TY - JOUR AB - Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates, leaf metabolites and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important. AU - Behr, J.H.* AU - Kuhl-Nagel, T.* AU - Sommermann, L.* AU - Moradtalab, N.* AU - Chowdhury, S.P. AU - Schloter, M. AU - Windisch, S.* AU - Schellenberg, I.* AU - Maccario, L.* AU - Sörensen, S.J.* AU - Rothballer, M. AU - Geistlinger, J.* AU - Smalla, K.* AU - Ludewig, U.* AU - Neumann, G.* AU - Grosch, R.* AU - Babin, D.* C1 - 69746 C2 - 55245 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. JO - FEMS Microbiol. Ecol. VL - 100 IS - 2 PB - Oxford Univ Press PY - 2024 SN - 0168-6496 ER - TY - JOUR AB - Eukaryotic organisms co-evolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, benefical / symbiotic or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term "Rhizosphere" to characterize the observation that a high density of saprophytic, beneficial and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing (QS) of bacteria is mediated by different auto-inducible metabolites in a density dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts. AU - Hartmann, A. AU - Binder, T. AU - Rothballer, M. C1 - 70680 C2 - 55812 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health. JO - FEMS Microbiol. Ecol. VL - 100 IS - 6 PB - Oxford Univ Press PY - 2024 SN - 0168-6496 ER - TY - JOUR AB - Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils. AU - Leifheit, E.F.* AU - Camenzind, T.* AU - Lehmann, A.* AU - Andrade Linares, D.R. AU - Fussan, M.* AU - Westhusen, S.* AU - Wineberger, T.M.* AU - Rillig, M.C.* C1 - 70245 C2 - 55462 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Fungal traits help to understand the decomposition of simple and complex plant litter. JO - FEMS Microbiol. Ecol. VL - 100 IS - 5 PB - Oxford Univ Press PY - 2024 SN - 0168-6496 ER - TY - JOUR AB - Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We demonstrated that plant growth characteristics were strongly related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce IAA and siderophores) exhibited greater relative abundance in high- and medium performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, Azohydromonas. Conversely, the network within low performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices. AU - Martins, R.B. AU - Radl, V. AU - Treder, K.* AU - Michałowska, D.* AU - Pritsch, K. AU - Schloter, M. C1 - 70810 C2 - 55939 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics. JO - FEMS Microbiol. Ecol. VL - 100 IS - 8 PB - Oxford Univ Press PY - 2024 SN - 0168-6496 ER - TY - JOUR AB - Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16- and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities. AU - Pinheiro Alves de Souza, Y. AU - Siani, R. AU - Albracht, C.* AU - Huang, Y.* AU - Eisenhauer, N.* AU - Vogel, A.* AU - Wagg, C.* AU - Schloter, M. AU - Schulz, S. C1 - 71045 C2 - 55872 TI - The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient. JO - FEMS Microbiol. Ecol. VL - 100 IS - 8 PY - 2024 SN - 0168-6496 ER - TY - JOUR AB - Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota. AU - Ohan, J. AU - Siani, R. AU - Kurth, J. AU - Sommer, V.* AU - Gläser, K.* AU - Karsten, U.* AU - Schloter, M. AU - Schulz, S. C1 - 68093 C2 - 54571 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps. JO - FEMS Microbiol. Ecol. VL - 99 IS - 8 PB - Oxford Univ Press PY - 2023 SN - 0168-6496 ER - TY - JOUR AB - Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations. AU - Sachs, C. AU - Kanaparthi, D. AU - Kublik, S. AU - Szalay, A.A. AU - Schloter, M. AU - Damgaard, L.R.* AU - Schramm, A.* AU - Lueders, T.* C1 - 64794 C2 - 52493 TI - Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns. JO - FEMS Microbiol. Ecol. VL - 98 IS - 5 PY - 2022 SN - 0168-6496 ER - TY - JOUR AB - A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial/archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial groups. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production. AU - Babin, D.* AU - Sommermann, L.* AU - Chowdhury, S.P. AU - Behr, J.H.* AU - Sandmann, M.* 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 - 61316 C2 - 50149 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories. JO - FEMS Microbiol. Ecol. VL - 97 IS - 4 PB - Oxford Univ Press PY - 2021 SN - 0168-6496 ER - TY - JOUR AB - Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing, and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with the 15.3-fold increase in Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS, and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific. AU - Duffner, C. AU - Holzapfel, S.* AU - Wunderlich, A.* AU - Einsiedl, F.* AU - Schloter, M. AU - Schulz, S. C1 - 60936 C2 - 49989 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Dechloromonas and close relatives prevail hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material. JO - FEMS Microbiol. Ecol. VL - 97 IS - 3 PB - Oxford Univ Press PY - 2021 SN - 0168-6496 ER - TY - JOUR AB - We report on a study that aimed at establishing a large soil-fungal culture collection spanning a wide taxonomic diversity and systematically screening the collection for bacterial associations. Fungal cultures were isolated from soil samples obtained from a natural grassland in eastern Germany and bacterial associations were assessed by PCR-amplification and sequencing of bacterial 16S rRNA. In addition, intraspecies genetic diversities of a subset of the isolated species were estimated by double-digest restriction associated DNA sequencing. A total of 688 fungal cultures, representing at least 106 fungal species from 36 different families, were obtained and even though clonal isolates were identified in almost all fungal species subjected to ddRAD-seq, relatively high genetic diversities could be observed in some of the isolated species. Sixty-nine % of the fungal isolates in our collection were found to be associated with bacteria and the most commonly identified bacterial genera were Pelomonas, Enterobacter and Burkholderia. Our results indicate that bacterial associations commonly occur in soil fungi, even if antibiotics are being applied during the isolation process, and provide a basis for the use of our culture collection in ecological experiments that want to acknowledge the importance of intraspecies genetic diversity. AU - Muller, L.A.H.* AU - Ballhausen, M.B.* AU - Andrade Linares, D.R. AU - Pinek, L.* AU - Golubeva, P.* AU - Rillig, M.C.* C1 - 61844 C2 - 50197 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Fungus-bacterium associations are widespread in fungal cultures isolated from a semi-arid natural grassland in Germany. JO - FEMS Microbiol. Ecol. VL - 97 IS - 5 PB - Oxford Univ Press PY - 2021 SN - 0168-6496 ER - TY - JOUR AB - In contrast to the pervasive occurrence of denitrification in soils, anammox (anaerobic ammonium oxidation) is a spatially restricted process that depends on specific ecological conditions. To identify the factors that constrain the distribution and activity of anammox bacteria in terrestrial environments, we investigated four different soil types along a catena with opposing ecological gradients of nitrogen and water content, from an amended pasture to an ombrotrophic bog. Anammox was detected by polymerase chain reaction (PCR) and quantitative PCR (qPCR) only in the nitrophilic wet meadow and the minerotrophic fen, in soil sections remaining water-saturated for most of the year and whose interstitial water contained inorganic nitrogen. Contrastingly, aerobic ammonia oxidizing microorganisms were present in all examined samples and outnumbered anammox bacteria usually by at least one order of magnitude. 16S rRNA gene sequencing revealed a relatively high diversity of anammox bacteria with one Ca. Brocadia cluster. Three additional clusters could not be affiliated to known anammox genera, but have been previously detected in other soil systems. Soil incubations using N-15-labeled substrates revealed that anammox processes contributed about <2% to total N-2 formation, leaving nitrification and denitrification as the dominant N-removal mechanism in these soils that represent important buffer zones between agricultural land and ombrotrophic peat bogs. AU - Bagnoud, A.* AU - Guye-Humbert, S.* AU - Schloter-Hai, B. AU - Schloter, M. AU - Zopfi, J.* C1 - 57677 C2 - 47855 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils. JO - FEMS Microbiol. Ecol. VL - 96 IS - 2 PB - Oxford Univ Press PY - 2020 SN - 0168-6496 ER - TY - JOUR AB - Virtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2 fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L (NaHCO3)-C-13. Incorporation of (HCO3)-C-13 - was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, C-13 incorporation into the tricarboxylic acid cycle increased with time and occurred via [4-C-13]oxaloacetate formed by carboxylation of pyruvate. The levels of C-13 incorporation were highest for growth on glucose and lowest on malate. Incorporation of C-13 into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from (HCO3)-C-13 - by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments. AU - Spona-Friedl, M. AU - Braun, A.