TY  - JOUR
AB  - The COVID-19 pandemic has increased interest in wastewater-based 
      epidemiology (WBE) as a reliable and cost-effective framework for 
      monitoring the spread of microbes. However, WBE frameworks have rarely 
      been applied to the study of fecal–oral transmissible diseases, except 
      for poliomyelitis. Here, we investigated the presence of hepatitis A 
      virus (HAV) and hepatitis E virus (HEV) in wastewater in Munich. We 
      collected wastewater samples between July 2020 and November 2023. A 
      total of 186 samples were processed using centrifugation and analyzed 
      for HAV- and HEV-RNA using RT-qPCR. As a reference, we used notification
       data from clinically or laboratory-diagnosed hepatitis A and E cases. 
      Lockdown stringency levels were derived from official documentation. Our
       results show that 87.6% of wastewater samples were positive for HEV at 
      concentrations of 9.0 × 101 to 2.5 × 105 copies/L, while HAV was only detectable in 7.5% of the samples at viral loads of 4.6 × 101 to 2.4 × 103
       copies/L. We also detected differences in HEV concentrations but not in
       case numbers when comparing lockdown and no-lockdown periods. This 
      study covers all but the first lockdowns in Bavaria. We present a unique
       real-world dataset evaluating the impact of lockdown interventions on 
      hepatitis A and E case numbers, as well as on the concentrations of HAV 
      and HEV in wastewater. Person-to-person spread and eating out appear to 
      have contributed to the transmission of HEV. In addition, the 
      consistently high HEV concentrations in sewage support the findings of 
      serological studies, indicating a substantial burden of undetected 
      subclinical infections.
AU  - Javanmardi, J.*
AU  - Schemmerer, M.*
AU  - Wallrafen-Sam, K.*
AU  - Neusser, J.*
AU  - Rubio‐Acero, R.*
AU  - Hoelscher, M.
AU  - Kletke, T.*
AU  - Boehm, B.O.*
AU  - Schneider, M.*
AU  - Waldeck, E.*
AU  - Hoch, M.*
AU  - Böhmer, M.M.*
AU  - Geldmacher, C.*
AU  - Hasenauer, J.
AU  - Wenzel, J.J.*
AU  - Wieser, A.*
C1  - 75804
C2  - 58000
SP  - 2379 - 2379
TI  - Continuous circulation of hepatitis E and A viruses during COVID-19 pandemic lockdowns in Munich, Germany—experience from three years of wastewater surveillance.
JO  - Microorganisms
VL  - 13
IS  - 10
PY  - 2025
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Viral meningitis poses a significant clinical challenge due to its rapid onset and potential progression to life-threatening encephalitis. Early detection of treatable viral pathogens such as Herpes simplex virus (HSV), Cytomegalovirus (CMV), and Varicella-zoster virus (VZV) is essential for initiating appropriate therapies. However, multiplex PCRs for the rapid and simultaneous detection of these pathogens are scarce due to the complex PCR design and the elaborate validation process using cerebrospinal fluid samples. In this study, we established and validated a novel multiplex PCR assay for detecting HSV, CMV, and VZV in cerebrospinal fluid samples and implemented the assay on a fully automated platform.
AU  - Luzius, T.
AU  - Jeske, S.
AU  - Baer, J.*
AU  - Goelnitz, U.*
AU  - Protzer, U.
AU  - Wettengel, J.M.
C1  - 73174
C2  - 56945
TI  - A multiplex polymerase chain reaction assay for the detection of herpes simplex virus, cytomegalovirus, and varicella-zoster virus in cerebrospinal Fluid.
JO  - Microorganisms
VL  - 13
IS  - 1
PY  - 2025
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
AU  - Daakour, S.*
AU  - Nelson, D.R.*
AU  - Fu, W.*
AU  - Jaiswal, A.*
AU  - Dohai, B.S.M.
AU  - Alzahmi, A.S.*
AU  - Koussa, J.*
AU  - Huang, X.*
AU  - Shen, Y.*
AU  - Twizere, J.C.*
AU  - Salehi-Ashtiani, K.*
C1  - 71560
C2  - 56305
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Adaptive evolution signatures in Prochlorococcus: Open reading frame (ORF)eome resources and insights from comparative genomics.
JO  - Microorganisms
VL  - 12
IS  - 8
PB  - Mdpi
PY  - 2024
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
AU  - Ishola, O.A.
AU  - Kublik, S.
AU  - Durai Raj, A.C.
AU  - Ohnmacht, C.
AU  - Schulz, S.
