Bacterial phylotypes associated with the digestive tract of the sea urchin Paracentrotus lividus and the ascidian <Emphasis Type="Italic">Microcosmus</Emphasis> sp.

We used sequencing and phylogenetic analysis of PCR-amplified 16S rRNA genes from bacteria that are associated with the esophagus/pharynx, stomach and intestine of two marine sympatric invertebrates but with different feeding mechanisms, namely the sea urchin Paracentrotus lividus (grazer) and the ascidian Microcomus sp. (suspension feeder). Amplifiable DNA was retrieved from all sections except the pharynx of the ascidian. Based on the inferred phylogeny of the retrieved sequences, the sea urchin’s esophagus is mainly characterized mostly by bacteria belonging to α-, γ-Proteobacteria and Bacteriodetes, most probably originating from the surrounding environment. The stomach revealed phylotypes that belonged to γ- and δ-Proteobacteria, Verrucomicrobia and Fusobacteria. Since the majority of their closest relatives are anaerobic species and they could be putative symbionts of the P. lividus stomach, in which anaerobic conditions also prevail. Seven out of eight phylotypes found in the sea urchin’s intestine belonged to sulfate reducing δ-Proteobacteria, and one to γ-Proteobacteria, with possible nutritional activities, i.e. degradation of complex organic compounds which is beneficial for the animal. The bacterial phylotypes of the ascidian digestive tract belonged only to the phyla of Actinobacteria and Proteobacteria. The stomach phylotypes of the ascidian were related to pathogenic bacteria possibly originating from the water column, while the intestine seemed to harbour putative symbiotic bacteria that are involved in the degradation of nitrogenous and other organic compounds, thus assisting ascidian nutrition. The text was submitted by the authors in English.     

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

In order to assess bacterial diversity within four surface sediment samples (0–5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (α, β, γ, δ and ε-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). α, γ, and δ-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The γ-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of γ-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.     

Seasonal changes and diversity of bacteria in Bohai Bay by RFLP analysis of PCR-amplified 16S rDNA gene fragments

Information about seasonal bacterial composition and diversity is of great value for exploitation of marine biological resources and improvement of ecological environment. Here PCR-amplified restriction fragment length polymorphism (PCR–RFLP) of 16S rRNA genes was used to evaluate seasonal bacterial diversity and community composition in Bohai Bay. A total of 24 bacterial communities were sampled from seawater and sediment of three representative sites in a whole seasonal cycle: spring (April), summer (July), autumn (October), and winter (January). Bacterial Genomic DNA was extracted and PCR-amplified to obtain 16S rDNA fragments which were cloned to construct 24 16s rDNA libraries. Clones of each library were selected randomly for PCR–RFLP analysis of rDNA fragments, and eventually 101 genotypes were identified by RFLP fingerprintings. These 101 genotypes were sequenced and their respective phylotype was identified through the Blast tool of NCBI (similarity 96–100%) and phylogenetic analyses. Among our phylotypes, 80.2% belonged to the genera α-Proteobacteria, β-proteobacteria,γ-Proteobacteria, δ-Proteobacteria, ε-proteobacteria, Flavobacteria, Cytophaga-Flavobacteria-Bacteroides, Verrucomicrobia, Firmicutes and Actinobacteria. Sequence analyses revealed that 47.5% (48) of clone sequences were similar to those of uncultured marine bacteria in the environment. In addition, bacterial diversity and composition clearly displayed seasonal variety. More genera were discovered in summer than any other seasons, and some special species appeared only in specific season.     