* AU - Huber, C.* AU - Eisenreich, W.* AU - Griebler, C. AU - Kappler, A.* AU - Elsner, M. C1 - 59007 C2 - 48539 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling. JO - FEMS Microbiol. Ecol. VL - 96 IS - 6 PB - Oxford Univ Press PY - 2020 SN - 0168-6496 ER - TY - JOUR AB - Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10-30 cm (topsoil) and 60-75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function. AU - Degrune, F.* AU - Dumack, K.* AU - Fiore-Donno, A.M.* AU - Bonkowski, M.* AU - Sosa-Hernández, M.A.* AU - Schloter, M. AU - Kautz, T.* AU - Fischer, D. AU - Rillig, M.C.* C1 - 55757 C2 - 46538 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Distinct communities of Cercozoa at different soil depths in a temperate agricultural field. JO - FEMS Microbiol. Ecol. VL - 95 IS - 4 PB - Oxford Univ Press PY - 2019 SN - 0168-6496 ER - TY - JOUR AB - Several studies have analyzed biogeographic distribution patterns of microbial communities across broad spatial scales. However, it is often unclear to what extent differences in community composition across different regions are caused by dispersal limitation or selection, and if selection is caused by local environmental conditions alone or additional broad-scale region-specific factors. This is especially true for groundwater environments, which have been understudied in this context relative to other non-subsurface habitats. Here, we analyzed microbial community composition based on exact 16S rRNA amplicon sequence variants (ASVs) from four geographically separated aquifers located in different regions along a latitudinal transect of similar to 700 km across Germany. Using a combination of variation partitioning and ecological null models revealed that differences in microbial community composition were mainly the product of selection imposed by local environmental conditions and to a smaller but still significant extent dispersal limitation and drift across regions. Only similar to 23% of the total variation in microbial community composition remained unexplained, possibly due to underestimated effects of dispersal limitation among local communities within regions and temporal drift. No evidence was found for selection due to region-specific factors independent of local environmental conditions. AU - Fillinger, L. AU - Hug, K. AU - Griebler, C. C1 - 57098 C2 - 47536 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers. JO - FEMS Microbiol. Ecol. VL - 95 IS - 11 PB - Oxford Univ Press PY - 2019 SN - 0168-6496 ER - TY - JOUR AU - Stott, M.* AU - Lueders, T. C1 - 54377 C2 - 45514 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Editorial: Deep life, kia ora! JO - FEMS Microbiol. Ecol. VL - 94 IS - 11 PB - Oxford Univ Press PY - 2018 SN - 0168-6496 ER - TY - JOUR AB - The availability of oxygen is often a limiting factor for the degradation of aromatic hydrocarbons in subsurface environments. However, while both aerobic and anaerobic degraders have been intensively studied, degradation betwixt, under micro-or hypoxic conditions has rarely been addressed. It is speculated that in environments with limited, but sustained oxygen supply, such as in the vicinity of groundwater monitoring wells, hypoxic degradation may take place. A large diversity of subfamily I.2.C extradiol dioxygenase genes has been previously detected in a BTEX-contaminated aquifer in Hungary. Older literature suggests that such catabolic potentials could be associated to hypoxic degradation. Bacterial communities dominated by members of the Rhodocyclaceae were found, but the majority of the detected C23O genotypes could not be affiliated to any known bacterial degrader lineages. To address this, a stable isotope probing (SIP) incubation of site sediments with C-13(7)-toluene was performed under microoxic conditions. A combination of 16S rRNA gene amplicon sequencing and T-RFLP fingerprinting of C23O genes from SIP gradient fractions revealed the central role of degraders within the Rhodocyclaceae in hypoxic toluene degradation. The main assimilators of C-13 were identified as members of the genera Quatrionicoccus and Zoogloea, and a yet uncultured group of the Rhodocyclaceae. AU - Táncsics, A.* AU - Szalay, A.A. AU - Farkas, M.* AU - Benedek, T.* AU - Szoboszlay, S.* AU - Szabó, I.* AU - Lueders, T. C1 - 53541 C2 - 44899 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - Stable isotope probing of hypoxic toluene degradation at the Siklos aquifer reveals prominent role of Rhodocyclaceae. JO - FEMS Microbiol. Ecol. VL - 94 IS - 6 PB - Oxford Univ Press PY - 2018 SN - 0168-6496 ER - TY - JOUR AB - Reduced nitrogen species are key nutrients for biological productivity in the oceans. Ammonium is often present in low and growth-limiting concentrations, albeit peaks occur during collapse of algal blooms or via input from deep sea upwelling and riverine inflow. Autotrophic phytoplankton exploit ammonium peaks by storing nitrogen intracellularly. In contrast, the strategy of heterotrophic bacterioplankton to acquire ammonium is less well understood. This study revealed the marine bacterium Phaeobacter inhibens DSM 17395, a Roseobacter group member, to have already depleted the external ammonium when only ~1/3 of the ultimately attained biomass is formed. This was paralleled by a three-fold increase in cellular nitrogen levels and rapid buildup of various nitrogen-containing intracellular metabolites (and enzymes for their biosynthesis) and biopolymers (DNA, RNA and proteins). Moreover, nitrogen-rich cells secreted potential RTX proteins and the antibiotic tropodithietic acid, perhaps to competitively secure pulses of external ammonium and to protect themselves from predation. This complex response may ensure growing cells and their descendants exclusive provision with internal nitrogen stocks. This nutritional strategy appears prevalent also in other roseobacters from distant geographical provenances and could provide a new perspective on the distribution of reduced nitrogen in marine environments, i.e. temporary accumulation in bacterioplankton cells. AU - Trautwein, K.* AU - Hensler, M.* AU - Wiegmann, K.* AU - Skorubskaya, E.* AU - Wöhlbrand, L.* AU - Wünsch, D.* AU - Hinrichs, C.* AU - Feenders, C.* AU - Müller, C. AU - Schell, K.* AU - Ruppersberg, H.S.* AU - Vagts, J.* AU - Koßmehl, S.* AU - Steinbüchel, A.* AU - Schmitt-Kopplin, P. AU - Wilkes, H.* AU - Hillebrand, H.* AU - Blasius, B.* AU - Schomburg, D.* AU - Rabus, R.* C1 - 54160 C2 - 45368 CY - Great Clarendon St, Oxford Ox2 6dp, England TI - The marine bacterium Phaeobacter inhibens secures external ammonium by rapid buildup of intracellular nitrogen stocks. JO - FEMS Microbiol. Ecol. VL - 94 IS - 10 PB - Oxford Univ Press PY - 2018 SN - 0168-6496 ER - TY - JOUR AB - © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. The enrichment culture BPL is able to degrade benzene with sulfate as electron acceptor and is dominated by an organism of the genus Pelotomaculum. Members of Pelotomaculum are usually known to be fermenters, undergoing syntrophy with anaerobic respiring microorganisms or methanogens. By using a metagenomic approach, we reconstructed a high-quality genome (∼2.97 Mbp, 99% completeness) for Pelotomaculum candidate BPL. The proteogenomic data suggested that (1) anaerobic benzene degradation was activated by a yet unknown mechanism for conversion of benzene to benzoyl-CoA; (2) the central benzoyl-CoA degradation pathway involved reductive dearomatization by a class II benzoyl-CoA reductase followed by hydrolytic ring cleavage and modified β-oxidation; (3) the oxidative acetyl-CoA pathway was utilized for complete oxidation to CO2. Interestingly, the genome of Pelotomaculum candidate BPL has all the genes for a complete sulfate reduction pathway including a similar electron transfer mechanism for dissimilatory sulfate reduction as in other Gram-positive sulfate-reducing bacteria. The proteome analysis revealed that the essential enzymes for sulfate reduction were all formed during growth with benzene. Thus, our data indicated that, besides its potential to anaerobically degrade benzene, Pelotomaculum candidate BPL is the first member of the genus that can perform sulfate reduction. AU - Dong, X. AU - Dröge, J.* AU - von Toerne, C. AU - Marozava, S. AU - McHardy, A.C.* AU - Meckenstock, R.U.