Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species

Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.     

Effect of the Earthworms Lumbricus terrestris and Aporrectodea caliginosa on Bacterial Diversity in Soil

Earthworms ingest large amounts of soil and have the potential to radically alter the biomass, activity, and structure of the soil microbial community. In this study, the diversity of eight bacterial groups from fresh soil, gut, and casts of the earthworms Lumbricus terrestris and Aporrectodea caliginosa were studied by single-strand conformation polymorphism (SSCP) analysis using both newly designed 16S rRNA gene-specific primer sets targeting Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Firmicutes and a conventional universal primer set for SSCP, with RNA and DNA as templates. In parallel, the study of the relative abundance of these taxonomic groups in the same samples was performed using fluorescence in situ hybridization. Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria were predominant in communities from the soil and worm cast samples. Representatives of classes Flavobacteria and Sphingobacteria (Bacteroidetes) and Pseudomonas spp. (low-abundant Gammaproteobacteria) were detected in soil and worm cast samples with conventional and taxon-targeting SSCP and through the sequence analysis of 16S rRNA clone libraries. Physiologically active unclassified Sphingomonadaceae (Alphaproteobacteria) and Alcaligenes spp. (Betaproteobacteria) also maintained their diversities during transit through the earthworm intestine and were found on taxon-targeting SSCP profiles from the soil and worm cast samples. In conclusion, our results suggest that some specific bacterial taxonomic groups maintain their diversity and even increase their relative numbers during transit through the gastrointestinal tract of earthworms.     

Viscera-Associated Bacterial Diversity Among Intertidal Gastropods from Northern-Atlantic Coast of Portugal

Culture-dependent evaluation of the bacteria was carried out on gastropods, such as Monodonta lineata, Gibbula umbilicalis, Nucella lapillus and Patella intermedia, and the environmental samples (biofilm and surrounding sea water) collected from six different locations of Northern Portugal coastal area to investigate the interactions between the microbes in the viscera of gastropods and in the environment. A total of 141 isolates and 39 operational taxonomic units were identified. Phylogenetic analysis based on the 16S rRNA gene showed that bacterial isolates are highly diverse and most of them were found in other marine environment. The observed bacterial diversity was distributed over five different classes (Gammaproteobacteria, Alphaproteobacteria, Flavobacteria, Bacilli and Actinobacteria) with the greatest number of 16S rRNA gene sequence derived from the Gammaproteobacteria (77 %). Vibrio is found to be the dominant one among the different bacterial species isolated. The results suggest that the microorganisms in the environment are maintained in the viscera of the gastropods which may have a key role in the metabolic functions.     

'Candidatus Lumbricincola', a novel lineage of uncultured Mollicutes from earthworms of family Lumbricidae

Molecular signatures of new, as yet uncultured mollicute-like organisms (MLOs) have been detected in total rRNA and DNA extracted from tissues, gut contents and casts of four species of the earthworm family Lumbricidae. The MLO 16S rRNA sequences exhibited low identity to those of known Mollicutes species and formed a monophyletic cluster distantly affiliated to the ' Candidatus Bacilloplasma' (84.9%) and almost equidistant to the other main phylogenetic group of Mollicutes (< 79.8%) and the classes Bacilli (< 79.5%) and Clostridia (< 76.1%). SSCP profiling and sequence analysis of bands and bacterial clones derived from the earthworms and substrata revealed high phylogenetic relatedness of MLOs in earthworms from different geographic locations (Russia and Germany), with no obvious host species specificity being observed. Fluorescence in situ hybridization (FISH) analysis with a nucleotide probe specific for the new MLO group localized them to the coelomic fluids of earthworms. A new taxonomic group within the Mollicutes , designated ' Candidatus Lumbricincola', is proposed to include these as yet uncultured organisms.     

Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It is noted that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.     

Seasonal and spatial variability of sediment bacterial communities inhabiting the large shallow Lake Balaton

Seasonal studies of surface sediment bacterial communities, from two basins with differing trophic states within Lake Balaton (Hungary), were carried out using molecular (denaturing gradient gel electrophoresis, DGGE) and cultivation-based techniques. The presence of polyphosphate accumulates was tested using Neisser staining, and phosphatase activity was investigated on organic phosphorus (P) compound. Aerobic viable cell counts were significantly higher in the eutrophic than mesotrophic basin in each season. The lowest viable counts were observed in the autumn and the highest in spring and summer month in both basins. The DGGE fingerprints of the samples reflected that the composition of sediment bacterial communities in the two basins were distinct in spring and summer, and similar in autumn, but similarly diverse in all seasons. On the basis of partial 16S rDNA sequences, the 216 strains were affiliated with six major bacterial lineages: Firmicutes; Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Common species characterized from both basins constituted up to 66% of all identified phylotypes. Strains related to Bacillus sp. were dominant in all but one sample. Isolates affiliated with Aeromonas sp. prevailed in the sample taken from the mesotrophic basin in spring. The majority of the strains showed excess poly-P accumulation. Association of Neisser staining and phosphatase activity test results suggested that excess poly-P accumulation serves as P storage for sediment bacteria. Our study implied the importance of Firmicutes, Actinobacteria, Alphaproteobacteria, and Aeromonas species in benthic bacterial P retention.     

