Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe

The phylogenetic structure and community composition were analysed in an existing data set of marine bacterioplankton communities to elucidate the evolutionary and ecological processes dictating the assembly. The communities were sampled from coastal waters at nine locations distributed worldwide and were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes. The analyses show that the local communities are phylogenetically different from each other and that a majority of them are phylogenetically clustered, i.e. the species (operational taxonomic units) were more related to each other than expected by chance. Accordingly, the local communities were assembled non-randomly from the global pool of available bacterioplankton. Further, the phylogenetic structures of the communities were related to the water temperature at the locations. In agreement with similar studies, including both macroorganisms and bacteria, these results suggest that marine bacterial communities are structured by “habitat filtering”, i.e. through non-random colonization and invasion determined by environmental characteristics. Different bacterial types seem to have different ecological niches that dictate their survival in different habitats. Other eco-evolutionary processes that may contribute to the observed phylogenetic patterns are discussed. The results also imply a mapping between phenotype and phylogenetic relatedness which facilitates the use of community phylogenetic structure analysis to infer ecological and evolutionary assembly processes.     

北极太平洋扇区海洋沉积物细菌多样性的系统发育分析

对北极太平洋扇区3个不同深度的海洋沉积物样品,采用PCR结合变性梯度凝胶电泳(DGGE)技术进行细菌16S rRNA基因V3区序列的系统发育分析。结果表明,同一个沉积物样品不同层次的DGGE电泳图谱不完全相同。从3个沉积物样品中共获得50条序列,大部分序列与从海洋环境尤其海洋沉积物获得的细菌16S rDNA序列相似性较高(88%~100%),归属于变形细菌(Proteobacteria)的gamma亚群、alpha亚群、beta亚群、epsilon亚群、delta亚群,Cytophaga_Flavobacterium_Bacteroides(CFB)群细菌和高G C含量的革兰氏阳性细菌等系统分类群,其中变形细菌(Proteobacteria)的gamma亚群为沉积物中的优势细菌类群。     

Phylogenetic characterization of the heterotrophic bacterial communities inhabiting a marine recirculating aquaculture system

Aims: The aim of the present work was to characterize the heterotrophic bacterial community of a marine recirculating aquaculture system (RAS). Methods and Results: An experimental RAS was sampled for the rearing water (RW) and inside the biofilter. Samples were analysed for bacterial abundances, community structure and composition by using a combination of culture‐dependent and ‐independent techniques. The most represented species detected among biofilter clones was Pseudomonas stutzeri, while Ruegeria spp. and Roseobacter spp. were more abundant among isolates. In comparison, the genera Roseobacter and Ruegeria were well represented in both the biofilter and the RW samples. A variety of possible bacterial pathogens (e.g. Vibrio spp., Erwinia spp. and Coxiella spp.) were also identified in this study. Conclusions: Results revealed that the bacterial community in the RW was quite different to that associated with the biofilter. Moreover, data obtained suggest that the whole bacterial community can be involved in maintaining an effective and a stable rearing environment (shelter effect). Significance and Impact of the Study: Improving the reliability and the sustainability of RAS depends on the correct management of the bacterial populations inside it. This study furnishes more accurate information on the bacterial populations and better clarifies the existing relationships between the bacterial flora in the RW and that associated with the biofilter.     

Horizontal heterogeneity of denitrifying bacterial communities in marine sediments by terminal restriction fragment length polymorphism analysis

Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (nosZ) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996. Sorenson's indices (pairwise similarity values) were calculated to permit comparison between samples. The similarities of benthic denitrifiers ranged from 0.80 to 0.85 for centimeter scale comparisons, from 0.52 to 0.79 for meter level comparisons, and from 0.23 to 0.53 for kilometer scale comparisons. Sorenson's indices for temporal comparisons varied from 0.12 to 0.74. A cluster analysis of the similarity values indicated that the composition of the denitrifier assemblages varied most significantly at the kilometer scale and between seasons at individual stations. Specific nosZ genes were identified which varied at centimeter, meter, or kilometer scales and may be associated with variability in meio- or macrofaunal abundance (centimeter scale), bottom topography (meter scale), or sediment characteristics (kilometer scale).     

