Publications

Chemoautotrophic bacteria belonging to the genus Sulfurimonas (class Campylobacteria) were previously identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle. S. denitrificans was further shown to be able to oxidize cyclooctasulfur (S ). However, at present the mechanism of activation and metabolism of cyclooctasulfur is not known. Here, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or S as the electron donor. While the overall expression profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of S . This included a higher abundance of expressed genes related to surface attachment in the presence of S , and the differential regulation of the sulfur-oxidation multienzyme complex (SOX), which in S. denitrificans is encoded in two gene clusters: soxABXY Z and soxCDY Z . While the proteins of both clusters were present with thiosulfate, only proteins of the soxCDY Z were detected at significant levels with S . Based on these findings a model for the oxidation of S is proposed. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxY Z among sulfur-oxidizing Campylobacteria.

Molecular hydrogen (H ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H -oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H ase sequences were assigned to group 1b and 1c [NiFe]-H ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H -scavengers in marine sediments.

Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.

To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.

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.

Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, (14)CO(2) fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of (13)CO(2), was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs.

Dispersal and colonization are important for the assembly and biodiversity of microbial communities. While emigration as the initial step of dispersal has become increasingly understood in model bacterial biofilms, the drivers of dispersal and colonization in complex biofilms remain elusive. We grew complex biofilms in microcosms from natural surface water in laminar and turbulent flow, and investigated dispersal and colonization patterns of fluorescently labeled cells and microbeads in nascent and mature biofilms. Settling occurred in nonrandom spatial patterns governed by the interplay of local flow patterns and biofilm topography. Settling was higher in treatments with nascent biofilms, with fewer cells remaining in the water column than in treatments with mature biofilms. The flow regime had no effect on settling velocity, even though in mature biofilms the formation of streamers under turbulent flow enhanced particle trapping compared with the laminar flow treatment. Hence, small-scale variations in the flow pattern seemed to be more important than the overall flow regime. Furthermore, spatial analysis of the colonizer patterns suggests that bacteria have moved in the biofilm after settling. Our results show that colonization of biofilms in a model stream environment is a heterogeneous process differently affected by biological and physical factors.

Coastal waters support ~90% of global fisheries and, as such, are an important food reserve for our planet1. Eutrophication of these waters, due to human activity, leads to severe oxygen depletion and the episodic occurrence of hydrogen sulphide a toxin for multi-cellular life with disastrous consequences for coastal ecosytems. Here, we show that an area of ~7,000 km2 of African shelf, covered by sulphidic water, was detoxified by blooming bacteria, which oxidized the biologically harmful sulphide to environmentally-harmless colloidal sulphur and sulphate. Combined chemical analyses, stoichiometric modelling, isotopic incubations, comparative 16S ribosomal RNA, functional gene sequence analyses and fluorescence in situ hybridization (FISH) indicate that the detoxification proceeded by chemolithotrophic oxidation of sulphide with nitrate and was mainly catalyzed by two discrete populations of Gamma- and Epsilonproteobacteria. Chemolithotrophic bacteria, accounting for ~20% of the bacterioplankton in sulphidic waters, created a buffer zone between the toxic sulphidic subsurface waters and the oxic surface waters, where fish and other nekton live. This is the first time that large-scale detoxification of sulphidic waters by chemolithotrophs has been shown in an open-ocean system. The data suggest that sulphide can be completely consumed by bacteria in the subsurface waters, and thus, can be overlooked by remote sensing or monitoring of shallow coastal waters. Consequently, sulphidic bottom waters on continental shelves may be more frequent than previously believed, and as such, could have an important but as-yet neglected effect on benthic communities.

Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.