* C1 - 51778 C2 - 43478 TI - Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate. JO - FEMS Microbiol. Ecol. VL - 93 IS - 3 PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - Chlorinated ethanes belong to the most common groundwater and soil contaminants. Of these, 1,2-dichloroethane (1,2-DCA) is a man-made, persistent and toxic contaminant, released due to improper waste treatment at versatile production sites. This study investigated the anaerobic transformation of 1,2-DCA by Dehalococcoides mccartyi strain 195 and strain BTF08 using triple-element compound-specific stable isotope analysis of carbon, chlorine and hydrogen for the first time. Isotope fractionation patterns for carbon (εCBTF08 = -28.4 ± 3.7‰; εC195 = -30.9 ± 3.6‰) and chlorine (εClBTF08 = -4.6 ± 0.7‰; εCl195 = -4.2 ± 0.5‰) within both investigated D. mccartyi strains, as well as the dual-element analysis (ΛBTF08 = 6.9 ± 1.2; Λ195 = 7.1 ± 0.2), supported identical reaction mechanisms for dehalogenation of 1,2-DCA. Hydrogen isotope fractionation analysis revealed dihaloelimination as prevalent reaction mechanism. Vinyl chloride as major intermediate could be excluded by performing the experiment in deuterated aqueous media. Furthermore, evaluation of the derived apparent kinetic isotope effects (AKIECBTF08 = 1.029/AKIEC195 = 1.031; AKIEClBTF08 = 1.005/AKIECl195 = 1.004) pointed towards simultaneous abstraction of both involved chlorine-substituents in a concerted matter. It was shown that D. mccartyi strain BTF08 and strain 195 are capable of complete, direct dihaloelimination of 1,2-DCA to ethene. AU - Franke, S.* AU - Lihl, C. AU - Renpenning, J.* AU - Elsner, M. AU - Nijenhuis, I.* C1 - 52219 C2 - 43856 CY - Oxford TI - Triple-element compound-specific stable isotope analysis of 1,2-dichloroethane for characterization of the underlying dehalogenation reaction in two Dehalococcoides mccartyi strains. JO - FEMS Microbiol. Ecol. VL - 93 IS - 12 PB - Oxford Univ Press PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. C-13-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. AU - Lueders, T. C1 - 51003 C2 - 42748 CY - Oxford TI - The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers. JO - FEMS Microbiol. Ecol. VL - 93 IS - 1 PB - Oxford Univ Press PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The ‘stable’ component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the ‘dynamic’ component comprised OTUs that were enriched at specific vegetation stages. AU - Pfeiffer, S.* AU - Mitter, B.* AU - Oswald, A.* AU - Schloter-Hai, B. AU - Schloter, M. AU - Declerck, S.* AU - Sessitsch, A.* C1 - 50310 C2 - 42087 CY - Oxford TI - Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development. JO - FEMS Microbiol. Ecol. VL - 93 IS - 2 PB - Oxford Univ Press PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - The stoichiometric constraints of algal growth are well understood, whereas there is less knowledge for heterotrophic bacterioplankton. Growth of the marine bacterium Phaeobacter inhibens DSM 17395, belonging to the globally distributed Roseobacter group, was studied across a wide concentration range of NH 4 + and PO 4 3- . The unique dataset covers 415 different concentration pairs, corresponding to 207 different molar N:P ratios (from 10 -2 to 10 5 ). Maximal growth (by growth rate and biomass yield) was observed within a restricted concentration range at N:P ratios (50-120) markedly above Redfield. Experimentally determined growth parameters deviated to a large part from model predictions based on Liebig's law of the minimum, thus implicating synergistic co-limitation due to biochemical dependence of resources. Internal elemental ratios of P. inhibens varied with external nutrient supply within physiological constraints, thus adding to the growing evidence that aquatic bacteria can be flexible in their internal elemental composition. Taken together, the findings reported here revealed that P. inhibens is well adapted to fluctuating availability of inorganic N and P, expected to occur in its natural habitat (e.g. colonized algae, coastal areas). Moreover, this study suggests that elemental variability in bacterioplankton needs to be considered in the ecological stoichiometry of the oceans. AU - Trautwein, K.* AU - Feenders, C.* AU - Hulsch, R.* AU - Ruppersberg, H.S.* AU - Strijkstra, A.* AU - Kant, M.* AU - Vagts, J.* AU - Wünsch, D.* AU - Michalke, B. AU - Maczka, M.* AU - Schulz, S.M.* AU - Hillebrand, H.* AU - Blasius, B.* AU - Rabus, R.* C1 - 51795 C2 - 43475 CY - Oxford TI - Non-Redfield, nutrient synergy and flexible internal elemental stoichiometry in a marine bacterium. JO - FEMS Microbiol. Ecol. VL - 93 IS - 5 PB - Oxford Univ Press PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - Predation is a fundamental mechanism of all food webs, but its drivers and organismic connectivities, especially at microbial level, are still poorly understood. Specifically, competitive carbon flows in the presence of multiple micropredators, as well as trophic links within and between microbial kingdoms have rarely been resolved. Here, using maize-planted agricultural soil as a model system, we have investigated the predation of amended bacterial prey by both prokaryotic and eukaryotic micropredators. We have queried how soil compartment (rhizosphere vs bulk soil) and nature of prey (Gram-positive vs Gram-negative) influence predation outcomes. We added 13C-labelled biomass of Pseudomonas putida and Arthrobacter globiformis to soil microcosms and found that P. putida was consumed much more rapidly. Bacteria and microeukaryotes specifically responsive to the biomass amendments were identified by RNA-stable isotope probing. Amongst the bacteria, only a few myxobacteria sequestered C from A. globiformis, whereas a considerable diversity of predatory bacteria incorporated C derived from P. putida. Diverse groups of heterotrophic protists, especially amoeba including Glaeseria, Hartmanella and Vahlkampfia spp., were observed to incorporate 13C from both amendments, but with pronounced niche differentiation between rhizosphere and bulk soil. This provides novel insights into niche partitioning between bacterial and eukaryotic micropredators in soil, driven not only by the nature of bacterial prey itself, but also by soil compartments. AU - Zhang, L. AU - Lueders, T. C1 - 51915 C2 - 43572 CY - Oxford TI - Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. JO - FEMS Microbiol. Ecol. VL - 93 IS - 9 PB - Oxford Univ Press PY - 2017 SN - 0168-6496 ER - TY - JOUR AB - Naturally occurring drying-rewetting events in soil have been shown to affect the dissipation of veterinary antibiotics entering soil by manure fertilization. However, knowledge of effects on the soil microbial community structure and resistome is scarce.Here, consequences of drying-rewetting cycles on effects of sulfadiazine (SDZ) in soil planted withDactylis glomerataL. were investigated in microcosms. Manure containing SDZ or not was applied to the pregrown grass and incubated for 56 days in a climate chamber. Water was added either daily or was reduced during two drying events of seven days, each followed by a recovery phase. Total community DNA was analyzed to reveal effects on the bacterial community structure and on the abundance ofsul1,sul2,intI1,intI2,qacE+qacEΔ1,traNandkorBgenes relative to 16S rRNA genes.16S rRNA gene based DGGE fingerprints indicated that drying-rewetting cycles modulated effects of SDZ on the bacterial community structure in the soil. Furthermore, the SDZ treatment increased the relative abundance of sulfonamide resistance and integrase genes compared to the control. However, this increase was not different between moisture regimes, indicating that drying-rewetting had only a negligible effect on the selection of the resistome by SDZ in the manured soil. AU - Jechalke, S.* AU - Radl, V. AU - Schloter, M. AU - Heuer, H.* AU - Smalla, K.* C1 - 48294 C2 - 41001 CY - Oxford TI - Do drying and rewetting cycles modulate effects of sulfadiazine spiked manure in soil? JO - FEMS Microbiol. Ecol. VL - 92 IS - 5 PB - Oxford Univ Press PY - 2016 SN - 0168-6496 ER - TY - JOUR AB - Beneficial microbes are applied to the soil and plant tissues directly or through seed inoculation, whereas soil application is preferred when there is risk of inhibitors or antagonistic microbes on the plant tissues. Insufficient survival of the microorganisms, hindrance in application of fungicides to the seeds and exposure to heat and sunlight in subsequent seed storage in conventional inoculation methods force to explore appropriate and efficient bacterial application method. Seed priming, where seeds are hydrated to activate metabolism without actual germination followed by drying, increases the germination, stand establishment and stress tolerance in different crops. Seed priming with living bacterial inoculum is termed as biopriming that involves the application of plant growth promoting rhizobacteria. It increases speed and uniformity of germination; also ensures rapid, uniform and high establishment of crops; and hence improves harvest quality and yield. Seed biopriming allows the bacteria to enter/adhere the seeds and also acclimatization of bacteria in the prevalent conditions. This review focuses on methods used for biopriming, and also the role in improving crop productivity and stress tolerance along with prospects of this technology. The comparison of methods being followed is also reviewed proposing biopriming as a promising technique for application of beneficial microbes to the seeds. AU - Mahmood, A. AU - Turgay, O.C.