通过焦磷酸测序揭示北极海水的微生物群落结构

This study aimed to determine the microbial community structure of seawater in(ICE-1) and out(FUBIAO) of the pack ice zone in the Arctic region.Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted.We conducted a detailed census of microbial communities by pyrosequencing.Analysis of the microbial community structures indicated that these two samples had high bacterial,archaeal and eukaryotic diversity.Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples,and their relative abundance were 51.29% and 35.39%,72.95%and 23.21%,respectively.Euryarchaeota was the most abundant archaeal phylum,and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1.As for the eukaryotes,no_rank_Eukaryota,Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO,accounting for 85.29% of the total reads.The relative abundance of the most abundant phylum in Sample ICE-1,no_rank_Eukaryota and no_rank_Metazoa,was up to 90.69% of the total reads.Alphaproteobacteria,Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level.There were also differences in the top ten abundant bacterial,archaeal and eukaryotic OTUs at the level of 97% similarity between the two 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.     

Distribution of ammonia-oxidizing Betaproteobacteria community in surface sediment off the Changjiang River Estuary in summer

The spatial distribution of ammonia-oxidizing Betaproteobacteria ( β AOB) was investigated by FISH (fluorescence in situ hybridization) and DGGE (denaturing gradient gel electrophoresis) techniques in the sediment off the Changjiang River Estuary.Sediment samples were collected from eight stations in June before the formation of hypoxia zone in 2006.The abundance of β AOB ranged from 1.87 × 10 5 to 3.53 × 10 5 cells/g of sediment.β AOB abundance did not present a negative correlation with salinity,whereas salinity was implicated as the primary factor affecting nitrification rates.The DGGE profiles of PCR-amplified amo A gene fragments revealed that the β AOB community structure of sample S2 separated from other samples at the level of 40% similarity.The variations in composition of β AOB were significantly correlated with the salinity,temperature,absorption ability of sediments and TOC. The statistical analysis indicates that the β AOB abundance was a main factor to influence nitrification rates with an influence ratio of 87.7% at the level of 40% biodiversity similarity.Considering the good correlation between β AOB abundance and nitrification estimates,the abundance and diversity of β AOB community could be expected as an indirect index of nitrification activity at the study sea area in summer.     

Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific “warm pool”

A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific ＂warm pool＂ （WP） was investigated and compared with that in a sediment sample from the eastern Pacific （EP） by phylogenetic analysis of 16S rDNA fragments. Five bacterial 16S rDNA clone libraries were constructed, and 133 clones with different restriction fragment length polymorphism （RFLP） patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample. The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides （CFB） group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria （SRB） were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.     

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China

In order to understand the diversity and distribution of the bacterial community in the coastal sediment of the Bohai Bay,China,high-throughput barcoded pyrosequencing of the 16 S r RNA gene was used.Metagenomic DNA was extracted from the sediment samples,and was sequenced using a 454 GS FLX Titanium system.At 97%similarity,the sequences were assigned to 22 884 operational taxonomic units(OTUs) which belonged to 41 phyla,84 classes,268 genera and 789 species.At the different taxonomic levels,both the dominants and their distribution varied significantly among the six coastal sediments.Proteobacteria was the first dominant phylum across all the six coastal sediments,representing 57.52%,60.66%,45.10%,60.92%,56.63% and 56.59%,respectively.Bacteroidetes was the second dominant phylum at Stas S1,S2 and S4,while Chloroflexi was the second dominant phylum at Stas S3,S5 and S6.At class level,γ-Proteobacteria was the first dominant class at Stas S1,S2,S4 and S6,while δ-Proteobacteria became the first dominant class at Stas S3 and S5.In addition,a large proportion of unclassified representatives have distributed at the different taxonomic levels.Canonical correspondence analysis(CCA) results indicated that the sediment texture,water depth(D),dissolved oxygen(DO),total nitrogen(TN) and nine EPA priority control polycyclic aromatic hydrocarbons(PAHs) including naphthalene,acenaphthylene,acenaphthene,fluorine,phenanthrene,fluoranthene,pyrene,benzo[a]anthracene and indeno[1,2,3-cd]pyrene were the important factors in regulating the bacterial community composition.Those results are very important to further understand the roles of bacterial community in the coastal biogeochemical cycles.     

