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.     

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.     

东、黄海鲐鱼群体遗传差异的RAPD分析

利用随机扩增多态DNA(RAPD)技术分别分析了五岛西部日本鲐、东海西部日本鲐和澳洲鲐三群体的样本,共产生226个分子标记,其中143个为多态性标记,多态百分率达到63.3%,每条引物产生的平均标记数为7.29。五岛西部日本鲐、东海西部日本鲐和澳洲鲐群体内遗传相似度分别为0.949、0.877和0.936,而群体间遗传距离依次为:五岛西部日本鲐-东海西部日本鲐(0.2357)<东海西部日本鲐-澳洲鲐(0.3030)<五岛西部日本鲐-澳洲鲐(0.3528),五岛西部日本鲐与东海西部日本鲐个体在UPGMA系统树独立聚类为两个类群,初步支持东、黄海的日本鲐存在东海西部和五岛西部的两个种群的观点。Shannon多样性指数表明,其遗传多样性大小依次为东海西部日本鲐、澳洲鲐、五岛西部日本鲐。     

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.     

Drivers of coastal bacterioplankton community diversity and structure along a nutrient gradient in the East China Sea

Anthropogenic nutrient discharge poses widespread threats to coastal ecosystems and has increased environmental gradients from coast to sea. Bacterioplankton play crucial roles in coastal biogeochemical cycling, and a variety of factors af fect bacterial community diversity and structure. We used 16 S r RNA gene pyrosequencing to investigate the spatial variation in bacterial community composition(BCC) across five sites on a coast-of fshore gradient in the East China Sea. Overall, bacterial alpha-diversity did not diff er across sites, except that richness and phylogenetic diversity were lower in the of fshore sites, and the highest alpha-diversity was found in the most landward site, with Chl-abeing the main factor. BCCs generally clustered into coastal and of fshore groups. Chl-a explained 12.3% of the variation in BCCs, more than that explained by either the physicochemical(5.7%) or spatial(8.5%) variables. Nutrients(particularly nitrate and phosphate), along with phytoplankton abundance, were more important than other physicochemical factors, co-explaining 20.0% of the variation in BCCs. Additionally, a series of discriminant families(primarily affiliated with Gammaproteobacteria and Alphaproteobacteria), whose relative abundances correlated with Chl-a, DIN, and phosphate concentrations, were identified, implying their potential to indicate phytoplankton blooms and nutrient enrichment in this marine ecosystem. This study provides insight into bacterioplankton response patterns along a coast-of fshore gradient, with phytoplankton abundance increasing in the of fshore sites. Time-series sampling across multiple transects should be performed to determine the seasonal and spatial patterns in bacterial diversity and community structure along this gradient.     

Characters of the Pco2 and CO2 Flux in the East China Sea in Autumn

Pco2 of air and seawater samples from the East China Sea(ECS) were measured in situ in autumn, 1994,Ocean currents,terrestrial fluviation,biological activities,etc.,Pco2 char-acters in air and seawater were investigated,CO2 flux and its character in the East China Sea are discussed on the basis of the Pco2 profiles of air and seawater,It was clear that the nearshore was the source of CO2;and tht the oulter sea area was the sink of CO2; and that the shelf area of the EXS is a net sink for atmospheric CO2 in autumn.     

Population genetic structure of the mantis shrimp Oratosquilla oratoria(Crustacea: Squillidae) in the Yellow Sea and East China Sea

The mantis shrimp O ratosquilla oratoria is an ecologically and economically important species in the Western Pacific. In present study, the population genetic structure of O ratosquilla oratoria from the Yellow Sea and East China Sea was examined with mitochondrial DNA control region sequences. In total, 394 samples were collected from 18 locations and 102 haplotypes were obtained. For the Yellow Sea, the overall nucleotide diversity and haplotype diversity were 0.006 9 and 0.946 8, respectively; while across all the East China Sea locations, the overall nucleotide diversity and haplotype diversity were 0.027 94 and 0.979 0, respectively. The results of AMOVA and pairwise F_(ST)(0.145 2, P 0.001) revealed moderate differentiation between the Yellow Sea and East China Sea populations of O. oratoria. However, neither the neighbor-joining tree nor haplotype network showed clades with geographic pattern, which indicated considerable gene flow was existed between the Yellow Sea and East China Sea, and supporting the high larval dispersal ability in this species. Mismatch distribution analysis and neutrality tests suggested that O. oratoria has undergone population expansion event, and the Pleistocene glacial cycles might have an impact on the historical demography of O. oratoria. The genetic information obtained in this study can provide useful information for sustainable improvements for capture fisheries management strategies.     

