Bacterial community shifts in different functional zones of a reservoir with ecological purification facilities

Ecological purification in a reservoir is an important strategy to control the level of nutrients in water.The bacterial community of such a reservoir is the main agent for pollutant degradation,which has not been fully documented.Taking the Jinze Reservoir,a freshwater source for Shanghai,China as the case,its spatial distributions of water and sediment bacteria were determined using 16 S rRNA gene-based Illumina MiSeq sequencing,and the environmental parameters were analyzed.The reservoir takes natural river water and functions as an ecological purification system,consisting of three functional zones,i.e.,pretreatment zone,ecological purification zone,and ecological sustaining zone.Results show that the concentrations of both total nitrogen(TN) and total phosphorus(TP) decreased considerably after the ecological treatment,and the concentration of dissolved oxygen(DO) in the ecological purification zone was boosted from that before pretreatment.In addition,patterns of bacterial communities in both water and sediment were similar and consisted of mainly Proteobacteria,Actinobacteria,and Bacteroidetes.However,difference in water bacterial composition was distinct in each functional zone,whereas the bacterial communities in sediment changed only slightly among sediment samples.Network analysis revealed nonrandom co-occurrence patterns of bacterial community composition in water and sediment,and Pseudomonas,unclassified Comamonadaceae,Variovorax,and Dechloromonas were the key taxa in the co-occurrence network.The bacterial taxa from the same module of the network had strong ecological connections,participated in C-cycles,and shared common trophic properties.PICRUSt analysis showed that bacteria were involved potentially in various essential processes;and the abundance of predicted xenobiotic biodegradation genes showed a decreasing trend in water samples from the inlet to the outlet of the reservoir.These results improve our current knowledge of the spatial distribution of bacteria in water and sediment in ecological purification reservoirs.     

Characterization of microbial communities in sediments of the South Yellow Sea

Illumina sequencing and quantitative PCR(qPCR) based on the 16 S ribosomal RNA(rRNA) gene were conducted to characterize the vertical distribution of bacterial and archaeal communities in the sediments of two sites from the South Yellow Sea. Both bacterial and archaeal communities showed a clear stratified distribution with sediment depth. The microbial communities in the upper layers were distinct from those in the deeper layers; the relative abundances of sequences of Thaumarchaeota, Gammaproteobacteria, and Actinobacteria were higher in the upper than in the deeper sediments, whereas the sequences of Bathyarchaeia, Lokiarchaeota, Euryarchaeota, Chloroflexi, and Deltaproteobacteria were relatively more abundant in the deeper sediments. Sediment depth and total organic carbon(TOC) can significantly influence both the bacterial and archaeal communities. Furthermore, bacterial and archaeal groups potentially involved in nitrogen, sulfur, and methane metabolism were detected in both sites. In our study, both ammonia-oxidizing bacteria( Nitrospira) and ammonia-oxidizing archaea( Candidatus Nitrosopumilus) were responsible for ammonia oxidization. Additionally, sulfur-reducing bacteria SEEP-SRB1 forming consortia with anaerobic methane-oxidizing archaea ANME-2 a-2 b were capable of anaerobic methane oxidation(AOM) in the 3400-02 sediment samples.     

Bacterial diversity, composition and temporal-spatial variation in the sediment of Jiaozhou Bay, China

Studies on the diversity and distribution of bacterial populations will improve the overall understanding of the global patterns of marine bacteria and help to comprehend local biochemical processes and environments. We evaluated the composition and the dynamics of bacterial communities in the sediment of Jiaozhou Bay (China) using PCR-denaturing gradient gel electrophoresis (DGGE). Sediment samples were collected from 10 different sites in May, August, and November 2008 and in February 2009. There was significant temporal variation in bacterial community composition at all sites. However, the spatial variation was very small. The DGGE analyses of bacterial communities were used to divide the 10 stations into three types. Canonical correspondence analysis (CCA) revealed that the changes in bacterial communities were driven by sediment properties. Sequence analysis of DGGE band-derived 16S rRNA gene fragments revealed that the dominant bacterial groups in the sediment were of the classes γ-proteobacteria and δ-proteobacteria and phyla Bacteroidetes and Nitrospirae. Our results provide considerable insight into the bacterial community structure in Jiaozhou Bay, China.     

