Bacterial Divisions Research Articles

Effect of Nutrient Loading on Bacterioplankton Community Composition in Lake Mesocosms

Changes in bacterioplankton community composition were followed in mesocosms set up in the littoral of Lake Vesijärvi, southern Finland, over two summers. Increasing nitrogen and phosphorus concentrations in the mesocosms represented different trophic states, from mesotrophic to hypertrophic. In 1998, the mesocosms were in a turbid state with a high biomass of phytoplankton, whereas in 1999, macrophytes proliferated and a clear-water state prevailed. The bacterial communities in the mesocosms also developed differently, as shown by denaturing gradient gel electrophoresis profiling of partial 16S rRNA gene fragments and by nonmetric multidimensional scaling analysis. In 1998, nutrient treatments affected the diversity and clustering of bacterial communities strongly, but in 1999, the bacterial communities were less diversified and not clearly affected by treatments. Canonical correspondence analysis indicated that bacterioplankton communities in the mesocosms were influenced by environmental physicochemical variables linked to the increasing level of eutrophication. Nitrogen concentration correlated directly with the bacterioplankton composition. In addition, the high nutrient levels had indirect effects through changes in the biomass and composition of phyto- and zooplankton. Sequencing analysis showed that the dominant bacterial divisions remained the same, but the dominant phylotypes changed during the 2-year period. The occurrence of Verrucomicrobia correlated with more eutrophic conditions, whereas the occurrence of Actinobacteria correlated with less eutrophic conditions.

Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents

The diversity of thermophilic prokaryotes inhabiting deep-sea hot vents was actively studied over the last two decades. The ever growing interest is reflected in the exponentially increasing number of novel thermophilic genera described. The goal of this paper is to survey the progress in this field made in the years 2000-2005. In this period, representatives of several new taxa of hyperthermophilic archaea were obtained from deep-sea environments. Two of these isolates had phenotypic features new for this group of organisms: the presence of an outer cell membrane (the genus Ignicoccus) and the ability to grow anaerobically with acetate and ferric iron (the genus Geoglobus). Also, our knowledge on the diversity of thermophilic bacteria from deep-sea thermal environments extended significantly. The new bacterial isolates represented diverse bacterial divisions: the phylum Aquificae, the subclass Epsilonproteobacteria, the order Thermotogales, the families Thermodesulfobacteriaceae, Deferribacteraceae, and Thermaceae, and a novel bacterial phylum represented by the genus Caldithrix. Most of these isolates are obligate or facultative lithotrophs, oxidizing molecular hydrogen in the course of different types of anaerobic respiration or microaerobic growth. The existence and significant ecological role of some of new bacterial thermophilic isolates was initially established by molecular methods.

Lateral gene transfer and phylogenetic assignment of environmental fosmid clones

Metagenomic data, especially sequence data from large insert clones, are most useful when reasonable inferences about phylogenetic origins of inserts can be made. Often, clones that bear phylotypic markers (usually ribosomal RNA genes) are sought, but sometimes phylogenetic assignments have been based on the preponderance of blast hits obtained with predicted protein coding sequences (CDSs). Here we use a cloning method which greatly enriches for ribosomal RNA-bearing fosmid clones to ask two questions: (i) how reliably can we judge the phylogenetic origin of a clone (that is, its RNA phylotype) from the sequences of its CDSs? and (ii) how much lateral gene transfer (LGT) do we see, as assessed by CDSs of different phylogenetic origins on the same fosmid? We sequenced 12 rRNA containing fosmid clones, obtained from libraries constructed using DNA isolated from Baltimore harbour sediments. Three of the clones are from bacterial candidate divisions for which no cultured representatives are available, and thus represent the first protein coding sequences from these major bacterial lineages. The amount of LGT was assessed by making phylogenetic trees of all the CDSs in the fosmid clones and comparing the phylogenetic position of the CDS to the rRNA phylotype. We find that the majority of CDSs in each fosmid, 57-96%, agree with their respective rRNA genes. However, we also find that a significant fraction of the CDSs in each fosmid, 7-44%, has been acquired by LGT. In several cases, we can infer co-transfer of functionally related genes, and generate hypotheses about mechanism and ecological significance of transfer.

Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir

The succession in bacterial community composition was studied over two years in the epilimnion and hypolimnion of two freshwater systems: a natural lake (Pavin Lake) and a lake-reservoir (Sep Reservoir). The bacterial community composition was determined by cloning-sequencing of 16S rRNA and by terminal restriction fragment length polymorphism. Despite large hydrogeological differences, in the Sep Reservoir and Pavin Lake the dominant bacteria were from the same taxonomic divisions, particularly Actinobacteria and Betaproteobacteria. In both ecosystems, these major bacterial divisions showed temporal fluctuations that were much less marked than those occurring at a finer phylogenetic scale. Nutrient availability and mortality factors, the nature of which differed from one lake to another, covaried with the temporal variations in the bacterial community composition at all sampling depths, whereas factors related to seasonal forces (temperature and outflow for Sep Reservoir) seemed to account only for the variation of the hypolimnion bacterial community composition. No seasonal reproducibility in temporal evolution of bacterial community from one year to the next was observed.

Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples

The goal of this research was to investigate the influence of the error rate of sequence determination on the differentiation of cloned SSU rRNA gene sequences for assessment of community structure. SSU rRNA cloned sequences from groundwater samples that represent different bacterial divisions were sequenced multiple times with the same sequencing primer. From comparison of sequence alignments with unedited data, confidence intervals were obtained from both a ‘double binomial’ model of sequence comparison and by non-parametric methods. The results indicated that similarity values below 0.9946 are likely derived from dissimilar sequences at a confidence level of 0.95, and not sequencing errors. The results confirmed that screening by direct sequence determination could be reliably used to differentiate at the species level. However, given sequencing errors comparable to those seen in this study, sequences with similarities above 0.9946 should be treated as the same sequence if a 95% confidence is desired.

In situ identification and characterization of the microbial community structure of full-scale enhanced biological phosphorous removal plants in Japan

Fluorescent in situ hybridization (FISH) and polyphosphate (polyP) staining methods were used to characterize the microbial community structure of 13 activated sludge samples taken from nine different Japanese wastewater treatment plants with and without enhanced biological phosphorous removal (EBPR) activities. FISH with published rRNA-targeted oligonucleotide probes for important bacterial groups involving in the EBPR process revealed that Rhodocyclus-related polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms from a gammaproteobacterial lineage GB were the predominant populations detected, representing 4–18% and 10–31% of EUBmix-stained cells, respectively, in those samples. However, a considerable proportion of Rhodocyclus-related PAO cells were observed with no polyP granules accumulated based on polyP staining. This was further supported by a poor correlation between Rhodocyclus-related PAO population and sludge total phosphorous (TP) contents. In contrast, high correlations between polyP-stained cells and sludge TP contents were observed. In particular, among those polyP-stained cells in samples Ariake_A2O and Nakano_AO, more than 85% of them could not be targeted by probe PAOmix. These non- Rhodocyclus-related PAOs included populations from other bacterial divisions and members of the Betaproteobacteria other than those in Rhodocyclus-related group.

Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes

The microbial diversity of intertidal hot springs on the seashore of northwest Iceland was examined by combining directed in situ enrichments, artificial support colonization, and mat sampling. Analysis of 16S rRNA genes revealed the presence of clones related to both marine and terrestrial, thermophilic, mesophilic, and psychrophilic microorganisms scattered among 11 bacterial divisions. No archaea were found. The species composition of the enrichments was affected by the length of the hot periods experienced at low tide and was very different from those found in the biomass. A total of 36 chitinase genes were detected by molecular screening of the samples with degenerate primers for glycoside hydrolase family 18. The chitinase gene diversity was at least twofold higher in the enrichment samples than in the controls, indicating that a much higher diversity of hydrolytic genes can be accessed with this approach.