AU  - Fösel, B.
AU  - Schloter, M.
C1  - 70034
C2  - 55371
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Comparative metagenomic analysis of bacteriophages and prophages in gnotobiotic mouse models.
JO  - Microorganisms
VL  - 12
IS  - 2
PB  - Mdpi
PY  - 2024
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - The intricate relationship between chronic lung diseases and viral infections is a significant concern in respiratory medicine. We explore how pre-existing lung conditions, including chronic obstructive pulmonary disease, asthma, and interstitial lung diseases, influence susceptibility, severity, and outcomes of viral infections. We also examine how viral infections exacerbate and accelerate the progression of lung disease by disrupting immune responses and triggering inflammatory pathways. By summarizing current evidence, this review highlights the bidirectional nature of these interactions, where underlying lung diseasesincrease vulnerability to viral infections, while these infections, in turn, worsen the clinical course. This review underscores the importance of preventive measures, such as vaccination, early detection, and targeted therapies, to mitigate adverse outcomes in patients with chronic lung conditions. The insights provided aim to inform clinical strategies that can improve patient management and reduce the burden of chronic lung diseases exacerbated by viral infections.
AU  - Suri, C.*
AU  - Pande, B.*
AU  - Sahithi, L.S.*
AU  - Sahu, T.*
AU  - Verma, H.K.
C1  - 72160
C2  - 56412
TI  - Interplay between lung diseases and viral infections: A comprehensive review.
JO  - Microorganisms
VL  - 12
IS  - 10
PY  - 2024
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Immunocompromised individuals are at higher risk of developing protracted and severe COVID-19, and understanding individual disease courses and SARS-CoV-2 immune responses in these individuals is of the utmost importance. For more than two years, we followed an immunocompromised individual with a protracted SARS-CoV-2 infection that was eventually cleared in the absence of a humoral neutralizing SARS-CoV-2 antibody response. By conducting an in-depth examination of this individual’s immune response and comparing it to a large cohort of convalescents who spontaneously cleared a SARS-CoV-2 infection, we shed light on the interplay between B- and T-cell immunity and how they interact in clearing SARS-CoV-2 infection.
AU  - Bunse, T.
AU  - Körber, N.
AU  - Wintersteller, H.*
AU  - Schneider, J.*
AU  - Graf, A.*
AU  - Radonić, A.*
AU  - Thuermer, A.*
AU  - von Kleist, M.*
AU  - Blum, H.*
AU  - Spinner, C.D.*
AU  - Bauer, T.
AU  - Knolle, P.A.*
AU  - Protzer, U.
AU  - Schulte, E.C.
C1  - 68424
C2  - 54651
TI  - T-cell-dominated immune response resolves protracted SARS-CoV-2 infection in the absence of neutralizing antibodies in an immunocompromised individual.
JO  - Microorganisms
VL  - 11
IS  - 6
PY  - 2023
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).
AU  - Sommermann, L.*
AU  - Babin, D.*
AU  - Behr, J.H.*
AU  - Chowdhury, S.P.
AU  - Sandmann, M.*
AU  - Windisch, S.*
AU  - Neumann, G.*
AU  - Nesme, J.*
AU  - Sørensen, S.J.*
AU  - Schellenberg, I.*
AU  - Rothballer, M.
AU  - Geistlinger, J.*
AU  - Smalla, K.*
AU  - Grosch, R.*
C1  - 66290
C2  - 53127
TI  - Long-term fertilization strategy impacts Rhizoctonia solani–microbe interactions in soil and rhizosphere and defense responses in lettuce.
JO  - Microorganisms
VL  - 10
IS  - 9
PY  - 2022
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Alcoholic fermentation is known to be a key stage in the winemaking process that directly impacts the composition and quality of the final product. Twelve wines were obtained from fermentations of Chardonnay must made with twelve different commercial wine yeast strains of Saccharomyces cerevisiae. In our study, FT-ICR-MS, GC-MS, and sensory analysis were combined with multivariate analysis. Ultra-high-resolution mass spectrometry (uHRMS) was able to highlight hundreds of metabolites specific to each strain from the same species, although they are characterized by the same technological performances. Furthermore, the significant involvement of nitrogen metabolism in this differentiation was considered. The modulation of primary metabolism was also noted at the volatilome and sensory levels. Sensory analysis allowed us to classify wines into three groups based on descriptors associated with white wine. Thirty-five of the volatile compounds analyzed, including esters, medium-chain fatty acids, superior alcohols, and terpenes discriminate and give details about differences between wines. Therefore, phenotypic differences within the same species revealed metabolic differences that resulted in the diversity of the volatile fraction that participates in the palette of the sensory pattern. This original combination of metabolomics with the volatilome and sensory approaches provides an integrative vision of the characteristics of a given strain. Metabolomics shine the new light on intraspecific discrimination in the Saccharomyces cerevisiae species.
