TY  - JOUR
AB  - Host-bacteria symbioses are specific and transgenerationaly stable. In hosts that acquire their symbionts from the environment, selective mechanisms are required to identify beneficial partners among environmental microorganisms. In Coreoidea stinkbugs, which house environmentally acquired symbionts in the midgut, bacterial competition shapes symbiont specificity whereby Caballeronia strains consistently outcompete other bacteria. Here, we show that competition within the gut also occurs among Caballeronia strains themselves, driving specificity at a finer taxonomic scale. The stinkbugs Riptortus pedestris and Coreus marginatus, when reared on the same soil sample, preferentially selected for α- and β-subclade Caballeronia, respectively. In a gnotobiotic infection system, representative strains from the α-, β-, and γ-subclades can independently colonize the midgut of both insect species in monoculture. However, in pairwise co-culture infections, each host exhibits selectivity for either α- or β-subclade strains, consistent with patterns observed in the soil inoculation experiment. In R. pedestris, we further find that both priority effects and displacement mechanisms shape interspecies competition outcomes. At the molecular level, metabolic capabilities, resistance to antimicrobial peptides, and chemotactic behavior determine symbiont competitive success. In R. pedestris, the reproductive fitness benefits conferred by the symbiosis align with the observed strain specificity in the tested strain panel, suggesting a functional link between symbiont selection and host fitness, despite these processes occurring at distinct stages of the symbiotic relationship. Our findings highlight that the gut in Coreoidea species constitutes a multifactorial, species-specific selective environment that contributes to the colonization of the symbiotic midgut region by the best-adapted Caballeronia strain.
AU  - Lextrait, G.*
AU  - Joardar, S.
AU  - Cossard, R.*
AU  - Kikuchi, Y.*
AU  - Ohbayashi, T.*
AU  - Mergaert, P.*
C1  - 76093
C2  - 58421
CY  - Great Clarendon St, Oxford Ox2 6dp, England
SP  - 13
TI  - Strict gut symbiont specificity in Coreoidea insects governed by interspecies competition within Caballeronia strains.
JO  - ISME J.
VL  - 19
IS  - 1
PB  - Oxford Univ Press
PY  - 2025
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Aerobic methanotrophy is strongly controlled by copper, and methanotrophs are known to use different mechanisms for copper uptake. Some methanotrophs secrete a modified polypeptide-methanobactin-while others utilize a surface-bound protein (MopE) and a secreted form of it (MopE*) for copper collection. As different methanotrophs have different means of sequestering copper, competition for copper significantly impacts methanotrophic activity. Herein, we show that Methylomicrobium album BG8, Methylocystis sp. strain Rockwell, and Methylococcus capsulatus Bath, all lacking genes for methanobactin biosynthesis, are not limited for copper by multiple forms of methanobactin. Interestingly, Mm. album BG8 and Methylocystis sp. strain Rockwell were found to have genes similar to mbnT that encodes for a TonB-dependent transporter required for methanobactin uptake. Data indicate that these methanotrophs "steal" methanobactin and such "theft" enhances the ability of these strains to degrade methylmercury, a potent neurotoxin. Further, when mbnT was deleted in Mm. album BG8, methylmercury degradation in the presence of methanobactin was indistinguishable from when MB was not added. Mc. capsulatus Bath lacks anything similar to mbnT and was unable to degrade methylmercury either in the presence or absence of methanobactin. Rather, Mc. capsulatus Bath appears to rely on MopE/MopE* for copper collection. Finally, not only does Mm. album BG8 steal methanobactin, it synthesizes a novel chalkophore, suggesting that some methanotrophs utilize both competition and cheating strategies for copper collection. Through a better understanding of these strategies, methanotrophic communities may be more effectively manipulated to reduce methane emissions and also enhance mercury detoxification in situ.
AU  - Kang-Yun, C.S.*
AU  - Liang, X.*
AU  - Dershwitz, P.*
AU  - Gu, W.*
AU  - Schepers, A.
AU  - Flatley, A.
AU  - Lichtmannegger, J.
AU  - Zischka, H.
AU  - Zhang, L.*
AU  - Lu, X.*
AU  - Gu, B.*
AU  - Ledesma, J.C.*
AU  - Pelger, D.J.*
AU  - DiSpirito, A.A.*
AU  - Semrau, J.D.*
C1  - 62643
C2  - 50988
CY  - Campus, 4 Crinan St, London, N1 9xw, England
SP  - 211–220
TI  - Evidence for methanobactin "Theft" and novel chalkophore production in methanotrophs: Impact on methanotrophic-mediated methylmercury degradation.
JO  - ISME J.
VL  - 16
PB  - Springernature
PY  - 2022
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.
AU  - Broadbent, A.A.D.*
AU  - Snell, H.S.K.*
AU  - Michas, A.
AU  - Pritchard, W.J.*
AU  - Newbold, L.*
AU  - Cordero, I.*
AU  - Goodall, T.*
AU  - Schallhart, N.*
AU  - Kaufmann, R.*
AU  - Griffiths, R.I.*
AU  - Schloter, M.