Phylogenetic diversity in sulphate-reducing bacterial communities from oxidised and reduced bottom sediments of the Barents Sea

In the bottom sediments from a number of the Barents Sea sites, including coastal areas of the Novaya Zemlya, Franz Josef Land, and Svalbard archipelagos, sulphate reduction rates were measured and the phylogenetic composition of sulphate-reducing bacterial (SRB) communities was analysed for the first time. Molecular genetic analysis of the sequences of the 16S rRNA and dsrB genes (the latter encodes the β-subunit of dissimilatory (bi)sulphite reductase) revealed significant differences in the composition of bacterial communities in different sampling stations and sediment horizons of the Barents Sea depending on the physicochemical conditions. The major bacteria involved in reduction of sulphur compounds in Arctic marine bottom sediments belonged to Desulfobulbaceae, Desulfobacteraceae, Desulfovibrionaceae, Desulfuromonadaceae, and Desulfarculaceae families, as well as to uncultured clades SAR324 and Sva0485. Desulfobulbaceae and Desulfuromonadaceae predominated in the oxidised (E_h = 154–226 mV) upper layers of the sediments (up to 9% and 5.9% from all reads of the 16S rRNA gene sequences in the sample, correspondingly), while in deeper, more reduced layers (E_h = ?210 to ?105 mV) the share of Desulfobacteraceae in the SRB community was also significant (up to 5%). The highest relative abundance of members of Desulfarculaceae family (3.1%) was revealed in reduced layers of sandy-clayey sediments from the Barents Sea area affected by currents of transformed (mixed, with changed physicochemical characteristics) Atlantic waters.

     

Topographic effects of coastal seas on the composition of the culturable bacterial communities in marine sediments

Five published indirect methods to estimate benthic secondary production of intertidal mudflats and a new proposed formulation based on quarter-power allometric scaling and the “Universal Temperature Dependence” of biological processes (UTD) were compared. For this purpose, a dataset consisting of an annual series of samples, taken from the Lagoon of Venice from March 1996 to March 1997, at sites characterised by different seagrass coverage was used. All methods resulted in that biomass and secondary production decreased progressively when moving from the seagrass meadow toward areas of unvegetated substrate, suggesting an influence of the available marine phanerogams on the neighbouring sites. The equation proposed in this paper gives results comparable with those obtained using empirical regression models from literature. The main conclusion from this study is that general equations proposed by the “metabolic theory of ecology” can be applied for indirect estimations of secondary production of benthic communities.     

Phylogenetic analysis of culturable marine bacteria in sediments from the South Korean Yellow Sea

Biogeochemical and microbiological characterization of marine sediments taken from the Yellow Sea of South Korea was carried out. One hundred and thirty six bacterial strains were isolated, characterized and phylogenetic relationship was evaluated. The gene sequences of 16S rDNA regions were examined to study the phylogenetic analysis of bacterial community in the marine sediments. Among 136 isolates, 5 bacterial isolates were identified as novel members, remaining 131 isolates were fall into 5 major linkages of bacterial phyla represented as follows: Firmicutes, alpha, gamma-Proteobacteria, High G + C and Bacteroidetes. Bacterial community in sediments mainly dominated by Firmicutes (58.77%) and followed by gamma-Pateobacteria (38.16%). Gamma-Proteobacteria domain highly diverged and mainly consists of the genera Vibrio, Marinobacterium, Photobacterium, Pseudoalteromonas, Oceanisphaera, Halomonas, Alteromonas, Stenotrophomonas and Pseudomonas. Total N and Organic matter content in Yellow Sea of South Korea were relatively high. The Total-N content in the sediments was varied from 177.31 to 1974.96 (mg/kg) and organic matter ranged from 0.82 to 4.23 (g/100 g). The current research work provides clear explanation obtained for the phylogenetic affiliation of the culturable bacterial community in sediments of South Korean Yellow Sea and revealed the relationship with biogeochemical characteristics of the sediments.     

Phospholipid analysis as a tool to study complex microbial communities in marine sediments.