Gill-symbiosis in mytilidae associated with wood fall environments

Bivalves belonging to the genera Idas and Adipicola were collected from wood fall environments in the west Pacific (Vanuatu islands) between 300 and 890 m depths in 2004. Bacterial symbionts were checked by three complementary techniques: histological and DAPI staining, in situ hybridization (FISH), and TEM. No bacteria were detected inside the gills of the two species, rejecting the endosymbiosis hypothesis. However, results from our study demonstrated the existence of ectosymbionts colonizing microvilli differentiated at the apical surface of the cells constituting the lateral zone of gill filaments. These ectosymbionts are γ-Proteobacteria due to their strong hybridization with the specific probe GAM42; in contrast no hybridization was obtained from either gills or other host tissues by using the oligonucleotide probes specific to α- β- and δ-Proteobacteria. Based on TEM observations, these Gram-negative bacterial symbionts are not methanotrophic due to the lack of concentric stacking of intracellular membranes in their cytoplasm. Such ectosymbionts may represent thioautotrophic bacteria as already described in various Mytilidae from hydrothermal vents and cold seeps. Unfortunately, no phylogenetic analysis could be done in this study to compare their DNA sequence to that of other marine invertebrate symbionts described to date.     

Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.     

The Community and Phylogenetic Diversity of Biological Soil Crusts in the Colorado Plateau Studied by Molecular Fingerprinting and Intensive Cultivation

We studied the bacterial communities in biological soil crusts (BSCs) from the Colorado Plateau by enrichment and cultivation, and by statistically analyzed denaturing gradient gel electrophoresis (DGGE) fingerprinting of environmental 16S rRNA genes, and phylogenetic analyses. Three 500-m-long transects, tens of km apart, consisting of 10 equally spaced samples each, were analyzed. BSC communities consistently displayed less richness (10–32 detectable DGGE bands per sample) and Shannon diversity (2.1–3.3) than typical soil communities, with apparent dominance by few members. In spite of some degree of small-scale patchiness, significant differences in diversity and community structure among transects was detectable, probably related to the degree of crust successional maturity. Phylogenetic surveys indicated that the cyanobacterium Microcoleus vaginatus was dominant, with M. steenstrupii second among phototrophs. Among the 48 genera of nonphototrophs detected, Actinobacteria (particularly Streptomyces spp.) were very common and diverse, with 18 genera and an average contribution to the total 16S rDNA amplificate of 11.8%. β-Proteobacteria and Bacteriodetes contributed around 10% each; Low-GC Gram-positives, α-Proteobacteria, Thermomicrobiales, and Acidobacteria were common (2–5%). However, the second largest contribution was made by deep-branching unaffiliated alleles (12.6%), with some of them representing candidate bacterial divisions. Many of the novel strains isolated are likely new taxa, and some were representatives of the phylotypes detected in the field. The mucoid or filamentous nature of many of these isolates speaks for their role in crust formation.     

Coexistence of Bacterial Sulfide Oxidizers, Sulfate Reducers, and Spirochetes in a Gutless Worm (Oligochaeta) from the Peru Margin

Olavius crassitunicatus is a small symbiont-bearing worm that occurs at high abundance in oxygen-deficient sediments in the East Pacific Ocean. Using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization, we examined the diversity and phylogeny of bacterial symbionts in two geographically distant O. crassitunicatus populations (separated by 385 km) on the Peru margin (water depth, ~300 m). Five distinct bacterial phylotypes co-occurred in all specimens from both sites: two members of the γ-Proteobacteria (Gamma 1 and 2 symbionts), two members of the δ-Proteobacteria (Delta 1 and 2 symbionts), and one spirochete. A sixth phylotype belonging to the δ-Proteobacteria (Delta 3 symbiont) was found in only one of the two host populations. Three of the O. crassitunicatus bacterial phylotypes are closely related to symbionts of other gutless oligochaete species; the Gamma 1 phylotype is closely related to sulfide-oxidizing symbionts of Olavius algarvensis, Olavius loisae, and Inanidrilus leukodermatus, the Delta 1 phylotype is closely related to sulfate-reducing symbionts of O. algarvensis, and the spirochete is closely related to spirochetal symbionts of O. loisae. In contrast, the Gamma 2 phylotype and the Delta 2 and 3 phylotypes belong to novel lineages that are not related to other bacterial symbionts. Such a phylogenetically diverse yet highly specific and stable association in which multiple bacterial phylotypes coexist within a single host has not been described previously for marine invertebrates.     

Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru margin

Olavius crassitunicatus is a small symbiont-bearing worm that occurs at high abundance in oxygen-deficient sediments in the East Pacific Ocean. Using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization, we examined the diversity and phylogeny of bacterial symbionts in two geographically distant O. crassitunicatus populations (separated by 385 km) on the Peru margin (water depth, approximately 300 m). Five distinct bacterial phylotypes co-occurred in all specimens from both sites: two members of the gamma-Proteobacteria (Gamma 1 and 2 symbionts), two members of the delta-Proteobacteria (Delta 1 and 2 symbionts), and one spirochete. A sixth phylotype belonging to the delta-Proteobacteria (Delta 3 symbiont) was found in only one of the two host populations. Three of the O. crassitunicatus bacterial phylotypes are closely related to symbionts of other gutless oligochaete species; the Gamma 1 phylotype is closely related to sulfide-oxidizing symbionts of Olavius algarvensis, Olavius loisae, and Inanidrilus leukodermatus, the Delta 1 phylotype is closely related to sulfate-reducing symbionts of O. algarvensis, and the spirochete is closely related to spirochetal symbionts of O. loisae. In contrast, the Gamma 2 phylotype and the Delta 2 and 3 phylotypes belong to novel lineages that are not related to other bacterial symbionts. Such a phylogenetically diverse yet highly specific and stable association in which multiple bacterial phylotypes coexist within a single host has not been described previously for marine invertebrates.     

Specific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments

Specific amplification of 16S rRNA gene fragments in combination with denaturing gradient gel electrophoresis (DGGE) was used to generate fingerprints of Chromatiaceae, green sulfur bacteria, Desulfovibrionaceae, and β-Proteobacteria. Sequencing of the gene fragments confirmed that each primer pair was highly specific for the respective phylogenetic group. Applying the new primer sets, the bacterial diversity in the chemoclines of a eutrophic freshwater lake, a saline meromictic lake, and a laminated marine sediment was investigated. Compared to a conventional bacterial primer pair, a higher number of discrete DGGE bands was generated using our specific primer pairs. With one exception, all 15 bands tested yielded reliable 16S rRNA gene sequences. The highest diversity was found within the chemocline microbial community of the eutrophic freshwater lake. Sequence comparison revealed that the six sequences of Chromatiaceae and green sulfur bacteria detected in this habitat all represent distinct and previously unknown phylotypes. The lowest diversity of phylotypes was detected in the chemocline of the meromictic saline lake, which yielded only one sequence each of the Chromatiaceae, β-2-Proteobacteria, and Desulfovibrionaceae, and no sequences of green sulfur bacteria. The newly developed primer sets are useful for the detection of previously unknown phylotypes, for the comparison of the microbial diversity between different natural habitats, and especially for the rapid monitoring of enrichments of unknown bacterial species. Received: 22 January 1999 / Accepted: 28 April 1999     

Bacterial symbionts in the hepatopancreas of isopods: diversity and environmental transmission

The midgut glands (hepatopancreas) of terrestrial isopods contain bacterial symbionts. We analysed the phylogenetic diversity of hepatopancreatic bacteria in isopod species from various suborders colonizing marine, semiterrestrial, terrestrial and freshwater habitats. Hepatopancreatic bacteria were absent in the marine isopod Idotea balthica (Valvifera). The symbiotic bacteria present in the midgut glands of the freshwater isopod Asellus aquaticus (Asellota) were closely related to members of the proteobacterial genera Rhodobacter, Burkholderia, Aeromonas or Rickettsiella, but differed markedly between populations. By contrast, species of the suborder Oniscidea were consistently colonized by the same phylotypes of hepatopancreatic bacteria. While symbionts in the semiterrestrial isopod Ligia oceanica (Oniscidea) were close relatives of Pseudomonas sp. (Gammaproteobacteria), individuals of the terrestrial isopod Oniscus asellus (Oniscidea) harboured either 'Candidatus Hepatoplasma crinochetorum' (Mollicutes) or 'Candidatus Hepatincola porcellionum' (Rickettsiales), previously described as symbionts of another terrestrial isopod, Porcellio scaber. These two uncultivated bacterial taxa were consistently present in each population of six and three different species of terrestrial isopods, respectively, collected in different geographical locations. However, infection rates of individuals within a population ranged between 10% and 100%, rendering vertical transmission unlikely. Rather, feeding experiments suggest that 'Candidatus Hepatoplasma crinochetorum' is environmentally transmitted to the progeny.     