AU  - Bahn, M.*
AU  - Bardgett, R.D.*
C1  - 61409
C2  - 50143
CY  - Campus, 4 Crinan St, London, N1 9xw, England
SP  - 2264–2275
TI  - Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt.
JO  - ISME J.
VL  - 15
PB  - Springernature
PY  - 2021
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Cyanobacterial mats were hotspots of biogeochemical cycling during the Precambrian. However, mechanisms that controlled O(2)release by these ecosystems are poorly understood. In an analog to Proterozoic coastal ecosystems, the Frasassi sulfidic springs mats, we studied the regulation of oxygenic and sulfide-driven anoxygenic photosynthesis (OP and AP) in versatile cyanobacteria, and interactions with sulfur reducing bacteria (SRB). Using microsensors and stable isotope probing we found that dissolved organic carbon (DOC) released by OP fuels sulfide production, likely by a specialized SRB population. Increased sulfide fluxes were only stimulated after the cyanobacteria switched from AP to OP. O(2)production triggered migration of large sulfur-oxidizing bacteria from the surface to underneath the cyanobacterial layer. The resultant sulfide shield tempered AP and allowed OP to occur for a longer duration over a diel cycle. The lack of cyanobacterial DOC supply to SRB during AP therefore maximized O(2)export. This mechanism is unique to benthic ecosystems because transitions between metabolisms occur on the same time scale as solute transport to functionally distinct layers, with the rearrangement of the system by migration of microorganisms exaggerating the effect. Overall, cyanobacterial versatility disrupts the synergistic relationship between sulfide production and AP, and thus enhances diel O(2)production.
AU  - Klatt, J.M.*
AU  - Gomez-Saez, G.V.*
AU  - Meyer, S.*
AU  - Ristova, P.P.*
AU  - Yilmaz, P.*
AU  - Granitsiotis, M.S.
AU  - Macalady, J.L.*
AU  - Lavik, G.*
AU  - Polerecky, L.*
AU  - Bühring, S.I.*
C1  - 59887
C2  - 49098
CY  - Macmillan Building, 4 Crinan St, London N1 9xw, England
SP  - 3024-3037
TI  - Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat.
JO  - ISME J.
VL  - 14
IS  - 12
PB  - Nature Publishing Group
PY  - 2020
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Cable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)(2) or Fe(OH)(3) were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.
AU  - Müller, H.*
AU  - Marozava, S.
AU  - Probst, A.J.*
AU  - Meckenstock, R.U.*
C1  - 57384
C2  - 47774
CY  - Macmillan Building, 4 Crinan St, London N1 9xw, England
SP  - 623-634
TI  - Groundwater cable bacteria conserve energy by sulfur disproportionation.
JO  - ISME J.
VL  - 14
IS  - 2
PB  - Nature Publishing Group
PY  - 2020
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - ( )Exploring adaptive strategies by which microorganisms function and survive in low-energy natural environments remains a grand goal of microbiology, and may help address a prime challenge of the 21st century: degradation of man-made chemicals at low concentrations ("micropollutants"). Here we explore physiological adaptation and maintenance energy requirements of a herbicide (atrazine)-degrading microorganism (Arthrobacter aurescens TC1) while concomitantly observing mass transfer limitations directly by compound-specific isotope fractionation analysis. Chemostat-based growth triggered the onset of mass transfer limitation at residual concentrations of 30 mu g L-1 of atrazine with a bacterial population doubling time (t(d)) of 14 days, whereas exacerbated energy limitation was induced by retentostat-based near-zero growth (t(d) = 265 days) at 12 +/- 3 mu g L-1 residual concentration. Retentostat cultivation resulted in (i) complete mass transfer limitation evidenced by the disappearance of isotope fractionation (epsilon C-13 = -0.45%o +/- 0.36 parts per thousand) and (ii) a twofold decrease in maintenance energy requirement compared with chemostat cultivation. Proteomics revealed that retentostat and chemostat cultivation under mass transfer limitation share low protein turnover and expression of stress-related proteins. Mass transfer limitation effectuated slow-down of metabolism in retentostats and a transition from growth phase to maintenance phase indicating a limit of similar or equal to 10 mu g L-1 for long-term atrazine degradation. Further studies on other ecosystem-relevant microorganisms will substantiate the general applicability of our finding that mass transfer limitation serves as a trigger for physiological adaptation, which subsequently defines a lower limit of biodegradation.
AU  - Kundu, K.
AU  - Marozava, S.
AU  - Ehrl, B.
AU  - Merl-Pham, J.
AU  - Griebler, C.
AU  - Elsner, M.
C1  - 56029
C2  - 46789
CY  - Macmillan Building, 4 Crinan St, London N1 9xw, England
SP  - 2236-2251
TI  - Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1.
JO  - ISME J.
VL  - 13
IS  - 9
PB  - Nature Publishing Group
PY  - 2019
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Since publication of the original article the authors noticed that co-author Christian Griebler’s second affiliation was not included. This has now been added to the HTML and PDF versions of the paper. Furthermore, Supplementary Table 3 was not uploaded with the rest of the Supplementary Information files. This is now available to view on the HTML of the original article. The authors would like to apologies for any inconvenience caused.
AU  - Kundu, K.
AU  - Marozava, S.
AU  - Ehrl, B.
