TY  - JOUR
AB  - Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
AU  - Shintani, M.*
AU  - Vestergaard, G.*
AU  - Milaković, M.*
AU  - Kublik, S.
AU  - Smalla, K.*
AU  - Schloter, M.
AU  - Udiković-Kolić, N.*
C1  - 68337
C2  - 54754
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 3035-3051
TI  - Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies.
JO  - Environ. Microbiol.
VL  - 25
IS  - 12
PB  - Wiley
PY  - 2023
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
AU  - Duffner, C.
AU  - Kublik, S.
AU  - Fösel, B.
AU  - Frostegård,*
AU  - Schloter, M.
AU  - Bakken, L.*
AU  - Schulz, S.
C1  - 64255
C2  - 52161
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 1887-1901
TI  - Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers.
JO  - Environ. Microbiol.
VL  - 24
IS  - 4
PB  - Wiley
PY  - 2022
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.
AU  - Ryan, M.J.*
AU  - Schloter, M.
AU  - Berg, G.*
AU  - Kinkel, L.L.*
AU  - Eversole, K.*
AU  - Macklin, J.A.*
AU  - Rybakova, D.*
AU  - Sessitsch, A.*
C1  - 60713
C2  - 49975
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 372-375
TI  - Towards a unified data infrastructure to support European and global microbiome research: A call to action.
JO  - Environ. Microbiol.
VL  - 23
IS  - 1
PB  - Wiley
PY  - 2021
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.
AU  - Kundu, K.
AU  - Weber, N.
AU  - Griebler, C.
AU  - Elsner, M.
C1  - 59298
C2  - 48734
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 3339-3356
TI  - Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions.
JO  - Environ. Microbiol.
VL  - 22
IS  - 8
PB  - Wiley
PY  - 2020
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Some temperate tree species are associated with very low soil nitrification rates, with important implications for forest N dynamics, presumably due to their potential for biological nitrification inhibition (BNI). However, evidence for BNI in forest ecosystems is scarce so far and the nitrifier groups controlled by BNI-tree species have not been identified. Here, we evaluated how some tree species can control soil nitrification by providing direct evidence of BNI and identifying the nitrifier group(s) affected. First, by comparing 28 year-old monocultures of several tree species, we showed that nitrification rates correlated strongly with the abundance of the nitrite oxidizers Nitrobacter (50- to 1000-fold changes between tree monocultures) and only weakly with the abundance of ammonia oxidizing archaea (AOA). Second, using reciprocal transplantation of soil cores between low and high nitrification stands, we demonstrated that nitrification changed 16 months after transplantation and was correlated with changes in the abundance of Nitrobacter, not AOA. Third, extracts of litter or soil collected from the low nitrification stands of Picea abies and Abies nordmanniana inhibited the growth of Nitrobacter hamburgensis X14. Our results provide for the first time direct evidence of BNI by tree species directly affecting the abundance of Nitrobacter.
AU  - Laffite, A.*
AU  - Florio, A.*
AU  - Andrianarisoa, K.S.*
AU  - des Chatelliers, C.C.*
AU  - Schloter-Hai, B.
AU  - Ndaw, S.M.*
AU  - Periot, C.*
AU  - Schloter, M.
AU  - Zeller, B.*
AU  - Poly, F.*
AU  - Le Roux, X.*
C1  - 57844
C2  - 47951
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 1141-1153
TI  - Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations.
JO  - Environ. Microbiol.
VL  - 22
IS  - 3
PB  - Wiley
PY  - 2020
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant-microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.
AU  - Chowdhury, S.P.
AU  - Babin, D.*
AU  - Sandmann, M.*
AU  - Jacquiod, S.*
AU  - Sommermann, L.*
AU  - Sørensen, S.J.*
AU  - Fliessbach, A.*
AU  - Mäder, P.*
AU  - Geistlinger, J.*
AU  - Smalla, K.*
AU  - Rothballer, M.
AU  - Grosch, R.*
C1  - 55860
C2  - 46621
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 2426-2439
TI  - Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce.
JO  - Environ. Microbiol.
VL  - 21
IS  - 7
PB  - Wiley
PY  - 2019
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Sediments accommodate the dominating share of groundwater microbiomes, however the processes that govern the assembly and succession of sediment-attached microbial communities in groundwater aquifers are not well understood. To elucidate these processes, we followed the microbial colonization of sterile sediments in in situ microcosms that were exposed to groundwater for almost 1 year at two distant but hydrologically connected sites of a pristine, shallow, porous aquifer. Our results revealed intriguing similarities between the community succession on the newly-colonized sediments and succession patterns previously observed for biofilms in other more dynamic aquatic environments, indicating that the assembly of microbial communities on surfaces may be governed by similar underlying mechanisms across a wide range of different habitats. Null model simulations on spatiotemporally resolved 16S rRNA amplicon sequencing data further indicated selection of specific OTUs rather than random colonization as the main driver of community assembly. A small fraction of persistent OTUs that had established on the sediments during the first 115 days dominated the final communities (68%-85%), suggesting a key role of these early-colonizing organisms, in particular specific genera within the Comamonadaceae and Oxalobacteraceae, for community assembly and succession during the colonization of the sediments. Overall, our study suggests that differences between planktonic and sediment-attached communities often reported for groundwater environments are not the result of purely stochastic events, but that sediment surfaces select for specific groups of microorganisms that assemble over time in a reproducible, non-random way.
AU  - Fillinger, L.
AU  - Zhou, Y.
AU  - Kellermann, C.S.
AU  - Griebler, C.
C1  - 54616
C2  - 45713
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 327-342
TI  - Non-random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer.
JO  - Environ. Microbiol.
VL  - 21
IS  - 1
PB  - Wiley
PY  - 2018
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Anaerobic degradation processes are very important to attenuate polycyclic aromatic hydrocarbons (PAHs) in saturated, anoxic sediments. However, PAHs are poorly degradable, leading to very slow microbial growth and thus resulting in only a few cultures that have been enriched and studied so far. Here, we report on a new phenanthrene-degrading, sulfate-reducing enrichment culture, TRIP1. Genome-resolved metagenomics and strain specific cell counting with FISH and flow cytometry indicated that the culture is dominated by a microorganism belonging to the Desulfobacteraceae family (60% of the community) and sharing 93% 16S rRNA sequence similarity to the naphthalene-degrading, sulfate-reducing strain NaphS2. The anaerobic degradation pathway was studied by metabolite analyses and revealed phenanthroic acid as the major intermediate consistent with carboxylation as the initial activation reaction. Further reduced metabolites were indicative of a stepwise reduction of the ring system. We were able to measure the presumed second enzyme reaction in the pathway, phenanthroate-CoA ligase, in crude cell extracts. The reaction was specific for 2-phenanthroic acid and did not transform other isomers. The present study provides first insights into the anaerobic degradation pathways of three-ringed PAHs. The biochemical strategy follows principles known from anaerobic naphthalene degradation, including carboxylation and reduction of the aromatic ring system.
AU  - Himmelberg, A.M.
AU  - Brüls, T.*
AU  - Farmani, Z.*
AU  - Weyrauch, P.*
AU  - Barthel, G.
AU  - Schrader, W.*
AU  - Meckenstock, R.U.*
C1  - 54019
C2  - 45211
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 3589-3600
TI  - Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture.
JO  - Environ. Microbiol.
VL  - 20
IS  - 10
PB  - Wiley
PY  - 2018
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this me tabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions.
AU  - Marozava, S.