* AU - Farooq, M.* AU - Hayat, R.* C1 - 49203 C2 - 41714 CY - Oxford TI - Seed biopriming with plant growth promoting rhizobacteria: A review. JO - FEMS Microbiol. Ecol. VL - 92 IS - 8 PB - Oxford Univ Press PY - 2016 SN - 0168-6496 ER - TY - JOUR AB - Incorporation of plant litter is a frequent agricultural practice to increase nutrient availability in soil and heavily relies on the activity of cellulose degrading microorganisms. Here we address the question how different tillage treatments affect soil microbial communities and their cellulose degrading potential in a long-term agricultural experiment. To identify potential differences in microbial taxonomy and functionality, we generated six soil metagenomes of conventional (CT) and reduced (RT) tillage-treated topsoil samples, which differed in their potential extracellular cellulolytic activity as well as microbial biomass. Taxonomic analysis of metagenomic data revealed few differences between RT and CT and a dominance of Proteobacteria and Actinobacteria, whereas eukaryotic phyla were not prevalent. Prediction of cellulolytic enzymes revealed glycoside hydrolase families 1, 3, 5, 94, auxiliary activity family 8 and carbohydrate binding module 2 as the most abundant in soil. These were annotated mainly to the phyla of Proteobacteria, Actinobacteria and Bacteroidetes. These results suggest that the observed higher cellulolytic activity in RT soils can be explained by a higher microbial biomass or changed expression levels but not by shifts in the soil microbiome. Overall this study reveals stability of soil microbial communities and cellulolytic gene composition under the investigated tillage treatments. AU - de Vries, M.C. AU - Schöler, A. AU - Ertl, J. AU - Xu, Z.* AU - Schloter, M. C1 - 45474 C2 - 37354 CY - Oxford TI - Metagenomic analyses reveal no differences in genes involved in cellulose degradation under different tillage treatments. JO - FEMS Microbiol. Ecol. VL - 91 IS - 7 PB - Oxford Univ Press PY - 2015 SN - 0168-6496 ER - TY - JOUR AB - Effluents from wastewater treatment plants (WWTPs) containing micro-organisms and residual nitrogen can stimulate nitrification in freshwater streams. We hypothesized that different ammonia-oxidizing (AOB) and nitrite-oxidizing (NOB) bacteria present in WWTP effluents differ in their potential to colonize biofilms in the receiving streams. In an experimental approach, we monitored biofilm colonization by nitrifiers in ammonium- or nitrite-fed microcosm flumes after inoculation with activated sludge. In a field study, we compared the nitrifier communities in a full-scale WWTP and in epilithic biofilms downstream of the WWTP outlet. Despite substantially different ammonia concentrations in the microcosms and the stream, the same nitrifiers were detected by fluorescence in situ hybridization in all biofilms. Of the diverse nitrifiers present in the WWTPs, only AOB of the Nitrosomonas oligotropha/ureae lineage and NOB of Nitrospira sublineage I colonized the natural biofilms. Analysis of the amoA gene encoding the alpha subunit of ammonia monooxygenase of AOB revealed seven identical amoA sequence types. Six of these affiliated with the N.oligotropha/ureae lineage and were shared between the WWTP and the stream biofilms, but the other shared sequence type grouped with the N.europaea/eutropha and N.communis lineage. Measured nitrification activities were high in the microcosms and the stream. Our results show that nitrifiers from WWTPs can colonize freshwater biofilms and confirm that WWTP-affected streams are hot spots of nitrification. AU - Mußmann, M.* AU - Ribot, M.* AU - von Schiller, D.* AU - Merbt, S.N.* AU - Augspurger, C.* AU - Karwautz, C. AU - Winkel, M.* AU - Battin, T.J.* AU - Marti, E.* AU - Daims, H.* C1 - 25909 C2 - 31989 SP - 104-115 TI - Colonization of freshwater biofilms by nitrifying bacteria from activated sludge. JO - FEMS Microbiol. Ecol. VL - 85 IS - 1 PB - Wiley-Blackwell PY - 2013 SN - 0168-6496 ER - TY - JOUR AB - A novel approach was developed to follow the successive utilization of organic carbon under anoxic conditions by microcalorimetry, chemical analyses of fermentation products and stable-isotope probing (SIP). The fermentation of 13C-labeled glucose was monitored over 4weeks by microcalorimetry in a stimulation experiment with tidal-flat sediments. Based on characteristic heat production phases, time points were selected for quantifying fermentation products and identifying substrate-assimilating bacteria by the isolation of intact ribosomes prior to rRNA-SIP. The preisolation of ribosomes resulted in rRNA with an excellent quality. Glucose was completely consumed within 2days and was mainly fermented to acetate. Ethanol, formate, and hydrogen were detected intermittently. The amount of propionate that was built within the first 3days stayed constant. Ribosome-based SIP of fully labeled and unlabeled rRNA was used for fingerprinting the glucose-degrading species and the inactive background community. The most abundant actively degrading bacterium was related to Psychromonas macrocephali (similarity 99%) as identified by DGGE and sequencing. The disappearance of Desulfovibrio-related bands in labeled rRNA after 3days indicated that this group was active during the first degradation phase only. In summary, ribosome-based SIP in combination with microcalorimetry allows dissecting distinct phases in substrate turnover in a very sensitive manner. AU - Graue, J.* AU - Kleindienst, S.* AU - Lüders, T. AU - Cypionka, H.* AU - Engelen, B.* C1 - 7589 C2 - 29579 SP - 78-87 TI - Identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing. JO - FEMS Microbiol. Ecol. VL - 81 IS - 1 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - CO2 fixation is one of the most important processes on the Earth's surface, but our current understanding of the occurrence and importance of chemolithoautotrophy in the terrestrial subsurface is poor. Groundwater ecosystems, especially at organically polluted sites, have all the requirements for autotrophic growth processes, and CO2 fixation is thus suggested to contribute significantly to carbon flux in these environments. We explored the potential for autotrophic CO2 fixation in microbial communities of a petroleum hydrocarbon-contaminated aquifer by detection of functional marker genes (cbbL, cbbM), encoding different forms of the key enzyme RubisCO of the CalvinBensonBassham cycle. Quantification of (red-like) cbbL genes revealed highest numbers at the upper fringe of the contaminant plume and the capillary fringe where reduced sulphur and iron species are regularly oxidized in the course of groundwater table changes. Functional gene sequences retrieved from this area were most closely related to sequences of different thiobacilli. Moreover, several cultures could be enriched from fresh aquifer material, all of which are able to grow under chemolithoautotrophic conditions. A novel, nitrate-reducing, thiosulfate-oxidizing bacterial strain, recently described as Thiobacillus thiophilus D24TNT sp. nov., was shown to carry and transcribe RubisCO large-subunit genes of form I and II. Enzyme tests proved the actual activity of RubisCO in this strain. AU - Kellermann, C. AU - Selesi, D. AU - Lee, N.* AU - Hugler, M.* AU - Esperschütz, J. AU - Hartmann, A. AU - Griebler, C. C1 - 7591 C2 - 29800 SP - 172-187 TI - Microbial CO2 fixation potential in a tar-oil-contaminated porous aquifer. JO - FEMS Microbiol. Ecol. VL - 81 IS - 1 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - Climate warming may induce shifts in soil microbial communities possibly altering the long-term carbon mineralization potential of soils. We assessed the response of the bacterial community in a forest soil to experimental soil warming (+4 °C) in the context of seasonal fluctuations. Three experimental plots were sampled in the fourth year of warming in summer and winter and compared to control plots by 16S rRNA gene pyrosequencing. We sequenced 17 308 amplicons per sample and analysed operational taxonomic units at genetic distances of 0.03, 0.10 and 0.25, with respective Good's coverages of 0.900, 0.977 and 0.998. Diversity indices did not differ between summer, winter, control or warmed samples. Summer and winter samples differed in community structure at a genetic distance of 0.25, corresponding approximately to phylum level. This was mainly because of an increase of Actinobacteria in winter. Abundance patterns of dominant taxa (> 0.06% of all reads) were analysed individually and revealed, that seasonal shifts were coherent among related phylogenetic groups. Seasonal community dynamics were subtle compared to the dynamics of soil respiration. Despite a pronounced respiration response to soil warming, we did not detect warming effects on community structure or composition. Fine-scale shifts may have been concealed by the considerable spatial variation. AU - Kuffner, M.* AU - Hai, B. AU - Rattei, T.