A culture-based study of the bacterial communities within the guts of nine longicorn beetle species and their exo-enzyme producing properties for degrading xylan and pectin

In this study, bacterial communities within the guts of several longicorn beetles were investigated by a culture-dependent method. A total of 142 bacterial strains were isolated from nine species of longicorn beetle, including adults and larvae. A comparison of their partial 16S rRNA gene sequences showed that most of the bacteria constituting the gut communities can typically be found in soil, plants and the intestines of animals, and approximately 10% were proposed as unreported. Phylogenetic analysis demonstrated that the bacterial species comprised 7 phyla, and approximately half were Gammaproteobacteria. Actinobacteria were the second most populous group (19%), followed by Firmicutes (13%) and Alphaproteobacteria (11%). Betaproteobacteria, Flavobacteria, and Acidobacteria were minor constituents. The taxonomic compositions of the isolates were variable according to the species of longicorn beetle. Particularly, an abundance of Actinobacteria existed in Moechotypa diphysis and Mesosa hirsute, which eat broadleaf trees; however, no Actinobacteria were isolated from Corymbia rubra and Monochamus alternatus, which are needle-leaf eaters. Considerable proportions of xylanase and pectinase producing bacteria in the guts of the longicorn beetles implied that the bacteria may play an important role in the digestion of woody diets. Actinobacteria and Gammaproteobacteria were the dominant xylanase producers in the guts of the beetles.     

Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits

During cold storage after milk collection, psychrotrophic bacterial populations dominate the microflora, and their extracellular enzymes, mainly proteases and lipases, contribute to the spoilage of dairy products. The diversity, dynamics, and enzymatic traits of culturable psychrotrophs in raw milk from four farms were investigated over a 10-month period. About 20% of the isolates were found to be novel species, indicating that there is still much to be learned about culturable psychrotrophs in raw milk. The psychrotrophic isolates were identified and classified in seven classes. Three classes were predominant, with high species richness (18 to 21 species per class) in different seasons of the year: Gammaproteobacteria in spring and winter, Bacilli in summer, and Actinobacteria in autumn. The four minor classes were Alphaproteobacteria, Betaproteobacteria, Flavobacteria, and Sphingobacteria. The dominant classes were found in all four dairies, although every dairy had its own unique "bacterial profile." Most but not all bacterial isolates had either lipolytic or both lipolytic and proteolytic activities. Only a few isolates showed proteolytic activity alone. The dominant genera, Pseudomonas and Acinetobacter (Gammaproteobacteria), showed mainly lipolytic activity, Microbacterium (Actinobacteria) was highly lipolytic and proteolytic, and the lactic acid bacteria (Lactococcus and Leuconostoc) displayed very minor enzymatic ability. Hence, the composition of psychrotrophic bacterial flora in raw milk has an important role in the determination of milk quality. Monitoring the dominant psychrotrophic species responsible for the production of heat-stable proteolytic and lipolytic enzymes offers a sensitive and efficient tool for maintaining better milk quality in the milk industry.     

Changes of bacterial communities in the rhizosphere of sugarcane under elevated concentration of atmospheric CO2