To complement information on microbial communities in marine sediments that can be obtained using microbiological methods, we developed an analytical procedure to trace microbial lipids in environmental samples. We focused on analyzing intact phospholipids as these membrane constituents are known to be biomarkers for viable cells. Analysis of intact phospholipids from a fractionated and preconcentrated sediment extract was achieved using liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). The combined analysis of phospholipid types and their fatty acid substituents allowed a differentiation between various groups of microorganisms living in the sediment. For comparison three strains of marine sulfate-reducing bacteria (SRB) were analysed for their lipid content.     

High bacterial diversity in permanently cold marine sediments.

A 16S ribosomal DNA (rDNA) clone library from permanently cold marine sediments was established. Screening 353 clones by dot blot hybridization with group-specific oligonucleotide probes suggested a predominance of sequences related to bacteria of the sulfur cycle (43.4% potential sulfate reducers). Within this fraction, the major cluster (19.0%) was affiliated with Desulfotalea sp. and other closely related psychrophilic sulfate reducers isolated from the same habitat. The cloned sequences showed between 93 and 100% similarity to these bacteria. Two additional groups were frequently encountered: 13% of the clones were related to Desulfuromonas palmitatis, and a second group was affiliated with Myxobacteria spp. and Bdellovibrio spp. Many clones (18.1%) belonged to the gamma subclass of the class Proteobacteria and were closest to symbiotic or free-living sulfur oxidizers. Probe target groups were further characterized by amplified rDNA restriction analysis to determine diversity within the groups and within the clone library. Rarefaction analysis suggested that the total diversity assessed by 16S rDNA analysis was very high in these permanently cold sediments and was only partially revealed by screening of 353 clones.     

Phylogenetic analysis of culturable marine bacteria in sediments from South Korean Yellow Sea

Biogeochemical and microbiological characterization of marine sediments taken from the Yellow Sea of South Korea was carried out. One hundred and thirty six bacterial strains were isolated, characterized and phylogenetic relationship was evaluated. The gene sequences of 16S rDNA regions were examined to study the phylogenetic analysis of bacterial community in the marine sediments. Among 136 isolates, 5 bacterial isolates were identified as novel members, remaining 131 isolates were fall into 5 major linkages of bacterial phyla represented as follows: Firmicutes,, -@Proteobacteria, High G + C and Bacteroidetes. Bacterial community in sediments mainly dominated by Firmicute (58.77%) and followed by @-Proteobacteria (38.16%). @-Proteobacteria domain highly diverged and mainly consists of the genera Vibrio, Marinobacterium, Photobacterium, Pseudoalteromonas, Oceanisphaera, Halomonas, Alteromonas, Stenotrophomas and Pseudomonas. Total N and Organic matter content in Yellow Sea of South Korea were relatively high. The Total-N content in the sediments was varied from 177.31 to 1974.96 (mg/kg) and organic matter ranged from 0.82 to 4.23 (g/100 g⁻¹). The current research work provides clear explanation obtained for the phylogenetic affiliation of the culturable bacterial community in sediments of South Korean Yellow Sea and revealed the relationship with biogeochemical characteristics of the sediments.     

Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater

The phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. These reactors were operated at both mesophilic (28 to 32 degrees C) and thermophilic (50 to 58 degrees C) temperatures. Community fingerprint analysis by denaturing gradient gel electrophoresis (DGGE) of the PCR-amplified V3 region of the 16S rRNA gene from the domain Bacteria revealed that these seven reactors supported three distinct microbial communities. A band-counting analysis of the PCR-DGGE results suggested that elevated reactor temperatures corresponded with reduced species richness. Cloning of nearly complete 16S rRNA genes also suggested a reduced species richness in the thermophilic reactors by comparing the number of clones with different nucleotide inserts versus the total number of clones screened. While these results imply that elevated temperature can reduce species richness, other factors also could have impacted the number of populations that were detected. Nearly complete 16S rDNA sequence analysis showed that the thermophilic reactors were dominated by members from the beta subdivision of the division Proteobacteria (beta-proteobacteria) in addition to anaerobic phylotypes from the low-G+C gram-positive and Synergistes divisions. The mesophilic reactors, however, included at least six bacterial divisions, including Cytophaga-Flavobacterium-Bacteroides, Synergistes, Planctomycetes, low-G+C gram-positives, Holophaga-Acidobacterium, and Proteobacteria (alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria and delta-proteobacteria subdivisions). The two PCR-based techniques detected the presence of similar bacterial populations but failed to coincide on the relative distribution of these phylotypes. This suggested that at least one of these methods is insufficiently quantitative to determine total community biodiversity-a function of both the total number of species present (richness) and their relative distribution (evenness).     