AU  - Merl-Pham, J.
AU  - Griebler, C.
AU  - Elsner, M.
C1  - 57011
C2  - 47431
CY  - Macmillan Building, 4 Crinan St, London N1 9xw, England
SP  - 323-323
TI  - Defining lower limits of biodegradation: Atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1 (vol 13, pg 2236, 2019).
JO  - ISME J.
VL  - 14
IS  - 1
PB  - Nature Publishing Group
PY  - 2019
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.
AU  - Zhao, Z.*
AU  - Gonsior, M.*
AU  - Schmitt-Kopplin, P.
AU  - Zhan, Y.*
AU  - Zhang, R.*
AU  - Jiao, N.*
AU  - Chen, F.*
C1  - 56387
C2  - 47047
SP  - 2551–2565
TI  - Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: Coupling of bacterial diversity and DOM chemodiversity.
JO  - ISME J.
VL  - 13
PY  - 2019
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H-2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H-2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.
AU  - Dong, X.
AU  - Greening, C.*
AU  - Brüls, T.*
AU  - Conrad, R.*
AU  - Guo, K.*
AU  - Blaskowski, S.*
AU  - Kaschani, F.*
AU  - Kaiser, M.*
AU  - Laban, N.A.*
AU  - Meckenstock, R.U.*
C1  - 53839
C2  - 45065
CY  - Macmillan Building, 4 Crinan St, London N1 9xw, England
SP  - 2039-2050
TI  - Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats.
JO  - ISME J.
VL  - 12
IS  - 8
PB  - Nature Publishing Group
PY  - 2018
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000 p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.
AU  - Karwautz, C.
AU  - Kus, G.*
AU  - Stöckl, M.
AU  - Neu, T.R.*
AU  - Lueders, T.
C1  - 51993
C2  - 43604
CY  - London
SP  - 87-100
TI  - Microbial megacities fueled by methane oxidation in a mineral spring cave.
JO  - ISME J.
VL  - 12
IS  - 1
PB  - Nature Publishing Group
PY  - 2018
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The classical quorum-sensing (QS) model is based on the assumption that diffusible signaling molecules accumulate in the culture medium until they reach a critical concentration upon which expression of target genes is triggered. Here we demonstrate that the hydrophobic signal N-hexadecanoyl-L-homoserine lactone, which is produced by Paracoccus sp., is released from cells by the aid of membrane vesicles (MVs). Packed into MVs, the signal is not only solubilized in an aqueous environment but is also delivered with varying propensities to different bacteria. We propose a novel MV-based mechanism for binary trafficking of hydrophobic signal molecules, which may be particularly relevant for bacteria that live in open aqueous environments.
AU  - Toyofuku, M.*
AU  - Morinaga, K.*
AU  - Hashimoto, Y.*
AU  - Uhl, J.
AU  - Shimamura, H.*
AU  - Inaba, H.*
AU  - Schmitt-Kopplin, P.
AU  - Eberl, L.*
AU  - Nomura, N.*
C1  - 50690
C2  - 42772
CY  - London
SP  - 1504-1509
TI  - Membrane vesicle-mediated bacterial communication.
JO  - ISME J.
VL  - 11
IS  - 6
PB  - Nature Publishing Group
PY  - 2017
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The Alphaproteobacterium Rhizobium radiobacter F4 (RrF4) was originally characterized as an endofungal bacterium in the beneficial endophytic Sebacinalean fungus Piriformospora indica. Although attempts to cure P. indica from RrF4 repeatedly failed, the bacterium can easily be grown in pure culture. Here, we report on RrF4’s genome and the beneficial impact the free-living bacterium has on plants. In contrast to other endofungal bacteria, the genome size of RrF4 is not reduced. Instead, it shows a high degree of similarity to the plant pathogenic R. radiobacter (formerly: Agrobacterium tumefaciens) C58, except vibrant differences in both the tumor-inducing (pTi) and the accessor (pAt) plasmids, which can explain the loss of RrF4’s pathogenicity. Similar to its fungal host, RrF4 colonizes plant roots without host preference and forms aggregates of attached cells and dense biofilms at the root surface of maturation zones. RrF4-colonized plants show increased biomass and enhanced resistance against bacterial leaf pathogens. Mutational analysis showed that, similar to P. indica, resistance mediated by RrF4 was dependent on the plant’s jasmonate-based induced systemic resistance (ISR) pathway. Consistent with this, RrF4- and P. indica-induced pattern of defense gene expression were similar. In clear contrast to P. indica, but similar to plant growth-promoting rhizobacteria, RrF4 colonized not only the root outer cortex but also spread beyond the endodermis into the stele. On the basis of our findings, RrF4 is an efficient plant growth-promoting bacterium.
AU  - Glaeser, S.P.*
AU  - Imani, J.*
AU  - Alabid, I.*
AU  - Guo, H.*
AU  - Kumar, N.*
AU  - Kämpfer, P.*
AU  - Hardt, M.*
AU  - Blom, J.*
AU  - Goesmann, A.*
AU  - Rothballer, M.
AU  - Hartmann, A.
AU  - Kogel, K.-H.*
C1  - 47156
C2  - 39121
SP  - 871-884
TI  - Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica.