Bacterial Diversity in Three Different Antarctic Cold Desert Mineral Soils

A bacterial phylogenetic survey of three environmentally distinct Antarctic Dry Valley soil biotopes showed a high proportion of so-called “uncultured” phylotypes, with a relatively low diversity of identifiable phylotypes. Cyanobacterial phylotypic signals were restricted to the high-altitude sample, whereas many of the identifiable phylotypes, such as the members of the Actinobacteria, were found at all sample sites. Although the presence of Cyanobacteria and Actinobacteria is consistent with previous culture-dependent studies of microbial diversity in Antarctic Dry Valley mineral soils, many phylotypes identified by 16S rDNA analysis were of groups that have not hitherto been cultured from Antarctic soils. The general belief that such “extreme” environments harbor a relatively low species diversity was supported by the calculation of diversity indices. The detection of a substantial number of uncultured bacterial phylotypes showing low BLAST identities (<95%) suggests that Antarctic Dry Valley mineral soils harbor a pool of novel psychrotrophic taxa.     

Bacterial Community Diversity in Undisturbed Perhumid Montane Forest Soils in Taiwan

The diversity and composition of soil bacterial communities in three topographic sites (summit, foot slope, and lakeshore) from subtropical montane forest ecosystem in Taiwan were examined by using 16S rRNA gene clone library analysis. This locality is temperate, perhumid, and has low soil acidity (pH < 4), which is an uncommon ecosystem in a monsoonal part of Southeast Asia. A total of 481 clones were sequenced and placed into ten phylogenetic groups according to their similarities to type strains of described organisms. Toposequence of the transect was investigated from summit to foot slope and at the lakeshore. More than 86% of the clones were affiliated with members of the Proteobacteria, Acidobacteria, and Actinobacteria. Within the Proteobacteria, the β-Proteobacteria was the most abundant, then α-Proteobacteria and γ-Proteobacteria. Based on the Shannon diversity index (H) analysis, the bacterial community in the foot slope was the most diverse (H = 0.86) and that in summit was the least diverse (H = 0.68). The composition and diversity of soil bacterial communities in the three sites suggested no trend with topographic change. Less than 20% of the sequences were Acidobacteria-affiliated clones. The low proportion of Acidobacteria observed may be related to the high soil moisture and anaerobic microhabitats. Moreover, Shannon diversity indices revealed these bacterial communities to have lower diversity than that of other temperate (H = 0.90) and tropical forest (H = 0.82) ecosystems. The extreme acidity of soil pH and high soil moisture of this forest may explain composition and reduced the diversity of these soil bacterial communities.     

Spatial heterogeneity of bacterial community structure in the sediments of the Pearl River estuary

Denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analytical methods were applied to investigate the spatial variation of bacterial community structure in the Pearl River estuary sediment and to address the relationship between microbial community composition and bottom water chemistry in ten different stations. Preliminary results of sequencing analysis of the excised DGGE bands suggested that α-Proteobacteria, γ-Proteobacteria, Acidobacteria and Actinobacteria were the dominant bacterial groups in the Pearl River estuary sediment. Results of multidimensional scaling analysis of these field data suggested that the composition of bacterial communities varied with sampling sites. Finally, canonical correspondence analysis of the data of environmental variables and bacterial community suggested that bacterial community structure was significantly influenced by the change of environmental variables (total phosphorus, nitrite, ammonium, dissolved oxygen, pH and salinity).     