Methods used to study bacterial diversity in the marine environment around Qingdao

Pollution has a considerable effect on biological communities, in terms of size and diversity of the populations. Yet, the precise consequences of human activity on microbial communities in the marine environment are poorly understood. Therefore, in an ongoing collaborative research programme between Heriot-Watt University and the Ocean University of Qingdao, bacteria were isolated in 1999 and 2000 from marine sediment, seawater, seaweed, fish and shellfish, taken from locations in Shandong Province adjacent to Qingdao. Sampling locations were comprised of industrial and aquacultural sites and a clean, control site. In order to analyse microbial diversity, a polyphasic approach was adopted for characterisation of these isolates, specifically through examination of key phenotypic traits, i.e. using Biolog GN MicroPlate^™ profiles, bacterial whole cell protein profiles and 16S and 23S rRNA gene sequences. These techniques yielded complex taxonomic data, which were subjected to statistical and cluster analyses. The application of these methods to studies of microbial communities is discussed.     

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.     

Response of microbial community to petroleum stress and phosphate dosage in sediments of Jiaozhou Bay,China

The dynamic microcosms were used to evaluate the effect of oil spills on microbial ecological system in marine sediment and the enhancement of nutrient on the oil removal. The function and structure of microbial community caused by the oil pollution and phosphate dosage were simultaneously monitored by dehydrogenase activity assay and PCR-denaturing gradient gel electrophoresis (DGGE) techniques. The results indicated that the amount of total bacteria in all dynamic microcosms declined rapidly with incubation time. The number of petroleum-degrading bacteria and the activity of sediment dehydrogenase were gradually enhanced by petroleum in the oil-treated microcosms, while they both showed no obvious response to phosphate dosage. In comparison, phosphate spiked heterotrophic bacteria and they showed a significant increase in amount. DGGE profiles indicated that petroleum dosage greatly changed community structure, and the bacteria belonged to class Deltaproteobacteria, and phyla Bacteroidetes and Chlorobi were enriched. This study demonstrated that petroleum input greatly impacted the microbial community structure and consequently the marine sediment petroleum-degrading activity was enhanced. Phosphate dosage would multiply heterotrophic bacteria but not significantly enhance the petroleum degradation.     

Shifts of sediment bacterial community and respiration along a successional gradient in a typical karst plateau lake wetland(China)

Bacteria are important regulators of carbon cycling in lakes and are central to sediment ecosystem processes. However, the sediment microbial communities and their respiratory responses to the lake wetland succession are poorly understood. In this study, we collected sediment samples from four different succession points(the Potamogeton lucens zone, the Scirpus tabernaemontani zone, the Scirpus triqueter zone, and the Juncus effusus zone) in the Caohai Wetland of the Guizhou Plateau(China). The bacterial communities at these succession points were studied using a high-throughput sequencing approach. The sediment microbial respiration(SR) was measured using static chambers in the field and basal respiration(BR) was determined in the laboratory. The results show that the dominant bacterial taxa in the sediment was Proteobacteria(34.7%), Chloroflexi(17.8%), Bacteroidetes(7.3%), Acidobacteria(6.6%), and Cyanobacteria(6.1%). Principal coordinate analysis showed that the microbial community structure differs significantly at different sampling points along the successional gradient, indicating that the bacterial community structure is sensitive to the lake wetland succession. Different hydrological regimes and soil characteristics such as NH_4~+-N, Fe~(2+), Mn~(2+), and sediment organic carbon(SOC) content may be important factors responsible for the differences in the sediment microbial characteristics of the different successional stages in the Caohai wetland. Additionally, it was found that the SR increased significantly from the P. lucens zone to the J. effusus zone, but BR had the opposite response. The shifts in the bacterial community structure along the successional gradient may be the main reason for the observed differences in sediment respiration.     

Microbial ecological associations in the surface sediments of Bohai Strait

Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China(average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational dif ference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.     

Structure and diversity dynamics of microbial communities at day and night: investigation of meromictic Lake Doroninskoe,Transbaikalia, Russia