* AU - Melodelima, C.* AU - Schloter, M. AU - Zechmeister-Boltenstern, S.* AU - Jandl, R.* AU - Schindlbacher, A.* AU - Sessitsch, A.* C1 - 8523 C2 - 30162 SP - 551-562 TI - Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. JO - FEMS Microbiol. Ecol. VL - 82 IS - 3 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - Acidovorax radicis N35, isolated from surface-sterilized wheat roots (Triticum aestivum), showed irreversible phenotypic variation in nutrient broth, resulting in a differing colony morphology. In addition to the wild-type form (rough colony type), a phenotypic variant form (smooth colony type) appeared at a frequency of 3.2 × 10(-3) per cell per generation on NB agar plates. In contrast to the N35 wild type, the variant N35v showed almost no cell aggregation and had lost its flagella and swarming ability. After inoculation, only the wild-type N35 significantly promoted the growth of soil-grown barley plants. After co-inoculation of axenically grown barley seedlings with differentially fluorescently labeled N35 and N35v cells, decreased competitive endophytic root colonization in the phenotypic variant N35v was observed using confocal laser scanning microscopy. In addition, 454 pyrosequencing of both phenotypes revealed almost identical genomic sequences. The only stable difference noted in the sequence of the phenotype variant N35v was a 16-nucleotide deletion identified in a gene encoding the mismatch repair protein MutL. The deletion resulted in a frameshift that revealed a new stop codon resulting in a truncated MutL protein missing a functional MutL C-terminal domain. The mutation was consistent in all investigated phenotype variant cultures and might be responsible for the observed phenotypic variation in A. radicis N35. AU - Li, D. AU - Rothballer, M. AU - Engel, M. AU - Hoser, J.D.S. AU - Schmidt, T. AU - Kuttler, C.* AU - Schmid, M. AU - Schloter, M. AU - Hartmann, A. C1 - 7185 C2 - 29530 SP - 751-762 TI - Phenotypic variation in Acidovorax radicis N35 influences plant growth promotion. JO - FEMS Microbiol. Ecol. VL - 79 IS - 3 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - no Abstract AU - Lüders, T. AU - Griebler, C. AU - Haggblom, M.* C1 - 7592 C2 - 29580 SP - 1 TI - Subsurface microbiology: The life below our feet. JO - FEMS Microbiol. Ecol. VL - 81 IS - 1 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - Seasonal patterns of groundwater and sediment microbial communities were explored in a hydrologically dynamic alpine oligotrophic porous aquifer, characterized by pronounced groundwater table fluctuations. Rising of the groundwater level in consequence of snow melting water recharge was accompanied by a dramatic drop of bacterial Shannon diversity in groundwater from H '=3.22+/-0.28 in autumn and winter to H '=1.31+/-0.35 in spring and summer, evaluated based on T-RFLP community fingerprinting. Elevated numbers of bacteria in groundwater in autumn followed nutrient inputs via recharge from summer rains and correlated well with highest concentrations of assimilable organic carbon. Sterile sediments incubated to groundwater in monitoring wells were readily colonized reaching maximum cell densities within 2months, followed by a consecutive but delayed increase and leveling-off of bacterial diversity. After 1year of incubation, the initially sterile sediments exhibited a similar number of bacteria and Shannon diversity when compared to vital sediment from a nearby river incubated in parallel. The river bed sediment microbial communities hardly changed in composition, diversity, and cell numbers during 1year of exposure to groundwater. Summing up, the seasonal hydrological dynamics were found to induce considerable dynamics of microbial communities suspended in groundwater, while sediment communities seem unaffected and stable in terms of biomass and diversity. AU - Zhou, Y. AU - Kellermann, C. AU - Griebler, C. C1 - 7597 C2 - 30136 SP - 230-242 TI - Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer. JO - FEMS Microbiol. Ecol. VL - 81 IS - 1 PB - Wiley-Blackwell PY - 2012 SN - 0168-6496 ER - TY - JOUR AB - no Abstract AU - Baldrian, P.* AU - Head, I.M.* AU - Prosser, J.I.* AU - Schloter, M. AU - Smalla, K.* AU - Tebbe, C.C.* C1 - 3760 C2 - 28896 SP - 1-2 TI - Ecology and metagenomics of soil microorganisms. JO - FEMS Microbiol. Ecol. VL - 78 IS - 1 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - A high percentage of photosynthetically assimilated carbon is released into soil via root exudates, which are acknowledged as the most important factor for the development of microbial rhizosphere communities. As quality and quantity of root exudates are dependent on plant genotype, the genetic engineering of plants might also influence carbon partitioning within the plant and thus microbial rhizosphere community structure. In this study, the carbon allocation patterns within the plant-rhizosphere system of a genetically modified amylopectin-accumulating potato line (Solanum tuberosum L.) were linked to microbial degraders of root exudates under greenhouse conditions, using (13)C-CO(2) pulse-chase labelling in combination with phospholipid fatty acid (PLFA) analysis. In addition, GM plants were compared with the parental cultivar as well as a second potato cultivar obtained by classical breeding. Rhizosphere samples were obtained during young leaf developmental and flowering stages. (13)C allocation in aboveground plant biomass, water-extractable organic carbon, microbial biomass carbon and PLFA as well as the microbial community structure in the rhizosphere varied significantly between the natural potato cultivars. However, no differences between the GM line and its parental cultivar were observed. Besides the considerable impact of plant cultivar, the plant developmental stage affected carbon partitioning via the plant into the rhizosphere and, subsequently, microbial communities involved in the transformation of root exudates. AU - Gschwendtner, S. AU - Esperschütz, J.* AU - Buegger, F. AU - Reichmann, M.* AU - Müller, M.* AU - Munch, J.-C.* AU - Schloter, M. C1 - 6199 C2 - 28562 SP - 564-575 TI - Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates. JO - FEMS Microbiol. Ecol. VL - 76 IS - 3 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type denitrifiers to scales >14 m for nirK-type denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil. AU - Keil, D.* AU - Meyer, A.H.* AU - Berner, D.* AU - Poll, C.* AU - Schützenmeister, A.* AU - Piepho, H.P.* AU - Vlasenko, A.* AU - Philippot, L.* AU - Schloter, M. AU - Kandeler, E.* AU - Marhan, S.* C1 - 6445 C2 - 28699 SP - 95-106 TI - Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils. JO - FEMS Microbiol. Ecol. VL - 77 IS - 1 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - An anaerobic naphthalene-degrading culture (N49) was enriched with ferric iron as electron acceptor. A closed electron balance indicated the total oxidation of naphthalene to CO(2) . In all growing cultures, the concentration of the presumed central metabolite of naphthalene degradation, 2-naphthoic acid, increased concomitantly with growth. The first metabolite of anaerobic methylnaphthalene degradation, naphthyl-2-methyl-succinic acid, was not identified in culture supernatants, which does not support a methylation to methylnaphthalene as the initial activation reaction of naphthalene, but rather a carboxylation, as proposed for other naphthalene-degrading cultures. Substrate utilization tests revealed that the culture was able to grow on 1-methyl-naphthalene, 2-methyl-naphthalene, 1-naphthoic acid or 2-naphthoic acid, whereas it did not grow on 1-naphthol, 2-naphthol, anthracene, phenanthrene, indane and indene. Terminal restriction fragment length polymorphism and 16S rRNA gene sequence analyses revealed that the microbial community of the culture was dominated by one bacterial microorganism, which was closely related (99% 16S sequence similarity) to the major organism in the iron-reducing, benzene-degrading enrichment culture BF [ISME J (2007) 1: 643; Int J Syst Evol Microbiol (2010) 60: 686]. The phylogenetic classification supports a new candidate species and genus of Gram-positive spore-forming iron-reducers that can degrade non-substituted aromatic hydrocarbons. It furthermore indicates that Gram-positive microorganisms might also play an important role in anaerobic polycyclic aromatic hydrocarbon-degradation. AU - Kleemann, R. AU - Meckenstock, R.U. C1 - 6797 C2 - 29305 SP - 488-496 TI - Anaerobic naphthalene degradation by Gram-positive, iron-reducing bacteria. JO - FEMS Microbiol. Ecol. VL - 78 IS - 3 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - Nitrogen management in soils has been considered as key to the sustainable use of terrestrial ecosystems and a protection of major ecosystem services. However, the microorganisms driving processes like nitrification, denitrification, N-fixation and mineralization are highly influenced by changing climatic conditions, intensification of agriculture and the application of new chemicals to a so far unknown extent. In this review, the current knowledge concerning the influence of selected scenarios of global change on the abundance, diversity and activity of microorganisms involved in nitrogen turnover, notably in agricultural and grassland soils, is summarized and linked to the corresponding processes. In this context, data are presented on nitrogen-cycling processes and the corresponding microbial key players during ecosystem development and changes in functional diversity patterns during shifts in land use. Furthermore, the impact of increased temperature, carbon dioxide and changes in precipitation regimes on microbial nitrogen turnover is discussed. Finally, some examples of the effects of pesticides and antibiotics after application to soil for selected processes of nitrogen transformation are also shown. AU - Ollivier, J.