Gut microbiota in nymph and adults of the giant mesquite bug (Thasus neocalifornicus) (Heteroptera: Coreidae) is dominated by Burkholderia acquired de novo every generation

The coreid bug Thasus neocalifornicus Brailovsky and Barrera, commonly known as the giant mesquite bug, is a ubiquitous insect of the southwestern United States. Both nymphs and adults are often found aggregated on mesquite trees (Prosopis spp.: Fabaceae) feeding on seedpods and plant sap. We characterized the indigenous bacterial populations of nymphs and adults of this species by using molecular and phylogenetic techniques and culturing methods. Results show that this insect's bacterial gut community has a limited diversity dominated by Burkholderia associates. Phylogenetic analysis by using 16s rRNA sequences suggests that these β-Proteobacteria are closely related to those symbionts obtained from other heteropteran midgut microbial communities but not to Burkholderia symbionts associated with other insect orders. These bacteria were absent from the eggs and were not found in all younger nymphs, suggesting that they are acquired after the insects have hatched. Rearing experiments of nymphs with potentially Burkholderia contaminated soil suggested that if this symbiont is not acquired, giant mesquite bugs experience higher mortality. Egg, whole-body DNA extractions of younger nymphs, and midgut DNA extractions of fifth-instar nymphs and adults also revealed the presence of α-Proteobacteria from the Wolbachia genus. However, this bacterium was also present in reproductive organs of adults, indicating that this symbiont is not specific to the gut.     

Yellowstone Lake: high-energy geochemistry and rich bacterial diversity

Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H(2)S, CH(4), CO(2) and H(2), although CH(4) and H(2) levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-μm-, 3.0-μm-, 0.8-μm- and 0.1-μm-pore-size filters, with the >0.1 to <0.8 μm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α- and β-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.     

Antibiotic exposure perturbs the bacterial community in the small brown planthopper Laodelphax striatellus

Bacteria symbionts in herbivores play an important role in host biology and ecology, and are affected by environmental factors such as temperature, diet, habitat, antibiotics and so on. However, the effects of antibiotics on the microbiome of the small brown planthopper Laodelphax striatellus (SBPH) remain unclear. Here, we studied the effects of tetracycline on the diversity and composition of bacterial colonies in different tissues of SBPH using high throughput sequencing of 16S ribosomal RNA amplicons. Our results show that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria were most abundant in SBPH, and the genera Asaia and Wolbachia were most abundant in all body parts of SBPH. Antibiotic treatment had persistent effects on the composition of the SBPH microbiome. Tetracycline depleted the population of Firmicutes, Bacteroidetes, Tenericutes and Fusobacteria, and nearly 100% eliminated Wolbachia, Bacteroides and Abiotrophia in SBPH. Together, these results suggest that antibiotic exposure affects the bacteria symbionts of different body parts in SBPH and will facilitate future studies of the bacterial symbionts of arthropod hosts.     

Culturable heterotrophic bacteria from the marine sponge <Emphasis Type="Italic">Dendrilla</Emphasis> <Emphasis Type="Italic">nigra</Emphasis>: isolation and phylogenetic diversity of actinobacteria

Culturable heterotrophic bacterial composition of marine sponge Dendrilla nigra was analysed using different enrichments. Five media compositions including without enrichment (control), enriched with sponge extract, with growth regulator (antibiotics), with autoinducers, and complete enrichment containing sponge extract, antibiotics, and autoinducers were developed. DNA hybridization assay was performed to explore host specific bacteria and ecotypes of culturable sponge-associated bacteria. Enrichment with selective inducers (AHLs and sponge extract) and regulators (antibiotics) considerably enhanced the cultivation potential of sponge-associated bacteria. It was found that Marinobacter (MSI032), Micromonospora (MSI033), Streptomyces (MSI051), and Pseudomonas (MSI057) were sponge-associated obligate symbionts. The present findings envisaged that “Micromonospora–Saccharomonospora–Streptomyces” group was the major culturable actinobacteria in the marine sponge D. nigra. The DNA hybridization assay was a reliable method for the analysis of culturable bacterial community in marine sponges. Based on the culturable community structure, the sponge-associated bacteria can be grouped (ecotypes) as general symbionts, specific symbionts, habitat flora, and antagonists.     