AU  - Bordet, F.*
AU  - Roullier-Gall, C.*
AU  - Ballester, J.*
AU  - Vichi, S.*
AU  - Quintanilla-Casas, B.*
AU  - Gougeon, R.D.*
AU  - Julien-Ortiz, A.*
AU  - Schmitt-Kopplin, P.
AU  - Alexandre, H.*
C1  - 63511
C2  - 51348
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Different wines from different yeasts? “Saccharomyces cerevisiae intraspecies differentiation by metabolomic signature and sensory patterns in wine”.
JO  - Microorganisms
VL  - 9
IS  - 11
PB  - Mdpi
PY  - 2021
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - This study aimed to investigate the effects of different levels of soil‐ and plant‐associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gai-ellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that lit-ter‐associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
AU  - Chiba, A.
AU  - Uchida, Y.*
AU  - Kublik, S.
AU  - Vestergaard, G.
AU  - Buegger, F.
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 61373
C2  - 50180
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Soil bacterial diversity is positively correlated with decomposition rates during early phases of maize litter decomposition.
JO  - Microorganisms
VL  - 9
IS  - 2
PB  - Mdpi
PY  - 2021
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacAdependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.
AU  - Lalaouna, D.*
AU  - Fochesato, S.*
AU  - Harir, M.
AU  - Ortet, P.*
AU  - Schmitt-Kopplin, P.
AU  - Heulin, T.*
AU  - Achouak, W.*
C1  - 61154
C2  - 50071
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Amplifying and fine-tuning Rsm sRNAs expression and stability to optimize the survival of Pseudomonas brassicacerum in nutrient-poor environments.
JO  - Microorganisms
VL  - 9
IS  - 2
PB  - Mdpi
PY  - 2021
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - The relationship between viruses (dominated by bacteriophages or phages) and lower gastrointestinal (GI) tract diseases has been investigated, whereas the relationship between gut bacteriophages and upper GI tract diseases, such as esophageal diseases, which mainly include Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC), remains poorly described. This study aimed to reveal the gut bacteriophage community and their behavior in the progression of esophageal diseases. In total, we analyzed the gut phage community of sixteen samples from patients with esophageal diseases (six BE patients and four EAC patients) as well as six healthy controls. Differences were found in the community composition of abundant and rare bacteriophages among three groups. In addition, the auxiliary metabolic genes (AMGs) related to bacterial exotoxin and virulence factors such as lipopolysaccharides (LPS) biosynthesis proteins were found to be more abundant in the genome of rare phages from BE and EAC samples compared to the controls. These results suggest that the community composition of gut phages and functional traits encoded by them were different in two stages of esophageal diseases. However, the findings from this study need to be validated with larger sample sizes in the future.
AU  - Ma, T.
AU  - Ru, J.
AU  - Xue, J.
AU  - Schulz, S.
AU  - Mirzaei, M.K.
AU  - Janssen, K.P.*
AU  - Quante, M.*
AU  - Deng, L.
C1  - 62794
C2  - 51063
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Differences in gut virome related to barrett esophagus and esophageal adenocarcinoma.
JO  - Microorganisms
VL  - 9
IS  - 8
PB  - Mdpi
PY  - 2021
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
AU  - Schulze-Makuch, D.*
AU  - Lipus, D.*
AU  - Arens, F.L.*
AU  - Baqué, M.*
AU  - Bornemann, T.L.V.*
AU  - Devere, J.P.*
AU  - Flury, M.*
AU  - Frösler, J.*
AU  - Heinz, J.*
AU  - Hwang, Y.*
AU  - Kounaves, S.P.*
AU  - Mangelsdorf, K.*
AU  - Meckenstock, R.U.*
AU  - Pannekens, M.*
AU  - Probst, A.J.*
AU  - Sáenz, J.S.
AU  - Schirmack, J.*
AU  - Schloter, M.
AU  - Schmitt-Kopplin, P.
AU  - Schneider, B.*
AU  - Uhl, J.
AU  - Vestergaard, G.*
AU  - Valenzuela, B.*
AU  - Zamorano, P.*
AU  - Wagner, D.*
C1  - 62052
C2  - 50617
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Microbial hotspots in lithic microhabitats inferred from dna fractionation and metagenomics in the atacama desert.