* AU - Töwe, S.* AU - Bannert, A.* AU - Hai, B. AU - Kastl, E.-M. AU - Meyer, A.H.* AU - Su, M. AU - Kleineidam, K. AU - Schloter, M. C1 - 3761 C2 - 28897 SP - 3-16 TI - Nitrogen turnover in soil and global change. JO - FEMS Microbiol. Ecol. VL - 78 IS - 1 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil-contaminated aquifer in Germany, where a specialized community of contaminant degraders codominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase α-subunit, bssA) genes detected in situ appeared to be more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with (13) C(7) -toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae in sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This and the absence of (13) C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy among anaerobic toluene degraders on site. AU - Pilloni, G. AU - von Netzer, F. AU - Engel, M. AU - Lüders, T. C1 - 6591 C2 - 28953 SP - 165-175 TI - Electron acceptor-dependent identification of key anaerobic toluene degraders at a tar-oil-contaminated aquifer by Pyro-SIP. JO - FEMS Microbiol. Ecol. VL - 78 IS - 1 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - The phylogenetic composition of bacterial communities in the rhizosphere of three potato cultivars grown at two distant field sites was analysed. Ribosomal gene fragments amplified from total community DNA were hybridized to PhyloChips. A total of 2432 operational taxonomic units (OTUs) were detected by the PhyloChips, of which 65% were found in the rhizosphere of all cultivars at both field sites. From all detected OTUs, 9% revealed a cultivar-dependent abundance at the one or the other field site and 4% at both sites. Differential abundance on the three cultivars was mainly observed for OTUs belonging to the Pseudomonadales, Actinomycetales and Enterobacteriales. More than 40% of OTUs belonging to Bradyrhizobiales, Sphingomonadales, Burkholderiales, Rhodocyclales, Xanthomonadales and Actinomycetales differed significantly in their abundance between the sites. A sequence analysis of six 16S rRNA gene clone libraries corresponded well with the taxonomic community structure evidenced by the PhyloChip hybridization. Most ribotypes matched OTUs detected by the PhyloChip. Those OTUs that responded to the potato cultivar at both field sites might be of interest in view of cultivar-specific effects on bacterial biocontrol strains and pathogens. AU - Weinert, N.* AU - Piceno, Y.* AU - Ding, G.C.* AU - Meincke, R.* AU - Heuer, H.* AU - Berg, G.* AU - Schloter, M. AU - Andersen, G.* AU - Smalla, K. C1 - 5704 C2 - 28443 CY - Oxford SP - 497-506 TI - PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: Many common and few cultivar-dependent taxa. JO - FEMS Microbiol. Ecol. VL - 75 IS - 3 PB - Wiley-Blackwell PY - 2011 SN - 0168-6496 ER - TY - JOUR AB - A toluene-degrading microbial consortium was enriched directly in a BTEX-contaminated aquifer under sulfate-reducing conditions using in situ microcosms consisting of toluene-loaded activated carbon pellets. Degradation of toluene and concomitant sulfide production by the consortium was subsequently demonstrated in laboratory microcosms. The consortium was physiologically and phylogenetically characterized by isotope tracer experiments using nonlabeled toluene, [13C]-alpha-toluene or [13C(7)]-toluene as growth substrates. Cells incubated with [13C]-alpha-toluene or [13C(7)]-toluene incorporated 8-15 at.% 13C and 51-57 at.% 13C into total lipid fatty acids, respectively, indicating a lower specific incorporation of 13C from [13C(7)]-toluene. In order to identify the toluene-assimilating bacteria, the incorporation of carbon from both [13C]-alpha-toluene and [13C(7)]-toluene into rRNA was analyzed by stable isotope probing. Time and buoyant density-resolved 16S rRNA gene-based terminal restriction fragment length polymorphism profiles, combined with cloning and sequencing, revealed that an uncultured bacterium (99% sequence similarity) related to the genus Desulfocapsa was the main toluene-degrading organism in the consortium. The ratio of the respective terminal restriction fragments changed over time, indicating trophic interactions within this consortium. AU - Bombach, P.* AU - Chatzinotas, A.* AU - Neu, T.R.* AU - Kästner, M.* AU - Lüders, T. AU - Vogt, C.* C1 - 37 C2 - 27097 SP - 237-246 TI - Enrichment and characterization of a sulfate-reducing toluene-degrading microbial consortium by combining in situ microcosms and stable isotope probing techniques. JO - FEMS Microbiol. Ecol. VL - 71 IS - 2 PB - Wiley-Blackwell PY - 2010 SN - 0168-6496 ER - TY - JOUR AB - The biocontrol strain Pseudomonas putida IsoF, which was isolated from a tomato rhizosphere, is a known N-acyl-homoserine lactone (AHL) producer with only one LuxI/LuxR-like quorum-sensing (QS) system. The production and degradation of AHLs were analysed in different growth phases of the bacterium. Using the analytical tools of ultra performance liquid chromatography and high resolution MS, it was possible to determine not only the various AHLs synthesized over time but also their degradation products. 3-oxo-decanoyl-homoserine lactone was found to be the dominant AHL, which reached its maximum in the early logarithmic growth phase. Although the pH of the medium was neutral, the AHLs were degraded thereafter rapidly to the corresponding homoserines and other metabolites. The proposed lactonase gene of P. putida IsoF could not be identified, because it is apparently quite different from hitherto described lactonases. The analytical data were used to calculate the rates and thresholds of AHL production by mathematical modelling, allowing quantitative predictions and a further understanding of the QS-based regulations in this bacterium. This study, combining microbiological, chemical and mathematical approaches, suggests that AHL degradation is an integral part of the whole autoinducer circuit of P. putida IsoF. AU - Fekete, A. AU - Kuttler, C.* AU - Rothballer, M. AU - Hense, B.A. AU - Fischer, D. AU - Buddrus-Schiemann, K. AU - Lucio, M. AU - Müller, J.* AU - Schmitt-Kopplin, P. AU - Hartmann, A. C1 - 5994 C2 - 27762 SP - 22-34 TI - Dynamic regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF. JO - FEMS Microbiol. Ecol. VL - 72 IS - 1 PB - Wiley-Blackwell Publishing Inc. PY - 2010 SN - 0168-6496 ER - TY - JOUR AB - The surface of tubers might be a reservoir for bacteria that are disseminated with seed potatoes or that affect postharvest damage. The numbers of culturable bacteria and their antagonistic potential, as well as bacterial community fingerprints were analysed from tubers of seven field-grown potato genotypes, including two lines with tuber-accumulated zeaxanthin. The plant genotype significantly affected the number of culturable bacteria only at one field site. Zeaxanthin had no effect on the bacterial plate counts. In dual culture, 72 of 700 bacterial isolates inhibited at least one of the potato pathogens Rhizoctonia solani, Verticillium dahliae or Phytophthora infestans, 12 of them suppressing all three. Most of these antagonists were identified as Bacillus or Streptomyces. From tubers of two plant genotypes, including one zeaxanthin line, higher numbers of antagonists were isolated. Most antagonists showed glucanase, cellulase and protease activity, which could represent mechanisms for pathogen suppression. PCR-DGGE fingerprints of the 16S rRNA genes of bacterial communities from the tuber surfaces revealed that the potato genotype significantly affected the Pseudomonas community structure at one site. However, the genotypes showed nearly identical fingerprints for Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Bacillus and Streptomycetaceae. In conclusion, tuber-associated bacteria were only weakly affected by the plant genotype. AU - Weinert, N.* AU - Meincke, R.* AU - Gottwald, C.* AU - Heuer, H.* AU - Schloter, M. AU - Berg, G.* AU - Smalla, K.