JO  - ISME J.
VL  - 10
IS  - 4
PY  - 2016
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The biodegradation of organic pollutants in aquifers is often restricted to the fringes of contaminant plumes where steep countergradients of electron donors and acceptors are separated by limited dispersive mixing. However, long-distance electron transfer (LDET) by filamentous 'cable bacteria' has recently been discovered in marine sediments to couple spatially separated redox half reactions over centimeter scales. Here we provide primary evidence that such sulfur-oxidizing cable bacteria can also be found at oxic-anoxic interfaces in aquifer sediments, where they provide a means for the direct recycling of sulfate by electron transfer over 1-2-cm distance. Sediments were taken from a hydrocarbon-contaminated aquifer, amended with iron sulfide and saturated with water, leaving the sediment surface exposed to air. Steep geochemical gradients developed in the upper 3 cm, showing a spatial separation of oxygen and sulfide by 9 mm together with a pH profile characteristic for sulfur oxidation by LDET. Bacterial filaments, which were highly abundant in the suboxic zone, were identified by sequencing of 16S rRNA genes and fluorescence in situ hybridization (FISH) as cable bacteria belonging to the Desulfobulbaceae. The detection of similar Desulfobulbaceae at the oxic-anoxic interface of fresh sediment cores taken at a contaminated aquifer suggests that LDET may indeed be active at the capillary fringe in situ.
AU  - Müller, H.
AU  - Bosch, J.
AU  - Griebler, C.
AU  - Damgaard, L.R.*
AU  - Nielsen, L.P.*
AU  - Lueders, T.
AU  - Meckenstock, R.U.
C1  - 48296
C2  - 39999
CY  - London
SP  - 2010-2019
TI  - Long-distance electron transfer by cable bacteria in aquifer sediments.
JO  - ISME J.
VL  - 10
IS  - 8
PB  - Nature Publishing Group
PY  - 2016
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Toxic freshwater cyanobacteria form harmful algal blooms that can cause acute toxicity to humans and livestock. Globally distributed, bloom-forming cyanobacteria Planktothrix either retain or lose the mcy gene cluster (encoding the synthesis of the secondary metabolite hepatotoxin microcystin or MC), resulting in a variable spatial/temporal distribution of (non)toxic genotypes. Despite their importance to human well-being, such genotype diversity is not being mapped at scales relevant to nature. We aimed to reveal the factors influencing the dispersal of those genotypes by analyzing 138 strains (from Europe, Russia, North America and East Africa) for their (i) mcy gene cluster composition, (ii) phylogeny and adaptation to their habitat and (iii) ribosomally and nonribosomally synthesized oligopeptide products. Although all the strains from different species contained at least remnants of the mcy gene cluster, various phylogenetic lineages evolved and adapted to rather specific ecological niches (for example, through pigmentation and gas vesicle protein size). No evidence for an increased abundance of specific peptides in the absence of MC was found. MC and peptide distribution rather depended on phylogeny, ecophysiological adaptation and geographic distance. Together, these findings provide evidence that MC and peptide production are primarily related to speciation processes, while within a phylogenetic lineage the probability that strains differ in peptide composition increases with geographic distance.
AU  - Kurmayer, R.*
AU  - Blom, J.F.*
AU  - Deng, L.
AU  - Pernthaler, J.*
C1  - 47170
C2  - 39128
SP  - 909-921
TI  - Integrating phylogeny, geographic niche partitioning and secondary metabolite synthesis in bloom-forming Planktothrix.
JO  - ISME J.
VL  - 9
IS  - 4
PY  - 2015
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.
AU  - Steinbach, A.*
AU  - Schulz, S.
AU  - Giebler, J.*
AU  - Schulz, S.
AU  - Pronk, G.J.*
AU  - Kögel-Knabner, I.*
AU  - Harms, H.*
AU  - Wick, L.Y.*
AU  - Schloter, M.
C1  - 43033
C2  - 35965
CY  - London
SP  - 1687-1691
TI  - Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.
JO  - ISME J.
VL  - 9
IS  - 7
PB  - Nature Publishing Group
PY  - 2015
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.
AU  - Tedersoo, L.*
AU  - Bahram, M.*
AU  - Cajthaml, T.*
AU  - Polme, S.*
AU  - Hiiesalu, I.*
AU  - Anslan, S.*
AU  - Harend, H.*
AU  - Buegger, F.
AU  - Pritsch, K.
AU  - Koricheva, J.*
AU  - Abarenkov, K.*
C1  - 46321
C2  - 37596
SP  - 346-362
TI  - Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.
JO  - ISME J.
VL  - 10
IS  - 2
PY  - 2015
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.
AU  - Daniel, H.*
AU  - Gholami, A.M.*
AU  - Berry, D.*
AU  - Desmarchelier, C.*
AU  - Hahne, H.*
AU  - Loh, G.*
AU  - Mondot, S.*
AU  - Lepage, P.*
AU  - Rothballer, M.
AU  - Walker, A.*
AU  - Böhm, C.*
AU  - Wenning, M.*
AU  - Wagner, M.*
AU  - Blaut, M.*
AU  - Schmitt-Kopplin, P.
