Epiphytic bacterial communities on two common submerged macrophytes in Taihu Lake: diversity and host-specificity

Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes: Vallisneria natans and Hydrilla verticillata in Taihu Lake, Jiangsu, China, using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes. The results show that: (1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria, and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria, including Burkholderiales, was the most abundant bacterial group on both plants. Cyanobacteria and Gammaproteobacteria were the second largest groups on V. natans and H. verticillata, respectively. Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations. Both ANOSIM of the T-RFLP data and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants. Therefore, the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific, which may aid in understanding the ecological functions of submerged macrophytes in general.     

Characterization of the bacterial communities associated with biofilters in two full-scale recirculating aquaculture systems

Bacteria play a major role in metabolizing ammonia and other metabolites in recirculating aquaculture systems(RASs). To characterize and compare the bacterial communities in the biofilters of two full-scale RASs for the culture of puffer fish, Takifugu rubripes, at different ages and densities were studied. In overall, 47 807 optimized reads of the 16 S rRNA gene with V4–V5 region were obtained from four biofilm samples collected after biofilm maturation. At 97% cut-off level, these sequences were clustered into 500 operational taxonomic units, and were classified into 19 bacterial phyla and 138 genera. At the phylum level, Proteobacteria and Bacteroidetes were the most abundant, followed by Nitrospirae and Planctomycetes. At the genus level, Colwellia, Marinifilum, Oceanospirillum, Lutibacter, Winogradskyella, Pseudoalteromonas, Arcobacter, and Phaeobacter were the top members. Nitrosomonas and Nitrospira were main ammonia-and nitrite-oxidizing bacteria. Differences in bacterial communities at different sampling dates and similarities of both biofilters were revealed in the Venn diagram and cluster analysis. Maintaining a good water quality and health offarmed fish in RASs depended on the correct management of the bacterial communities. This study provides more accurate information on the bacterial communities associated with the bifilters of both RASs.     

Characterization of dominant and cellulolytic bacterial communities along the gut of silver carp Hypophthalmichthys molitrix during cyanobacterial blooms

Silver carp is one of the most important planktivorous fish in Chinese aquaculture and plays a significant role controlling cyanobacterial blooms. A balanced gut microbiota is crucial for growth and health of the host because of its important roles in immune defense, digestion of complex carbohydrates, and production of enterocytes. In our study, the dominant bacterial and cellulolytic bacterial( Clostridium I, Clostridium III, Clostridium XIVab, and Fibrobacter) communities in the contents and mucus of the silver carp gut(foregut, midgut, and hindgut) were analyzed by denaturing gradient gel electrophoresis and quantitative polymerase chain reaction(q PCR) analyses. The results revealed that the dominant and cellulolytic bacterial communities were significantly different among gut regions as well as in contents and mucus. Bacterial diversity and richness in contents and mucus increased along the gut and were higher in contents than those in local mucus. A sequence analysis of gut samples exhibited the conservative phylotypes of Proteobacteria, Actinobacteria, and Firmicutes. The gut of silver carp harbored an abundance of cellulolytic bacteria, particularly Clostridium XIV ab. The foregut segment had the highest proportions of the four cellulolytic bacteria, followed by the midgut and hindgut. However, the proportions of cellulolytic species in the silver carp gut was much lower than those in the terrestrial vertebrate gastrointestinal tract. We conclude that gut bacteria could help silver carp obtain energy from cyanobacteria, which may be why silver carp can maintain high growth rates during cyanobacterial blooms.     