AU  - Vargas-López, R.*
AU  - Tian, Y.*
AU  - Merl-Pham, J.
AU  - Braster, M.*
AU  - Meckenstock, R.U.
AU  - Smidt, H.*
AU  - Röling, W.F.M.*
AU  - Westerhoff, H.V.*
C1  - 53673
C2  - 44943
CY  - 111 River St, Hoboken 07030-5774, Nj Usa
SP  - 2652-2669
TI  - Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats.
JO  - Environ. Microbiol.
VL  - 20
IS  - 7
PB  - Wiley
PY  - 2018
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - The cyclohexane derivative cis-2-(carboxymethyl)cyclohexane-1-carboxylic acid [(1R,2R)-/(1S,2S)-2-(carboxymethyl)cyclohexane-1-carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate-reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis-isomer, verifying that this is a true intermediate and not a dead-end product. Mass-spectrometric analyses confirmed that conversion is performed by an acyl-CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl-group. We propose that a novel kind of ring-opening lyase is involved in the further catabolic pathway proceeding via pimeloyl-CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring-cleavage is achieved via hydratases, this lyase might represent a new ring-opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl-CoA and glutaryl-CoA was proved in cell free extracts, yielding 2,3-dehydropimeloyl-CoA, 3-hydroxypimeloyl-CoA, 3-oxopimeloyl-CoA, glutaconyl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA and acetyl-CoA as observable intermediates. This indicates a link to central metabolism via β-oxidation, a non-decarboxylating glutaryl-CoA dehydrogenase and a subsequent glutaconyl-CoA decarboxylase.
AU  - Weyrauch, P.
AU  - Zaytsev, A.V.*
AU  - Stephan, S.*
AU  - Kocks, L.*
AU  - Schmitz, O.J.*
AU  - Golding, B.T.*
AU  - Meckenstock, R.U.*
C1  - 51543
C2  - 43301
CY  - Hoboken
SP  - 2819-2830
TI  - Conversion of cis-2-carboxycyclohexylacetyl-CoA in the downstream pathway of anaerobic naphthalene degradation.
JO  - Environ. Microbiol.
VL  - 19
IS  - 7
PB  - Wiley
PY  - 2017
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study glycerol was injected in an aquifer contaminated with cis-dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance of Firmicutes, Bacteriodetes and sulfate reducing Deltaproteobacteria. In line with (13) C cDCE enrichment and increased Dehalococcoides mccartyi (Dcm) numbers, dechlorination was observed towards the end of the field experiment, albeit being incomplete with accumulation of vinyl chloride. This was concurrent with i) decreased concentrations of dissolved organic carbon (DOC), reduced relative abundances of fermenting and sulfate reducing bacteria that have been suggested to promote Dcm growth by providing electron donor (H2 ) and essential corrinoid cofactors, ii) increased sulfate concentration and increased relative abundance of Epsilonproteobacteria and Deferribacteres as putative oxidizers of reduced sulfur compounds. Strong correlations of DOC, relative abundance of fermenters and sulfate reducers, and dechlorination imply the importance of syntrophic interactions to sustain robust dechlorination. Tracking microbial and environmental parameters that promote/preclude enhanced reductive dechlorination should aid development of sustainable bioremediation strategies.
AU  - Atashgahi, S.*
AU  - Lu, Y.*
AU  - Zheng, Y.*
AU  - Saccenti, E.*
AU  - Suarez-Diez, M.*
AU  - Ramiro-Garcia, J.*
AU  - Eisenmann, H.*
AU  - Elsner, M.
AU  - Stams, A.J.*
AU  - Springael, D.*
AU  - Dejonghe, W.*
AU  - Smidt, H.*
C1  - 49492
C2  - 40702
TI  - Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol.
JO  - Environ. Microbiol.
PY  - 2016
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus, but conversely also take up and immobilize P. Therefore, we analyzed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic DNA. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the datasets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harbored by Rhizobiales, Actinomycetales and Acidobacteriales.
AU  - Bergkemper, F.
AU  - Schöler, A.
AU  - Engel, M.
AU  - Lang, F.*
AU  - Krüger, J.*
AU  - Schloter, M.
AU  - Schulz, S.
C1  - 47573
C2  - 39172
CY  - Hoboken
SP  - 1988-2000
TI  - Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems.
JO  - Environ. Microbiol.
VL  - 18
IS  - 6
PB  - Wiley-blackwell
PY  - 2016
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - The plant pathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce several other secondary metabolites (SMs). Although much progress has been made in the field of secondary metabolism, the transcriptional regulation of SM biosynthesis is complex and still incompletely understood. Environmental conditions, global as well as pathway-specific regulators, and chromatin remodelling have been shown to play major roles. Here, the role of FfSge1, a homologue of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for formation of conidia and pathogenicity, but is involved in vegetative growth. Transcriptome analysis of the mutant Δffsge1 compared to the wild type, as well as comparative chemical analysis between the wild type, Δffsge1 and OE:FfSGE1, revealed that FfSge1 functions as a global activator of secondary metabolism in F. fujikuroi. Double mutants of FfSGE1 and other SM regulatory genes brought insights into the hierarchical regulation of secondary metabolism. In addition, FfSge1 is also required for expression of a yet uncharacterised SM gene cluster containing a non-canonical non-ribosomal peptide synthetase.
AU  - Michielse, C.B.*
AU  - Studt, L.*
AU  - Janevska, S.*
AU  - Sieber, C.M.K.
AU  - Arndt, B.*
AU  - Espino, J.J.*
AU  - Humpf, H.U.*
AU  - Güldener, U.
AU  - Tudzynski, B.*
C1  - 31972
C2  - 34921
CY  - Hoboken
SP  - 2690–2708
TI  - The global regulator FfSge1 is required for expression of secondary metabolite gene clusters, but not for pathogenicity in Fusarium fujikuroi.
JO  - Environ. Microbiol.
VL  - 17
IS  - 8
PB  - Wiley-blackwell
PY  - 2015
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Within the complex of deep, hypersaline anoxic lakes (DHALs) of the Mediterranean Ridge, we identified a new, unexplored DHAL and named it 'Lake Kryos' after a nearby depression. This lake is filled with magnesium chloride (MgCl2)-rich, athalassohaline brine (salinity>470 practical salinity units), presumably formed by the dissolution of Messinian bischofite. Compared with the DHALDiscovery, it contains elevated concentrations of kosmotropic sodium and sulfate ions, which are capable of reducing the net chaotropicily of MgCl2-rich solutions. The brine of Lake Kryos may therefore be biologically permissive at MgCl2 concentrations previously considered incompatible with life. We characterized the microbiology of the seawater-Kryos brine interface and managed to recover mRNA from the 2.27-3.03M MgCl2 layer (equivalent to 0.747-0.631 water activity), thereby expanding the established chaotropicity window-for-life. The primary bacterial taxa present there were Kebrit Deep Bacteria 1 candidate division and DHAL-specific group of organisms, distantly related to Desulfohalobium. Two euryarchaeal candidate divisions, Mediterranean Sea Brine Lakes group 1 and halophilic cluster 1, accounted for >85% of the rRNA-containing archaeal clones derived from the 2.27-3.03M MgCl2 layer, but were minority community-members in the overlying interface-layers. These findings shed light on the plausibility of life in highly chaotropic environments, geochemical windows for microbial extremophiles, and have implications for habitability elsewhere in the Solar System.