AU  - Kuster, B.*
AU  - Haller, D.*
AU  - Clavel, T.*
C1  - 27521
C2  - 32711
SP  - 295–308
TI  - High-fat diet alters gut microbiota physiology in mice.
JO  - ISME J.
VL  - 8
IS  - 2
PB  - Nature Publishing
PY  - 2014
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with (13)C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills.
AU  - Kleindienst, S.*
AU  - Herbst, F.A.*
AU  - Stagars, M.*
AU  - von Netzer, F.
AU  - von Bergen, M.*
AU  - Seifert, J.*
AU  - Peplies, J.*
AU  - Amann, R.*
AU  - Musat, F.*
AU  - Lueders, T.
AU  - Knittel, K.*
C1  - 31049
C2  - 34152
CY  - London
SP  - 2029-2044
TI  - Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps.
JO  - ISME J.
VL  - 8
IS  - 10
PB  - Nature Publishing Group
PY  - 2014
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. This study focused on gut and liver metabolomics of two different mouse strains, the C57BL/6J (C57J) and the C57BL/6N (C57N) fed with high-fat diet (HFD) for 3 weeks, causing diet-induced obesity in C57N, but not in C57J mice. Furthermore, a 16S-ribosomal RNA comparative sequence analysis using 454 pyrosequencing detected significant differences between the microbiome of the two strains on phylum level for Firmicutes, Deferribacteres and Proteobacteria that propose an essential role of the microbiome in obesity susceptibility. Gut microbial and liver metabolomics were followed by a combinatory approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography time of tlight MS/MS with subsequent multivariate statistical analysis, revealing distinctive host and microbial metabolome patterns between the C57J and the C57N strain. Many taurine-conjugated bile acids (TBAs) were significantly elevated in the cecum and decreased in liver samples from the C57J phenotype likely displaying different energy utilization behavior by the bacterial community and the host. Furthermore, several metabolite groups could specifically be associated with the C57N phenotype involving fatty acids, eicosanoids and urobilinoids. The mass differences based metabolite network approach enabled to extend the range of known metabolites to important bile acids (BAs) and novel taurine conjugates specific for both strains. In summary, our study showed clear alterations of the metabolome in the gastrointestinal tract and liver within a HFD-induced obesity mouse model in relation to the host-microbial nutritional adaptation.
AU  - Walker, A.
AU  - Pfitzner, B.
AU  - Neschen, S.
AU  - Kahle-Stephan, M.
AU  - Harir, M.
AU  - Lucio, M.
AU  - Moritz, F.
AU  - Tziotis, D.
AU  - Witting, M.
AU  - Rothballer, M.
AU  - Engel, M.
AU  - Schmid, M.
AU  - Endesfelder, D.
AU  - Klingenspor, M.
AU  - Rattei, T.*
AU  - zu Castell, W.
AU  - Hrabě de Angelis, M.
AU  - Hartmann, A.
AU  - Schmitt-Kopplin, P.
C1  - 31552
C2  - 34566
SP  - 2380-2396
TI  - Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet.
JO  - ISME J.
VL  - 8
IS  - 12
PY  - 2014
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1(-/-) and wild-type mice, as determined by 454 pyrosequencing of bacterial 16S rRNA (gene) amplicons, metatranscriptomics and quantitative fluorescence in situ hybridization of selected phylotypes. The bacterial families Ruminococcaceae, Bacteroidaceae, Enterobacteriaceae, Deferribacteraceae and Verrucomicrobiaceae increased in relative abundance in DSS-treated mice. Comparative 16S rRNA sequence analysis at maximum possible phylogenetic resolution identified several indicator phylotypes for DSS treatment, including the putative mucin degraders Akkermansia and Mucispirillum. The analysis additionally revealed strongly contrasting abundance changes among phylotypes of the same family, particularly within the Lachnospiraceae. These extensive phylotype-level dynamics were hidden when reads were grouped at higher taxonomic levels. Metatranscriptomic analysis provided insights into functional shifts in the murine intestinal microbiota, with increased transcription of genes associated with regulation and cell signaling, carbohydrate metabolism and respiration and decreased transcription of flagellin genes during inflammation. These findings (i) establish the first in-depth inventory of the mouse gut microbiota and its metatranscriptome in the DSS colitis model, (ii) reveal that family-level microbial community analyses are insufficient to reveal important colitis-associated microbiota shifts and (iii) support a scenario of shifting intra-family structure and function in the phylotype-rich and phylogenetically diverse Lachnospiraceae in DSS-treated mice.
AU  - Berry, D.*
AU  - Schwab, C.*
AU  - Milinovich, G.*
AU  - Reichert, J.*
AU  - Ben Mahfoudh, K.*
AU  - Decker, T.-M.*
AU  - Engel, M.
AU  - Hai, B.
AU  - Hainzl, E.*
AU  - Heider, S.*
AU  - Kenner, L.*
AU  - Müller, M.*
AU  - Rauch, I.*
AU  - Strobl, B.*
AU  - Wagner, M.*
AU  - Schleper, C.*
AU  - Urich, T.*
AU  - Loy, A.*
C1  - 10951
C2  - 30430
SP  - 2091-2106
TI  - Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis.