Impact of redox-stratification on the diversity and distribution of bacterial communities in sandy reef sediments in a microcosm

Relationships between microbial communities and geochemical environments are important in marine microbial ecology and biogeochemistry. Although biogeochemical redox stratification has been well documented in marine sediments, its impact on microbial communities remains largely unknown. In this study, we applied denaturing gradient gel electrophoresis (DGGE) and clone library construction to investigate the diversity and stratification of bacterial communities in redox-stratified sandy reef sediments in a microcosm. A total of 88 Operational Taxonomic Units (OTU) were identified from 16S rRNA clone libraries constructed from sandy reef sediments in a laboratory microcosm. They were members of nine phyla and three candidate divisions, including Proteobacteria (Alpha-, Beta-, Gamma-, Delta-, and Epsilonproteobacteria), Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, Verrucomicrobia, Spirochaetes, and the candidate divisions WS3, SO31 and AO19. The vast majority of these phylotypes are related to clone sequences from other marine sediments, but OTUs of Epsilonproteobacteria and WS3 are reported for the first time from permeable marine sediments. Several other OTUs are potential new bacterial phylotypes because of their low similarity with reference sequences. Results from the 16S rRNA, gene clone sequence analyses suggested that bacterial communities exhibit clear stratification across large redox gradients in these sediments, with the highest diversity found in the anoxic layer (15–25 mm) and the least diversity in the suboxic layer (3–5 mm). Analysis of the nosZ, and amoA gene libraries also indicated the stratification of denitrifiers and nitrifiers, with their highest diversity being in the anoxic and oxic sediment layers, respectively. These results indicated that redox-stratification can affect the distribution of bacterial communities in sandy reef sediments.     

Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats

The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.     

Sediment bacterial communities are more complex in coastal shallow straits than in oceanic deep straits

Straits are ideal models to investigate the bacterial community assembly in complex hydrological environments. However, few studies have focused on bacterial communities in them. Here, comparable bacterial communities in costal shallow Bohai Strait(BS) and oceanic deep Fram Strait(FS) were studied. The Shannon and Chao1 indices were both higher in BS than in FS. The relative abundances of the classes Deltaproteobacteria and Bacilli and the family Halieaceae were higher in BS than in FS, in contrast to the families OM1_clade and JTB255_marine_benthic_group, revealing typical characteristics of bacterial communities in coastal and oceanic regions. Cluster analysis based on the Bray-Curtis index showed that samples were clustered by depth layer in FS and BS, indicating that structures of bacterial communities would diff er with increasing water depth in straits. Additionally, the cluster relationships among samples in abundant and rare communities were both similar to those in entire communities. However, the dissimilarities among samples showed a descending order as rare communities, entire communities and abundant communities. Network analysis indicated that the BS network was obviously more complex than the FS network. Filamentous bacteria Desulfobulbaceae exhibited high degree values in BS but not in FS, indicating key roles of Desulfobulbaceae in the BS. Our study provides different and common evidences for understanding microbial ecology in coastal shallow and oceanic deep straits.     

Metagenomic approach revealed effects of forest thinning on bacterial communities in the forest soil of Mt. Janggunbong,South Korea

The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes. Human activity, particularly harvesting or thinning, affects the soil microbiome in forests by altering environmental conditions, such as vegetation, microclimate, and soil physicochemical properties. The purpose of this study was to investigate the effects on forest thinning on the diversity and composition of the soil bacterial community. From next-generation sequencing results of the 16S rRNA gene, we examined differences in soil bacterial diversity and community composition before and after thinning at Mt. Janggunbong, South Korea. We identified 40 phyla, 103 classes, 192 orders, 412 families, 947 genera, and 3,145 species from the soil samples. Acidobacteria and Proteobacteria were the most dominant bacterial phyla in the forest soil of Mt. Janggunbong. Soil bacterial diversity measures (richness, Shannon diversity index, and evenness) at the phylum level increased after thinning, whereas species-level taxonomic richness decreased after thinning. Thinning provided new opportunities for bacterial species in Chloroflexi, Verrucomicrobia, Nitrospirae, and other nondominant bacterial taxa, especially for those not found in Mt. Janggunbong before thinning, to settle and adapt to the changing environment. Our results suggested that thinning affected the diversity and composition of soil bacterial communities in forests and mountains.     