It is believed that climate change will influence most of interactions that sustain life on Earth. Among these, the recruitment exerted by plants in their roots vicinity can change, leading to differential assemblages of microbiomes in the rhizosphere. We approached this issue analyzing the variations in the composition of bacterial communities in the rhizosphere of sugarcane cultivated under two concentrations of atmospheric CO₂ (350 or 700 ppm). In addition to the analysis of bacterial community, the use of DNA‐SIP allowed the comparison of bacterial groups assimilating roots exudates (based on ¹³C‐labeled DNA) in both conditions, in a period of 8 days after the CO₂ pulse. The separation of ¹³C‐DNA indicated the low but increasing frequency of labeling in the rhizosphere, as averages of 0.6, 2.4 and 5.0% of total DNA were labeled after 2, 4, and 8 days after the ¹³CO₂ pulse, respectively. Based on large‐scale sequencing of the V6 region in the gene 16S rRNA, we found an increase in the bacterial diversity in the ¹³C‐DNA along the sampling period. We also describe the occurrence of distinct bacterial groups assimilating roots exudates from sugarcane cultivated under each CO₂ concentration. Bacilli, Gammaproteobacteria, and Clostridia showed high affinity for the C‐sources released by sugarcane under 350 ppm of CO₂, while under elevated concentration of CO₂, the assimilation of roots exudates was prevalently made by members of Bacilli and Betaproteobacteria. The communities became more similar along time (4 and 8 days after CO₂ pulse), in both concentrations of CO₂, electing Actinobacteria, Sphingobacteriia, and Alphaproteobacteria as the major cross‐feeders on sugarcane exudates. In summary, we described the bacterial groups with higher affinity to assimilate roots exudates in the rhizosphere of sugarcane, and also demonstrated that the rhizosphere community can be differentially assembled in a future scenario with increased contents of CO₂.     

Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China

Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems.     

Bacterial community composition and diversity of a full-scale integrated fixed-film activated sludge system as investigated by pyrosequencing

The integrated fixed-film activated sludge (IFAS) system is a variation of the activated sludge wastewater treatment process, in which hybrid suspended and attached biomass is used to treat wastewater. Although the function and performance of the IFAS system are well studied, little is known about its microbial community structure. In this study, the composition and diversity of the bacterial community of suspended and attached biomass samples were investigated in a full-scale IFAS system using a highthroughput pyrosequencing technology. Distinct bacterial community compositions were examined for each sample and appeared to be important for its features different from conventional activated sludge processes. The abundant bacterial groups were Betaproteobacteria (59.3%), Gammaproteobacteria (8.1%), Bacteroidetes (5.2%), Alphaproteobacteria (3.9%), and Actinobacteria (3.2%) in the suspended sample, whereas Actinobacteria (14.6%), Firmicutes (13.6%), Bacteroidetes (11.6%), Betaproteobacteria (9.9%), Gammaproteobacteria (9.25%), and Alphaproteobacteria (7.4%) were major bacterial groups in the attached sample. Regarding the diversity, totals of 3,034 and 1,451 operational taxonomic units were identified at the 3% cutoff for the suspended and attached samples, respectively. Rank abundance and community analyses demonstrated that most of the diversity was originated from rare species in the samples. Taken together, the information obtained in this study will be a base for further studies relating to the microbial community structure and function of the IFAS system.     

添加不同益生菌对草鱼养殖水体菌群结构的影响

为评价添加不同益生菌对草鱼养殖水体菌群结构的影响,研究采用454焦磷酸测序技术分析其水体菌群结构。结果表明:添加益生菌后的处理组（枯草芽孢杆菌BS、光合细菌PSB和复合菌CB）其微生物多样性高于对照组（Control）。在门的水平,Control和CB样品中变形菌（Proteobacteria）为优势菌,PSB和BS中变形菌（Proteobacteria）和放线菌（Actinobacteria）所占比例差别不大。与Control相比,其他三组中拟杆菌（Bacteroidetes）和放线菌（Actinobacteria）都增加。对变形菌深入分析发现,在PSB,BS和 CB 样品中,-变形杆菌为优势菌,接下来是-变形杆菌纲、-变形杆菌纲和-变形杆菌纲。对拟杆菌分析发现,除对照外,其他样品中黄杆菌纲（Flavobacteria）为优势菌。在对照和处理组中,-变形杆菌、-变形杆菌、-变形杆菌和拟杆菌门在目的水平组成也有差异。以上结果表明,水体中添加益生菌能增加水体菌群多样性,改变菌群结构。       

黑龙江大豆胞囊线虫胞囊可培养细菌多样性

【目的】了解黑龙江省大豆田大豆胞囊线虫胞囊可培养细菌的多样性。【方法】运用稀释平板法和16SrDNA基因序列的系统发育分析对胞囊可培养细菌多样性进行研究。【结果】用NA培养基从胞囊上分离90株具有不同菌落形态的细菌。16S rDNA序列分析结果表明:90株菌株分属于7个属22个种。46株属于变形菌门γ亚群(Gammaproteobacteria),32株属于厚壁菌门(Firmicutes),10株属于变形菌门β亚群(Betaproteobacteria),2株属于变形菌门ɑ亚群(Alphaproteobacteria)。假单胞菌属(Pseudomonas)和芽孢杆菌属(Bacillus)为优势菌属。【结果】黑龙江省大豆胞囊线虫胞囊中存在丰富的细菌物种多样性,这些细菌对大豆胞囊线虫可能具有一定的生理生态作用。     