AU  - Yakimov, M.M.*
AU  - la Cono, V.L.*
AU  - Spada, G.L.*
AU  - Bortoluzzi, G.*
AU  - Messina, E.*
AU  - Smedile, F.*
AU  - Arcadi, E.*
AU  - Borghini, M.*
AU  - Ferrer, M.*
AU  - Schmitt-Kopplin, P.
AU  - Hertkorn, N.
AU  - Cray, J.A.*
AU  - Hallsworth, J.E.*
AU  - Golyshin, P.N.*
AU  - Giuliano, L.*
C1  - 43227
C2  - 36331
CY  - Hoboken
SP  - 364-382
TI  - Microbial community of the deep-sea brine Lake Kryos seawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA.
JO  - Environ. Microbiol.
VL  - 17
IS  - 2
PB  - Wiley-blackwell
PY  - 2015
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Polycyclic aromatic hydrocarbons are among the most hazardous environmental pollutants. However, in contrast to aerobic degradation, the respective degradation pathways in anaerobes are greatly unknown which has so far prohibited many environmental investigations. In this work, we studied the enzymatic dearomatization reactions involved in the degradation of the PAH model compounds naphthalene and 2-methylnaphthalene in the sulfate-reducing enrichment culture N47. Cell extracts of N47 grown on naphthalene catalysed the sodium dithionite-dependent four-electron reduction of the key intermediate 2-naphthoyl-coenzyme A (NCoA) to 5,6,7,8-tetrahydro-2-naphthoyl-CoA (THNCoA). The NCoA reductase activity was independent of ATP and was, surprisingly, not sensitive to oxygen. In cell extracts in the presence of various electron donors the product THNCoA was further reduced by a two-electron reaction to most likely a conjugated hexahydro-2-naphthoyl-CoA isomer (HHNCoA). The reaction assigned to THNCoA reductase strictly depended on ATP and was oxygen-sensitive with a half-life time between 30s and 1min when exposed to air. The rate was highest with NADH as electron donor. The results indicate that two novel and completely different dearomatizing ring reductases are involved in anaerobic naphthalene degradation. While the THNCoA reducing activity shows some properties of ATP-dependent class I benzoyl-CoA reductases, NCoA reduction appears to be catalysed by a previously unknown class of dearomatizing aryl-carboxyl-CoA reductases.
AU  - Eberlein, C.*
AU  - Johannes, J.
AU  - Mouttaki, H.
AU  - Sadeghi, M.*
AU  - Golding, B.T.*
AU  - Boll, M.*
AU  - Meckenstock, R.U.
C1  - 25747
C2  - 31913
SP  - 1832-1841
TI  - ATP-dependent/-independent enzymatic ring reductions involved in the anaerobic catabolism of naphthalene.
JO  - Environ. Microbiol.
VL  - 15
IS  - 6
PB  - Wiley-Blackwell
PY  - 2013
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl(3) precipitation and DNase, (iii) FeCl(3) precipitation and DNase + CsCl and (iv) FeCl(3) precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl(3) -precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl(3) and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.
AU  - Hurwitz, B.L.*
AU  - Deng, L.
AU  - Poulos, B.T.*
AU  - Sullivan, M.B.*
C1  - 10805
C2  - 30370
SP  - 1428-1440
TI  - Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.
JO  - Environ. Microbiol.
VL  - 15
IS  - 5
PB  - Wiley-Blackwell
PY  - 2013
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Over the last 5 years proteogenomics (using mass spectroscopy to identify proteins predicted from genomic sequences) has emerged as a promising approach to the high-throughput identification of protein N-termini, which remains a problem in genome annotation. Comparison of the experimentally determined N-termini with those predicted by sequence analysis tools allows identification of the signal peptides and therefore conclusions on the cytoplasmic or extracytoplasmic (periplasmic or extracellular) localization of the respective proteins. We present here the results of a proteogenomic study of the signal peptides in Escherichia coliK-12 and compare its results with the available experimental data and predictions by such software tools as SignalP and Phobius. A single proteogenomics experiment recovered more than a third of all signal peptides that had been experimentally determined during the past three decades and confirmed at least 31 additional signal peptides, mostly in the known exported proteins, which had been previously predicted but not validated. The filtering of putative signal peptides for the peptide length and the presence of an eight-residue hydrophobic patch and a typical signal peptidase cleavage site proved sufficient to eliminate the false-positive hits. Surprisingly, the results of this proteogenomics study, as well as a re-analysis of the E.coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates.
AU  - Ivankov, D.N.*
AU  - Payne, S.H.*
AU  - Galperin, M.Y.*
AU  - Bonissone, S.*
AU  - Pevzner, P.A.*
AU  - Frishman, D.
C1  - 24323
C2  - 31518
SP  - 983-990
TI  - How many signal peptides are there in bacteria?
JO  - Environ. Microbiol.
VL  - 15
IS  - 4
PB  - Wiley-Blackwell
PY  - 2013
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Metagenomics generates and tests hypotheses about dynamics and mechanistic drivers in wild populations, yet commonly suffers from insufficient (< 1 ng) starting genomic material for sequencing. Current solutions for amplifying sufficient DNA for metagenomics analyses include linear amplification for deep sequencing (LADS), which requires more DNA than is normally available, linker-amplified shotgun libraries (LASLs), which is prohibitively low throughput, and whole-genome amplification, which is significantly biased and thus non-quantitative. Here, we adapt the LASL approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a reconditioning PCR step to increase yield and minimize late-cycle PCR artefacts, and empirically documenting the quantitative capability of the optimized method with both laboratory isolate and wild community viral DNA. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with G + C content amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent, the first of which we tested and present data for here.
AU  - Duhaime, M.B.*
AU  - Deng, L.
AU  - Poulos, B.T.*
AU  - Sullivan, M.B.*
C1  - 8621
C2  - 30265
SP  - 2526-2537
TI  - Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: A rigorous assessment and optimization of the linker amplification method.
JO  - Environ. Microbiol.
VL  - 14
IS  - 9
PB  - Wiley-Blackwell
PY  - 2012
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Melioidosis is an emerging infectious disease of humans and animals in the tropics caused by the soil bacterium Burkholderia pseudomallei. Despite high fatality rates, the ecology of B. pseudomallei remains unclear. We used a combination of field and laboratory studies to investigate B. pseudomallei colonization of native and exotic grasses in northern Australia. Multivariable and spatial analyses were performed to determine significant predictors for B. pseudomallei occurrence in plants and soil collected longitudinally from field sites. In plant inoculation experiments, the impact of B. pseudomallei upon these grasses was studied and the bacterial load semi-quantified. Fluorescence in situ hybridization and confocal laser scanning microscopy were performed to localize the bacteria in plants. Burkholderia pseudomallei was found to inhabit not only the rhizosphere and roots but also aerial parts of specific grasses. This raises questions about the potential spread of B. pseudomallei by grazing animals whose droppings were found to be positive for these bacteria. In particular, B. pseudomallei readily colonized exotic grasses introduced to Australia for pasture. The ongoing spread of these introduced grasses creates new habitats suitable for B. pseudomallei survival and may be an important factor in the evolving epidemiology of melioidosis seen both in northern Australia and elsewhere globally.
AU  - Kaestli, M.*
AU  - Schmid, M.
AU  - Mayo, M.*
AU  - Rothballer, M.
AU  - Harrington, G.*
AU  - Richardson, L.*
AU  - Hill, A.*
AU  - Hill, J.*
AU  - Tuanyok, A.*
AU  - Keim, P.*
AU  - Hartmann, A.
