Phylogenetic diversity of winter bacterioplankton of eutrophic siberian reservoirs as revealed by 16S rRNA gene sequence

Using 16S rRNA gene sequence analyses we investigated the bacterial diversity of winter bacterioplankton of two eutrophic Siberian reservoirs. These reservoirs show similarity in phytoplankton community composition in spring and autumn but tend to differ in summer in exhibiting cyanobacterial bloom. Forty-eight unique partial 16S RNA gene sequences retrieved from two libraries were mostly affiliated with the class Actinobacteria, b subdivision of the class Proteobacteria, and the phylum Cytophaga-Flavobacterium-Bacteroides. The clone library of the pond exhibiting summer cyanobacterial bloom showed more diversity in sequence composition. A significant number of bacterial 16S rRNA gene clones were closely related to freshwater bacteria previously found in different aquatic ecosystems. This finding confirms the assumption that some bacterial clades are globally distributed.     

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were present in all samples. The largest number of reads belonged to Firmicutes (43.7% of total bacterial sequences), Verrucomicrobia (4.1%), Proteobacteria (3.8%), and Bacteroidetes (3.7%). The less abundant Actinobacteria, Cyanobacteria, and TM7 phyla presented here have not been previously described in the gut contents or feces of horses. Unclassified sequences represented 38.1% of total bacterial sequences; therefore, the equine fecal microbiome diversity is likely greater than that described. This is the first study to characterize the fecal bacterial community in horses by the use of 16S rRNA gene amplicon pyrosequencing, expanding our knowledge of the fecal microbiota of forage-fed horses.     

Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific)

The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.     

Phylogenetic diversity of bacteria in an earth-cave in Guizhou province, southwest of China

The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0%), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.     

Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide

Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO(2) in single or multifactorial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experiments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO(2) . Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO(2) on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO(2) or other climate factors. The Acidobacteria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi-quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO(2) on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be harbingers of more substantive changes in less abundant, more sensitive taxa that can only be detected by deeper surveys. Representative bacterial 16S rRNA gene clone sequences were deposited in GenBank with Accession No. JQ366086–JQ387568.     

Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria

The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems.     

Novel and Unexpected Prokaryotic Diversity in Water and Sediments of the Alkaline,Hypersaline Lakes of the Wadi An Natrun,Egypt

The phylogenetic diversity of the bacterial and archaeal community in the water and sediments of three large lakes of the Wadi An Natrun was investigated using 16S rRNA clone libraries. The bacterial community was diverse: 769 clones formed 345 operational taxonomic units (OTUs) defined at 99% 16S rRNA sequence identity. The bacterial community in both the water and sediments of the lakes was dominated by clones affiliated with the low G + C Gram-type-positive group, alpha-proteobacteria, and Bacteroidetes, (11-39, 11-30, and 10-37% of OTUs observed, respectively), patterns that have been observed in previously described alkaline, athalassohaline systems. However, a relatively high proportion of Firmicutess-related clones in the water of the lakes and alpha-proteobacteria in the sediments was observed. The bacterial community composition of the water and sediment of the same lake and of different lakes was significantly different (p < 0.05). Operational taxonomic units related to the gamma-proteobacteria were more abundant in the sediment of Lake Fazda, whereas the sediment of Lake UmRisha was dominated by members of the delta-proteobacteria. The proportion of gamma-proteobacterial and Bacteroidetes-affiliated OTUs were predominant in the water of Lake UmRisha and differed significantly from other lake waters (chi-squared analysis, p < or = 0.01). The more oxygenated and dilute nature of Lake Hamra was reflected in its microbial community composition, with the abundance of Bacillales sequences in the water, the absence of Halanaerobiales, Clostridiales, and Archaea in the water, and the presence of representatives of more phyla such as the Actinobacteria, Spirochaetes, and Verrucomicrobia. The archaeal community composition appeared less diverse: 589 clones resulted in 198 OTUs defined at 99% 16S rRNA sequence identity, and all sequences fell into the phylum Euryarchaeota. Phylogenetic analysis showed that many of the sequences were distantly related (83-90% 16S rRNA sequence identity) to cultured and uncultured archaea, with many clones forming clusters that branched deeply within the Euryarchaeota. Forty-two and 53% of the bacterial and archaeal clones had less than 90% 16S rRNA sequence identity to previously described sequences. This indicates that the water and sediments of the Wadi An Natrun harbor a unique and novel prokaryotic diversity that is different from what has been described among other alkaline, athalassohaline lakes.     

