北极海洋沉积物细菌和古菌群落结构分析

This study was to investigate bacterial and archaeal community structure of pan-Arctic Ocean sediments by pyrosequencing.In total,investigation of three marine sediments revealed 15 002 bacterial and 4 362 archaeal operational taxonomic units(OTUs) at the 97% similarity level.Analysis of community structure indicated that these three samples had high bacterial and archaeal diversity.The most relatively abundant bacterial group in Samples CC1 and R05 was Proteobacteria,while Firmicutes was dominant in Sample BL03.Thaumarchaeota was the most relatively abundant archaeal phylum in Samples CC1 and R05,and the relative abundance of Thaumarchaeota was almost as high as that of Euryarchaeota in Sample BL03.These two phyla accounted for nearly 100% of the archaeal OTUs.δ-Proteobacteria and γ-Proteobacteria were the two most relatively abundant classes at Proteobacterial class level,and their relative abundance was more than 60% in Samples CC1 and R05.There were also differences in the top 10 relatively abundant bacterial and archaeal OTUs among the three samples at the 97% similarity,and only 12 core bacterial OTUs were detected.Overall,this study indicated that there were distinct microbial communities and many unique OTUs in these three samples.     

渤海沉积物中细菌群落结构和基因丰度的空间分布特征

This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.     

Microbial community structure and diversity in deep-sea hydrothermal vent sediments along the Eastern Lau Spreading Centre

The aim of this study is to investigate microbial structures and diversities in five active hydrothermal fields’ sediments along the Eastern Lau Spreading Centre (ELSC) in the Lau Basin (southwest Pacific). Microbial communities were surveyed by denatured gradient gel electrophoresis (DGGE) and clone library analysis of 16S rRNA genes. The differences in microbial community structures among sediment samples from the five deep-sea hydrothermal sites were revealed by DGGE profiles. Cluster analysis of DGGE profiles separated the five hydrothermal samples into two groups. Four different 16S rRNA gene clone libraries, representing two selected hydrothermal samples (19-4TVG8 and 19-4TVG11), were constructed. Twenty-three and 32 phylotypes were identified from 166 and 160 bacterial clones respectively, including Proteobacteria, Bacteroidetes, Firmicutes, Nitrospirae and Planctomycetes. The phylum Proteobacteria is dominant in both bacterial libraries with a predominance of Gamma-Proteobacteria. A total of 31 and 25 phylotypes were obtained from 160 and 130 archaeal clones respectively, including Miscellaneous Crenarchaeotic Group, Marine Group Ⅰ and Ⅲ, Marine Benthic Group E, Terrestrial Hot Spring Crenarchaeota and Deep-sea Hydrothermal Vent Euryarchaeota. These results show a variety of clones related to those involved in sulfur cycling, suggesting that the cycling and utilization of sulfur compounds may extensively occur in the Lau Basin deep-sea hydrothermal ecosystem.     

施肥对盐沼沉积物微生物生物量和细菌群落组成的影响

The effects of nitrogen(N) addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis(DGGE) in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer(urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg(nitrogen content in sediment) and different forms of N fertilizers(urea,(NH_4)_2SO_4, and NH_4NO_3, each supplied at 0.2 g/kg(calculated by nitrogen).The fertilizers were applied 1–4 times during the plant-growing season in May, July, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N.Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance,and alters the structure of bacterial community.     

Heterotrophic bacteria of the Dapeng Bay in the South China Sea: community structure, abundance, and the relationships of culturablity with environmental factors

The community composition,abundance and culturablity of heterotrophic bacterioplankton in the Dapeng Bay of the South China Sea were investigated by morphological method,bacterial cultivation and biochemical methods over an annual cycle.Aeromonas and Pseudomonas were the predominant genera among the Gram-negative bacteria.The bacterioplankton abundance fluctuated from 2.07×10 8 to 2.44×10 9 cells/dm 3 ,and culturable bacteria abundance ranged between 0.1×10 6 and 16.07×10 6 CFU/dm 3 .The Culturablity of heterotrophic bacteria ranged between 0.01% and 1.31%.The relationship between bacterial culturablity and the environmental factors was also studied in different sites of the Dapeng Bay.Throughout the bay,a significantly positive relationship was evidenced between bacterial culturability and temperature,meanswhile bacterial culturability was significantly inversely related with salinity.The positive relationship was shown at the central bay while a negative relationship was observed at the bay mouth and there was no significant correlation at top bay between bacterial culturablity and chlorophyll a of sea water.A positive relationship was found between culturability and DIN all the bay,but DIP showed a significantly negative relationship with bacterial culturability only at the mouth of the bay.     

Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer

Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their diversity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization (FISH) showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic (AAP) bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria (Alpha, Beta and Gamma subclasses), Bacteroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone libraries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammapro-teobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.     

Spatial and temporal variations of macro-and mesozooplankton community in the Huanghai Sea (Yellow Sea) and East China Sea in summer and winter

The study was conducted during two cruises of June–August 2006 (summer),and January–February 2007 (winter) in the Huanghai (Yellow) Sea and East China Sea.Spatial and temporal variations of zooplankton abundance,biomass and community structure and its relation to currents and water masses over the continental shelf were examined.A total of 584 zooplankton species/taxa and 28 planktonic larvae were identified during the two surveys.Copepods were the most abundant component among these identified groups.Zooplankton abundance and biomass fluctuated widely and showed distinct heterogeneity in the shelf waters.Five zooplankton assemblages were identified with hierarchical cluster analysis during this study,and they were Huanghai Sea Assemblage,Changjiang Estuary Assemblage,Coastal Assemblage,East China Sea Mixed-water Assemblage and East China Sea Offshore Assemblage.Seasonal changes of zooplankton community composition and its geographical distribution were detected,and the locations of the faunistic areas overlap quite well with water masses and current systems.So we suggest that the zooplankton community structure and its changes were determined by the water masses in the Huanghai Sea and East China Sea.The results of this research can provide fundamental information for the long-term monitoring of zooplankton ecology in the shelf of Huanghai Sea and East China Sea.     

2010年西北冰洋浮游植物区域差异与环境关系

Global warming has caused Arctic sea ice to rapidly retreat,which is affecting phytoplankton,the primary producers at the base of the food chain,as well as the entire ecosystem.However,few studies with large spatial scales related to the Arctic Basin at high latitude have been conducted.This study aimed to investigate the relationship between changes in phytoplankton community structure and ice conditions.Fifty surface and 41 vertically stratified water samples from the western Arctic Ocean(67.0°–88°26′N,152°–178°54′W) were collected by the Chinese icebreaker R/V Xuelong from July 20 to August 30,2010 during China's fourth Arctic expedition.Using these samples,the species composition,spatial distribution,and regional disparities of phytoplankton during different stages of ice melt were assessed.A total of 157 phytoplankton taxa(5 μm) belonging to 69 genera were identified in the study area.The most abundant species were Navicula pelagica and Thalassiosira nordenskioeldii,accounting for 31.23% and 14.12% of the total phytoplankton abundance,respectively.The average abundance during the departure trip and the return trip were 797.07×10~2 cells/L and 84.94×10~2 cells/L,respectively.The highest abundance was observed at Sta.R09 in the north of Herald Shoal,where Navicula pelagica was the dominant species accounting for 59.42% of the abundance.The vertical distribution of phytoplankton abundance displayed regional differences,and the maximum abundances were confined to the lower layers of the euphotic zone near the layers of the halocline,thermocline,and nutricline.The species abundance of phytoplankton decreased from the low-latitude shelf to the high-latitude basin on both the departure and return trips.The phytoplankton community structure in the shallow continental shelf changed markedly during different stages of ice melt,and there was shift in dominant species from centric to pennate diatoms.Results of canonical correspondence analysis(CCA) showed that there were two distinct communities of phytoplankton in the western Arctic Ocean,and water temperature,ice coverage and silicate concentration were the most important environmental factors affecting phytoplankton distribution in the surveyed sea.These findings will help predict the responses of phytoplankton to the rapid melting of Arctic sea ice.     