AU  - Currie, B.J.*
C1  - 5455
C2  - 29331
SP  - 2058–2070
TI  - Out of the ground: Aerial and exotic habitats of the melioidosis bacterium Burkholderia pseudomallei in grasses in Australia.
JO  - Environ. Microbiol.
VL  - 14
IS  - 8
PB  - Blackwell Publishing Ltd.
PY  - 2012
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Polycyclic aromatic hydrocarbons such as naphthalene are recalcitrant environmental pollutants that are only slowly metabolized by bacteria under anoxic conditions. Based on metabolite analyses of culture supernatants, carboxylation or methylation of naphthalene have been proposed as initial enzymatic activation reactions in the pathway. However, the extremely slow growth of anaerobic naphthalene degraders with doubling times of weeks and the little biomass obtained from such cultures hindered the biochemical elucidation of the initial activation reaction, so far. Here, we provide biochemical evidence that anaerobic naphthalene degradation is initiated via carboxylation. Crude cell extracts of the sulfate-reducing enrichment culture N47 converted naphthalene and (13) C-labelled bicarbonate to 2-[carboxyl-(13) C]naphthoic acid at a rate of 0.12 nmol min(-1)  mg protein(-1) . The enzyme, namely naphthalene carboxylase, catalysed a much faster exchange of (13) C-labelled bicarbonate with the carboxyl group of 2-[carboxyl-(12) C]naphthoic acid at a rate of 3.2 nmol min(-1)  mg protein(-1) , indicating that the rate limiting step of the carboxylation reaction is the activation of the naphthalene molecule rather than the carboxylation itself. Neither the carboxylation nor the exchange reaction activities necessitate the presence of ATP or divalent metal ions and they were not inhibited by avidin or EDTA. The new carboxylation reaction is unprecedented in biochemistry and opens the door to understand the anaerobic degradation of polycyclic aromatic hydrocarbons which are among the most hazardous environmental contaminants.
AU  - Mouttaki, H.
AU  - Johannes, J.
AU  - Meckenstock, R.U.
C1  - 10684
C2  - 30328
SP  - 2770-2774
TI  - Identification of naphthalene carboxylase as a prototype for the anaerobic activation of non-substituted aromatic hydrocarbons.
JO  - Environ. Microbiol.
VL  - 14
IS  - 10
PB  - Blackwell Publishing Ltd.
PY  - 2012
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - P>Anaerobic degradation of polycyclic aromatic hydrocarbons (PAHs) is an important process during natural attenuation of aromatic hydrocarbon spills. However, knowledge about metabolic potential and physiology of organisms involved in anaerobic degradation of PAHs is scarce. Therefore, we introduce the first genome of the sulfate-reducing Deltaproteobacterium N47 able to catabolize naphthalene, 2-methylnaphthalene, or 2-naphthoic acid as sole carbon source. Based on proteomics, we analysed metabolic pathways during growth on PAHs to gain physiological insights on anaerobic PAH degradation. The genomic assembly and taxonomic binning resulted in 17 contigs covering most of the sulfate reducer N47 genome according to general cluster of orthologous groups (COGs) analyses. According to the genes present, the Deltaproteobacterium N47 can potentially grow with the following sugars including d-mannose, d-fructose, d-galactose, alpha-d-glucose-1P, starch, glycogen, peptidoglycan and possesses the prerequisites for butanoic acid fermentation. Despite the inability for culture N47 to utilize NO3- as terminal electron acceptor, genes for nitrate ammonification are present. Furthermore, it is the first sequenced genome containing a complete TCA cycle along with the carbon monoxide dehydrogenase pathway. The genome contained a significant percentage of repetitive sequences and transposase-related protein domains enhancing the ability of genome evolution. Likewise, the sulfate reducer N47 genome contained many unique putative genes with unknown function, which are candidates for yet-unknown metabolic pathways.
AU  - Bergmann, F.
AU  - Selesi, D.
AU  - Weinmaier, T.*
AU  - Tischler, P.*
AU  - Rattei, T.*
AU  - Meckenstock, R.U.
C1  - 5474
C2  - 28462
CY  - Malden, USA
SP  - 1125-1137
TI  - Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47.
JO  - Environ. Microbiol.
VL  - 13
IS  - 5
PB  - Wiley-Blackwell
PY  - 2011
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - In situ mesocosm experiments using a calcareous sand flat from a coastal area of the island of Mallorca in the Mediterranean Sea were performed in order to study the response of sulfate-reducing bacteria (SRB) to controlled crude oil contamination, or heavy contamination with naphthalene. Changes in the microbial community caused by the contamination were monitored by a combination of comparative sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, cultivation approaches and metabolic activity rates. Our results showed that crude oil and naphthalene negatively influenced the total microbial community as the natural increase in cell numbers due to the seasonal dynamics was attenuated. However, both contaminants enhanced the sulfate reduction rates, as well as the culturability of SRB. Our results suggested the presence of autochthonous deltaproteobacterial SRBs that were able to degrade crude oil or polycyclic aromatic hydrocarbons such as naphthalene in anaerobic sediment layers.
AU  - Suárez-Suárez, A.*
AU  - López-López, A.*
AU  - Tovar-Sánchez, A.*
AU  - Yarza, P.*
AU  - Orfila, A.*
AU  - Terrados, J.*
AU  - Arnds, J.*
AU  - Marques, S.*
AU  - Niemann, H.*
AU  - Schmitt-Kopplin, P.
AU  - Amann, R.*
AU  - Rosselló-Mora, R.*
C1  - 6460
C2  - 28736
CY  - Oxford
SP  - 1488-1499
TI  - Response of sulfate-reducing bacteria to an artificial oil-spill in a coastal marine sediment.
JO  - Environ. Microbiol.
VL  - 13
IS  - 6
PB  - Wiley-Blackwell
PY  - 2011
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Summary Anaerobic benzene degradation was studied with a highly enriched iron-reducing culture (BF) composed of mainly Peptococcaceae-related Gram-positive microorganisms. The proteomes of benzene-, phenol- and benzoate-grown cells of culture BF were compared by SDS-PAGE. A specific benzene-expressed protein band of 60 kDa, which could not be observed during growth on phenol or benzoate, was subjected to N-terminal sequence analysis. The first 31 amino acids revealed that the protein was encoded by ORF 138 in the shotgun sequenced metagenome of culture BF. ORF 138 showed 43% sequence identity to phenylphosphate carboxylase subunit PpcA of Aromatoleum aromaticum strain EbN1. A LC/ESI-MS/MS-based shotgun proteomic analysis revealed other specifically benzene-expressed proteins with encoding genes located adjacent to ORF 138 on the metagenome. The protein products of ORF 137, ORF 139 and ORF 140 showed sequence identities of 37% to phenylphosphate carboxylase PpcD of A. aromaticum strain EbN1, 56% to benzoate-CoA ligase (BamY) of Geobacter metallireducens and 67% to 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX) of A. aromaticum strain EbN1 respectively. These genes are proposed as constituents of a putative benzene degradation gene cluster ( approximately 17 kb) composed of carboxylase-related genes. The identified gene sequences suggest that the initial activation reaction in anaerobic benzene degradation is probably a direct carboxylation of benzene to benzoate catalysed by putative anaerobic benzene carboxylase (Abc). The putative Abc probably consists of several subunits, two of which are encoded by ORFs 137 and 138, and belongs to a family of carboxylases including phenylphosphate carboxylase (Ppc) and 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX).
AU  - Abu Laban, N.
AU  - Selesi, D.