Phylogenetic affiliation and quantification of psychrophilic sulfate-reducing isolates in marine Arctic sediments.

Thirteen psychrophilic sulfate-reducing isolates from two permanently cold fjords of the Arctic island Spitsbergen (Hornsund and Storfjord) were phylogenetically analyzed. They all belonged to the delta subclass of Proteobacteria and were widely distributed within this group, indicating that psychrophily is a polyphyletic property. A new 16S rRNA-directed oligonucleotide probe was designed against the largest coherent cluster of these isolates. The new probe, as well as a set of available probes, was applied in rRNA slot blot hybridization to investigate the composition of the sulfate-reducing bacterial community in the sediments. rRNA related to the new cluster of incompletely oxidizing, psychrophilic isolates made up 1.4 to 20.9% of eubacterial rRNA at Storfjord and 0.6 to 3. 5% of eubacterial rRNA at Hornsund. This group was the second-most-abundant group of sulfate reducers at these sites. Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments.     

Phylogenetic diversity of gram-positive bacteria cultured from marine sediments

Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class Actinobacteria while the remaining 65 (34.4%) were members of the class Bacilli. Using a sequence identity value of >/=98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.     

Biodegradation of free phytol by bacterial communities isolated from marine sediments under aerobic and denitrifying conditions

Biodegradation of (E)-phytol [3,7,11, 15-tetramethylhexadec-2(E)-en-1-ol] by two bacterial communities isolated from recent marine sediments under aerobic and denitrifying conditions was studied at 20 degrees C. This isoprenoid alcohol is metabolized efficiently by these two bacterial communities via 6,10, 14-trimethylpentadecan-2-one and (E)-phytenic acid. The first step in both aerobic and anaerobic bacterial degradation of (E)-phytol involves the transient production of (E)-phytenal, which in turn can be abiotically converted to 6,10,14-trimethylpentadecan-2-one. Most of the isoprenoid metabolites identified in vitro could be detected in a fresh sediment core collected at the same site as the sediments used for the incubations. Since (E)-phytenal is less sensitive to abiotic degradation at the temperature of the sediments (15 degrees C), the major part of (E)-phytol appeared to be biodegraded in situ via (E)-phytenic acid. (Z)- and (E)-phytenic acids are present in particularly large quantities in the upper section of the core, and their concentrations quickly decrease with depth in the core. This degradation (which takes place without significant production of phytanic acid) is attributed to the involvement of alternating beta-decarboxymethylation and beta-oxidation reaction sequences induced by denitrifiers. Despite the low nitrate concentration of marine sediments, denitrifying bacteria seem to play a significant role in the mineralization of (E)-phytol.     

Evidence for bacterial urea production in marine sediments

Abstract The quantitative importance of bacteria in urea production and turnover in a defaunated sediment from a Danish estuary was studied. After collecting the sediment, benthic infauna was removed by sieving, followed by anoxic pre-incubation for a week. Yeast extract was added to half of the samples. The urea concentration, urea production/turnover rates and the net ammonium production rate, were followed during a 338 h incubation. The urea concentration was highest in the enriched sediment, although urea production and turnover rates were the same in the enriched and control sediment, indicating that the urea concentration was controlled by the urea turnover rate constant, k _urea. Net ammonium production, urea concetrations and teh urea turnover declined towards the end of the experiment. Comparison of the net ammonium production rate and the urea turnover rate in the enriched and control treatments, showed that urea hydrolysis accounted for up to 100% of the ammonium produced, from all sources. More than 98% of the urea which was hydrolyzed, originated from production during incubation. This suggests that urea was a major nitrogen excretion product from bacteria in this sediment, and that bacteria could also be an important source of urea in other marine sediments.     

Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island)

Bacterial community composition and succession were examined over the course of the summer season in the Great South Bay, Long Island, NY, USA, using a 16S rDNA clone library approach. There was a progression of changes in dominant species in the libraries during the summer of 1997. The July library had several groups dominant, the SAR407 relatives of the alpha-Proteobacteria (24%) and the SAR86 (18%), sulfur-oxidizing symbiont relatives (8%) of the gamma-Proteobacteria, and unidentified Cytophaga-Flexibacter representatives (22%). In August, the Cytophaga-Flexibacter (Gelidibacter sp. and unidentified Cytophaga-Flexibacter representative) and Cyanobacteria (Synechococcus sp.) increased to 28% and 14%, respectively. High GC Gram-positives appeared at 18%, and beta-Proteobacteria (Ralstonia sp.) at 10%. By September these groups had either declined or were absent, while the SAR86 cluster, Pseudoalteromonas and Alteromonas of the gamma-Proteobacteria were dominant in the community (61%). The dominance of open ocean bacteria along with the presence of Aureococcus anophagefferens (Pelagophyceae) in July suggests possible open ocean coupling to bloom events. Many clones in this study were related to previously described clones from a wide distribution of marine environments, substantiating the cosmopolitan nature of pelagic bacteria. Only one isolated bacterium was closely related to 16S rDNA found in the August library.     

Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans.

The extent of the diversity of marine prokaryotes is not well known, primarily because of poor cultivability. However, new techniques permit the characterization of such organisms without culturing, via 16S rRNA sequences obtained directly from biomass. We performed such an analysis by polymerase chain reaction amplification with universal primers on five oligotrophic open-ocean samples: from 100-m (three samples) and 500-m depths in the western California Current (Pacific Ocean) and from a 10-m depth in the Atlantic Ocean near Bermuda. Of 61 clones, 90% were in clusters of two or more related marine clones obtained by ourselves or others. We report 15 clones related to clone SAR 11 found earlier near Bermuda (S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, and K. G. Field, Nature [London] 345:60-63, 1990), 11 related to marine cyanobacteria, 9 clustered in a group affiliated with gram-positive bacteria, 9 in an archaeal cluster we recently described (mostly from the 500-m sample), 4 in a novel gamma-proteobacterial cluster, and 6 in three two-membered clusters (including other archaea). One clone was related to flavobacteria. Only the cyanobacteria plus one other clone, related to Roseobacter denitrificans (formerly Erythrobacter longus Och114), were within 10% sequence identity to any previously sequenced cultured organism in a major data base. We never found more than two occurrences of the same sequence in a sample, although four times we found identical sequences between samples, two of which were between oceans; one of these sequences was also identical to SAR 11.(ABSTRACT TRUNCATED AT 250 WORDS)     

Phylogenetic and physiological characterization of organic waste-degrading bacterial communities

One of the greatest challenges in contemporary society is to reduce and treat household solid waste. The choice of inoculum to be used for start-up in reactors that degrade organic waste is critical to the success of organic waste treatment. In this study, the functional diversity, phylogenetic identification, and biogas production of bacterial communities from six inoculum sources were investigated. We used BIOLOG EcoPlates to evaluate the metabolic abilities of the bacterial communities, followed 16S rRNA gene sequence analysis to determine the phylogenetic affiliation of the bacteria responsible for carbon consumption. We observed great diversity in the physiological profiles. Of the six inocula tested, the sludge from an upflow anaerobic sludge blanket reactor (SRU) contained the most diverse, metabolically versatile microbiota and was characterized by the highest level of biogas production. By contrast, the sludge of the anaerobic lagoon (SAL) showed the worst performance in BIOLOG EcoPlates assays, but it exhibited the most diversity and generated the second largest amount of biogas. The bacterial isolates retrieved from BIOLOG EcoPlates were characterized as aerobic and/or facultative anaerobic, and were mainly Gram-negative. Phylogenetic analysis revealed that the isolates belonged to three major phyla: Proteobacteria, Firmicutes and Actinobacteria, represented by 33 genera. Proteobacteria exhibited the most diversity. The distribution of the bacterial genera differed considerably among the six inocula. Pseudomonas and Bacillus, which are able to degrade a wide range of proteins and carbohydrates, predominated in five of the six inocula. Analysis of the bacterial communities in this study indicates that both SRU and SAL microbiota are candidates for start-up inocula in anaerobic reactors. These start-up inocula must be studied further in order to identify their practical applications in degrading organic waste.