Bacterial,archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

We studied the microbial diversity in the sediment from the Kongsfjorden, Svalbard, Arctic, in the summer of 2005 based on the analysis of 16S rRNA and 18S rRNA gene clone libraries. The sequences of the cloned 16S rRNA and 18S rRNA gene inserts were used to determine the species identity or closest relatives by comparison with sequences of known species. Compared to the other samples acquired in Arctic and Antarctic, which are different from that of ours, the microbial diversity in our sediment is much higher. The bacterial sequences were grouped into 11 major lineages of the domain Bacteria: Proteobacteria (include α-, β-, γ-, δ-, and ε-Proteobacteria); Bacteroidetes; Fusobacteria; Firmicutes; Chloroflexi; Chlamydiae; Acidobacteria; Actinobacteria; Planctomycetes; Verrucomicrobiae and Lentisphaerae. Crenarchaeota were dominant in the archaeal clones containing inserts. In addition, six groups from eukaryotes including Cercozoa, Fungi, Telonema, Stramenopiles, Alveolata, and Metazoa were identified. Remarkably, the novel group Lentisphaerae was reported in Arctic sediment at the first time. Our study suggested that Arctic sediment as a unique habitat may contain substantial microbial diversity and novel species will be discovered.     

Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes

In an effort to better understand the factors contributing to patterns in freshwater bacterioplankton community composition and diversity, we coupled automated ribosomal intergenic spacer analysis (ARISA) to analysis of 16S ribosomal RNA (rRNA) gene sequences to follow the persistence patterns of 46 individual phylotypes over 3 years in Crystal Bog Lake. Additionally, we sought to identify linkages between the observed phylotype variations and known chemical and biological drivers. Sequencing of 16S rRNA genes obtained from the water column indicated the presence of phylotypes associated with the Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, TM7 and Verrucomicrobia phyla, as well as phylotypes with unknown affiliation. Employment of the 16S rRNA gene/ARISA method revealed that specific phylotypes varied independently of the entire bacterial community dynamics. Actinobacteria, which were present on greater than 95% of sampling dates, did not share the large temporal variability of the other identified phyla. Examination of phylotype relative abundance patterns (inferred using ARISA fragment relative fluorescence) revealed a strong correlation between the dominant phytoplankton succession and the relative abundance patterns of the majority of individual phylotypes. Further analysis revealed covariation among unique phylotypes, which formed several distinct bacterial assemblages correlated with particular phytoplankton communities. These data indicate the existence of unique persistence patterns for different common freshwater phylotypes, which may be linked to the presence of dominant phytoplankton species.     

Fine-scale vertical distribution of bacteria in the East Pacific deep-sea sediments determined via 16S rRNA gene T-RFLP and clone library analyses

Although the deep-sea sediments harbor diverse and novel bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking, considering the vast area and volume of the deep-sea sedimentary environments. Sediment bacteria vertical distribution and community structure were studied of the E272 site in the East Pacific Ocean with the molecular methods of 16S rRNA gene T-RFLP (terminal restriction fragment length polymorphism) and clone library analyses. Layered distribution of the bacterial assemblages was detected by both methods, indicating that the shallow sediments (40 cm in depth) harbored a diverse and distinct bacterial composition with fine-scale spatial heterogeneity. Substantial bacterial diversity was detected and nine major bacterial lineages were obtained, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Nitrospirae, Planctomycetes, Proteobacteria, and the candidate divisions OP8 and TM6. Three subdivisions of the Proteobacteria presented in our libraries, including the α-, γ- and δ-Proteobacteria. Most of our sequences have low similarity with known bacterial 16S rRNA genes, indicating that these sequences may represent as-yet-uncultivated novel bacteria. Most of our sequences were related to the GenBank nearest neighboring sequences retrieved from marine sediments, especially from deep-sea methane seep, gas hydrate or mud volcano environments. Several sequences were related to the sequences recovered from the deep-sea hydrothermal vent or basalt glasses-bearing sediments, indicating that our deep-sea sampling site might be influenced to certain degree by the nearby hydrothermal field of the East Pacific Rise at 13°N. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.