* C1 - 5410 C2 - 27558 SP - 114-123 TI - Bacterial diversity on the surface of potato tubers in soil and the influence of the plant genotype. JO - FEMS Microbiol. Ecol. VL - 74 IS - 1 PB - Wiley-Blackwell PY - 2010 SN - 0168-6496 ER - TY - JOUR AB - Despite its high chemical stability, benzene is known to be biodegradable with various electron acceptors under anaerobic conditions. However, our understanding of the initial activation reaction and the responsible prokaryotes is limited. In the present study, we enriched a bacterial culture that oxidizes benzene to carbon dioxide under sulfate-reducing conditions. Community analysis using terminal restriction fragment length polymorphism, 16S rRNA gene sequencing and FISH revealed 95% dominance of one phylotype that is affiliated to the Gram-positive bacterial genus Pelotomaculum showing that sulfate-reducing Gram-positive bacteria are involved in anaerobic benzene degradation. In order to get indications of the initial activation mechanism, we tested the substrate utilization, performed cometabolism tests and screened for putative metabolites. Phenol, toluene, and benzoate could not be utilized as alternative carbon sources by the benzene-degrading culture. Cometabolic degradation experiments resulted in retarded rates of benzene degradation in the presence of phenol whereas toluene had no effect on benzene metabolism. Phenol, 2-hydroxybenzoate, 4-hydroxybenzoate, and benzoate were identified as putative metabolites in the enrichment culture. However, hydroxylated aromatics were shown to be formed abiotically. Thus, the finding of benzoate as an intermediate compound supports a direct carboxylation of benzene as the initial activation mechanism but additional reactions leading to its formation cannot be excluded definitely. AU - Abu Laban, N.M.F.H. AU - Selesi, D. AU - Jobelius, C.* AU - Meckenstock, R.U. C1 - 685 C2 - 26172 SP - 300-311 TI - Anaerobic benzene degradation by Gram-positive sulfate-reducing bacteria. JO - FEMS Microbiol. Ecol. VL - 68 IS - 3 PB - Wiley-Blackwell Publishing, Inc PY - 2009 SN - 0168-6496 ER - TY - JOUR AB - The use of groundwater as a carrier of thermal energy is an important source of sustainable heating and cooling. However, the effects of thermal use on geochemical and biological aquifer characteristics are poorly understood. Here, we have assessed the impacts of heat discharge on an uncontaminated, shallow aquifer by monitoring the hydrogeochemical, bacterial and faunal parameters at an active thermal discharge facility. The observed variability between wells was considerable. Yet, no significant temperature impacts on bacterial or faunal abundance and on bacterial productivity were observed. Also, we did not observe an improved survival or growth of coliforms with temperature. In contrast, the diversity of bacterial terminal restriction fragment (T-RF) length polymorphism fingerprints and faunal populations was either positively or negatively affected by temperature, respectively, and the abundance of selected T-RFs was clearly temperature dependent. Canonical correspondence analysis indicated that both the impact of temperature and of surface water from a nearby river, were important drivers of aquifer biotic variability. These results demonstrate that aquifer thermal energy discharge can affect aquifer bacteria and fauna, while at the same time controlling only a minor part of the total seasonal and spatial variability and therefore posing no likely threat to ecosystem functioning and drinking water protection in uncontaminated, shallow aquifers. AU - Brielmann, H. AU - Griebler, C. AU - Schmidt, S.I. AU - Michel, R.* AU - Lüders, T. C1 - 1109 C2 - 26164 SP - 273-286 TI - Effects of thermal energy discharge on shallow groundwater ecosystems. JO - FEMS Microbiol. Ecol. VL - 68 IS - 3 PB - Wiley-Blackwell Publishing, Inc PY - 2009 SN - 0168-6496 ER - TY - JOUR AB - The aromatic hydrocarbon biphenyl is a widely distributed environmental pollutant. Whereas the aerobic degradation of biphenyl has been extensively studied, knowledge of the anaerobic biphenyl-oxidizing bacteria and their biochemical degradation pathway is scarce. Here, we report on an enrichment culture that oxidized biphenyl completely to carbon dioxide under sulfate-reducing conditions. The biphenyl-degrading culture was dominated by two distinct bacterial species distantly affiliated with the Gram-positive genus Desulfotomaculum. Moreover, the enrichment culture has the ability to grow with benzene and a mixture of anthracene and phenanthrene as the sole source of carbon, but here the microbial community composition differed substantially from the biphenyl-grown culture. Biphenyl-4-carboxylic acid was identified as an intermediate in the biphenyl-degrading culture. Moreover, 4-fluorobiphenyl was converted cometabolically with biphenyl because in addition to the biphenyl-4-carboxylic acid, a compound identified as its fluorinated analog was observed. These findings are consistent with the general pattern in the anaerobic catabolism of many aromatic hydrocarbons where carboxylic acids are found to be central metabolites. AU - Selesi, D. AU - Meckenstock, R.U. C1 - 1247 C2 - 26123 SP - 86-93 TI - Anaerobic degradation of the aromatic hydrocarbon biphenyl by a sulfate-reducing enrichment culture. JO - FEMS Microbiol. Ecol. VL - 68 IS - 1 PB - Wiley-Blackwell PY - 2009 SN - 0168-6496 ER - TY - JOUR AB - Herbaspirillum frisingense is a diazotrophic betaproteobacterium isolated from C4-energy plants, for example Miscanthus sinensis. To demonstrate endophytic colonization unequivocally, immunological labeling techniques using monospecific polyclonal antibodies against two H. frisingense strains and green fluorescent protein (GFP)-fluorescence tagging were applied. The polyclonal antibodies enabled specific in situ identification and very detailed localization of H. frisingense isolates Mb11 and GSF30(T) within roots of Miscanthusxgiganteus seedlings. Three days after inoculation, cells were found inside root cortex cells and after 7 days they were colonizing the vascular tissue in the central cylinder. GFP-tagged H. frisingense strains could be detected and localized in uncut root material by confocal laser scanning microscopy and were found as endophytes in cortex cells, intercellular spaces and the central cylinder of barley roots. Concerning the production of potential plant effector molecules, H. frisingense strain GSF30(T) tested positive for the production of indole-3-acetic acid, while Mb11 was shown to produce N-acylhomoserine lactones, and both strains were able to utilize 1-aminocyclopropane-1-carboxylate (ACC), providing an indication of the activity of an ACC-deaminase. These results clearly present H. frisingense as a true plant endophyte and, although initial greenhouse experiments did not lead to clear plant growth stimulation, demonstrate the potential of this species for beneficial effects on the growth of crop plants. AU - Rothballer, M. AU - Eckert, B. AU - Schmid, M. AU - Fekete, A. AU - Schloter, M. AU - Lehner, A.* AU - Pollmann, S.* AU - Hartmann, A. C1 - 490 C2 - 25718 SP - 85-95 TI - Endophytic root colonization of gramineous plants by Herbaspirillum frisingense. JO - FEMS Microbiol. Ecol. VL - 66 IS - 1 PB - Wiley-Blackwell PY - 2008 SN - 0168-6496 ER - TY - JOUR AB - Antibiotic-resistant bacteria, nutrients and antibiotics that enter the soil by means of manure may enhance the proportion of bacteria displaying antibiotic resistance among soil bacteria and may affect bacterial community structure and function. To investigate the effect of manure and amoxicillin added to manure on soil bacterial communities, microcosm experiments were performed with two soil types and the following treatments: (1) nontreated, (2) manure-treated, (3) treated with manure supplemented with 10 mg amoxicillin kg(-1) soil and (4) treated with manure supplemented with 100 mg amoxicillin kg(-1) soil, with four replicates per treatment. Manure significantly increased the total CFU count and the amoxicillin-resistant CFU count of both soil types. However, only the soil with a history of manure treatment showed a significant increase in the relative number of amoxicillin-resistant bacteria as a result of amoxicillin amendment. The majority of plasmids exogenously isolated from soil originated from soil treated with amoxicillin-supplemented manure. All 16 characterized plasmids carried the bla-TEM gene, and 10 of them belonged to the IncN group. The bla-TEM gene was detected in DNA directly extracted from soil by dot-blot hybridization of PCR amplicons and showed an increased abundance in soil samples treated with manure. Molecular fingerprint analysis of 16S rRNA gene fragments amplified from soil DNA revealed significant effects of manure and amoxicillin on the bacterial community of both soils. AU - Binh, C.T.* AU - Heuer, H.* AU - Gomes, N.C.* AU - Kotzerke, A.* AU - Fulle, M.* AU - Wilke, B.M.* AU - Schloter, M. AU - Smalla, K.