Intercellular and intracellular signalling systems that globally control the expression of virulence genes in plant pathogenic bacteria

Plant pathogenic bacteria utilize complex signalling systems to control the expression of virulence genes at the cellular level and within populations. Quorum sensing (QS), an important intercellular communication mechanism, is mediated by different types of small molecules, including N‐acyl homoserine lactones (AHLs), fatty acids and small proteins. AHL‐mediated signalling systems dependent on the LuxI and LuxR family proteins play critical roles in the virulence of a wide range of Gram‐negative plant pathogenic bacteria belonging to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Xanthomonas spp. and Xylella fastidiosa, members of the Gammaproteobacteria, however, possess QS systems that are mediated by fatty acid‐type diffusible signal factors (DSFs). Recent studies have demonstrated that Ax21, a 194‐amino‐acid protein in Xanthomonas oryzae pv. oryzae, plays dual functions in activating a rice innate immune pathway through binding to the rice XA21 pattern recognition receptor and in regulating bacterial virulence and biofilm formation as a QS signal molecule. In xanthomonads, DSF‐mediated QS systems are connected with the signalling pathways mediated by cyclic diguanosine monophosphate (c‐di‐GMP), which functions as a second messenger for the control of virulence gene expression in these bacterial pathogens.     

Bacterial diversity in the sediment from polymetallic nodule fields of the Clarion-Clipperton Fracture Zone

The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.     

Ubiquitous Dissolved Inorganic Carbon Assimilation by Marine Bacteria in the Pacific Northwest Coastal Ocean as Determined by Stable Isotope Probing

In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM ¹³C-NaHCO₃, doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.     

Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.     

Diversity of bacterial endophytes in roots of Mexican husk tomato plants (Physalis ixocarpa) and their detection in the rhizosphere

Endophytic bacterial diversity was estimated in Mexican husk tomato plant roots by amplified rDNA restriction analysis and sequence homology comparison of the 16S rDNA genes. Sixteen operational taxonomic units from the 16S rDNA root library were identified based on sequence analysis, including the classes Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Bacilli. The predominant genera were Stenotrophomonas (21.9%), Microbacterium (17.1%), Burkholderia (14.3%), Bacillus (14.3%), and Pseudomonas (10.5%). In a 16S rDNA gene library of the same plant species' rhizosphere, only common soil bacteria, including Stenotrophomonas, Burkholderia, Bacillus, and Pseudomonas, were detected. We suggest that the endophytic bacterial diversity within the roots of Mexican husk tomato plants is a subset of the rhizosphere bacterial population, dominated by a few genera.     

河口细菌群落多样性及其控制因素:以切萨皮克湾为例

咸淡水的混合和重要营养盐与有机物的再循环,使得河口成为地球上生产力较高而动态变化明显的水生生态系统.一个典型的河口区断面中,细菌群落包含了一些从淡水到海洋的过渡类型:例如α-变形菌(Alphaproteobacteria)、p-变形菌(Betaproteobacteria)、γ-变形菌(Gammaproteobacteria)、蓝细菌(Cyanobactenia)[聚球藻(Synechococcus)]、拟杆菌(Bacteroidetes)、放线细菌(Actinobacteria)和疣微菌(Verrucomicrobia)等.此外,河口也包含其独特的细菌群落:SAR11组、玫瑰杆菌属(Roseobacter)、SAR86和放线细菌(Actinobacteria)的一些进化亚枝(subclades),表明海湾或者大型温带河口区细菌类群具有区域生态适应性.以研究较多的美国切萨皮克湾(Chesapeake Bay)为例,其细菌群落呈现出显著的季节性变化和周期性的年际变化特征;这些变化除了受水的滞留时间和细菌生长速度影响外,还可能受其他许多环境因子的影响.其中叶绿素a和水温变化的影响最大,其他环境因子如溶解氧、铵态氮、亚硝酸盐和硝酸盐以及病毒的丰度也有影响.近年来,基于群落水平的基因组学(genomics)和后基因组学(postgenomics)(转录组学和蛋白质组学)技术应用于研究自然条件下微生物群落错综复杂的基因多样性和表达,提供了揭示水环境中微生物群落组成和新功能基因的途径.     

Leaf-Associated Bacterial and Fungal Taxa Shifts in Response to Larvae of the Tree Hole Mosquito, <Emphasis Type="Italic">Ochlerotatus triseriatus</Emphasis>

Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system.