JO  - ISME J.
VL  - 6
IS  - 11
PB  - Nature Publishing Group
PY  - 2012
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Alkanes are major constituents of plant-derived waxy materials. In this study, we investigated the abundance, community structure and activity of bacteria harbouring the alkane monooxygenase gene alkB, which catalyses a major step in the pathway of aerobic alkane degradation in the litter layer, the litter-soil interface and in bulk soil at three time points during the degradation of maize and pea plant litter (2, 8 and 30 weeks) to improve our understanding about drivers for microbial performance in different soil compartments. Soil cores of different soil textures (sandy and silty) were taken from an agricultural field and incubated at constant laboratory conditions. The abundance of alkB genes and transcripts (by qPCR) as well as the community structure (by terminal restriction fragment polymorphism fingerprinting) were measured in combination with the concentrations and composition of alkanes. The results obtained indicate a clear response pattern of all investigated biotic and abiotic parameters depending on the applied litter material, the type of soil used, the time point of sampling and the soil compartment studied. As expected the distribution of alkanes of different chain length formed a steep gradient from the litter layer to the bulk soil. Mainly in the two upper soil compartments community structure and abundance patterns of alkB were driven by the applied litter type and its degradation. Surprisingly, the differences between the compartments in one soil were more pronounced than the differences between similar compartments in the two soils studied. This indicates the necessity for analysing processes in different soil compartments to improve our mechanistic understanding of the dynamics of distinct functional groups of microbes.
AU  - Schulz, S.
AU  - Giebler, J.*
AU  - Chatzinotas, A.*
AU  - Wick, L.Y.*
AU  - Fetzer, I.*
AU  - Welzl, G.
AU  - Harms, H.*
AU  - Schloter, M.
C1  - 8452
C2  - 30120
SP  - 1763-1774
TI  - Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments.
JO  - ISME J.
VL  - 6
IS  - 9
PB  - Nature Pub. Group
PY  - 2012
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions.
AU  - Brankatsch, R.*
AU  - Töwe, S.*
AU  - Kleineidam, K.
AU  - Schloter, M.
AU  - Zeyer, J.*
C1  - 4790
C2  - 28367
SP  - 1025-1037
TI  - Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield.
JO  - ISME J.
VL  - 5
IS  - 6
PB  - Nature Publ. Group
PY  - 2011
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.
AU  - Engel, A.S.*
AU  - Meisinger, D.B.*
AU  - Porter, M.L.*
AU  - Payn, R.A.*
AU  - Schmid, M.
AU  - Stern, L.A.*
AU  - Schleifer, K.H.*
AU  - Lee, N.M.*
C1  - 40
C2  - 27067
SP  - 98-110
TI  - Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).
JO  - ISME J.
VL  - 4
IS  - 1
PB  - Nature Publ. Group
PY  - 2010
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
AU  - Peña, A.*
AU  - Teeling, H.*
AU  - Huerta-Cepas, J.*
AU  - Santos, F.*
AU  - Yarza, P.*
AU  - Brito-Echeverría, J.*
AU  - Lucio, M.
AU  - Schmitt-Kopplin, P.
AU  - Meseguer, I.*
AU  - Schenowitz, C.*
AU  - Dossat, C.*
AU  - Barbe, V.*
AU  - Dopazo, J.*
AU  - Rosselló-Mora, R.*
AU  - Schüler, M.*
AU  - Glöckner, F.O.*
AU  - Amann, R.*
AU  - Gabaldón, T.*
AU  - Antón, J.*
C1  - 1437
C2  - 27288
SP  - 882-895
TI  - Fine-scale evolution: Genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.
JO  - ISME J.
VL  - 4
IS  - 7
PB  - Nature Publ. Group
PY  - 2010
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. On incubation of fresh sediments with (13)C(7)-toluene, the production of both sulfide and (13)CO(2) was clearly coupled to the (13)C-labeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only ∼50%, pointing toward high ratios of heterotrophic CO(2)-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders. These findings demonstrate that the importance of non-proteobacterial populations in anaerobic aromatics degradation, as well as their specific ecophysiology in the subsurface may still be largely ungrasped.
AU  - Winderl, C.
AU  - Penning, H.
AU  - von Netzer, F.
AU  - Meckenstock, R.U.
AU  - Lüders, T.
C1  - 4192
C2  - 27428
SP  - 1314-1325
TI  - DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment.
JO  - ISME J.
VL  - 4
IS  - 10
PB  - International Society for Microbial Ecology
PY  - 2010
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The relative importance of size and composition of microbial communities in ecosystem functioning is poorly understood. Here, we investigated how community composition and size of selected functional guilds in the nitrogen cycle correlated with agroecosystem functioning, which was defined as microbial process rates, total crop yield and nitrogen content in the crop. Soil was sampled from a 50-year fertilizer trial and the treatments comprised unfertilized bare fallow, unfertilized with crop, and plots with crop fertilized with calcium nitrate, ammonium sulfate, solid cattle manure or sewage sludge. The size of the functional guilds and the total bacterial community were greatly affected by the fertilization regimes, especially by the sewage sludge and ammonium sulfate treatments. The community size results were combined with previously published data on the composition of the corresponding communities, potential ammonia oxidation, denitrification, basal and substrate-induced respiration rates, in addition to crop yield for an integrated analysis. It was found that differences in size, rather than composition, correlated with differences in process rates for the denitrifier and ammonia-oxidizing archaeal and total bacterial communities, whereas neither differences in size nor composition was correlated with differences in process rates for the ammonia-oxidizing bacterial community. In contrast, the composition of nitrate-reducing, denitrifying and total bacterial communities co-varied with primary production and both were strongly linked to soil properties.