Shifts in Rhizoplane Communities of Aquatic Plants after Cadmium Exposure

In this study we present the comparative molecular analysis of bacterial communities of the aquatic plant Lemna minor from a contaminated site (RCP) and from a laboratory culture (EPA), as well as each of these with the addition of cadmium. Plants were identified as L. minor by analysis of the rpl16 chloroplast region. Comparative bacterial community studies were based on the analyses of 16S rRNA clone libraries, each containing about 100 clones from the root surfaces of plants. Bacterial communities were compared at three phylogenetic levels of resolution. At the level of bacterial divisions, differences in diversity index scores between treatments, with and without cadmium within the same plant type (EPA or RCP), were small, indicating that cadmium had little effect. When we compared genera within the most dominant group, the beta-proteobacteria, differences between unamended and cadmium-amended libraries were much larger. Bacterial diversity increased upon cadmium addition for both EPA and RCP libraries. Analyses of diversity at the phylotype level showed parallel shifts to more even communities upon cadmium addition; that is, percentage changes in diversity indices due to cadmium addition were the same for either plant type, indicating that contamination history might be independent of disturbance-induced diversity shifts. At finer phylogenetic levels of resolution, the effects of cadmium addition on bacterial communities were very noticeable. This study is a first step in understanding the role of aquatic plant-associated microbial communities in phytoremediation of heavy metals.

Novel Major Bacterial Candidate Division within a Municipal Anaerobic Sludge Digester

In a previous study, we analyzed the molecular diversity of Planctomycetales by PCR amplification and sequencing of 16S rRNA clone libraries generated from a municipal wastewater plant, using planctomycete-specific and universal primer sets (R. Chouari, D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir, Appl. Environ. Microbiol. 69:7354-7363, 2003). Only a small fraction (4%) of the 16S rRNA gene sequences of the digester clone library corresponded to the Planctomycetales division. Importantly, 85.9% of the digester clone sequences are grouped into two different clusters named WWE1 (81.4% of the sequences) and WWE2 (4.5%) and are distantly affiliated with unidentified bacterial sequences retrieved from a methanogenic reactor community and from a termite gut, respectively. In phylogenetic analysis using 16S rRNA gene sequence representatives of the main phylogenetic bacterial divisions, the two clusters are monophyletic, branch apart from each other, and are distantly related to Planctomycetales and other bacterial divisions. A novel candidate division is proposed for WWE1, while the WWE2 cluster strongly affiliates with the recently proposed Lentisphearae phylum. We designed and validated a 16S rRNA probe targeting WWE1 16S rRNA sequences by both fluorescent in situ hybridization (FISH) and dot blot hybridization (DBH). Results of FISH analysis show that WWE1 representative microorganisms are rods or filamentous shaped, while DBH shows that WWE1 accounts for 12% of the total bacterial rRNA within the anaerobic digester. The remaining 16S rRNA gene sequences are affiliated with Verrucomicrobia or recently described candidate divisions with no known pure culture representatives, such as OD1, BRC1, or NBL-UPA2, making up less than 3.5% of the clone library, respectively. This inventory expands the known diversity of the latter bacterial division-level lineages.

Molecular diversity and biomass of epilithic biofilms from intertidal rocky shores in the Gulf of Mexico

Epilithic biofilms play key roles in rocky shore ecosystems. The diversity and biomass of epilithic biofilms were determined along a subtropical intertidal rocky shore at Xpicob, Southern Gulf of Mexico (Campeche, Mexico). Biofilm diversity was assessed by polymerase chain reaction (PCR) amplification of partial 16 S rRNA genes using single-strand conformation polymorphism (SSCP). Triplicate 2 cm×2 cm biofilm samples per site were taken randomly from 0.6 m×0.6 m quadrats located in two sampling sites, established 20 m apart within a homogeneous calcareous intertidal platform. Twenty-two partial rRNA sequences, belonging to four bacterial divisions (Cyanobacteria, Bacteroidetes, Actinobacteria and Proteobacteria), were recovered from these biofilms; of these, cyanobacteria were the most abundant (41%). The occurrence of cyanobacterial sequences in most samples, along with the detection of high levels of chlorophyll a and phycobiliprotein, indicates that these organisms are dominant within the biofilms. Consistent with previous reports, thick-sheathed cyanobacteria such as those found in this study (Xenococcus, Myxosarcina and Chroococcidiopsis) are typical in habitats in intertidal zones. In addition, most of the detected organisms from other bacterial lineages had closest relatives displaying biofilm phenotypes that suggested stressful conditions (i.e. desiccation) prevailed in the intertidal shores; this was selecting for biofilm-forming or thick-sheathed organisms as an ecological adaptation to withstand the conditions. Unweighted pair-group method with arithmetic mean (UPGMA) analysis of SSCP profiles indicated that there was significant spatial heterogeneity in biofilm community composition across different scales of analysis and that this heterogeneity was related to the distance at which samples were taken. This analysis showed that certain organisms appeared to be station specific and that the biofilm community structure varied even on a small scale (1 cm). Since no significant differences in bulk sea water or substratum physicochemistry were observed, these results suggest that small-scale variability of environmental conditions, surface properties and/or biological interactions (i.e. allelopathy) may be important factors structuring these biofilm communities.

