DNA-DNA Solution Hybridization Studies of the Bacterial Symbionts of Hydrothermal Vent Tube Worms (Riftia pachyptila and Tevnia jerichonana)

The giant tube worm, Riftia pachyptila (phylum Vestimentifera), is known only from four widely separated sulfide-rich deep-sea hydrothermal vent systems. This invertebrate is nourished by intracellular, chemoautotrophic bacterial symbionts which reside in a specialized trophosome tissue. The symbiont has not been cultured independently and is believed to be acquired de novo by host larvae of each generation. In the current study, R. pachyptila symbiont DNA was purified from the two most distant sites on the basis of its difference in density versus host DNA. These two standards were hybridized against trophosome DNAs of 13 individuals from the Guaymas Basin, Galapagos Rift, and 13 degrees N vents. This indicated that all R. pachyptila symbionts are conspecific and that the variability in DNA-DNA hybridization (relative binding ratio [RBR]) was comparable within or between widely separated vents. The symbiont of another tube worm, Tevnia jerichonana, was found to be the same as that of R. pachyptila, the first case in which distinct hosts possess the same sulfur bacterial symbiont. By contrast, Lamellibrachia sp. (same class as T. jerichonana) showed insignificant RBR with the R. pachyptila symbiont. DNA derived from solely eucaryotic tissue of R. pachyptila showed a surprisingly high RBR (20 to 50) with density-separated DNA standards. With DNAs obtained from physically separated symbionts, independent solution hybridization experiments confirmed the above-described conclusions. Possible explanations for this host-symbiont homology are discussed.     

Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach

We have constructed a large fosmid library from a mesophilic anaerobic digester and explored its 16S rDNA diversity using a high-density filter DNA–DNA hybridization procedure. We identified a group of 16S rDNA sequences forming a new bacterial lineage named WWE3 (Waste Water of Evry 3). Only one sequence from the public databases shares a sequence identity above 80% with the WWE3 group which hence cannot be affiliated to any known or candidate prokaryotic division. Despite representing a non-negligible fraction (5% of the 16S rDNA sequences) of the bacterial population of this digester, the WWE3 bacteria could not have been retrieved using the conventional 16S rDNA amplification procedure due to their unusual 16S rDNA gene sequence. WWE3 bacteria were detected by polymerase chain reaction (PCR) in various environments (anaerobic digesters, swine lagoon slurries and freshwater biofilms) using newly designed specific PCR primer sets. Fluorescence in situ hybridization (FISH) analysis of sludge samples showed that WWE3 microorganisms are oval-shaped and located deep inside sludge flocs. Detailed phylogenetic analysis showed that WWE3 bacteria form a distinct monophyletic group deeply branching apart from all known bacterial divisions. A new bacterial candidate division status is proposed for this group.     

Lipid composition of deep-sea hydrothermal vent tubeworm Riftia pachyptila, crabs Munidopsis subsquamosa and Bythograea thermydron, mussels Bathymodiolus sp. and limpets Lepetodrilus spp

Lipid composition was determined for hydrothermal vent species collected by the Deep Submergence Vehicle ALVIN from chimneys at 2,500 m depth on the East Pacific Rise. These are the first lipid biomarker studies for most of these species. Lipid content was low and dominated by polar lipid in the vestimentiferan tubeworm Riftia pachyptila, mussels Bathymodiolus sp. and limpets Lepetodrilus spp. The galatheid (Munidopsis subsquamosa) and most brachyuran adult (Bythograea thermydron) crabs were characterized by higher storage lipid (triacylglycerol). Total polyunsaturated fatty acids were similar in R. pachyptila plume and body, but higher in the posterior part of the soft body, which had more docosahexaenoic acid (2-5% of total FA) compared to the anterior and plume (< or =0.3%). Two sulphur-oxidizing bacterial markers, 16:1(n-7)c and 18:1(n-7)c, were high in R. pachyptila and mussel (up to 23%), but lower in both crab species (4-17%). R. pachyptila had greater nonmethylene interrupted diunsaturated fatty acids (8-13%) than all other species (2-8%). R. pachyptila may desaturate and elongate 18:1(n-7)c to obtain essential polyunsaturated fatty acids 20:5(n-3) and 20:4(n-6). The sterol composition of R. pachyptila included similar amounts of cholesterol and desmosterol, whereas the other species had a more diverse sterol composition. These differences in lipids, fatty acids and sterols reflect diverse nutritional strategies and possibly temperature regimes in these species.     

Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing

Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in tidal flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gamma-and Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in tidal flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which were further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.     

Richness and diversity of bacteria in the Nansha carbonate platform (Core MD05-2896), South China Sea

We explored the bacterial diversity and vertical distribution along a sediment core (MD05-2896) from the coral reefs of the Nansha carbonate platform in the South China Sea. Bacterial diversity is determined by 16S rRNA molecular survey from twelve subsamples A, obtained via cloning, sequencing and phylogenetic analyses. We estimated the species richness by parametric and nonparametric models, which identified 326 ± 40 (SE) bacteria species. The dominant bacterial groups included Planctomycetes, Deltaproteobacteria, and candidate division OP3, which constituting 23.7, 10.4, and 9.5 % of bacterial 16S rRNAclone libraries, respectively. The observed stratification of bacterial communities was correlated with C/N ratio. This study improves our understanding of the species–environment relationship in the sub-sea floor sediment.     

Catabolism of pyrimidine nucleotides in the deep-sea tube worm Riftia pachyptila

The present study describes the distribution and properties of enzymes of the catabolic pathway of pyrimidine nucleotides in Riftia pachyptila, a tubeworm living around deep-sea hydrothermal vents and known to be involved in a highly specialized symbiotic association with a bacterium. The catabolic enzymes, 5'-nucleotidase, uridine phosphorylase, and uracil reductase, are present in all tissues of the worm, whereas none of these enzymatic activities were found in the symbiotic bacteria. The 5'-nucleotidase activity was particularly high in the trophosome, the symbiont-harboring tissue. These results suggest that the production of nucleosides in the trophosome may represent an alternative source of carbon and nitrogen for R. pachyptila, because these nucleosides can be delivered to other parts of the worm. This process would complement the source of carbon and nitrogen from organic metabolites provided by the bacterial assimilatory pathways. The localization of the enzymes participating in catabolism, 5'-nucleotidase and uridine phosphorylase, and of the enzymes involved in the biosynthesis of pyrimidine nucleotides, aspartate transcarbamylase and dihydroorotase, shows a non-homogeneous distribution of these enzymes in the trophosome. The catabolic enzymes 5'-nucleotidase and uridine phosphorylase activities increase from the center of the trophosome to its periphery. In contrast, the anabolic enzymes aspartate transcarbamylase and dihydroorotase activities decrease from the center toward the periphery of the trophosome. We propose a general scheme of anatomical and physiological organization of the metabolic pathways of the pyrimidine nucleotides in R. pachyptila and its bacterial endosymbiont.     

DNA base composition and genome size of the prokaryotic symbiont in Riftia pachyptila (Pogonophora)

Abstract It has been proposed that Riftia pachyptila , a pogonophoran tube worm abundant at hydrothermal deep sea vents, metabolizes solely via a chemoautotrophic symbiosiols. The symbionts resemble sulfur oxidizing bacteria and form the specific 'trophosome' tissue. Samples of DNA purified from trophosome and vestimentum (muscle) tissues of R. pachyptila were comparatively characterized by thermal denaturation studies, and by analysis of renaturation kinetics. The results show that the great majority of trophosome DNA is homogeneous and prokaryotic with a base ratio of approx. 58 mol% G + C. Its genome size (genetic complexity) is typical of free-living bacteria. Approx. 5% of trophosome DNA appears to be invertebrate DNA equivalent to that found in the vestimentum tissue which lacks symbionts.     

Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria

Culture-independent molecular phylogenetic methods were used to explore the breadth of diversity and environmental distribution of members of the division-level "candidate" phylogenetic group WS6, recently discovered in a contaminated aquifer and with no cultivated representatives. A broad diversity of WS6-affiliated sequences were cloned from 7 of 12 environments investigated: mainly from anaerobic sediment environments. The number of sequences representing the WS6 candidate division was increased from 3 to 60 in this study. The extent of phylogenetic divergence (sequence difference) in this candidate division was found to be among the largest of any known bacterial division. This indicates that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty. These results provide a framework for the further study of these evidently important kinds of organisms and tools, the sequences, with which to do so.     

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria

The diversity of bacterial species in the human oral cavity is well recognized, but a high proportion of them are presently uncultivable. Candidate division TM7 bacteria are almost always detected in metagenomic studies but have not yet been cultivated. In this paper, we identified candidate division TM7 bacterial phylotypes in mature plaque samples from around orthodontic bonds in subjects undergoing orthodontic treatment. Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes. The bacteria formed filaments of 20 to 200 μm in length within agar plate colonies and in monospecies biofilms on salivary pellicle and exhibited some unusual morphological characteristics by transmission electron microscopy, including a trilaminated cell surface layer and dense cytoplasmic deposits. Proteomic analyses of cell wall protein extracts identified abundant polypeptides predicted from the TM7 partial genomic sequence. Pleiomorphic phenotypes were observed when the candidate division TM7 bacterium was grown in dual-species biofilms with representatives of six different oral bacterial genera. The TM7 bacterium formed long filaments in dual-species biofilm communities with Actinomyces oris or Fusobacterium nucleatum. However, the TM7 isolate grew as short rods or cocci in dual-species biofilms with Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, or Streptococcus gordonii, forming notably robust biofilms with the latter two species. The ability to cultivate TM7 axenically should majorly advance understanding of the physiology, genetics, and virulence properties of this novel candidate division oral bacterium.     

Microbial Community of a Hydrothermal Mud Vent Underneath the Deep-Sea Anoxic Brine Lake Urania (Eastern Mediterranean)

The composition of a metabolically active prokaryotic community thriving in hydrothermal mud fluids of the deep-sea hypersaline anoxic Western Urania Basin was characterized using rRNA-based phylogenetic analysis of a clone library. The physiologically active prokaryotic assemblage in this extreme environment showed a great genetic diversity. Most members of the microbial community appeared to be affiliated to yet uncultured organisms from similar ecosystems, i.e., deep-sea hypersaline basins and hydrothermal vents. The bacterial clone library was dominated by phylotypes affiliated with the epsilon-Proteobacteria subdivision recognized as an ecologically significant group of bacteria inhabiting deep-sea hydrothermal environments. Almost 18% of all bacterial clones were related to delta-Proteobacteria, suggesting that sulfate reduction is one of the dominant metabolic processes occurring in warm mud fluids. The remaining bacterial phylotypes were related to alpha- and beta-Proteobacteria, Actinobacteria, Bacteroides, Deinococcus-Thermus, KB1 and OP-11 candidate divisions. Moreover, a novel monophyletic clade, deeply branched with unaffiliated 16S rDNA clones was also retrieved from deep-sea sediments and halocline of Urania Basin. Archaeal diversity was much lower and detected phylotypes included organisms affiliated exclusively with the Euryarchaeota. More than 96% of the archaeal clones belonged to the MSBL-1 candidate order recently found in hypersaline anoxic environments, such as endoevaporitic microbial mats, Mediterranean deep-sea mud volcanoes and anoxic basins. Two phylotypes, represented by single clones were related to uncultured groups DHVE-1 and ANME-1. Thus, the hydrothermal mud of hypersaline Urania Basin seems to contain new microbial diversity. The prokaryotic community was significantly different from that occurring in the upper layers of the Urania Basin since 60% of all bacterial and 40% of all archaeal phylotypes were obtained only from mud fluids. The uniqueness of the composition of the active prokaryotic community could be explained by the complex environmental conditions at the site. The interaction of oxygenated warm mud fluids with the cold hypersaline brine of the Urania Basin seems to simultaneously select for various metabolic processes, such as aerobic and anaerobic heterotrophy, sulfide- and methane-dependent chemotrophy along with anaerobic oxidation of methane, sulfate- and metal-reduction.     