Preliminary study on community structures of meiofauna in the middle and eastern Chukchi Sea

Sediment core samples were collected from 17 stations in the middle and eastern Chukchi Sea during the sixth Chinese National Arctic Research Expedition(CHINARE-Arctic) in summer 2014.The samples were analyzed for composition,abundance,biomass,vertical distribution,size spectra,and ecological indexes of meiofauna.A total of 14 meiofauna taxa were detected,and the free-living marine nematodes comprised the most dominant taxon,accounting for 97.21% of the average abundance.The abundance and biomass of meiofauna were within ranges of(218.12±85.83)-(7 239.38±1 557.15) ind./(10 cm~2) and(130.28±52.17)-(3 309.56±1 751.80) μg/(10 cm~2),with average values of(2 391.90±1 966.19) ind./(10 cm~2) and(1 549.73±2 042.85) μg/(10 cm~2)(according to dry weight)respectively.Furthermore,91.26% of the individuals were distributed in the top layer of 0-5 cm of surface sediment,and 90.84% had sizes of 32-250 μm.Group diversity index of meiofauna in the survey area was low,and the variation of abundance was the main difference in meiofauna communities among all stations.Abundance and biomass of meiofauna were not significantly correlated with environmental factors except concentration of nutrient Si in bottom seawater.Abundance of meiofauna in shallow water of marginal seas in the Pacific sector of the Arctic Ocean is likely at a same level and higher than that in most of China sea areas,suggesting that the shallow water of the summer Chukchi Sea is a continental shelf area with rich resources of meiofauna.The Chukchi Sea is important for studying the ecosystem of the Arctic Ocean and environmental responses.However,studies on meiofauna in the Chukchi Sea are still not enough,and in the future,natural and human disturbances may increase due to global warming,the Arctic channel opening,and other factors.Thus,more studies on meiofauna should be required,in order to know more about how the Arctic benthic community would alter.     

Seasonal variability in free-living marine nematode community structure in a sandy beach of the Taiping Bay of Qingdao, China

Nematode assemblage composition, trophic structure and biodiversity were followed over an annual cycle in a sandy beach of the Taiping Bay of Qingdao, China. Nematode assemblage in the sandy beach maintained a high genus diversity （75 genera）. Mlero- laimus and Bathylaimus were the dominant genus of the nematode assemblage, accounting for 66% of the total nematode abundance. The nematodes＇ dominant trophic structure changed seasonally as a response to the seasonal changes in food quality. Epigrowth-feeder nematodes （2A） were the dominant trophic groups in the trophic structure with the highest abundance in spring because of phytoplankton bloom, while the feeding type （ 1 B） showed higher abundance in summer that was due to the increasing of sediment detritus after spring bloom. Furthermore, species diversity and evenness calculated on nematodes identified to the genus level displayed significant temporal changes, which was also reflected by the index of trophic diversity. According to the cluster analysis, the nematode community structure of the whole year was clearly separated into two periods （A and B）. Biota-Envlron- ment matching （BIOENV） results showed that seawater temperature, sediment Chl a and grain size were responsible for the nema- tode community structure variation in spring and summer period （Period A）. However, seawater/interstitial water temperature, interstitial water dissolved oxygen concentration,interstitial water salinity, and sediment Ph a a were more important in constructing the autumn and winter period （Period B） nematode community structure.     

Comparison of community structures between particle-associated and free-living prokaryotes in tropical and subtropical Pacific Ocean surface waters

The subtropical and tropical regions of the Pacific Ocean are less productive than other oceanic regions. Although particle association should be an important strategy for heterotrophic prokaryotes to survive in such environments, we have little information on particle-associated (PA) prokaryotes in these regions. The specific aim of this study was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the North Pacific Subtropical Gyre, the South Pacific Subtropical Gyre, and an eastern equatorial region of the Pacific Ocean. Community profiles and phylogenetic identities were obtained by denaturing gradient gel electrophoresis, 454-pyrosequencing, and cloning followed by Sanger sequencing of 16Sr RNA gene amplicons. The distribution patterns of some abundant groups in three regions and two lifestyles (PA and FL) are shown in this study. Also, the PA community structures of bacteria differed from the FL ones and exhibited higher diversity than the FL ones, while the archaeal community structures did not show significant differences between PA and FL assemblages. We found that specific phylotypes of Gammaproteobacteria and Flavobacteria were abundant in PA bacterial assemblages, suggesting that they prefer to attach and consume particulate organic matter. In summary, the surface seawater PA assemblages represent very different bacterial and archaeal community structures between three different oceanic regions, each of which had distinct PA and FL community structures. These results imply that environmental factors determine microbial community structures.     