Patterns in the Composition of Microbial Communities from a Subtropical River: Effects of Environmental,Spatial and Temporal Factors

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO₄-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NO_x-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.     

Diversity of bacteria at various depths in the southern part of lake Baikal as detected by 16S rRNA sequencing

Phylogenetic analysis of the bacterial community inhabiting the water of Lake Baikal was performed on the basis of 16S rRNA sequencing. The composition of the bacterial community was shown to vary significantly with depth. Cyanobacteria were dominant species at the surface of the lake. At a moderate depth (400 m), actinomycete relatives were most abundant. At a great depth and near the bottom, the community was composed mainly of proteobacteria and cyanobacteria (the latter are probably brought from the surface layers by vertical near-shore water fluxes). Most of the bacterial 16S rRNA sequences detected exhibited low similarity to those known and formed separate clusters in the phylogenetic tree, which may indicate the endemic nature of the corresponding bacteria.     

Diversity and abundance of uncultured cytophaga-like bacteria in the Delaware estuary

The Cytophaga-Flavobacterium group is known to be abundant in aquatic ecosystems and to have a potentially unique role in the utilization of organic material. However, relatively little is known about the diversity and abundance of uncultured members of this bacterial group, in part because they are underrepresented in clone libraries of 16S rRNA genes. To circumvent a suspected bias in PCR, a primer set was designed to amplify 16S rRNA genes from the Cytophaga-Flavobacterium group and was used to construct a library of these genes from the Delaware Estuary. This library had several novel Cytophaga-like 16S rRNA genes, of which about 40% could be grouped together into two clusters (DE clusters 1 and 2) defined by sequences initially observed only in the Delaware library; the other 16S rRNA genes were classified into an additional four clades containing sequences from other environments. An oligonucleotide probe was designed for the cluster with the most clones (DE cluster 2) and was used in fluorescence in situ hybridization assays. Bacteria in DE cluster 2 accounted for about 10% of the total prokaryotic abundance in the Delaware Estuary and in a depth profile of the Chukchi Sea (Arctic Ocean). The presence of DE cluster 2 in the Arctic Ocean was confirmed by results from 16S rRNA clone libraries. The contribution of this cluster to the total bacterial biomass is probably larger than is indicated by the abundance of its members, because the average cell volume of bacteria in DE cluster 2 was larger than those of other bacteria and prokaryotes in the Delaware Estuary and Chukchi Sea. DE cluster 2 may be one of the more abundant bacterial groups in the Delaware Estuary and possibly other marine environments.     

Diversity of bacterial community in freshwater of Woopo wetland

Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.     

Connecting through space and time: catchment-scale distributions of bacteria in soil,stream water and sediment

Terrestrial and aquatic environments are linked through hydrological networks that transport abiotic components from upslope environments into aquatic ecosystems. However, our understanding of how bacteria are transported through these same networks is limited. Here, we applied 16S rRNA gene sequencing to over 500 soil, stream water and stream sediment samples collected within a native forest catchment to determine the extent to which bacterial communities in these habitats are connected. We provide evidence that while the bacterial communities in each habitat were significantly distinct from one another (PERMANOVA pairwise P < 0.001), the bacterial communities in soil and stream samples were weakly connected to each other when stream sediment sample locations were downhill of surface runoff flow paths. This pattern decreased with increasing distance between the soil and sediment samples. The connectivity between soil and stream water samples was less apparent and extremely transient; the greatest similarity between bacterial communities in soil and stream water overall was when comparing stream samples collected 1 week post soil sampling. This study shows how bacterial communities in soil, stream water and stream sediments are connected at small spatial scales and provides rare insights into the temporal dynamics of terrestrial and aquatic bacterial community connectivity.     