AU  - Rattei, T.*
AU  - Tischler, P.*
AU  - Meckenstock, R.U.
C1  - 5685
C2  - 27432
SP  - 2783-2796
TI  - Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture.
JO  - Environ. Microbiol.
VL  - 12
IS  - 10
PB  - Society for Applied Microbiology and Blackwell Publishing Ltd.
PY  - 2010
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - The flow of carbon under sulfate-reducing conditions within a benzene-mineralizing enrichment culture was analysed using fully labelled [13C6]-benzene. Over 180 days of incubation, 95% of added 13C-benzene was released as 13C-carbon dioxide. DNA extracted from cultures that had degraded different amounts of unlabelled or 13C-labelled benzene was centrifuged in CsCl density gradients to identify 13C-benzene-assimilating organisms by density-resolved terminal restriction fragment length polymorphism analysis and cloning of 16S rRNA gene fragments. Two phylotypes showed significantly increased relative abundance of their terminal restriction fragments in 'heavy' fractions of 13C-benzene-incubated microcosms compared with a 12C-benzene-incubated control: a member of the Cryptanaerobacter/Pelotomaculum group within the Peptococcaceae, and a phylotype belonging to the Epsilonproteobacteria. The Cryptanaerobacter/Pelotomaculum phylotype was the most frequent sequence type. A small amount of 13C-methane was aceticlastically produced, as concluded from the linear relationship between methane production and benzene degradation and the detection of Methanosaetaceae as the only methanogens present. Other phylotypes detected but not 13C-labelled belong to several genera of sulfate-reducing bacteria, that may act as hydrogen scavengers for benzene oxidation. Our results strongly support the hypothesis that benzene is mineralized by a consortium consisting of syntrophs, hydrogenotrophic sulfate reducers and to a minor extent of aceticlastic methanogens.
AU  - Herrmann, S.*
AU  - Kleinsteuber, S.*
AU  - Chatzinotas, A.*
AU  - Kuppardt, S.*
AU  - Lüders, T.
AU  - Richnow, H.H.*
AU  - Vogt, C.*
C1  - 450
C2  - 27105
SP  - 401-411
TI  - Functional characterization of an anaerobic benzene-degrading enrichment culture by DNA stable isotope probing.
JO  - Environ. Microbiol.
VL  - 12
IS  - 2
PB  - Blackwell
PY  - 2010
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Marine pelagic redoxclines are zones of high dark CO2 fixation rates, which can correspond up to 30% of the surface primary production. However, despite this significant contribution to the pelagic carbon cycle, the identity of most chemolithoautotrophic organisms is still unknown. Therefore, the aim of this study was to directly link the dark CO2 fixation capacity of a pelagic redoxcline in the central Baltic Sea (Landsort Deep) with the identity of the main chemolithoautotrophs involved. Our approach was based on the analysis of natural carbon isotope signatures in fatty acid methyl esters (FAMEs) and on measurements of CO2 incorporation in C-13-bicarbonate pulse experiments. The incorporation of C-13 into chemolithoautotrophic cells was investigated by rRNA-based stable isotope probing (RNA-SIP) and FAME analysis after incubation for 24 and 72 h under in situ conditions. Our results demonstrated that fatty acids indicative of Proteobacteria were significantly enriched in C-13 slightly below the chemocline. RNA-SIP analyses revealed that two different Gammaproteobacteria and three closely related Epsilonproteobacteria of the Sulfurimonas cluster were active dark CO2-fixing microorganisms, with a time-dependent community shift between these groups. Labelling of Archaea was not detectable, but after 72 h of incubation the C-13-label had been transferred to a potentially bacterivorous ciliate related to Euplotes sp. Thus, RNA-SIP provided direct evidence for the contribution of chemolithoautotrophic production to the microbial food web in this marine pelagic redoxcline, emphasizing the importance of dark CO2-fixing Proteobacteria within this habitat.
AU  - Glaubitz, S.*
AU  - Lüders, T.
AU  - Abraham, W.R.*
AU  - Jost, G.*
AU  - Jürgens, K.*
AU  - Labrenz, M.*
C1  - 1452
C2  - 25972
SP  - 326-337
TI  - 13C-isotope analyses reveal that chemolithoautotrophic Gamma- and Epsilonproteobacteria feed a microbial food web in a pelagic redoxcline of the central Baltic Sea.
JO  - Environ. Microbiol.
VL  - 11
IS  - 2
PB  - Wiley-Blackwell
PY  - 2009
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Crucial steps in geochemical cycles are in many cases performed by more than one group of microorganisms, but the significance of this functional redundancy with respect to ecosystem functioning is poorly understood. Ammonia-oxidizing archaea (AOA) and their bacterial counterparts (AOB) are a perfect system to address this question: although performing the same transformation step, they belong to well-separated phylogenetic groups. Using pig manure amended with different concentrations of sulfadiazine (SDZ), an antibiotic that is frequently used in veterinary medicine, it was possible to affect AOB and AOA to different degrees. Addition of manure stimulated growth of AOB in both soils and, interestingly, also growth of AOA was considerably stimulated in one of the soils. The antibiotic treatments decreased the manure effect notably on AOB, whereas AOA were affected to a lower extent. Model calculations concerning the respective proportions of AOA and AOB in ammonia oxidation indicate a substantial contribution of AOA in one of the soils that further increased under the influence of SDZ, hence indicating functional redundancy between AOA and AOB.
AU  - Schauss, K.
AU  - Focks, A.*
AU  - Leininger, S.*
AU  - Kotzerke, A.*
AU  - Heuer, H.*
AU  - Thiele-Bruhn, S.*
AU  - Sharma, S.
AU  - Wilke, B.M.*
AU  - Matthies, M.*
AU  - Smalla, K.*
AU  - Munch, J.-C.
AU  - Amelung, W.*
AU  - Kaupenjohann, M.*
AU  - Schloter, M.
AU  - Schleper, C.*
C1  - 284
C2  - 26068
SP  - 446-456
TI  - Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils.
JO  - Environ. Microbiol.
VL  - 11
IS  - 2
PB  - Wiley-Blackwell
PY  - 2009
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Inoculation of leguminous seeds with selected rhizobial strains is practised in agriculture to ameliorate the plant yield by enhanced root nodulation and nitrogen uptake of the plant. However, effective symbiosis between legumes and rhizobia does not only depend on the capacity of nitrogen fixation but also on the entire nitrogen turnover in the rhizosphere. We investigated the influence of seed inoculation with two indigenous Sinorhizobium meliloti strains exhibiting different efficiency concerning plant growth promotion on nitrogen turnover processes in the rhizosphere during the growth of alfalfa. Quantification of six target genes (bacterial amoA, nirK, nirS, nosZ, nifH and archaeal amoA) within the nitrogen cycle was performed in rhizosphere samples before nodule formation, at bud development and at the late flowering stage. The results clearly demonstrated that effectiveness of rhizobial inocula is related to abundance of nifH genes in the late flowering phase of alfalfa. Moreover, other genes involved in nitrogen turnover had been affected by the inocula, e.g. higher numbers of amoA copies were observed during flowering when the more effective strain had been inoculated. However, the respective gene abundances differed overall to a greater extent between the three plant development stages than between the inoculation variants.
AU  - Babić, K.H.
AU  - Schauss, K.
AU  - Hai, B.
AU  - Sikora, S.*
AU  - Redzepovic, S.*
AU  - Radl, V.
AU  - Schloter, M.