Diversity and geographical distribution of resting stages of eukaryotic algae in the surface sediments from the southern Chinese coastline based on metabarcoding partial 18S rDNA sequences

Surface sediment samples were collected from sixteen sites of the southern Chinese coastline in this study. Diversity of eukaryotic microalgae was examined using high-throughput sequencing of 18S rDNA to understand the community structure and geological distribution of microalgal resting stages. A total of 218 operational taxonomic units (OTUs) were detected for eukaryotic algae, and only 75 OTUs (34.40%) were detected into species level. The algal communities were composed of sixty-four genera belonged to twelve classes of four phyla. Dinoflagellates were the most abundant and diversified group, which accounted for the average of 56.26% and 53.70% DNA reads and OTUs, respectively. Dinoflagellates were dominated by Protoperidinium, Euduboscquella, Amylax, and Paragymnodinium. Chaetoceros, Thalassiosira, and Skeletonema were abundant in diatoms, while Pedospumella and Paraphysomonas in Chrysophyceae were the most abundant genera due to their massive occurrence in some particular sites. The high abundance of Protoperidinium sequences suggested the high nutrient levels in the southern Chinese coastline. Nineteen of the detected OTUs were assigned to harmful and/or bloom-forming microalgae. The wide occurrence of the toxic dinoflagellate Azadinium poporum and high abundance of Alexandrium pacificum in some particular sites suggested the potential risk of human poisoning.     

Prokaryotic community composition revealed by denaturing gradient gel electrophoresis in the East Sea

To understand the temporal and spatial variation of the prokaryotic community in the East Sea, their composition was determined by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE)-sequencing techniques. The investigations were conducted twice annually in 2007 and 2009 in coastal and offshore stations. Prokaryotic abundance (PA), leucine incorporation rate, and other environmental parameters were also measured. By using the DGGE approach, we obtained 283 bacterial sequences and 160 archaeal sequences. The most frequently detected bacterial phylotypes during the investigations belonged to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. However, their relative compositions differed in time and space. Although Alphaproteobacteria and Bacteroidetes were the dominant groups in the surface water in May 2007 and in May and October 2007, Gammaproteobacteria was dominant in mesopelagic samples. However, Gammaproteobacteria was overwhelmingly dominant in most samples in August 2009. Although Deltaproteobacteria was rarely found as a dominant bacterial group, it occupied the highest fraction in a mesopelagic sample in October 2007. Epsilonproteobacteria also showed a similar trend, although its maximal dominance was found in a mesopelagic sample in August 2009. The archaeal community was dominated overwhelmingly by members of the Euryarchaeota in most of the investigations. However, Nitrosopumilales was dominant in aphotic samples in August 2009. Further, their spatiotemporal composition at the family level changed more dynamically in the East Sea. These temporal and spatial distributions of the prokaryotic community were influenced mainly by seawater temperature and depth in the East Sea.     

基于第二代测序技术的条斑紫菜(Pyropia yezoensis)贝壳丝状体附生菌群研究

条斑紫菜(Pyropia yezoensis)贝壳丝状体黄斑病给育苗产业造成危害,但目前对健康状态下的菌群结构及其发病后变化仍缺乏认识。本研究基于第二代测序技术和16S r RNA序列分析,对健康和患病丝状体的细菌组成与变化进行比较。测序共产生1.6Gb配对末端序列,获得了第一个高通量的条斑紫菜贝壳丝状体细菌群落数据集。通过数据分析共识别出7,833种可操作分类单元(operational taxonomic units,OTUs),比对确定为18个细菌门。相对于健康样本,黄斑病丝状体样本的微生物多样性显著增加。主坐标分析和非加权组平均法(unweighted pair group method using arithmetic average,UPGMA)聚类均将健康和黄斑病丝状体分成不同的组,且健康组样本间的距离明显小于黄斑病组。上述结果说明,健康贝壳丝状体保持着相似的微生物群落结构,而患病后的丝状体则发生了不同的变化;健康样本和黄斑病样本组间差异显著的细菌属有39个,其中29个在健康样本中的相对丰度明显高于病患组样本。本研究从菌群生态角度分析了健康贝壳丝状体微生物菌群结构、发病后菌群的变化及其对丝状体生长的潜在作用,为丝状体病害的检测和预防提供有价值的信息。     