Bacterial Diversity in Spent Mushroom Compost Assessed by Amplified rDNA Restriction Analysis and Sequencing of Cultivated Isolates

Spent mushroom compost (SMC) is the residual by-product of commercial Agaricus spp. cultivation, and it is mainly composed of a thermally treated cereal straw/animal manure mixture colonized by the fungal biomass. Research on the valorization of this material is mainly focusing on its use as soil conditioner and plant fertilizer. An investigation of the bacterial diversity in SMC was performed using molecular techniques in order to reveal the origin of SMC microflora and its potential effect on soil microbial communities after incorporation into agricultural soils. The bacterial population was estimated by the plate count method to a mean of 2.7 10(9) colony forming units (cfu) per g of dry weight, while the numbers of Gram-positive and Gram-negative bacteria were 1.9 10(9) and 4.9 10(8) cfu per g dw respectively as estimated by enumeration on semi-selective media. Fifty bacterial isolates were classified into 14 operational taxonomic units (OTUs) following ARDRA-PCR of the 16S rDNA gene. Sequencing of the 16S rDNA amplicon assigned 12 of the 14 OTUs to Gram-positive bacteria, associated with the genera Bacillus, Paenibacillus, Exiguobacterium, Staphylococcus, Desemzia, Carnobacterium, Brevibacterium, Arthrobacter and Microbacterium of the bacterial divisions Firmicutes and Actinobacteria. Two bacterial groups have phylogenetic links with the genera Comamonas and Sphingobacterium, which belong to beta-Proteobacteria and Bacteroidetes respectively. Two potentially novel bacteria are reported, which are associated with the genera Bacillus and Microbacterium. Most of the bacteria identified are of environmental origin, while strains related to species usually isolated from insects, animal and clinical sources were also detected. It appears that bacterial diversity in SMC is greatly affected by the origin of the initial material, its thermal pasteurization treatment and the potential unintended colonization of the mushroom substrate during the cultivation process.

Phylogenetic diversity of bacteria in the leachate of a full-scale recirculating landfill

We analyzed the phylogenetic composition of bacterial community in the effluent leachate of a full-scale recirculating landfill using a culture-independent molecular approach. 16S rRNA genes were amplified directly from leachate DNA with universally conserved and Bacteria-specific rDNA primers and cloned. The clone library was screened by restriction fragment length polymorphism, and representative rDNA sequences were determined. Many bacterial sequences displaying relatively low levels of similarity to any other hitherto reported rDNA sequences were retrieved. A total of 103 bacterial sequence types were found in 195 analyzed clones. Roughly 90% of the sequence types were affiliated with low-G + C gram-positive bacteria, the Chlamydiae/Verrucomicrobia group and with the Cytophaga–Flexibacter–Bacteroides group, where the clone distribution was 53%, 21% and 19%, respectively. The other 10 sequence types represented 7% of the total clones, and they were either affiliated with well-recognized bacterial divisions Planctomycetes, Spirochaetes, Proteobacteria and Actinobacteria, or grouped within two recently proposed candidate divisions OP9 and OP11. The most frequent sequence type represented less than 10% of the total bacterial 16S rRNA gene sequences, and the 15 more frequent sequence types accounted for at least 47% of these sequences. Some rRNA gene sequences clustered with genera or taxa that were classically identified within anaerobic treatment systems. These results indicate that, despite recent expansion, our knowledge on the microbial diversity in anaerobic treatment systems is still limited.

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.

Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro

Construction of 16S rDNA libraries was undertaken to examine the structure of free-living bacterial communities in the estuarine system Ria de Aveiro, Portugal. Samples were collected in April 2002, from two sites representing marine (station N1) and brackish (station I6) water zones. Clones were characterized by RFLP patterns and sequence analysis of representative clones revealed that both libraries were clearly dominated by α- proteobacteria, followed by γ- proteobacteria and β- proteobacteria. Clones affiliated with the δ- proteobacteria, Verrucomicrobia, Bacteroidetes and Actinobacteria were exclusive of station I6 and sequences related to the Firmicutes were only found in station N1. Sequences retrieved are included in only a few major bacterial divisions and in general, shared a high degree of homology with sequences deposited in nucleotide databases, and recovered from aquatic environments of diverse geographic regions. Differences between the two sites may reflect adaptation to different environmental conditions, especially salinity. The pattern of prokaryotic diversity is comparable to other coastal and estuarine environments previously studied.

Thermophilic bacterial DNA polymerases with reverse-transcriptase activity.

Conserved motifs found in known bacterial polI DNA polymerase sequences were identified, and degenerate PCR primers were designed for PCR amplification of an internal portion of polI genes from all bacterial divisions. We describe here a method that has allowed the rapid identification and isolation of 13 polI genes from a diverse selection of thermophilic bacteria and report on the biochemical characteristics of nine of the purified recombinant enzymes. Several enzymes showed significant reverse-transcriptase activity in the presence of Mg2+, particularly the polymerases from Bacillus caldolyticus EA1, Caldibacillus cellovorans CompA.2, and Clostridium stercorarium.

Molecular Phylogenetic Analysis of Archaea and Bacteria in Wind Cave, South Dakota

The diversity of bacteria and archaea was characterized from sediments collected from Wind Cave located in Wind Cave National Park in the Black Hills of South Dakota. Wind Cave is a limestone dissolution cave with strata that started forming over 300 million years ago, making it one of the oldest in the world. Previous work suggested that the cave was largely a detritus based system ultimately dependent upon allochthonous energy and carbon from photosynthesis of the overlying vegetation, and algae growing near lights along the tour routes. In this work, we used a molecular phylogenetic approach to characterize the microbial structure and infer a corresponding ecosystem function where appropriate. Four bacterial divisions and subdivisions were found in the culture collection, which represented 14 phylotypes, whereas 12 divisions and subdivisions were identified in the clonal analysis comprising 49 phylotypes. The predominant groups were the γ-Proteobacteria and Acidobacteria. Although a few of the clones resembled sequences from other cave and subterranean systems, no cave-specific bacterial community was evident in this work. Archaeal phylotypes (20 Crenarchaeota and 2 Euryarchaeota) were detected, with a large proportion of the Crenarchaeota resembling sequences from a South African gold mine. One archaeal cluster in particular appears to be specific to the subterranean environment. Most of the microbial sequences were not related to known chemolithoautotrophs, therefore we conclude that this particular community is likely detritus based where allochthonous energy and carbon are transported into the cave by infiltrating waters.

New perspective on uncultured bacterial phylogenetic division OP11.

Organisms belonging to the OP11 candidate phylogenetic division of Bacteria have been detected only in rRNA-based sequence surveys of environmental samples. Preliminary studies indicated that such organisms represented by the sequences are abundant and widespread in nature and highly diverse phylogenetically. In order to document more thoroughly the phylogenetic breadth and environmental distribution of this diverse group of organisms, we conducted further molecular analyses on environmental DNAs. Using PCR techniques and primers directed toward each of the five described subdivisions of OP11, we surveyed 17 environmental DNAs and analyzed rRNA gene sequences in 27 clonal libraries from 14 environments. Ninety-nine new and unique sequences were determined completely, and approximately 200 additional clones were subjected to partial sequencing. Extensive phylogenetic comparisons of the new sequences to those representing other bacterial divisions further resolved the phylogeny of the bacterial candidate division OP11 and identified two new candidate bacterial divisions, OP11-derived 1 (OD1) and Sulphur River 1 (SR1). The widespread environmental distribution of representatives of the bacterial divisions OD1, OP11, and SR1 suggests potentially conspicuous biogeochemical roles for these organisms in their respective environments. The information on environmental distribution offers clues for attempts to culture landmark representatives of these novel bacterial divisions, and the sequences are specific molecular signatures that provide for their identification in other contexts.