C1  - 1377
C2  - 25611
SP  - 2922-2930
TI  - Influence of different Sinorhizobium meliloti inocula on abundance of genes involved in nitrogen transformations in the rhizosphere of alfalfa (Medicago sativa L.).
JO  - Environ. Microbiol.
VL  - 10
IS  - 11
PB  - Blackwell
PY  - 2008
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Anaerobic benzene degradation is an important process in contaminated aquifers but is poorly understood due to the scarcity of microbial cultures for study. We have enriched a ferric iron-reducing culture that completely mineralizes benzene to CO2. With 13C6-labelled benzene as the growth substrate, ring-labelled benzoate was identified as a major intermediate by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis of culture supernatants. With increasing incubation time, 13C7-labelled benzoate appeared, indicating that the carboxyl group of benzoate derived from CO2 that was produced from mineralization of labelled benzene. This was confirmed by growing the culture in 13C-bicarbonate-buffered medium with unlabelled benzene as the substrate, as the label appeared in the carboxyl group of benzoate produced. Phenol was also identified as an intermediate at high concentration. However, it was clearly shown that phenol was formed abiotically by autoxidation of benzene during the sampling and analysis procedure as a result of exposure to air. The results suggest that, in our culture, anaerobic benzene degradation proceeds via carboxylation and that caution should be exercised in interpreting hydroxylated benzene derivatives as metabolic intermediates of anaerobic benzene degradation.
AU  - Kunapuli, U.
AU  - Griebler, C.
AU  - Beller, H.R.*
AU  - Meckenstock, R.U.
C1  - 2026
C2  - 25295
SP  - 1703-1712
TI  - Identification of intermediates formed during anaerobic benzene degradation by an iron-reducing enrichment culture.
JO  - Environ. Microbiol.
VL  - 10
IS  - 7
PB  - Blackwell
PY  - 2008
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (Delta G) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI BLAST, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
AU  - Loy, A.*
AU  - Arnold, R.C.
AU  - Tischler, P.
AU  - Rattei, T.
AU  - Wagner, M.*
AU  - Horn, M.*
C1  - 1963
C2  - 25944
SP  - 2894-2898
TI  - probeCheck - a central resource for evaluating oligonucleotide probe coverage and specificity.
JO  - Environ. Microbiol.
VL  - 10
IS  - 10
PB  - Wiley-Blackwell
PY  - 2008
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Based on lipid analyses, 16S rRNA/rRNA gene single-strand conformation polymorphism fingerprints and methane flux measurements, influences of the fertilization regime on abundance and diversity of archaeal communities were investigated in soil samples from the long-term (103 years) field trial in Bad Lauchstädt, Germany. The investigated plots followed a gradient of increasing fertilization beginning at no fertilization and ending at the 'cattle manure' itself. The archaeal phospholipid etherlipid (PLEL) concentration was used as an indicator for archaeal biomass and increased with the gradient of increasing fertilization, whereby the concentrations determined for organically fertilized soils were well above previously reported values. Methane emission, although at a low level, were occasionally only observed in organically fertilized soils, whereas the other treatments showed significant methane uptake. Euryarchaeotal organisms were abundant in all investigated samples but 16S rRNA analysis also demonstrated the presence of Crenarchaeota in fertilized soils. Lowest molecular archaeal diversity was found in highest fertilized treatments. Archaea phylogenetically most closely related to cultured methanogens were abundant in these fertilized soils, whereas Archaea with low relatedness to cultured microorganisms dominated in non-fertilized soils. Relatives of Methanoculleus spp. were found almost exclusively in organically fertilized soils or cattle manure. Methanosarcina-related microorganisms were detected in all soils as well as in the cattle manure, but soils with highest organic application rate were specifically dominated by a close phylogenetic relative of Methanosarcina thermophila. Our findings suggest that regular application of cattle manure increased archaeal biomass, but reduced archaeal diversity and selected for methanogenic Methanoculleus and Methanosarcina strains, leading to the circumstance that high organic fertilized soils did not function as a methane sink at the investigated site anymore.
AU  - Gattinger, A.
AU  - Höfle, M.G.*
AU  - Schloter, M.
AU  - Embacher, A.
AU  - Böhme, F.*
AU  - Munch, J.-C.
AU  - Labrenz, M.*
C1  - 5597
C2  - 24322
SP  - 612-624
TI  - Traditional cattle manure application determines abundance, diversity and activity of methanogenic Archaea in arable European soil.
JO  - Environ. Microbiol.
VL  - 9
IS  - 3
PB  - Blackwell
PY  - 2007
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Lower Kane Cave, Wyoming (USA), has hydrogen sulfide-bearing springs that discharge into the cave passage. The springs and cave stream harbour white filamentous microbial mats dominated by Epsilonproteobacteria. Recently, novel 16S rRNA gene sequences from the phylum Acidobacteria, subgroup 7, were found in these cave mats. Although Acidobacteria are ubiquitously distributed in many terrestrial and marine habitats, little is known about their ecophysiology. To investigate this group in Lower Kane Cave in more detail, a full-cycle rRNA approach was applied based on 16S and 23S rRNA gene clone libraries and the application of novel probes for fluorescence in situ hybridization. The 16S and 23S rRNA gene clone libraries yielded seven and six novel acidobacterial operational taxonomic units (OTUs) respectively. The majority of the OTUs were affiliated with subgroups 7 and 8. One OTU was affiliated with subgroup 6, and one OTU could not be assigned to any of the present acidobacterial subgroups. Fluorescence in situ hybridization distinguished two morphologically distinct, rod-shaped cells of the acidobacterial subgroups 7 and 8. Although the ecophysiology of Acidobacteria from Lower Kane Cave will not be fully resolved until cultures are obtained, acidobacterial cells were always associated with the potentially chemolithoautotrophic epsilon- or gammaproteobacterial filaments, suggesting perhaps a lifestyle based on heterotrophy or chemoorganotrophy.
AU  - Meisinger, D.B.*
AU  - Zimmermann, J.*
AU  - Ludwig, W.*
AU  - Schleifer, K.H.*
AU  - Wanner, G.*
AU  - Schmid, M.
AU  - Bennett, P.C.*
AU  - Engel, A.S.*
AU  - Lee, N.M.*
C1  - 3154
C2  - 24635
SP  - 1523-1534
TI  - In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA).
JO  - Environ. Microbiol.
VL  - 9
IS  - 6
PB  - Blackwell
PY  - 2007
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Pseudomonas brassicacearum forms phenotypic variants in vitro as well as in planta during root colonization under natural conditions, leading to subpopulations (phase I and II cells) that differ in colony morphology and production of exoenzymes/secondary metabolites. The maximal concentration of cadmium allowing both variants growth was 25 muM; however, phase II cells accumulated fivefold higher Cd than phase I cells, even though both variants showed the same growth rate and kinetics, comprising a long stasis period (50 h). The whole transcriptome analysis of both variants in response to Cd was investigated using the home-made DNA microarrays. This analysis revealed completely different adaptation mechanisms developed by each variant to withstand and grow in the presence of the toxic. A re-organization of the cell wall to limit Cd entrance was noticed for phase I cells, as genes encoding levan exopolymers were downregulated at the expense of an upregulation of genes encoding alginate, and an upregulation of transporters such as cadA, and a downregulation of copper transporters. Phase II cells were unable to prevent Cd entrance and recruited genes under the control of oxyR and soxR regulation to face osmotic and oxidant stresses generated by Cd. Putrescine and spermidine metabolism appeared to play a central role in Cd tolerance. Microarray data were validated by biological analyses such as motility, oxidative stress assay, metabolite profiling with ICR-FT/MS and UPLC, capillary electrophoresis analysis of biogenic amines.