AU  - Hallin, S.*
AU  - Jones, C.M.*
AU  - Schloter, M.
AU  - Philippot, L.*
C1  - 1511
C2  - 25974
SP  - 597-605
TI  - Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment.
JO  - ISME J.
VL  - 3
IS  - 5
PB  - Nature Publ. Group
PY  - 2009
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Extensive physiological analyses of different microbial community members in many samples are difficult because of the restricted number of target populations that can be investigated in reasonable time by standard substrate-mediated isotope-labeling techniques. The diversity and ecophysiology of Rhodocyclales in activated sludge from a full-scale wastewater treatment plant were analyzed following a holistic strategy based on the isotope array approach, which allows for a parallel functional probing of different phylogenetic groups. Initial diagnostic microarray, comparative 16S rRNA gene sequence, and quantitative fluorescence in situ hybridization surveys indicated the presence of a diverse community, consisting of an estimated number of 27 operational taxonomic units that grouped in at least seven main Rhodocyclales lineages. Substrate utilization profiles of probe-defined populations were determined by radioactive isotope array analysis and microautoradiography-fluorescence in situ hybridization of activated sludge samples that were briefly exposed to different substrates under oxic and anoxic, nitrate-reducing conditions. Most detected Rhodocyclales groups were actively involved in nitrogen transformation, but varied in their consumption of propionate, butyrate, or toluene, and thus in their ability to use different carbon sources in activated sludge. This indicates that the functional redundancy of nitrate reduction and the functional versatility of substrate usage are important factors governing niche overlap and differentiation of diverse Rhodocyclales members in this activated sludge.
AU  - Hesselsoe, M.*
AU  - Füreder, S.*
AU  - Schloter, M.
AU  - Bodrossy, L.*
AU  - Iversen, N.*
AU  - Roslev, P.*
AU  - Nielsen, P.H.*
AU  - Wagner, M.*
AU  - Loy, A.*
C1  - 1468
C2  - 26114
SP  - 1349-1364
TI  - Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge.
JO  - ISME J.
VL  - 3
IS  - 12
PB  - Nature Publ. Group
PY  - 2009
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - We constructed an experimental model system to study the effects of grazing by a common soil amoeba, Acanthamoeba castellanii, on the composition of bacterial communities in the rhizosphere of Arabidopsis thaliana. Amoebae showed distinct grazing preferences for specific bacterial taxa, which were rapidly replaced by grazing tolerant taxa in a highly reproducible way. The relative proportion of active bacteria increased although bacterial abundance was strongly decreased by amoebae. Specific bacterial taxa had disappeared already two days after inoculation of amoebae. The decrease in numbers was most pronounced in Betaproteobacteria and Firmicutes. In contrast, Actinobacteria, Nitrospira, Verrucomicrobia and Planctomycetes increased. Although other groups, such as betaproteobacterial ammonia oxidizers and Gammaproteobacteria did not change in abundance, denaturing gradient gel electrophoresis with specific primers for pseudomonads (Gammaproteobacteria) revealed both specific changes in community composition as well as shifts in functional genes (gacA) involved in bacterial defence responses. The resulting positive feedback on plant growth in the amoeba treatment confirms that bacterial grazers play a dominant role in structuring bacteria-plant interactions. This is the first detailed study documenting how rapidly protozoan grazers induce shifts in rhizosphere bacterial community composition.
AU  - Rosenberg, K.*
AU  - Bertaux, J.*
AU  - Krome, K.*
AU  - Hartmann, A.
AU  - Scheu, S.*
AU  - Bonkowski, M.*
C1  - 394
C2  - 26939
SP  - 675-684
TI  - Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana.
JO  - ISME J.
VL  - 3
IS  - 6
PB  - Nature Publ. Group
PY  - 2009
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The influence of switches in grassland management to or from grazing on the dynamics of nitrifier activity, as well as the abundance of ammonia-oxidizing bacteria, AOB and ammonia-oxidizing archeae, AOA, was analyzed for two years after changing management. Additionally community structure of AOB was surveyed. Four treatments were compared in mesocosms: grazing on previously grazed grassland (G-G); no grazing on ungrazed grassland (U-U); grazing on ungrazed grassland (U-G) and cessation of grazing on grazed grassland (G-U). Nitrifier activity and abundance were always higher for G-G than U-U treatments and AOB community structure differed between these treatments. AOA abundance was in the same range as AOB abundance and followed the same trend. Grazing led to a change in AOB community structure within <5 months and a subsequent (5-12 months) increase in nitrifier activity and abundance. In contrast, cessation of grazing led to a decrease in nitrifier activity and abundance within <5 months and to a later (5-12 months) change in AOB community structure. Activity in G-U and U-G was similar to that in U-U and G-G, respectively, after 12 months. Sequence analysis of 16S rRNA gene clones showed that AOB retrieved from soils fell within the Nitrosospira lineage and percentages of AOB related to known Nitrosospira groups were affected by grazing. These results demonstrate that AOB and AOA respond quickly to changes in management. The selection of nitrifiers adapted to novel environmental conditions was a prerequisite for nitrification enhancement in U-G, whereas nitrification decrease in G-U was likely due to a partial starvation and decrease in the abundance of nitrifiers initially present. The results also suggest that taxonomic affiliation does not fully infer functional traits of AOB.