Extreme environmental conditions are key factors in the formation of the structure and diversity of microbial communities. In meromictic ecosystems, extreme conditions and a stable stratification of physical, chemical and biological parameters lead to diversity and heterogeneity of microenvironments. Lake Doroninskoe is located in an extreme geographical area and diff ers from other known meromictic reservoirs of the world by a low level of illumination in the chemocline and a rare type of alkaline water in sedimentary rocks formed by evaporative concentration. To understand the key factors that shape the composition and structure of the microbial community, the macro-and micro-variations in space and time are of great importance. We investigated the short-term dynamics of the structure and diversity of microbial communities of the meromictic soda lake, Lake Doroninskoe, at day and night using highthroughput sequencing and bioinformatics. Metagenomic analysis of 16 S rRNA gene amplicons showed that the microbial communities had a high taxonomic diversity both at day and night. Sixteen bacterial and three archaeal phyla were identified. Proteobacteria were dominant and comprised 75% during the day, increasing to 90% at night. Metabolically stable denitrifying bacteria that were able to use a variety of alternative electron acceptors and electron donors were prevalent in Lake Doroninskoe. They belonged to the families Enterobacteriaceae(class Gammaproteobacteria) and Alcaligenaceae(class Betaproteobacteria). Statistically significant differences between day and night microbial communities were found. During the day, the microbial community was the most diverse. We discuss the peculiarities of the underexplored shortterm dynamics of the structure and diversity of the microbial communities of the meromictic soda Lake Doroninskoe, and propose topics for prospective studies.     

Bacterial communities fluctuate in abundance and diversity under simulated oil-contaminated seawater conditions

Marine bacteria have recently been identified as a potent solution for petroleum hydrocarbon degradation in response to hazardous oceanic oil spills. In this study, a mesocosm experiment simulating a petroleum spill event was performed to investigate changes in the abundance, structure, and productivity of bacterial communities in response to oil pollution. Cultured heterotrophic bacteria and total bacteria showed a consistent trend involving an immediate decrease in abundance, followed by a slight increase, and a steady low-level thereafter. However, the changing trend of bacterial productivity based on bacterial biomass and bacterial volume showed the opposite trend. In addition, the density of oil-degrading bacteria increased initially, then subsequently declined. The change in the bacterial community structure at day 0 and day 28 were also analyzed by amplified ribosomal DNA restriction analysis(ARDRA), which indicated that the species diversity of the bacterial community changed greatly after oil pollution. Alphaproteobacteria(40.98%)replaced Epsilonproteobacteria(51.10%) as the most abundant class, and Gammaproteobacteria(38.80%)became the second most dominant class in the whole bacterial community. The bacterial communities in oil-contaminated seawater(32 genera) became much more complex than those found in the natural seawater sample(16 genera). The proportion of petroleum-degrading bacteria in the oil-contaminated seawater also increased. In this study, culture-dependent and culture-independent approaches were combined to elucidate changes in both bacterial productivity and community structure. These findings will contribute to a better understanding of the role that bacteria play in material cycling and degradation in response to oil pollution.     

Temporal and spatial variations of bacterial community compositions in two estuaries of Chaohu Lake

The distinctive estuary hydrodynamics and nutrient input make the estuary ecosystem play a key role in lake ecosystems. The Nanfei River and Zhaohe River are two main inlets of Chaohu Lake, Anhui, East China. We selected estuaries of the two rivers as representative areas to study temporal and spatial changes of bacterial communities. In August (summer) and November (autumn) 2016 and February (winter) and May (spring) 2017, 16 water and sediment samples were collected from the estuaries. Physicochemical characteristics indicate significant differences in the nutritional status and eutrophication index of the estuaries due mainly to organic input. Examination of the number of operational taxonomic units, the diversity index, the community composition, and redundancy analysis revealed the following. First, the existence of varying degrees of seasonal differences in the distribution of almost all bacteria. In addition, the species diversity in the sediment samples was higher than that in the water samples, and the dominant species differed also among these samples. Second, a large number of unknown genera were detected, especially in the sediment samples, such as unclassified Xanthomonadales incertae sedis, unclassified Anaerolineaceae, and unclassified Alcaligenaceae. Last, TP, TN, and TOC were the main influential factors that affected the bacterial community structure.     

Spatial variations of bacterial community composition in sediments of the Jiaozhou Bay,China