Expanding the Known Diversity and Environmental Distribution of an Uncultured Phylogenetic Division of Bacteria

Culture-independent molecular phylogenetic methods were used to explore the breadth of diversity and environmental distribution of members of the division-level “candidate” phylogenetic group WS6, recently discovered in a contaminated aquifer and with no cultivated representatives. A broad diversity of WS6-affiliated sequences were cloned from 7 of 12 environments investigated: mainly from anaerobic sediment environments. The number of sequences representing the WS6 candidate division was increased from 3 to 60 in this study. The extent of phylogenetic divergence (sequence difference) in this candidate division was found to be among the largest of any known bacterial division. This indicates that organisms representing the WS6 phylogenetic division offer a broad diversity of undiscovered biochemical and metabolic novelty. These results provide a framework for the further study of these evidently important kinds of organisms and tools, the sequences, with which to do so.     

Electing a candidate: a speculative history of the bacterial phylum OP10

In 1998, a cultivation‐independent survey of the microbial community in Obsidian Pool, Yellowstone National Park, detected 12 new phyla within the Domain Bacteria. These were dubbed ‘candidate divisions’ OP1 to OP12. Since that time the OP10 candidate division has been commonly detected in various environments, usually as part of the rare biosphere, but occasionally as a predominant community component. Based on 16S rRNA gene phylogeny, OP10 comprises at least 12 class‐level subdivisions. However, despite this broad ecological and evolutionary diversity, all OP10 bacteria have eluded cultivation until recently. In 2011, two reference species of OP10 were taxonomically validated, removing the phylum from its ‘candidate’ status. Construction of a highly resolved phylogeny based on 29 universally conserved genes verifies its standing as a unique bacterial phylum. In the following paper we summarize what is known and what is suspected about the newest described bacterial phylum, the Armatimonadetes.     

Microbial diversity in alpine tundra wet meadow soil: novel Chloroflexi from a cold, water-saturated environment

Cold, water-saturated soils play important biogeochemical roles, yet almost nothing is known about the identity and habitat of microbes active under such conditions. We investigated the year-round microenvironment of an alpine tundra wet meadow soil in the Colorado Rocky Mountains, focusing on the biogeochemistry and microbial diversity of spring snowmelt--a dynamic time for alpine ecosystems. In situ measurements revealed spring and autumn periods of long-term temperature stability near 0 degrees C, and that deeper soil (30 cm) was more stable than surface soil, with more moderate summers and winters, and longer isothermal phases. The soil was saturated and water availability was limited by freezing rather than drying. Analyses of bioavailable redox species showed a shift from Mn reduction to net Fe reduction at 2-3 cm depth, elevated SO4(2-) and decreased soluble Zn at spring snowmelt. Terminal restriction fragment length polymorphism profiles detected a correlated shift in bacterial community composition at the surface to subsurface transition. Bacterial and archaeal small-subunit rRNA genes were amplified from saturated spring soil DNA pooled along a depth profile. The most remarkable feature of these subsurface-biased libraries was the high relative abundance of novel, uncultivated Chloroflexi-related sequences comprising the third largest bacterial division sampled, and representing seven new Chloroflexi subdivisions, thereby dramatically expanding the known diversity of this bacterial division. We suggest that these novel Chloroflexi are active at near -0 degrees C temperatures, under likely anoxic conditions, and utilize geochemical inputs such as sulfide from upslope weathering.     