Bacterial diversity in the bacterioneuston (sea surface microlayer): the bacterioneuston through the looking glass

The bacterioneuston is defined as the community of bacteria present within the neuston or sea surface microlayer. Bacteria within this layer were sampled using a membrane filter technique and bacterial diversity was compared with that in the underlying pelagic coastal seawater using molecular ecological techniques. 16S rRNA gene libraries of approximately 500 clones were constructed from both bacterioneuston and the pelagic water samples and representative clones from each library were sequenced for comparison of bacterial diversity. The bacterioneuston was found to have a significantly lower bacterial diversity than the pelagic seawater, with only nine clone types (ecotaxa) as opposed to 46 ecotaxa in the pelagic seawater library. Surprisingly, the bacterioneuston clone library was dominated by 16S rRNA gene sequences affiliated to two groups of organisms, Vibrio spp. which accounted for over 68% of clones and Pseudoalteromonas spp. accounting for 21% of the library. The dominance of these two 16S rRNA gene sequence types within the bacterioneuston clone library was confirmed in a subsequent gene probing experiment. 16S rRNA gene probes specific for these groups of bacteria were designed and used to probe new libraries of 1000 clones from both the bacterioneuston and pelagic seawater DNA samples. This revealed that 57% of clones from the bacterioneuston library hybridized to a Vibrio sp.-specific 16S rRNA gene probe and 32% hybridized to a Pseudoalteromonas sp.-specific 16S rRNA gene probe. In contrast, the pelagic seawater library resulted in only 13% and 8% of 16S rRNA gene clones hybridizing to the Vibrio sp. and Pseudoalteromonas sp. probes respectively. Results from this study suggest that the bacterioneuston contains a distinct population of bacteria and warrants further detailed study at the molecular level.     

The first results of a study of the phylogenetic diversity of microorganisms in southern Baikal sediments from the area of subsurface depositions of methane hydrates

Phylogenetic analysis of the bacterial communities in Lake Baikal bottom sediments in the region of subsurface methane hydrate depositions has been carried out using data on 16S rRNA sequences. The composition of these microbial communities is shown to be different in different horizons. Methanotrophic bacteria are found in the surface layer (0-5 cm), and uncultured bacteria constitute a great portion of this population. In deeper sediment layers (92-96 cm), achange in the microbial community occurs; specifically, a decreased homology with the known sequences is observed. The new sequences form separate clusters on a phylogenetic tree, indicating the possibly endemic nature of the bacteria revealed. Organisms related to the genus Pseudomonas constitute the main portion of the population. An archaea-related sequence was found in a horizon containing gas hydrate crystals (100-128 cm). Uncultured bacteria remain predominant.     

Bacterial diversity in worker adults of Apis mellifera capensis and Apis mellifera scutellata (Insecta: Hymenoptera) assessed using 16S rRNA sequences

High-fidelity PCR of 16S rRNA sequences was used to identify bacteria associated with worker adults of the honeybee subspecies Apis mellifera capensis and Apis mellifera scutellata. An expected approximately 1.5-kb DNA band, representing almost the entire length of the 16S rRNA gene, was amplified from both subspecies and cloned. Ten unique sequences were obtained: one sequence each clustered with Bifidobacterium (Gram-positive eubacteria), Lactobacillus (Gram-positive eubacteria), and Gluconacetobacter (Gram-negative alpha-proteobacteria); two sequences each clustered with Simonsiella (beta-proteobacteria) and Serratia (gamma-proteobacteria); and three sequences each clustered with Bartonella (alpha-proteobacteria). Although the sequences relating to these six bacterial genera initially were obtained from either A. m. capensis or A. m. scutellata or both, newly designed honeybee-specific 16S rRNA primers subsequently amplified all sequences from all individual workers of both subspecies. Attempts to amplify these sequences from eggs have failed. However, the wsp primers designed to amplify Wolbachia DNA from arthropods, including these bees, consistently produced a 0.6-kb DNA band from individual eggs, indicating that amplifiable bacterial DNA was present. Hence, the 10 bacteria could have been acquired orally from workers or from other substrates. This screening of 16S rRNA sequences from A. m. capensis and A. m. scutellata found sequences related to Lactobacillus and Bifidobacterium which previously had been identified from other honeybee subspecies, as well as sequences related to Bartonella, Gluconacetobacter, Simonsiella/Neisseria, and Serratia, which have not been identified previously from honeybees.     

Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings

A molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in Austria and Germany. The applied molecular method included PCR amplification of genes encoding the small subunit rRNA of bacteria (16S rDNA), genetic fingerprinting by denaturing gradient gel electrophoresis (DGGE), construction of 16S rDNA clone libraries, and comparative phylogenetic sequence analyses. The bacterial community of one red-pigmented biofilm sampled in Herberstein (Austria) contained bacteria phylogenetically related to the genera Saccharopolyspora, Nocardioides, Pseudonocardia, Rubrobacter, and to a Kineococcus-like bacterium. The bacterial community of the second red-pigmented biofilm sampled in Herberstein contained bacteria related to Arthrobacter, Comamonas, and to Rubrobacter. Rubrobacter-related 16S rDNA sequences were the most abundant. In the red-pigmented biofilm sampled in Burggen (Germany), only Rubrobacter-related bacteria were identified. No Rubrobacter-related bacteria were detected in non-rosy biofilms. The majority of sequences (70%) obtained from the bacterial communities of the three investigated rosy biofilms were related to sequences of the genus Rubrobacter (red-pigmented bacteria), demonstrating a correlation between Rubrobacter-related bacteria and the phenomenon of rosy discolouration of masonry and lime wall paintings.     