Variations of bacterial and fungal communities along a primary successional chronosequence in the Hailuogou glacier retreat area (Gongga Mountain,SW China)

New terrestrial habitats have emerged and a primary succession has developed in the retreat area(29°34'N, 102°00'E, 2951–2886 m) after the retreat of the Hailuogou glacier. To investigate soil microbial changes along the primary successional chronosequence, mixed soil samples were collected at six sites at different ages(2 young sites, 2 mid-aged sites, and 2 old sites). The RNA was extracted and amplified. Bacterial 16 S r RNA and fungal 18 S r RNA were analyzed using high-throughput 454 pyrosequencing analysis. Overall, pyrosequencing showed that Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria were the main bacterial phyla, and the fungal communities were strongly dominated by the phyla Ascomycota and Basidiomycota in the retreat area. The Shannon diversity index(Hshannon) of bacteria was 6.5 – 7.9, and that of fungi was 2.2 – 4.1 in these sites. For the bacterial communities, diversity and evenness values were highest on the mid-age sites and wererelatively low on the young and old sites. A similar trend was observed for the fungal communities. In contrast, soil properties showed significant linear distributional trends(increase or decrease) with the age of the site. Combining the linear change patterns of soil properties, the highest values of bacterial and fungal evenness and diversity in the mid-aged sites indicated that there was less environmental stress and more niches for microbial communities in the middle successional stage compare with other stages. In addition, our analysis showed that microbial communities were the main drivers that build a soil organic matter pool to expedite pedogenesis for ecosystem succession. This primary succession in the Hailuogou glacier retreat area is developing rapidly compared with that in other glacier retreats.     

珠江口盆地北部早—中中新世滨线迁移轨迹与沉积体系演化

根据三维地震和钻测井资料,研究珠江口盆地北部珠江组—韩江组层序划分及沉积演化特征,明确珠江口盆地北部早—中中新世沉积体系演化与海平面变化的关系;通过识别不同类型的前积倾斜层特征,分析早—中中新世滨线迁移趋势,建立滨线迁移轨迹与层序旋回及海平面变化的对应关系。结果表明:珠江口盆地北部陆架区早—中中新世珠江组—韩江组划分为2个二级层序(CS1和CS2)和8个三级层序(S1-S8),研究区识别5种前积倾斜层,并划分为上升海侵型、下降海退型和下降海侵型3种滨线迁移轨迹类型。珠江组沉积早期,陆架边缘三角洲体系自陆架边缘向陆地退积,逐渐演化为内陆架三角洲而形成上升海侵型滨线迁移轨迹;珠江组沉积晚期—韩江组沉积早期,三角洲体系开始向盆地方向推进,逐渐演化为外陆架三角洲体系,滨线迁移轨迹呈下降海退型;韩江组沉积晚期,三角洲体系再次后退至内陆架区而形成下降海侵型滨线迁移轨迹。研究区滨线迁移轨迹与区域性海平面变化具有良好的对应关系。该结果对研究区油气勘探具有指导意义。     

Quantitative division of succession and spatial patterns among different stand developmental stages in Changbai Mountains

Broadleaf-Korean pine forests exhibit high species richness and distinctive species composition, which are currently becoming more dominant among natural forests in Changbai Mountains of northeastern China. Understanding the ecological process of restored vegetation is quite important for ecosystem reconstruction. Distinguishing stand development stages and analyzing the dynamic spatial patterns could provide insights into significant community coexistence mechanisms. In the present study, eight permanent study areas were established according to the substituting space for time method in Changbai Mountains of north-eastern China. The optimal division method was used to quantify the successional series into different stand development stages, and the point pattern analysis method(L(r) function) was used to analyse the dynamic changes in spatial patterns and interspecific associations. Our results suggested that:(1) The stand development process was divided into five stages: the first three stages were poplar-birch secondary forests in different stages of recovery, the fourth stage was thespruce-fir mixed forest, and the last stage was the primary broadleaf-Korean pine forest;(2) The spatial pattern showed an aggregated distribution at a small scale and changed to a random distribution as the scale increased in poplar-birch secondary forests, but the spatial pattern appeared to be randomly distributed in spruce-fir mixed forest and broadleafKorean pine forest;(3) The interspecific associations between pioneer species and climax species changed from negative to positive among the different stand stages, and environmental resources were shared among these species. Interspecific differences in shade tolerance among the tree species were key determinants of forest dynamics and structure. Our study is vital to the understanding of the forest development; thus, the spatial change features should receive greater attention when forest management is being planned and restoration strategies are being developed for the Changbai Mountains.     