On the deep sea demersal fish communities of the East China Sea

Cluster analysis of data on the species similarity index offish samples taken at various sampling stations of different depths by the R /V " Dongfang " of the East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Science, during the deep sea demersal fish resources survey in May - November, 1981, showed deep sea demersal fish fauna of the western part of the East China Sea can be grouped into the following communities :1)The outer continental shelf community ,2)The continental slope community, and3)The western Okinawa Trough community .The authors found that not only the species diversity index, but also the species similarity index are important criteria to reflect the structure of biotic community.     

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.     

Chemical hydrography of coastal upwelling in the East China Sea

Based on the field data obtained during cruises on the shelf of the East China Sea from 1997 to 1999, seasonal variations of coastal upwelling on the inner shelf are discussed by using cross-shelf transect profiles and horizontal distributions of chemical and hydrographic variables. Results show that the coastal upwelling was year-round, but the areas and intensities of the upwelling were quite different in season. The coastal upwelling occurred in all of the coastal areas of the region in spring and summer, but in autumn only in the area off Zhejiang Province, and in winter in the area off Fujian Prov- ince. It was the strongest in summer and the weakest in winter. Geographically, it was the strongest in the area off Zhejiang Province and the weakest in the southmost or northmost parts of the East China Sea. The estimated nutrient fluxes upward into euphotic zone through coastal upwelling were quite large, es- pecially for phosphate, which contributed significantly to primary production and improved the nutrient structure of the coastal ecosystem in the East China Sea.     

Sedimentary response to volcanic activity in the Okinawa Trough since the last deglaciation

To investigate the relationship between volcanic activity and sediment record on regional and temporal scales,158 surface sediment samples were collected from the East China Sea Shelf to the northern Okinawa Trough (OT),and two cores recovered in the northern and southern OT,respectively.Mineralogy,grain-size,and geochemical analyses of those samples show that:1) volcanic glass,volcanic-type pyroxene,hypersthenes,and magnetite increase in sediment influenced by volcanic activity;2) sediment grain sizes (and...     

Benthic nutrient recycling in shallow coastal waters of the Bohai Sea

Sediment-water fluxes of N and P species in the Bohai Sea were investigated in September-October 1998 and April-May 1999. The benthic fluxes of nutrient species were determined by incubating sediment core samples with bottom seawater bubbled with air or nitrogen. NO^-2,NH4, dissolved organic nitrogen (DON) and phosphorus (DOP), total dissolved nitrogen (TDN) and phosphorus (TDP), and PO4^3- showed a net exchange flux from seawater to sediment, while NO^-3, dissolved inorganic nitrogen (DIN) and SiO3^2- were released from sediment to seawater in the Bohai Sea. Sediment-water nutrient exchange increases DIN and reduces the phosphorus load in the Bohai Sea. The release of silicate from sediment to overlying seawater reduces potential silicate limitation of primary production resulted from decrease of riverine discharge.The exchange flux of nutrients showed no obvious seasonal variation. The present study showed that the concentrations and composition of nutrients in the water column were affected by suspended sediment, and that not all the exchangeable phosphate in sediment could be released via sediment resuspension.     

Characteristics of Vertical Distributions of Fatty Acids in Surface Sediments of the Yellow Sea and East China Sea

Fatty acids(FAs) in sediment collected from three different stations in the Yellow Sea and the East China Sea were analyzed for their distributions and to determine evidence of harmful algal blooms in the sediment core.Less diverse FAs were found in the Yellow Sea(YS) station,whereas in the two stations of the East China Sea(ECS) the FAs were more diverse.Concentrations of some FA species in the two ECS stations displayed an occasional surge in their vertical profile.The highest concentration of FAs was found in the surface layer of station QT3(43.28 μg g~(-1)).Monounsaturated FAs were more susceptible to degradation compared to their saturated counterparts,and changes of 16:0,18:2 and 20:5 accounted for the most variability in total concentrations of FAs as those species made up most of the quantified FAs.The origins of the major fraction of FAs were attributed to autotrophic sources,and bacterial FAs accounted for only a small fraction of the total FAs in the region.Nutrient availability was a possible regulating factor controlling bacteria abundances in marine sediments in the ECS and the YS.A principal component analysis(PCA) was applied to analyze the FA dataset and to reveal the principal environmental factors that control the composition of FAs in the sediments.PC2,which explains 15% of the variance,was estimated to reflect the diagenetic effects on the FA compositional changes in sediments influenced by bacterial degradation.     