JO  - Microorganisms
VL  - 9
IS  - 5
PB  - Mdpi
PY  - 2021
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - The analysis of the gut microbiome with respect to health care prevention and diagnostic purposes is increasingly the focus of current research. We analyzed around 2000 stool samples from the KORA (Cooperative Health Research in the Region of Augsburg) cohort using high-throughput 16S rRNA gene amplicon sequencing representing a total microbial diversity of 2089 operational taxonomic units (OTUs). We evaluated the combination of three different components to assess the reflection of obesity related to microbiota profiles: (i) four prediction methods (i.e., partial least squares (PLS), support vector machine regression (SVMReg), random forest (RF), and M5Rules); (ii) five OTU data transformation approaches (i.e., no transformation, relative abundance without and with log-transformation, as well as centered and isometric log-ratio transformations); and (iii) predictions from nine measurements of obesity (i.e., body mass index, three measures of body shape, and five measures of body composition). Our results showed a substantial impact of all three components. The applications of SVMReg and PLS in combination with logarithmic data transformations resulted in considerably predictive models for waist circumference-related endpoints. These combinations were at best able to explain almost 40% of the variance in obesity measurements based on stool microbiota data (i.e., OTUs) only. A reduced loss in predictive performance was seen after sex-stratification in waist-height ratio compared to other waist-related measurements. Moreover, our analysis showed that the contribution of OTUs less prevalent and abundant is minor concerning the predictive power of our models.
AU  - Troll, M.
AU  - Brandmaier, S.
AU  - Reitmeier, S.*
AU  - Adam, J.
AU  - Sharma, S.
AU  - Sommer, A.
AU  - Bind, M.A.*
AU  - Neuhaus, K.*
AU  - Clavel, T.*
AU  - Adamski, J.
AU  - Haller, D.*
AU  - Peters, A.
AU  - Grallert, H.
C1  - 58851
C2  - 48406
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Investigation of adiposity measures and operational taxonomic unit (OTU) data transformation procedures in stool samples from a German Cohort Study using machine learning algorithms.
JO  - Microorganisms
VL  - 8
IS  - 4
PB  - Mdpi
PY  - 2020
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Mechanisms used by plants to respond to water limitation have been extensively studied. However, even though the inoculation of beneficial microbes has been shown to improve plant performance under drought stress, the inherent role of soil microbes on plant response has been less considered. In the present work, we assessed the importance of the soil microbiome for the growth of barley plants under drought stress. Plant growth was not significantly affected by the disturbance of the soil microbiome under regular watering. However, after drought stress, we observed a significant reduction in plant biomass, particularly of the root system. Plants grown in the soil with disturbed microbiome were significantly more affected by drought and did not recover two weeks after re-watering. These effects were accompanied by changes in the composition of endophytic fungal and bacterial communities. Under natural conditions, soil-derived plant endophytes were major colonizers of plant roots, such as Glycomyces and Fusarium, whereas, for plants grown in the soil with disturbed microbiome seed-born bacterial endophytes, e.g., Pantoea, Erwinia, and unclassified Pseudomonaceae and fungal genera normally associated with pathogenesis, such as Gibberella and Gaeumannomyces were observed. Therefore, the role of the composition of the indigenous soil microbiota should be considered in future approaches to develop management strategies to make plants more resistant towards abiotic stress, such as drought.
AU  - Yang, L.
AU  - Schröder, P.
AU  - Vestergaard, G.*
AU  - Schloter, M.
AU  - Radl, V.
C1  - 60063
C2  - 49203
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Response of barley plants to drought might be associated with the recruiting of soil-borne endophytes.
JO  - Microorganisms
VL  - 8
IS  - 9
PB  - Mdpi
PY  - 2020
SN  - 2076-2607
ER  - 

TY  - JOUR
AB  - Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ.
AU  - Pilloni, G.
AU  - Bayer, A.
AU  - Ruth-Anneser, B.
AU  - Fillinger, L.
AU  - Engel, M.
AU  - Griebler, C.
AU  - Lueders, T.
C1  - 55492
C2  - 46276
CY  - St Alban-anlage 66, Ch-4052 Basel, Switzerland
TI  - Dynamics of hydrology and anaerobic hydrocarbon degrader communities in a tar-oil contaminated aquifer.
JO  - Microorganisms
VL  - 7
IS  - 2
PB  - Mdpi
PY  - 2019
SN  - 2076-2607
ER  -