The identity and abundance of potentially active sulfate-reducing bacteria (SRB) in several metre deep sediments of a tidal sand flat in the German Wadden Sea were assessed by directed cultivation and cultivation-independent CARD-FISH analysis (catalysed reporter deposition fluorescence in situ hybridization). Presumably abundant SRB from different sediment layers between 0.5 and 4 m depth were selectively enriched in up to million-fold diluted cultures supplemented with lactate, acetate or hydrogen. Partial 16S rRNA gene sequences obtained from highest dilution steps showing sulfide formation indicated growth of deltaproteobacterial SRB belonging to the Desulfobulbaceae and the Desulfobacteraceae as well as of members of the Firmicutes. Subsequent isolation resulted in 10 novel phylotypes of both litho- and organotrophic sulfate-reducing Deltaproteobacteria. Molecular pre-screening identified six isolates as members of the Desulfobulbaceae, sharing highest identities with either candidatus 'Desulfobacterium corrodens' (95-97%) or Desulfobacterium catecholicum (98%), and four isolates as members of Desulfobacteraceae, being related to either Desulfobacter psychrotolerans (98%) or Desulfobacula phenolica (95-97%). Relatives of D. phenolica were exlusively isolated from 50 and 100 cm deep sediments with 10 and 2 mM of pore water sulfate respectively. In contrast, relatives of D. corrodens, D. psychrotolerans and D. catecholicum were also obtained from layers deeper than 100 cm and with less than 2 mM sulfate. The high in situ abundance of members of both families in sediment layers beneath 50 cm could be confirmed via CARD-FISH analysis performed with a set of six SRB-specific oligonucleotide probes. Moreover, SRB represented a numerically significant fraction of the microbial community throughout the sediment (up to 7%) and reached even higher cell numbers in deep, sulfate-poor layers than in the sulfate-rich surface sediment. This relatively large community size of potentially active SRB in deep sandy sediments might on the one hand be a result of their syntrophic association with other anaerobes. Our results furthermore support the hypothesis that enhanced advective pore water transport might supply nutrients to microbial communities in deep sandy sediments and point to their so far unrecognized contribution to biogeochemical processes in Wadden Sea sediments.

Anaerobic enrichments with H2 as electron donor and thiosulfate/polysulfide as electron acceptor at pH 10 and 0.6 M total Na+ yielded two non sulfate-reducing representatives of reductive sulfur cycle from soda lake sediments. Strain AHT 1 was isolated with thiosulfate as the electron acceptor from north-eastern Mongolian soda lakes and strain AHT 2-with polysulfide as the electron acceptor from Wadi al Natrun lakes in Egypt. Both isolates represented new phylogenetic lineages: AHT 1-within Clostridiales and AHT 2-within the Deltaproteobacteria. Both bacteria are obligate anaerobes with respiratory metabolism. Both grew chemolithoautotrophically with H2 as the electron donor and can use thiosulfate, elemental sulfur and polysulfide as the electron acceptors. AHT 2 also used nitrate as acceptor, reducing it to ammonia. During thiosulfate reduction, AHT 1 excreted sulfite. dsrAB gene was not found in either strain. Both strains were moderate salt-tolerant (grow up to 2 M total Na+) true alkaliphiles (grow between pH 8.5 and 10.3). On the basis of the phenotypic and phylogenetic data, strains AHT 1 and AHT 2 are proposed as new genera and species Dethiobacter alkaliphilus and Desulfurivibrio alkaliphilus, respectively.

The aim of this study was to investigate the supposed vertical diel migration and the accompanying physiology of Beggiatoa bacteria from hypersaline microbial mats. We combined microsensor, stable-isotope, and molecular techniques to clarify the phylogeny and physiology of the most dominant species inhabiting mats of the natural hypersaline Lake Chiprana, Spain. The most dominant morphotype had a filament diameter of 6 to 8 microm and a length varying from 1 to >10 mm. Phylogenetic analysis by 16S rRNA gene comparison revealed that this type appeared to be most closely related (91% sequence identity) to the narrow (4-microm diameter) nonvacuolated marine strain MS-81-6. Stable-isotope analysis showed that the Lake Chiprana species could store nitrate intracellularly to 40 mM. The presence of large intracellular vacuoles was confirmed by fluorescein isothiocyanate staining and subsequent confocal microscopy. In illuminated mats, their highest abundance was found at a depth of 8 mm, where oxygen and sulfide co-occurred. However, in the dark, the highest Beggiatoa densities occurred at 7 mm, and the whole population was present in the anoxic zone of the mat. Our findings suggest that hypersaline Beggiatoa bacteria oxidize sulfide with oxygen under light conditions and with internally stored nitrate under dark conditions. It was concluded that nitrate storage by Beggiatoa is an optimal strategy to both occupy the suboxic zones in sulfidic sediments and survive the dark periods in phototrophic mats.