Seasonal distribution of macrobenthos and its relationship with environmental factors in Yellow Sea and East China Sea

Macrobenthos samples were collected from the Yellow and East China Seas in four seasons during 2011 to 2012. The seasonal distribution of macrobenthos and its relationship with environmental factors were analyzed. A total of 562 macrobenthic species were identified, with polychaetes and mollusks accounting for 67% of the total number of species. A similarity percentage(SIMPER) analysis showed that the dominant species were bivalve mollusks in the Yellow Sea and small-sized polychaetes in the East China Sea. A two-factor analysis of variance showed significant seasonal variations in species number, density and diversity index, and significant regional differences of biomass and density. Two-factor community similarity analysis also showed significant seasonal and regional differences in macrobenthic communities. Canonical correspondence analysis indicated that the main environmental factors af fecting the macrobenthic communities were water depth, temperature, dissolved oxygen, and inorganic nitrogen. The results demonstrate significant regional differences and seasonal variations in macrobenthos in the two seas. Sediment properties and water mass characteristics are speculated to be the causes of regional differences.     

Stratigraphic Division Based on Minor Elements in the Sediment Core Q43 from the Outer Shelf of the East China Sea： Approached Through Correspondence Analysis and Fuzzy Cluster Analysis

The multivariate statistical techniques, principal component analysis, Q-mode factor analysis, correspondence analysis and fuzzy C-means clustering were applied to analyzing the datasets of minor element concentrations in sediment samples of a core collected from the outer shelf of the East China Sea. According to the analysis results, the sediment core Q43 can be divided into three strata with different features in minor elements. The first stratum (unit Ⅰ) is characterized by higher concentrations of V, Cr, Cd and Sc, which are active and inactive elements. The second stratum (unit Ⅱ) is controlled by ultrastable elements V, Ti, Cr, Th, Sc, Pb, etc. The third stratum (unit Ⅲ) is dominated by Ni, Co, Ba, Rb and Mn, which are authigenic and volcanogenic elements. The geochemical features of the core Q43 show environmental changes in the depositional process from the Late Pleistocene to Holocene.     

Molecular analyses of bacterioplankton communities with highly abundant Vibrio clades: a case study in Bohai Sea coastal waters

We investigated the bacterioplankton abundance,community composition and the associated Vibrio clades of natural seawater in Bohai Sea coastal waters.Seawater samples(10 L in triplicate)were collected at 0.5,3,and 5 m depths near the coastal aquaculture zone of the Bohai Sea on May 12,2016.Real-time PCR and 16 S rRNA gene amplicon high-throughput sequencing methods were employed by which 485 operational taxonomic units(OTUs)at a 97% sequence similarity level were generated.Gammaproteobacteria,Alphaproteobacteria,and Bacteroidetes were the most abundant groups,accounting for 49.5%,23.5%,and 18.9% ofthe total assemblage,respectively.Obvious variations in Pseudoalteromonas,Vibrio,and Octadecabacter,which were the most abundant genera,could be observed among different samples.Notably,the results of Vibrio-specific real-time PCR indicated that Vibrio had extremely high 16 S rRNA gene copy numbers.The 16 S rRNA gene sequencing results across all the samples also indicated that they occupied a large proportion of the total assemblage.Both the alpha diversity and major bacterioplankton group Pseudoalteromonas had significant correlations with the concentration of PO43-.Overall,studies on bacterioplankton communities with highly abundant Vibrio clades can provide interesting insight into the microbial function and health assessment of the Bohai Sea coastal ecosystem.     