Acute toxicity and biodegradation of endosulfan by the polychaeta Perinereis aibuhitensis in an indoor culture

The polychaete Perinereis aibuhitensis, a key species in estuarine ecosystems, can improve the culture condition of sediment. Endosulfan is an organochlorine pesticide used globally to control insects and mites; however, it is a source of pollution in aquaculture as a result of runoff or accidental release. In this study, we evaluated the toxicity of endosulfan to polychaeta and its ability to improve polluted sediment. Specifically, the effects of a series of endosulfan concentrations (0, 1.25, 2.5, 5, 10, 15, and 20 mg/L) were investigated, and the results indicated that the 24-h median lethal concentration (24-h LC₅₀) was 55.57 mg/L, while the 48-h median lethal concentration (48-h LC₅₀) was 15.56 mg/L, and the safe concentration was about 1.556 mg/L. In a 30-d exposure experiment, the animal specimen could decompose endosulfan effectively while improving endosulfan-polluted aquatic sediment.     

DETERMINANTS OF STRUCTURE IN AQUATIC NON-PELAGIC PROTOZOAN COMMUNITIES

Although microbes have traditionally been used as models for testing ecological theory, research on the organization of these communities has largely been isolated from other areas of community ecology. Early studies indicated that microbial populations can form dynamic, interacting assemblages. Observations of distributional patterns suggest that certain deterministic forces regulate community structure. It appears that protozoans are tolerant of a wide range of environmental conditions although evidence for this is largely based on gross environmental analyses. Laboratory studies have suggested the importance of negative and positive biotic interactions in determining community membership, but little field evidence for this exists. The importance of transport processes in controlling community composition is being increasingly recognized. All three types of processes likely act to regulate the colonization and successional dynamics of these communities. A simple model is presented to promote the devel     

AMMONIUM UPTAKE AND REGENERATION FLUXES OF THE MICROPLANKTON COMMUNITIES IN JIAOZHOU BAY

The results from four cruises(Nov.1991—Jul.1992)to examine fluxes of ammonium uptake andregeneration in the surface layer of Jiaozhou Bay are presented.Seasonal variations of the two fluxeswere in the order:summer>spring>autumn>winter.Diel patterns were characterized by higher uptake inthe daytime and higher regeneration at night.Averaged uptake and regeneration fluxes on an annual scalewere 0.073 and 0.053 μmol·L~(-1)·h~(-1)respectively.Regeneration fluxes were always less than uptakefluxes throughout the year.The longest turnover time was 16.34 d(in winter),and the shortest one was0.68 d(in summer).The major uptake flux was contributed by the smallest fraction-picoplankton.Theextents of light-dependence of ammouium uptake by different size fractions were in the order:netplankton>nanoplankton>picoplankton..     

Dissolved organic matter and its role in red tide succession in the East China Sea in spring

Dissolved fluorescent organic matter was measured using fluorescence excitation-emission matrix spectroscopy at three temporal points during a Synechococcus bloom after diatom bloom dispersion in spring, 2007. Carbohydrate and dissolved organic carbon were also analyzed. The relationship between organic matter and red tide succession was examined. The results show that after the diatom bloom, tyrosine-like fluorescence B intensity was very high within the water column and exhibited a negative correlation wi...     