AU  - Pages, D.*
AU  - Sanchez, L.*
AU  - Conrod, S.*
AU  - Gidrol, X.*
AU  - Fekete, A.
AU  - Schmitt-Kopplin, P.
AU  - Heulin, T.*
AU  - Achouak, W.*
C1  - 351
C2  - 24763
SP  - 2820-2835
TI  - Exploration of intraclonal adaptation mechanisms of Pseudomonas brassicacearum facing cadmium toxicity.
JO  - Environ. Microbiol.
VL  - 9
IS  - 11
PB  - Blackwell
PY  - 2007
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Acetate is an important intermediate in the decomposition of organic matter in anoxic freshwater sediments. Here, we identified distinct microorganisms active in its oxidation and transformation to methane in the anoxic methanogenic layers of Lake Kinneret (Israel) profundal sediment by rRNA-based stable isotope probing (RNA-SIP). After 18 days of incubation with amended [U-C-13]acetate we found that archaeal 16S rRNA was C-13-labelled to a far greater extent than bacterial rRNA. We identified acetoclastic methanogens related to Methanosaeta concilii as being most active in the degradation and assimilation of acetate. Oxidation of the acetate-methyl group played only a minor role, but nevertheless 'heavy' C-13-labelled bacterial rRNA templates were identified. 'Heavy' bacteria were mainly affiliated with the Betaproteobacteria (mostly Rhodocyclales and Nitrosomonadales), the Nitrospira phylum (related to 'Magnetobacterium bavaricum' and Thermodesulfovibrio yellowstonii), and also with the candidate phylum 'Endomicrobia'. However, the mode of energy gain that allowed for the assimilation of C-13-acetate by these bacterial groups remains unknown. It may have involved syntrophic oxidation of acetate, reduction of chlorinated compounds, reduction of humic substances, fermentation of organic compounds, or even predation of C-13-labelled Methanosaeta spp. In summary, this SIP experiment shows that acetate carbon was predominantly consumed by acetoclastic methanogens in profundal Lake Kinneret sediment, while it was also utilized by a small and heterogeneous community of bacteria.
AU  - Schwarz, J.I.*
AU  - Lüders, T.
AU  - Eckert, W.*
AU  - Conrad, R.*
C1  - 4943
C2  - 24186
SP  - 223-237
TI  - Identification of acetate-utilizing Bacteria and Archaea in methanogenic profundal sediments of Lake Kinneret (Israel) by stable isotope probing of rRNA.
JO  - Environ. Microbiol.
VL  - 9
IS  - 1
PB  - Blackwell
PY  - 2007
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Benzylsuccinate synthase (Bss) is the key enzyme of anaerobic toluene degradation and has been found in all anaerobic toluene degrading bacterial isolates tested. However, only a few pure cultures capable of anaerobic toluene oxidation are available to date, and it is important to understand the relevance of these model organisms for in situ bioremediation of hydrocarbon-contaminated aquifers. Due to their phylogenetic dispersal, it is not possible to specifically target anaerobic toluene degraders using marker rRNA genes. We therefore established an assay targeting a ~794 bp fragment within the Bss alpha-subunit (bssA) gene, which allows for the specific detection and affiliation of both known and unknown anaerobic degraders. Three distinct tar-oil-contaminated aquifer sites were screened for intrinsic bssA gene pools in order to identify and compare the diversity of hydrocarbon degraders present at these selected sites. We were able to show that local diversity patterns of degraders were entirely distinct, apparently highly specialized and well-adapted to local biogeochemical settings. Discovered at one of the sites were bssA genes closely related to that of Geobacter spp., which provides evidence for an importance of iron reduction for toluene degradation in these sediments. Retrieved from the other two sites, dominated by sulfate reduction, were previously unidentified bssA genes and also deeply branching putative bssA homologues. We provide evidence for a previously unrecognized diversity of anaerobic toluene degraders and also of other hydrocarbon degraders using fumarate-adding key reactions in contaminated aquifers. These findings enhance our current understanding of intrinsic hydrocarbon-degrading microbial communities in perturbed aquifers and may have potential for the future assessment and prediction of natural attenuation based on degradation genes.
AU  - Winderl, C.
AU  - Schaefer, S.
AU  - Lüders, T.
C1  - 3440
C2  - 24370
SP  - 1035-1046
TI  - Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker.
JO  - Environ. Microbiol.
VL  - 9
IS  - 4
PB  - Blackwell
PY  - 2007
SN  - 1462-2912
ER  - 

TY  - JOUR
AU  - Jahn, M.K.*
AU  - Haderlein, S.B.*
AU  - Meckenstock, R.U.
C1  - 4050
C2  - 23477
SP  - 362-367
TI  - Reduction of Prussian Blue by the two iron-reducing microorganisms Geobacter metallireducens and Shewanella alga.
JO  - Environ. Microbiol.
VL  - 8
PY  - 2006
SN  - 1462-2912
ER  - 

TY  - JOUR
AU  - Safinowski, M.*
AU  - Meckenstock, R.U.
C1  - 4255
C2  - 23476
SP  - 347-352
TI  - Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture.
JO  - Environ. Microbiol.
VL  - 8
PY  - 2006
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - During the last years, the number of human infections caused by opportunistic pathogens has increased dramatically. One natural reservoir of opportunistic pathogens is the rhizosphere, the zone around roots that is influenced by the plant. Due to a high content of nutrients, this habitat is a ‘microbial hot-spot’, where bacterial abundances including those with strong antagonistic traits are enhanced. Various bacterial genera, including Burkholderia, Enterobacter, Herbaspirillum, Ochrobactrum, Pseudomonas, Ralstonia, Staphylococcus and Stenotrophomonas, contain root-associated strains that can encounter bivalent interactions with both plant and human hosts. Mechanisms responsible for colonization of the rhizosphere and antagonistic activity against plant pathogens are similar to those responsible for colonization of human organs and tissues, and pathogenicity. Multiple resistances against antibiotics are not only found with clinical strains but also with strains isolated from the rhizosphere. High competition, the occurrence of diverse antibiotics in the rhizosphere, and enhanced horizontal gene transfer rates in this microenvironment appear to contribute to the high levels of natural resistances. While opportunistic bacteria from the rhizosphere have some properties in common, each of these emerging pathogens has its own features, which are discussed in detail for Burkholderia, Ochrobactrum and Stenotrophomonas.
AU  - Berg, G.*
AU  - Eberl, L.*
AU  - Hartmann, A.
C1  - 3901
C2  - 23209
SP  - 1673-1685
TI  - The rhizosphere as a reservoir for opportunistic human pathogenic bacteria.
JO  - Environ. Microbiol.
VL  - 7
IS  - 11
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Fluorescence in situ hybridization, associated with confocal laser scanning microscopy or epifluorescence microscopy with deconvolution system, has allowed the detection of a community of intracellular bacteria in non-axenic samples of the ectomycorrhizal fungus Laccaria bicolor S238N. The endobacteria, mainly α-proteobacteria, were present in more than half of the samples, which consisted of ectomycorrhizae, fungal mats and fruit bodies, collected in the glasshouse or in the forest. Acridine orange staining suggests that the endobacteria inhabit both live and dead fungal cells. The role of these endobacteria remains to be clarified.
AU  - Bertaux, J.*
AU  - Schmid, M.*
AU  - Hutzler, P.