Fish community diversity in the middle continental shelf of the East China Sea

The status of fishery stocks in the coastal waters of China is far from ideal, mainly due to climate change and the impacts of human activities (e.g., pollution and overfishing). Thus, the restoration and protection of fishery resources have become critical and complex. The stability and balanced structure of the fish community is a basic foundation for the protection of fishery resources. Based on data collected from bottom trawls by the R/V Beidou in continental shelf of the East China Sea in November 2006 and February 2007, changes in the composition and diversity of fish species and functional groups were analyzed. The research area was divided into offshore waters and inshore waters by the two-way indicator species analysis (TWIA). The results showed that the dominant species were different between offshore waters and inshore waters and also varied with the survey time. The most abundant family was Sciaenidae and Teraponidae in November 2006, Sciaenidae, Engraulidae and Triglidae were most abundant in February 2007. The species belonged mainly to mobile piscivores (G6), benthivores/piscivores (G4), benthivores (G3) and planktivores (G1), and the dominant species in November 2006 were commercial species (e.g. Larimichthys polyactis and Trichiurus japonicus), but small-sized species were dominant in February 2007 (e.g., Harpadon nehereus, Benthosema pterotum, Champsodon capensis, and Acropoma japonicum). The species diversity showed a similar trend as the functional group diversity. Stations with higher diversity were mainly distributed in inshore waters in February 2007, whereas higher diversity was found in offshore waters in November 2006. The highest biomass and species number were found in G6 group, followed by the G4, G5 and G1 groups. The distribution of the number of individuals of each functional group showed the opposite trend as that of the biomass distribution. In addition, the size spectra were mainly concentrated around 3–29 cm, and the individual number of fish species gradually decreased with the increase in body size, but the relative biomass showed a moderate fluctuation in each size class. These changes showed that species with faster growth rate and earlier maturity age became dominant in continental shelf of the East China Sea. So the variations in biological characteristics of fish should be fully considered in maintaining sustainable utilization of fishery resource.     

Microbial diversity in Huguangyan Maar Lake of China revealed by high-throughput sequencing

Huguangyan Maar Lake is a typical maar lake in the southeast of China.It is well preserved and not disturbed by anthropogenic activities.In this study,microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method.We found significant differences between the microbial community compositions of the water and the sediment.The sediment samples contained more diverse Bacteria and Archaea than did the water samples.Actinobacteria,Betaproteobacteria,Cyanobacteria,and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria,Anaerolineae,Nitrospira,and Dehalococcoidia were the major bacterial groups in the sediment.As for Archaea,Woesearchaeota(DHVEG-6),unclassified Archaea,and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water,whereas the Miscellaneous Crenarchaeotic Group,Thermoplasmata,and Methanomicrobia were significantly more abundant in the sediment.Interactions between Bacteria and Archaea were common in both the water column and the sediment.The concentrations of major nutrients(NO_3~-,PO_4~(3-),SiO_3~(2-)and NH_4~+)shaped the microbial population structures in the water.At the higher phylogenetic levels including phylum and class,many of the dominant groups were those that were also abundant in other lakes;however,novel microbial populations(unclassified)were often seen at the lower phylogenetic levels.Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.     

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.     

Study on the seasonal variation of the suspended sediment distribution and transportation in the East China Seas based on SeaWiFS data

The monthly mean suspended sediment concentration in the upper layer of the East China Seas was derived from theretrieval of the monthly binned SeaWiFS Level 3 data during 1998 to 2006.The seasonal variation and spatial distribution of thesuspended sediment concentration in the study area were investigated.It was found that the suspended sediment distribution presentsapparent spatial characteristics and seasonal variations,which are mainly affected by the resuspension and transportation of the sus-pended sediment in the study area.The concentration of suspended sediment is high inshore and low offshore,and river mouths aregenerally high concentration areas.The suspended sediment covers a much wider area in winter than in summer,and for the samesite the concentration is generally higher in winter.In the Yellow and East China Seas the suspended sediment spreads farther to theopen sea in winter than in summer,and May and October are the transitional periods of the extension.Winds,waves,currents,ther-mocline,halocline,pycnocline as well as bottom sediment feature and distribution in the study area are important influencing factorsfor the distribution pattern.If the 10mg L-1 contour line is taken as an indicator,it appears that the transportation of suspended sedi-ment can hardly reach 124°00'E in summer or 126°00'E in winter,which is due to the obstruction of the Taiwan Warm Current andthe Kuroshio Current in the southern Yellow Sea and the East China Sea.