* C1 - 3479 C2 - 24888 SP - 290-302 TI - Short-term effects of amoxicillin on bacterial communities in manured soil. JO - FEMS Microbiol. Ecol. VL - 62 IS - 3 PB - Wiley-Blackwell PY - 2007 SN - 0168-6496 ER - TY - JOUR AB - In this study the influence of different farming systems on microbial community structure was analyzed using soil samples from the DOK long-term field experiment in Switzerland, which comprises organic (BIODYN and BIOORG) and conventional (CONFYM and CONMIN) farming systems as well as an unfertilized control (NOFERT). We examined microbial communities in winter wheat plots at two different points in the crop rotation (after potatoes and after maize). Employing extended polar lipid analysis up to 244 different phospholipid fatty acids (PLFA) and phospholipid ether lipids (PLEL) were detected. Higher concentrations of PLFA and PLEL in BIODYN and BIOORG indicated a significant influence of organic agriculture on microbial biomass. Farmyard manure (FYM) application consistently revealed the strongest, and the preceding crop the weakest, influence on domain-specific biomass, diversity indices and microbial community structures. Esterlinked PLFA from slowly growing bacteria (k-strategists) showed the strongest responses to long-term organic fertilization. Although the highest fungal biomass was found in the two organic systems of the DOK field trial, their contribution to the differentiation of community structures according to the management regime was relatively low. Prokaryotic communities responded most strongly to either conventional or organic farming management. AU - Esperschütz, J. AU - Gattinger, A. AU - Mäder, P.* AU - Schloter, M. AU - Fließbach, A.* C1 - 3004 C2 - 24445 SP - 26-37 TI - Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations. JO - FEMS Microbiol. Ecol. VL - 61 IS - 1 PB - Wiley-Blackwell PY - 2007 SN - 0168-6496 ER - TY - JOUR AU - Bathe, S.* AU - Achouak, W.* AU - Hartmann, A. AU - Heulin, T.* AU - Schloter, M. AU - Lebuhn, M. C1 - 2115 C2 - 23572 SP - 272-280 TI - Genetic and phenotypic microdiversity of Ochrobactrum spp.. JO - FEMS Microbiol. Ecol. VL - 56 PB - Wiley PY - 2006 SN - 0168-6496 ER - TY - JOUR AU - Gantner, S. AU - Schmid, M. AU - Dürr, C. AU - Schuhegger, R. AU - Steidle, A.* AU - Hutzler, P. AU - Langebartels, C. AU - Eberl, L.* AU - Hartmann, A. AU - Dazzo, F.B.* C1 - 4461 C2 - 23994 SP - 188-194 TI - In situ quantification of the spatial scale of calling distances and population density-independent N-acylhomoserine lactone-mediated communication by rhizobacteria colonized on plant roots. JO - FEMS Microbiol. Ecol. VL - 56 PB - Wiley PY - 2006 SN - 0168-6496 ER - TY - JOUR AU - Kutter, S. AU - Hartmann, A. AU - Schmid, M. C1 - 3985 C2 - 23992 SP - 262-271 TI - Colonization of barley (Hordeum vulgare) with Salmonella enterica and Listeria spp. JO - FEMS Microbiol. Ecol. VL - 56 PB - Wiley PY - 2006 SN - 0168-6496 ER - TY - JOUR AB - Fractionation of stable carbon isotopes upon degradation of trichlorobenzenes was studied under aerobic and anaerobic conditions. Mineralization of 1,2,4-trichlorobenzene by the aerobic strain Pseudomonas sp. P51 which uses a dioxygenase for the initial enzymatic reaction was not accompanied by a significant isotope fractionation. In contrast, reductive dehalogenation by the anaerobic strain Dehalococcoides sp. strain CBDB1 revealed average isotope enrichment factors (eta) between -3.1 and -3.7 for 1,2,3- and 1,2,4-trichlorobenzene, respectively. The significant isotope fractionation during reductive dehalogenation would allow tracing the in situ biodegradation of halogenated benzenes in contaminated anoxic aquifers, whereas the lack of isotope fractionation during aerobic transformation limits the use of this approach in oxic environments. AU - Griebler, C.* AU - Adrian, L.* AU - Meckenstock, R.U. AU - Richnow, H.H.* C1 - 2004 C2 - 21787 SP - 313-321 TI - Stable carbon isotope fractionation during aerobic and anaerobic transformation of trichlorobenzene. JO - FEMS Microbiol. Ecol. VL - 48 PB - Wiley PY - 2004 SN - 0168-6496 ER - TY - JOUR AU - Meckenstock, R.U. AU - Safinowski, M.* AU - Griebler, C.* C1 - 2717 C2 - 22133 SP - 27-36 TI - Anaerobic degradation of polycyclic aromatic hydrocarbons. JO - FEMS Microbiol. Ecol. VL - 49 PB - Wiley PY - 2004 SN - 0168-6496 ER - TY - JOUR AB - It is frequently observed in aromatic hydrocarbons such as benzene, toluene, ethylbenzene, xylene (BTEX)-contaminated aquifers that toluene degrades faster than xylenes and benzene. In sediment column experiments which were run with a mixture of BTEX compounds toluene degradation started after a lag period of several weeks. When we omitted toluene from the culture medium o-xylene degradation started. Xylene degradation could be inhibited by adding toluene back to the medium and could be recovered when toluene was omitted again. This was observed repeatedly when toluene concentrations higher than 20 muM were added. Two sulphate-reducing bacterial species, isolated from the column material, were used to investigate the degradation behaviour in detail. Strain TRMI degraded exclusively toluene, strain OX39 degraded preferentially o-xylene and toluene only after an adaptation period of more than 90 days when added as the sole substrate. Growth and o-xylene degradation of strain OX39 were inhibited by toluene concentrations as low as 40 muM, whereas, in contrast, toluene degradation by strain TRMI was not inhibited by o-xylene concentrations up to 0.5 mM. Both the column data and the batch experiments indicated that two Organisms were responsible for the toluene/xylene degradation in the sediment column. One strain degraded only toluene and was not effected by xylene and the second degraded xylene and was inhibited by toluene. Our findings offer an explanation that the observed differential degradation of BTEX compounds in contaminated aquifers could originate from a partial metabolic inhibition of xylene-degrading organisms by toluene. AU - Meckenstock, R.U. AU - Warthmann, R.J.* AU - Schäfer, W.* C1 - 4952 C2 - 21725 SP - 381-386 TI - Inhibition of anaerobic microbial o-xylene degradation by toluene in sulfidogenic sediment columns and pure cultures. JO - FEMS Microbiol. Ecol. VL - 47 IS - 3 PB - Wiley PY - 2004 SN - 0168-6496 ER - TY - JOUR AB - Methanotrophic bacteria play an important role in regulating the methane flux from rice fields to the atmosphere. The abundance of methane-oxidizing bacteria is very heterogeneous along the rice root as revealed by most probable number (MPN) counts and by scanning confocal laser microscopy (SCLM). Two methanotrophic strains. Rp1 and Rp2, were isolated from high dilutions of MPN counts from the rhizoplane of rice roots grown in natural rice field soil. We used monoxenically grown rice plants to relocalize these strains on and in rice roots by means of polyclonal antisera and 16S rRNA probes. Strain Rp1 was even detected in xylem vessels. The two isolates also were able to recolonize roots grown in natural soil under competitive conditions. We found large colonies in deep grooves on the root surface between iron oxide precipitates. Some cells also were observed in the root cortex. The distribution of methane-oxidizing bacteria probably reflects the changing availability of methane and oxygen in the rhizosphere. AU - Gilbert, B.* AU - Aßmus, B. AU - Hartmann, A. AU - Frenzel, P.* C1 - 23029 C2 - 31172 SP - 117-128 TI - In situ localization of two methanotrophic strains in the rhizosphere of rice plants. JO - FEMS Microbiol. Ecol. VL - 25 IS - 2 PB - Wiley PY - 1998 SN - 0168-6496 ER - TY - JOUR AB - We determined the actual (no tryptophan, Trp, addition) and potential (Trp 0.1 g l(-1) added) production of indolic and phenolic compounds produced in different culture media by Paenibacillus polymyxa strains which had been isolated from different proximity to wheat roots. The production of indole-3-acetic acid (IAA) and related indolic metabolites by all strains tested was greatly enhanced upon Trp addition, suggesting that Trp is important as IAA precursor. A gradual decrease in potential IAA and an increase in potential indole-3-ethanol and indole-3-lactic acid production by strains isolated from non-rhizosphere soil (NRS) over rhizosphere soil (RS) to the rhizoplane (RP) were obtained. The NRS strain showed also a higher (potential) production of oxidized compounds such as indole-3-carboxylic and benzoic acid besides IAA. The determined metabolic differences indicate together with previous results on genetic and physiological parameters of P. polymyxa populations that plant roots select different P. polymyxa subpopulations. Our results suggest that the selected genotypes are differentially adapted to the decreasing oxygen pressure from NRS to RP. Possible effects of the probably microhabitat-specific metabolic profiles of the P. polymyxa isolates for plant growth are discussed. AU - Lebuhn, M. AU - Heulin, T.* AU - Hartmann, A. C1 - 23133 C2 - 31047 SP - 325-334 TI - Production of auxin and other indolic and phenolic compounds by Paenibacillus polymyxa strains isolated from different proximity to plant roots. JO - FEMS Microbiol. Ecol. VL - 22 IS - 4 PB - Wiley PY - 1997 SN - 0168-6496 ER -