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.     

Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes

Glycosaminoglycans (GAGs) are polysaccharides that are typically present in a wide diversity of animal tissue. Most common GAGs are well-characterized and pharmaceutical applications exist for many of these compounds, e.g. heparin and hyaluronan. In addition, also bacterial glycosaminoglycan-like structures exist. Some of these bacterial GAGs have been characterized, but until now no bacterial GAG has been found that possesses the modifications that are characteristic for many of the animal GAGs such as sulfation and C5-epimerization. Nevertheless, the latter conversion may also occur in bacterial and archaeal GAGs, as some prokaryotic polysaccharides have been demonstrated to contain L-iduronic acid. However, experimental evidence for the enzymatic synthesis of L-iduronic acid in prokaryotes is as yet lacking. We therefore performed an in silico screen for D-glucuronyl C5-epimerases in prokaryotes. Multiple candidate C5-epimerases were found, suggesting that many more microorganisms are likely to exist possessing an L-iduronic acid residue as constituent of their cell wall polysaccharides.     

The molecular biology of plastid division in higher plants

Plastids are essential plant organelles vital for life on earth, responsible not only for photosynthesis but for many fundamental intermediary metabolic reactions. Plastids are not formed de novo but arise by binary fission from pre-existing plastids, and plastid division therefore represents an important process for the maintenance of appropriate plastid populations in plant cells. Plastid division comprises an elaborate pathway of co-ordinated events which include division machinery assembly at the division site, the constriction of envelope membranes, membrane fusion and, ultimately, the separation of the two new organelles. Because of their prokaryotic origin bacterial cell division has been successfully used as a paradigm for plastid division. This has resulted in the identification of the key plastid division components FtsZ, MinD, and MinE, as well as novel proteins with similarities to prokaryotic cell division proteins. Through a combination of approaches involving molecular genetics, cell biology, and biochemistry, it is now becoming clear that these proteins act in concert during plastid division, exhibiting both similarities and differences compared with their bacterial counterparts. Recent efforts in the cloning of the disrupted loci in several of the accumulation and replication of chloroplasts mutants has further revealed that the division of plastids is controlled by a combination of prokaryote-derived and host eukaryote-derived proteins residing not only in the plastid stroma but also in the cytoplasm. Based on the available data to date, a working model is presented showing the protein components involved in plastid division, their subcellular localization, and their protein interaction properties.     

Pyrosequencing Reveals Bacterial Diversity in the Rhizosphere of Three Phragmites australis Ecotypes

Here we present the use of high-throughput DNA pyrosequencing to assess bacterial diversity in the rhizosphere of three Phragmites australis ecotypes from the Hexi Corridor, China. In total, 43404 sequences were obtained for the three ecotypes, representing 31 phyla and a small amount of unclassified bacteria. The predominant bacterial groups in the rhizosphere of P. australis were Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes. The bacterial community structure varied with the different degrees of wetland degradation, which were exhibited by the three P. australis ecotypes in the study area. At the phylum level, the Caldiserica, Chlamydiae, Deferribacteres, Lentisphaerae, and candidate division WS3 were only detected in the swamp reed (SR) sample. Then, δ-proteobacteria, Acidobacteria, Cyanobacteria and Fusobacteria decreased, the Actinobacteria increased with the degree of degradation from SR through salt meadow reed (SMR) to dune reed (DR). The functional bacterial genera also varied with wetland degradation. The sulfur and sulfate-reducing, nitrifying and nitrogen-fixing bacteria were more abundant in the rhizosphere of the SR sample. Methane-oxidizing bacteria were abundant in the SR and DR samples but less so in the SMR. In our study, pyrosequencing of different P. australis ecotypes provided insight into the structural variation of the rhizosphere bacterial community. This study gave a database for the use of bacteria in the protection and ecological restoration of wetland.     

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.     

Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys

The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO(2) and H(2) produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.     

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.