Molecular Phylogenetic Analysis of a Bacterial Community in an Oligotrophic Cave Environment

While much work has been carried out on cave communities that obtain energy from measurable exogenous energy sources (surface organics, sulfide or nitrite), very little work has been carried out on communities that subsist in regions of nutrient scarcity. In this study we generated a 16S SSU-rDNA clone library from an oligotrophic, bacterial community that occurs on a wall in Fairy Cave, Glenwood Springs, Colorado, in the absence of observable energy sources. Thirty-eight unique phylotypes based on restriction fragment length polymorphisms were identified and sequenced. Phylogenetic analysis of the sequences revealed that these phylotypes did not correspond to any known sequence, but were related to organisms in the bacterial divisions Proteobacteria, Actinobacteria, Cytophagales and the Low G+C gram-positive bacterial relatedness group. Comparative metabolic analysis suggests that the bacterial community subsists using a complex metabolic network, with input from trace organics within the environment or fixation of atmospheric gases using lithotrophic metabolism. Community distribution of these phylotypes is unique from previous observations in caves using cultivation, suggesting that many of the species identified are sufficiently adapted to the oligotrophic lifestyle and thus remain resistant to cultivation using standard techniques. Such oligotrophic microbial communities may reflect the principal form of life in subaerial cave environments.

Partitioning of bacterial communities between travertine depositional facies at Mammoth Hot Springs, Yellowstone National Park, U.S.A.

A culture-independent molecular survey indicates that the composition of bacterial communities is distinctly partitioned between travertine depositional facies in the surface drainage system of Spring AT-1 at Angel Terrace, Mammoth Hot Springs, Yellowstone National Park. PCR (polymerase chain reaction) amplification and sequencing of 16S rRNA genes with universally conserved bacterial primers has identified over 553 unique partial and 104 complete gene sequences (derived from more than 14 000 clones), affiliated with 221 unique species that represent 21 bacterial divisions. These sequences exhibited < 12% similarity in bacterial community composition between each of the travertine depositional facies. This implies that relatively little downstream bacterial transport and colonization took place despite the rapid and continuous flow of spring water from the high-temperature to low-temperature facies. These results suggest that travertine depositional facies, which are independently determined by the physical and chemical conditions of the hot spring drainage system, effectively predict bacterial community composition as well as the morphology and chemistry of travertine precipitation.

Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge.

We report here a molecular survey based on 16S rRNA genes of the bacterial diversity found in two deep-sea vent niches at the Mid-Atlantic Ridge: hydrothermal sediment (Rainbow site), and microcolonizers made of three different substrates (organic-rich, iron-rich and pumice) that were exposed for 15 days to a vent emission. Bacterial diversity in sediment samples was scattered through many bacterial divisions. The most abundant and diverse environmental sequences (phylotypes) in our libraries corresponded to the Gammaproteobacteria, followed by the Acidobacteria. We detected members of all the subdivisions within the Proteobacteria. Myxobacterial lineages were the most represented within the delta subdivision. Phylotypes ascribing to the Cytophaga-Flavobacterium-Bacteroides, Planctomycetales, high and low G + C Gram-positives, Nitrospirae, and the candidate division TM7 were also identified. Compared to this broad taxonomic coverage, microcolonizers were almost exclusively colonized by epsilonproteobacteria, although these exhibited considerable morphological and phylogenetic in-group diversity. No specificity for any of the substrates tested was seen. This observation further supports the idea of the ecological dominance of epsilonproteobacteria in the fluid-seawater interface environment. Because oxidation of reduced S species and/or sulphur-reduction is thought to be essential for their energetic metabolism in these areas, we mapped different oxidation states of S in individual bacterial filaments from the iron-rich microcolonizer. For this, we used high-resolution, non-destructive synchrotron micro-X-ray Absorption Near-Edge Spectroscopy (micro-XANES), which revealed the co-existence of different S oxidation states, from sulphide to sulphate, at the level of individual cells. This suggests that these cells were metabolizing sulphur in situ.