In addition to the taxonomic profiling, functional analysis of annotated sequences revealed no major differences between samples regarding application of the inoculant strain.
AU  - Kröber, M.*
AU  - Wibberg, D.*
AU  - Grosch, R.*
AU  - Eikmeyer, F.*
AU  - Verwaaijen, B.*
AU  - Chowdhury, S.P.
AU  - Hartmann, A.
AU  - Pühler, A.*
AU  - Schlüter, A.*
C1  - 31553
C2  - 34567
CY  - Lausanne
TI  - Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing.
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.
AU  - Magalhães, C.M.*
AU  - Machado, A.*
AU  - Frank-Fahle, B.
AU  - Lee, C.K.*
AU  - Cary, S.C.*
C1  - 32560
C2  - 35144
CY  - Lausanne
TI  - The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys.
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and might be a useful agent to stimulate bioremediation of hydrocarbons in contaminated soils. - See more at: http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00096/abstract#sthash.kWHdc5jQ.dpuf
AU  - Wallisch, S.
AU  - Gril, T.
AU  - Dong, X.
AU  - Welzl, G.
AU  - Bruns, C.*
AU  - Heath, E.*
AU  - Engel, M.
AU  - Suhaldoc, M.*
AU  - Schloter, M.
C1  - 30786
C2  - 33858
CY  - Lausanne
TI  - Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons.
JO  - Front. Microbiol.
VL  - 5
PB  - Frontiers Research Foundation
PY  - 2014
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - In a field experiment, the impact of repeated application of the antibiotic sulfadiazine (SDZ)-contaminated pig manure was assessed on functional microbial communities involved in ammonia and nitrite oxidation in the root-rhizosphere complexes (RRCs) of diverse plants composing a pasture. We surveyed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) as well as Nitrobacter- and Nitrospira-like nitrite-oxidizing bacteria (NOB) by quantitative PCR (qPCR), and the diversity of amoA AOA and Nitrobacter-like nxrA amplicons using a cloning-sequencing approach. Whereas the first SDZ-contaminated manure application caused only slight effects on the investigated microbial communities and did not change the diversity and abundance pattern significantly, the second application of SDZ-contaminated manure induced an up to 15-fold increased ratio of AOA:AOB and a reduction of nrxA genes. The diversity of AOA amoA increased after the second application of SDZ-contaminated manure compared to the control treatment whereas a clear reduction of nrxA OTUs was visible in the same samples. The results indicate that the application of SDZ may principally affect nitrite oxidation by NOB and alternative pathways like nitrite reduction might be favored under these conditions.
AU  - Ollivier, J.
AU  - Schacht, D.
AU  - Kindler, R.*
AU  - Groeneweg, J.*
AU  - Engel, M.
AU  - Wilke, B.-M.*
AU  - Kleineidam, K.
AU  - Schloter, M.
C1  - 22750
C2  - 30923
TI  - Effects of repeated application of sulfadiazine-contaminated pig manure on the abundance and diversity of ammonia and nitrite oxidizers in the root-rhizosphere complex of pasture plants under field conditions.
JO  - Front. Microbiol.
VL  - 4
PB  - Frontiers Media
PY  - 2013
SN  - 1664-302X
ER  - 

TY  - JOUR
AB  - The diazotrophic, bacterial endophyte Herbaspirillum frisingense GSF30(T) has been identified in biomass grasses grown in temperate climate, including the highly nitrogen-efficient grass Miscanthus. Its genome was annotated and compared with related Herbaspirillum species from diverse habitats, including H. seropedicae, and further well-characterized endophytes. The analysis revealed that Herbaspirillum frisingense lacks a type III secretion system that is present in some related Herbaspirillum grass endophytes. Together with the lack of components of the type II secretion system, the genomic inventory indicates distinct interaction scenarios of endophytic Herbaspirillum strains with plants. Differences in respiration, carbon, nitrogen and cell wall metabolism among Herbaspirillum isolates partially correlate with their different habitats. Herbaspirillum frisingense is closely related to strains isolated from the rhizosphere of phragmites and from well water, but these lack nitrogen fixation and metabolism genes. Within grass endophytes, the high diversity in their genomic inventory suggests that even individual plant species provide distinct, highly diverse metabolic niches for successful endophyte-plant associations.
AU  - Straub, D.*
AU  - Rothballer, M.
AU  - Hartmann, A.
AU  - Ludewig, U.*
C1  - 27578
C2  - 32730
CY  - Lausanne
TI  - The genome of the endophytic bacterium H. frisingense GSF30T identifies diverse strategies in the Herbaspirillum genus to interact with plants.
JO  - Front. Microbiol.
VL  - 4
PB  - Forntiers Research Foundation
PY  - 2013
SN  - 1664-302X
ER  -