AU  - Hartmann, A.
AU  - Garbaye, J.*
AU  - Frey-Klett, P.*
C1  - 3740
C2  - 23213
SP  - 1786-1795
TI  - Occurrence and distribution of endobacteria in the plant-associated mycelium of the ectomycorrhizal fungus Laccaria bicolor S238N.
JO  - Environ. Microbiol.
VL  - 7
IS  - 11
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Detailed studies on the relation of structure and function of microbial communities in a sediment depth profile scarcely exist. We determined as functional aspect the vertical distribution of the acetotrophic and hydrogenotrophic CH4 production activity by measuring production rates and stable 13C/12C-isotopic signatures of CH4 in the profundal sediment of Lake Dagow. The structural aspect was determined by the composition of the methanogenic community by quantifying the abundance of different archaeal groups using 'real-time' polymerase chain reaction and analysis of terminal restriction fragment length polymorphism (T-RFLP). Methane production rates in the surface sediment (0-3 cm depth) were higher in August than in May, but strongly decreased with depth (down to 20 cm). The delta13C of the produced CH4 and CO2 indicated an increase in isotopic fractionation with sediment depth. The relative contribution of hydrogenotrophic to total methanogenesis, which was calculated from the isotopic signatures, increased with depth from about 22% to 38%. Total numbers of microorganisms were higher in August than in May, but strongly decreased with depth. The increase of microorganisms from May to August mainly resulted from Bacteria. The Archaea, on the other hand, exhibited a rather constant abundance, but also decreased with depth from about 1 x 10(8) copies of the archaeal 16S rRNA gene per gram of dry sediment at the surface to 4 x 10(7) copies per gram at 15-20 cm depth. T-RFLP analysis combined with phylogenetic analysis of cloned sequences of the archaeal 16S rRNA genes showed that the methanogenic community consisted mainly of Methanomicrobiales and Methanosaetaceae. The relative abundance of Methanosaetaceae decreased with depth, whereas that of Methanomicrobiales slightly increased. Hence, the vertical distribution of the functional characteristics (CH4 production from acetate versus H2/CO2) was reflected in the structure of the community consisting of acetotrophic (Methanosaetaceae) versus hydrogenotrophic (Methanomicrobiales) phenotypes.
AU  - Chan, O.C.*
AU  - Claus, P.*
AU  - Casper, P.*
AU  - Ulrich, A.*
AU  - Lüders, T.*
AU  - Conrad, R.*
C1  - 4805
C2  - 22918
SP  - 1139-1149
TI  - Vertical distribution of structure and function of the methanogenic archael community in Lake Dagow sediment.
JO  - Environ. Microbiol.
VL  - 7
IS  - 8
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Methane is formed on rice roots mainly by CO2 reduction. The present study aimed to identify the active methanogenic populations responsible for this process. Soil-free rice roots were incubated anaerobically under an atmosphere of H2/13CO2 or N2/13CO2 with phosphate or carbonate (marble) as buffer medium. Nucleic acids were extracted and fractionated by caesium trifluoroacetate equilibrium density gradient centrifugation after 16-day incubation. Community analyses were performed for gradient fractions using terminal restriction fragment polymorphism analysis (T-RFLP) and sequencing of the 16S rRNA genes. In addition, rRNA was extracted and analysed at different time points to trace the community change during the 16-day incubation. The Methanosarcinaceae and the yet-uncultured archaeal lineage Rice Cluster-I (RC-I) were predominant in the root incubations when carbonate buffer and N2 headspace were used. The analysis of [13C]DNA showed that the relative 16S rRNA gene abundance of RC-I increased whereas that of the Methanosarcinaceae decreased with increasing DNA buoyant density, indicating that members of RC-I were more active than the Methanosarcinaceae. However, an unexpected finding was that RC-I was suppressed in the presence of high H2 concentrations (80%, v/v), which during the early incubation period caused a lower CH4 production compared with that with N2 in the headspace. Eventually, however, CH4 production increased, probably because of the activity of Methanosarcinaceae, which became prevalent. Phosphate buffer appeared to inhibit the activity of the Methanosarcinaceae, resulting in lower CH4 production as compared with carbonate buffer. Under these conditions, Methanobacteriaceae were the prevalent methanogens. Our study suggests that the active methanogenic populations on rice roots change in correspondence to the presence of H2 (80%, v/v) and the type of buffer used in the system.
AU  - Lu, Y.*
AU  - Lüders, T.
AU  - Friedrich, M.W.*
AU  - Conrad, R.*
C1  - 969
C2  - 22490
SP  - 326-336
TI  - Detecting active methanogenic populations on rice roots using stable isotope probing.
JO  - Environ. Microbiol.
VL  - 7
IS  - 3
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Inoculation of wheat roots with Azospirillum brasilense results in an increase of plant growth and yield, which is proposed to be mainly due to the bacterial production of indole-3-acetic acid in the rhizosphere. Field inoculation experiments had revealed more consistent plant growth stimulation using A. brasilense strain Sp245 as compared with the strain Sp7. Therefore, the in situ expression of the key gene ipdC (indole-3-pyruvate decarboxylase) was examined in these two strains. Within the ipdC promoter of strain Sp245 a region of 150 bases was identified, which was missing in strain Sp7. Thus, three different translational ipdC promoter fusions with gfpmut3 were constructed on plasmid level: the first contained the part of the Sp245 promoter region homologous to strain Sp7, the second was bearing the complete promoter region of Sp245 including the specific insertion and the third comprised the Sp7 promoter region. By comparing the fluorescence levels of these constructs after growth on mineral medium with and without inducing amino acids, it could be demonstrated that ipdC expression in A. brasilense Sp245 was subject to a stricter control compared with strain Sp7. Microscopic detection of these reporter strains colonizing the rhizoplane documented for the first time an in situ expression of ipdC.
AU  - Rothballer, M.
AU  - Schmid, M.
AU  - Fekete, A.
AU  - Hartmann, A.
C1  - 4606
C2  - 23211
SP  - 1839-1846
TI  - Comparative in situ analysis of ipdC-gfpmut3 promoter fusions of Azospirillum brasilense strains Sp7 and Sp245.
JO  - Environ. Microbiol.
VL  - 7
IS  - 11
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH4 production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester-linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso- and anteiso-branched fatty acids related to the amount of straight-chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.
AU  - Wagner, D.E.*
AU  - Lipski, A.*
AU  - Embacher, A.
AU  - Gattinger, A.
C1  - 4466
C2  - 22728
SP  - 1582-1592
TI  - Methane fluxes in permafrost habitats of the Lena Delta: Effects of microbial community structure and organic matter quality.
JO  - Environ. Microbiol.
VL  - 7
IS  - 10
PY  - 2005
SN  - 1462-2912
ER  - 

TY  - JOUR
AB  - Desulfotalea psychrophila is a marine sulfate-reducing δ-proteobacterium that is able to grow at in situ temperatures below 0°C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute  to  the  global  cycles  of  carbon  and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C4-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a β-oxidation complex and typical Desulfovibrio cytochromes, such as c553, c3 and ncc. D. psychrophila encodes more than 30 two-component regulatory  systems,  including  a  new  Ntr  subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
AU  - Rabus, R.*
AU  - Rattei, T.
C1  - 4102
C2  - 22394
SP  - 887-902
TI  - The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold arctic sediments.
JO  - Environ. Microbiol.
VL  - 6
IS  - 9
PY  - 2004
SN  - 1462-2912
ER  -