北极深海沉积物中细菌和古菌群落结构研究

在北极深海沉积物生态系统中,微生物的群落结构由有机质输入、能量的可用性及其他环境因素决定.然而,全球气候变暖及其导致的冰盖提前融化正在影响微生物的多样性.为描述北极深海沉积物中的微生物群落结构及其与环境因素的相关性,我们利用罗氏454对北极深海沉积物样品的16S rDNA扩增子进行了测序,对细菌和古菌群落的丰富度、成分、结构及其系统发育分类地位进行了描述.硫还原和化能有机营养类是细菌群落中的主要类群;而古细菌群落主要是由微生物的关系最为密切的氨氧化奇古菌门(96.66%)和产甲烷古生菌界(3.21%).这项研究描述了北极极点附近深海沉积物(> 3500米)中的微生物多样性,将为以后研究类似环境中微生物代谢过程和途径等功能分析奠定基础.     

Spatial and temporal variability of planktonic archaeal abundance in the Humboldt Current System off Chile

The latest advances in the field of microbial ecology have shown that planktonic Archaea are one of the most abundant unicellular microorganisms of the oceans. However, no information is available on the contribution this group makes to the prokaryote assemblages that inhabit the eastern South Pacific Ocean. Here, we describe the relative abundance and vertical distribution of planktonic Archaea off northern and central-southern Chile. Data come from several cruises and a 45-month time series at a station located on the shelf off central-southern Chile. Both the taxonomic composition of the prokaryote community and its relative abundance were determined using quantitative dot blot 16S-rRNA hybridizations. Total Archaea in central-southern Chile made up 6–87% of the prokaryote rRNA in the water column and did not present evidence of any seasonal pattern. Crenarchaea were the most abundant archaeal group at this site and were significantly associated with the ammonium concentration (r²=0.16, p=0.0003, n=80). Archaeal abundance in the time series was usually greater in the deeper layer (>50 m), with contributions reaching up to ∼90% of the prokaryote rRNA on certain occasions, and decreasing towards the surface. Important increments in the relative abundance of total Archaea were observed on given dates at the surface of the time-series station off central-southern Chile. Off northern Chile, total Archaea normally contributed from ∼10% to 50% of the prokaryote rRNA found between 10 and 1000 m, and were generally important in the mesopelagic realm. Our results indicate that Archaea constitute an important fraction of the prokaryote assemblage in the water column of the Humboldt Current System, especially in the oxygen minimum zone.     

Filter-feeder macroinvertebrates as key players in culturable bacteria biodiversity control: a case of study with Sabella spallanzanii (Polychaeta: Sabellidae)

The present study investigates the effect of the filtering activity of Sabella spallanzanii on the culturable heterotrophic bacterial community through the comparison of the bacterial diversity in transplanted polychaetes and the surrounding seawater. For isolation of culturable heterotrophic bacteria, seawater samples as well as polychaete homogenates were plated in triplicates onto Bacto Marine Agar 2216 (Difco). All the colonies grown were isolated, subcultured and identified by several morphological, biochemical and cultural methods. Some bacterial genera showed higher average abundances in polychaetes than in seawater (i.e. Lucibacterium and Photobacterium). Aeromonas represented a conspicuous component of the bacterial community both in S. spallanzanii and seawater. The presence of Cytophaga and Pseudomonas was also relevant in the examined seawater samples. The selective concentrations of some bacterial genera inside S. spallanzanii either by grazing on bacteria or their capability as bacterial reservoirs, provides evidence for the role of macrobenthic invertebrates as key determinants for microbial diversity.