Net-phytoplankton communities in the Western Boundary Currents and their environmental correlations

This study investigated net-phytoplankton biomass, species composition, the phytoplankton abundance horizontal distribution, and the correlations between net-phytoplankton communities and mesoscale structure that were derived from the net samples taken from the Western Boundary Currents during summer, 2014. A total of 199 phytoplankton species belonging to 61 genera in four phyla were identified. The dominant species included C limacodium frauenfeldianum, Thalassiothrix longissima, Rhizosolenia styliformis var. styliformis, Pyrocystis noctiluca, Ceratium trichoceros, and Trichodesmium thiebautii. Four phytoplankton communities were divided by cluster analysis and the clusters were mainly associated with the North Equatorial Counter Current(NECC), the North Equatorial Current(NEC), the Subtropical Counter Current(STCC), and the Luzon Current(LC), respectively. The lowest phytoplankton cell abundance and the highest T richodesmium filament abundance were recorded in the STCC region. The principal component analysis showed that T. thiebautii preferred warm and nutrient poor water. There was also an increase in phytoplankton abundance and biomass near 5°N in the NECC region, where they benefit from upwellings and eddies.     

Characterization of bacterial communities associating with larval development of Yesso Scallop (<Emphasis Type="Italic">Patinopecten yessoensisis</Emphasis> Jay, 1857) by high-throughput sequencing

Bacterial community presumably plays an essential role in inhibiting pathogen colonization and maintaining the health of scallop larvae, but limiting data are available for Yesso scallop (Patinopecten yessoensisis Jay, 1857) larval development stages. The aim of this study was to characterize and compare the bacterial communities associating with Yesso scallop larval development at fertilized egg S1, trochophora S2, D-shaped larvae S3, umbo larvae S4, and juvenile scallop S5 stages by Illumina high-throughput sequencing. Genomic DNA was extracted from the larvae and their associating bactera, and a gene segment covering V3-V4 region of 16S rRNA gene was amplified and sequenced using an Illumina Miseq sequencer. Overall, 106760 qualified sequences with an average length of 449 bp were obtained. Sequences were compared with those retrieved from 16S rRNA gene databases, and 4 phyla, 7 classes, 15 orders, 21 families, 31 genera were identified. Proteobacteria was predominant phylum, accounting for more than 99%, at all 5 larval development stages. At genus level, Pseudomonas was dominant at stages S1 (80.60%), S2 (87.77%) and S5 (68.71%), followed by Photobacterium (17.06%) and Aeromonas (1.64%) at stage S1, Serratia (6.94%), Stenotrophomonas (3.08%) and Acinetobacter (1.2%) at stage S2, Shewanella (25.95%) and Pseudoalteromonas (4.57%) at stage S5. Moreover, genus Pseudoalteromonas became dominant at stages S3 (44.85%) and S4 (56.02%), followed by Photobacterium (29.82%), Pseudomonas (11.86%), Aliivibrio (8.60%) and Shewanella (3.39%) at stage S3, Pseudomonas (18.16%), Aliivibrio (14.29%), Shewanella (4.11%), Psychromonas (4.04%) and Psychrobacter (1.81%) at stage S4. From the results, we concluded that the bacterial community changed significantly at different development stages of Yesso Scallop larvae.     

Soil microbial population dynamics along a chronosequence of moist evergreen broad-leaved forest succession in southwestern China

Little is known about whether soil microbial population dynamics are correlated with forest succession.To test the hypotheses that(1) soil microbial composition changes over successional stages,and(2) soil microbial diversity is positively correlated with plant species diversity,we determined the soil microbial populations,community composition,and microflora diversity in evergreen broad-leaved forests along a chronosequence of vegetation succession from 5 to 300 years in southwestern China.The soil microbi...     

A taxonomical and ecological survey of rotiffer communities in Krottensee (Austria)

The composition and distribution of benthic, periphytic and planktonic rotifers in different habitats in Krottensee were investigated. Sixty-five rotifer taxa were identified, their relative abundance estimated. Classification of the data set by cluster analysis allowed the recognition of distinct habitat groups confined to acid bog ponds, macrophytes, sediments and open water. Five groups of rotifer taxa were identified on the basis of their habitat preferences and the occurrence of the taxa. Highest diversities were found on macrophytes and in acid bog ponds.