Spatial variations of sediment microbes pose a great challenge for the estimation of anthropogenic influence on biogeochemical processes, yet remain very unclear in coastal ecosystems. Surface sediments in 9 stations from the eutrophic Jiaozhou Bay, China, were sampled, DNA was extracted within the sediments, and the 16 S rDNA was sequenced with the Illumina Hiseq sequencing. Results reveal considerable heterogeneity of sediment bacteria in the Jiaozhou Bay, of which Proteobacteria and Bacteroidetes accounted for over 75%. Bacterial alpha-diversity indices decreased generally from the outside to the inner part of the bay and from the offshore to the nearshore area. Bacterial community structures of S3, S4, S7, and S8 clustered, those of S5, S13, and S14 grouped together, while those of S6 and S10 were distinct from each other and from those of the other stations. Major class Gammaproteobacteria were more abundant at the stations with mesoeutrophic to eutrophic levels(S4, S5, S8, and S10) and less abundant at oligotrophic stations(S6, S13, and S14), while Deltaproteobacteria had an opposite distribution pattern. Overall, bacterial community composition transitioned from being Xanthomonadales-dominant at S4 and S8 to being unidentifed_Gammaproteobacteria-dominant at S5, S6, S13, and S14, while in other stations there were comparable orders. The biogeochemical processes correspondingly changed from being nitrogen cycling-dominant at S4 and S8 to being sulfur cycling-dominant at S5, S6, S13, and S14. The bacterial distribution patterns were especially affected by the factors(dissolved organic phosphorus, DOP) in the overlying seawater due to the habitat status of P-insu fficiency in the bay. Both orders Xanthomonadales and Alteromonadales could serve as bioindicators of anthropogenic pollution to different pollution types. At last, divergent distribution patterns of individual bacterial populations in the bay were revealed, the influential environmental gradients were clarified, and the uncertainty of microbes was reduced, helping to predict environmental functions in coastal areas.     

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.     

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.     

Microbial diversity in the sediments of the southern Mariana Trench

Microbial diversity in the abyssal sediments beneath the seafloor of 30, 94, and 151 cm near the southern end of the Mariana Trench was analyzed in the Illumina HiSeq 2500 platform. Results show that the microbial populations were dominated by bacteria but merely no archaea were identified at the three depths. In the bacterial community,Proteobacteria and Firmicutes dominated the total taxon tags, followed by Bacteroidetes, Actinobacteria, Planctomycetes, Cyanobacteria, and Chloroflexi, which together account for over 99% of the total population. Similar to that in the seawater in the trench, the operational taxonomic units(OTUs) belonging to Gammaproteobacteria from the sediment samples showed high abundance.However, common bacterial OTUs in the water of the trench including Nitrospirae and Marinimicrobia were hardly found in the sediments from the southern Mariana Trench or the hadal region. Therefore, this study documented for the first time the compositions of microbial diversity in the trench sediments, revealed the difference in microbial diversity in water and sediment of the trench and will enrich the knowledge on the microbial diversity in the abyssal areas.     

湛江高桥红树林区虾类群落的时空变化

研究2005-2008年广东省湛江市英罗湾高桥3个红树林区(红坎、两头流、西村)虾类群落的变化特征,并分析虾类群落组成与水质指标(盐度,pH)和沉积物指标(pH、可溶性盐、有机质、黏土、粉砂、砂砾)的相关性。结果表明:3个区域捕获虾类13596尾,属3科5属9种,刀额新对虾是高桥虾类的优势种;虾类种类年际变化较大,年间相似度平均为70.4,区域间相似度平均为60.6;红坎虾类多样性较丰富,两头流虾类的优势种明显,各年优势度指数均达0.95以上;3个区域的主要生态因子年间差异不显著(P>0.05);红坎3个采样点的底质性状较复杂,其沉积物特性差异显著(P<0.05),两头流和西村的底质性状较为单一,其沉积物特性均差异不显著(P>0.05)。群落变化特征和沉积物性状有显著相关关系,表明高桥虾类的渔获量受人为因素影响,多样性和分布受环境影响。     

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.     

Analysis of petroleum hydrocarbons in mangrove sediments of Red Sea of Yemen

A field work has been carried out to identify the occurrence of oil and oil products pollution in mangrove sediment from Red Sea of Yemen. The concentration of total petroleum hydrocarbons is from 700 ng/g at Kamaran Island station to 400 ng/g at Al-Hodiedah station, and the total organic carbon ( TOC) in samples ranges from 0.07% at Dhubab station to 0.03% at Kamaran Island station. This pollution is as a result of localized oil pollution and /or heavy ship traffic in the Red Sea and Gulf of Aden.     

Analysis of petroleum hydrocarbons in mangrove sediments of Red Sea of Yemen

A field work has been carried out to identify the occurrence of oil and oil products pollution in mangrove sediment from Red Sea of Yemen. The concentration of total petroleum hydrocarbons is from 700ng/g at Kamaran Island station to 400 ng/g at Al-Hodiedah station, and the total organic carbon （TOC） in samples ranges from 0. 07% at Dhubab station to 0. 03% at Kamaran Island station. This pollution is as a result of localized oil pollution and/or heavy ship traffic in the Red Sea and Gulf of Aden.