AU  - Le Roux, X.*
AU  - Poly, F.*
AU  - Currey, P.*
AU  - Commeaux, C.*
AU  - Hai, B.
AU  - Nicol, G.W.*
AU  - Prosser, J.I.*
AU  - Schloter, M.
AU  - Attard, E.*
AU  - Klumpp, K.*
C1  - 4029
C2  - 25137
SP  - 221-232
TI  - Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure.
JO  - ISME J.
VL  - 2
IS  - 2
PB  - Nature Publ. Group
PY  - 2008
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - The biogeography of prokaryotes and the effect of geographical barriers as evolutionary constraints are currently subjected to great debate. Some clear-cut evidence for geographic isolation has been obtained by genetic methods but, in many cases, the markers used are too coarse to reveal subtle biogeographical trends. Contrary to eukaryotic microorganisms, phenotypic evidence for allopatric segregation in prokaryotes has never been found. Here we present, for the first time, a metabolomic approach based on ultrahigh resolution mass spectrometry to reveal phenotypic biogeographical discrimination. We demonstrate that strains of the cosmopolitan extremophilic bacterium Salinibacter ruber, isolated from different sites in the world, can be distinguished by means of characteristic metabolites, and that these differences can be correlated to their geographical isolation site distances. The approach allows distinct degrees of discrimination for isolates at different geographical scales. In all cases, the discriminative metabolite patterns were quantitative rather than qualitative, which may be an indication of geographically distinct transcriptional or posttranscriptional regulations
AU  - Rosselló-Mora, R.*
AU  - Lucio, M.
AU  - Peña, A.*
AU  - Brito-Echeverría, J.*
AU  - López-López, A.*
AU  - Valens-Vadell, M.*
AU  - Frommberger, M.
AU  - Antón, J.*
AU  - Schmitt-Kopplin, P.
C1  - 3387
C2  - 25159
SP  - 242-253
TI  - Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber.
JO  - ISME J.
VL  - 2
IS  - 3
PB  - Nature Publ. Group
PY  - 2008
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - Here, we present a detailed functional and phylogenetic characterization of an iron-reducing enrichment culture maintained in our lab with benzene as sole carbon and energy source. We used DNA-stable isotope probing to identify microbes within the enrichment most active in the assimilation of (13)C-label. When (12)C(6)- and (13)C(6)-benzene were added as comparative substrates, marked differences in the quantitative buoyant density distribution became apparent especially for uncultured microbes within the Gram-positive Peptococcaceae, closely related to environmental clones retrieved from contaminated aquifers world wide and only distantly related to cultured representatives of the genus Thermincola. Prominent among the other constituents of the enrichment were uncultured Deltaproteobacteria, as well as members of the Actinobacteria. Although their presence within the enrichment seems to be stable they did not assimilate (13)C-label as significantly as the Clostridia within the time course of our experiment. We hypothesize that benzene degradation in our enrichment involves an unusual syntrophy, where members of the Clostridia primarily oxidize benzene. Electrons from the contaminant are both directly transferred to ferric iron by the primary oxidizers, but also partially shared with the Desulfobulbaceae as syntrophic partners. Alternatively, electrons may also be quantitatively transferred to the partners, which then reduce the ferric iron. Thus our results provide evidence for the importance of a novel clade of Gram-positive iron-reducers in anaerobic benzene degradation, and a role of syntrophic interactions in this process. These findings shed a totally new light on the factors controlling benzene degradation in anaerobic contaminated environments.
AU  - Kunapuli, U.
AU  - Lüders, T.
AU  - Meckenstock, R.U.
C1  - 3530
C2  - 24861
SP  - 643-653
TI  - The use of stable isotope probing to identify key iron-reducing microorganisms involved in anaerobic benzene degradation.
JO  - ISME J.
VL  - 1
IS  - 7
PB  - Nature Publ. Group
PY  - 2007
SN  - 1751-7362
ER  - 

TY  - JOUR
AB  - In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.
AU  - Radl, V.*
AU  - Gattinger, A.
AU  - Chronakova, A.*
AU  - Nemcová, A.*
AU  - Cuhel, J.*
AU  - Simek, M.*
AU  - Munch, J.-C.
AU  - Schloter, M.
AU  - Elhottova, D.*
C1  - 4314
C2  - 24597
SP  - 443-452
TI  - Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils.
JO  - ISME J.
VL  - 1
IS  - 5
PB  - Nature Publ. Group
PY  - 2007
SN  - 1751-7362
ER  -