Phylogenetic analysis of a microbial community involved in anaerobic oxidation of ammonium nitrogen

The phylogenetic diversity of a microbial community involved in anaerobic oxidation of ammonium nitrogen in the DEAMOX process was studied. Analysis of clone libraries containing 16S rRNA gene inserts of Bacteria, (including Planctomycetes) and Archaea revealed the presence of nucleotide sequences of the microorganisms involved in the main reactions of the carbon, nitrogen, and sulfur cycles, including nitrifying, denitrifying, and ANAMMOX bacteria. In the bacterial clone library, 16S rRNA gene sequences of representatives of the phyla Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Verrucomicrobia, Lentisphaerae, Spirochaetales, and Planctomycetes, as well as of some new groups, were detected. In the archaeal clone library, nucleotide sequences of methanogens belonging to the orders Methanomicrobiales, Methanobacteriales, and Methanosarcinales were found. It is possible that both ANAMMOX bacteria and bacteria of the genus Nitrosomonas are involved in anaerobic ammonium oxidation in the DEAMOX reactor. Many sequences were similar to those from the clone libraries obtained previously from the ANAMMOX community of marine sediments. It is also probable that the DEAMOX reactions occur in natural ecosystems (in marine and freshwater sediments and the oceanic water column), thereby providing for the coupling of the nitrogen and sulfur cycles.     

Assessing the Viability of Bacterial Species in Drinking Water by Combined Cellular and Molecular Analyses

The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining (“live/dead staining” indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the DNA- and RNA-based overall community structure differed substantially, (2) the community retrieved from RNA and DNA reflected different bacterial species, classified as 53 phylotypes (with only two common phylotypes), (3) the percentage of phylotpes with intact membranes or damaged cells were comparable for RNA- and DNA-based analyses, and (4) the retrieved species were primarily of aquatic origin. The pronounced difference between phylotypes obtained from DNA extracts (dominated by Betaproteobacteria, Bacteroidetes, and Actinobacteria) and from RNA extracts (dominated by Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria) demonstrate the relevance of concomitant RNA and DNA analyses for drinking water studies. Unexpected was that a comparable fraction (about 21%) of phylotypes with membrane-injured cells was observed for DNA- and RNA-based analyses, contradicting the current understanding that RNA-based analyses represent the actively growing fraction of the bacterial community. Overall, we think that this combined approach provides an interesting tool for a concomitant phylogenetic and viability analysis of bacterial species of drinking water.     

Community composition of the marine bacterioplankton in Kongsfjorden (Spitsbergen) as revealed by 16S rRNA gene analysis

Phylogenetic diversity of the marine bacterioplankton in Kongsfjorden (Spitsbergen) was investigated by 16S rRNA gene analysis. Community fingerprint analysis by PCR-denaturing gradient gel electrophoresis revealed that there was no apparent difference of bacterioplankton community composition between sampling locations in the fjord. A higher biodiversity was observed in bottom water of station 3 in the central part of the fjord. By 16S rRNA gene clone library analysis, sequences detected both in surface and bottom water of station 3 fell into eight putative divisions, including Proteobacteria (Alpha, Beta, Gamma and Delta), Bacteroidetes, Actinobacteria, Verrucomicrobia and unidentified bacteria, in addition to chloroplasts of algae. Sequences representing Planctomycetes were only observed in bottom water. Compared to the preponderance of clones representing Gammaproteobacteria (36.5%) and Alphaproteobacteria (29.4%) in bottom water, Alphaproteobacteria (43.6%) and algae (27.7%) constituted two dominant fractions in surface water. Cloned sequences showed 82.1–100% similarity to those described sequences. It suggests that, attributing to the influence of ocean currents as well as freshwater input in the summer, the bacterial community in Kongsfjorden may consist of a mixture of cosmopolitan and uniquely endemic phylotypes.