Community structure of zooplankton in the Lembeh Strait, Bitung, and Wori Beach, Manado, North Sulawesi, Indonesia

The community structure of zooplankton has been conducted in the Lembeh Strait in Bitung and Wori Beach in Manado, North Sulawesi in October 2015. Sampling of this research was conducted in 22 sampling sites along the strait. Zooplankton samples were collected from 22 stations, by NORPAC 300 μm net that was vertically hauled from maximum 10 m depth up to the surface water. The samples were poured into the bottle with formalin of 4%as preservative. The results showed that there were 43 taxa of zooplankton. The abundance of zooplankton was between 21.216–4 193.776 ind./m~3. The dominant taxa were copepod, especially Calanoida. The composition of zooplankton was relatively similar in all stations. We showed the abundance, dominance, composition and distribution of zooplankton at this research. More extensive studies concerning zooplankton is required to understand zooplankton biodiversity as a whole especially on the geographical and spatial distribution to describe population and community dynamic in the Lembeh Strait and Wori Beach.     

Effects of organic carbon consumption on denitrifier community composition and diversity along dissolved oxygen vertical profiles in lake sediment surface

At present,the understanding of the dynamics of denitrifiers at different dissolved oxygen(DO)layers under organic carbon consumption within the surface sediments remains inadequate.In this study,high-throughput sequencing and quantitative PCR targeting nirS gene were used to analyze the denitrifier abundance dynamics,community composition,and structure for aerobic(DO 0.5-6.9 mg/L),hypoxic-anoxic(DO 0-0.5 mg/L),and anoxic(DO 0 mg/L)layers in surface sediments under organic carbon consumption.Based on the analysis of nirS gene abundance,the values of denitrifying bacteria decreased with organic carbon consumption at different DO layers.When the bacterial species abundance at the genus level were compared between the high-carbon and low-carbon sediments,there was significant increase in 6 out of 36,7 out of 36 and 6 out of 36 genera respectively for the aerobic,hypoxic-anoxic and anoxic layers.On the other hand,14 out of 36,9 out of 36 and 15 out of 36 genera showed significant decrease in bacterial species abundance respectively for the aerobic,hypoxic-anoxic and anoxic layers.Additionally,14 out of 36,20 out of 36,and 15 out of 36 genera had no change in bacterial species abundance respectively for the aerobic,hypoxic-anoxic,and anoxic layers.This indicates that the carbon utilization ability of different denitrifiers on each DO layers was generally different from each other.Diversity of denitrifying bacteria also presented significant differences in different DO layers between the high-and low-carbon content sediment layers.Moreover,under the high-carbon and low-carbon content,the abundance of nirS gene showed a high peak within the hypoxic-anoxic regions,suggesting that this region might be the main distribution area for the denitrifying bacteria within the surface sediments.Furthermore,community of unique denitrifiers occurred in different DO layers and the adaptive changes of the denitrifier community followed the organic carbon consumption.     

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.     

Phylogenetic diversity of Type I polyketide synthase genes from sediments of Ardley Island in Antarctica

The diversity of modular polyketide synthase (PKS) genes in sediments of Ardley Island in Antarctica, was studied by restriction fragment length polymorphism (RFLP) analysis. Phylogenetic analysis of 14 amino acid (AA) sequences indicates that the identified ketosynthase (KS) domains were clustered with those from diverse bacterial groups, including Cyanobacteria, γ-Proteobacteria, Actinobacteria, Firmicutes, and some unidentified microorganisms from marine sponge, bryozoan and other environmental samples. The obtained KS domains showed 43%-81% similarity at the AA level to reference sequences in GenBank. Six identified KS domains showed diverse sequences of the motif (VQTACSTS) that was used to identify the hybrid PKS/nonribosomal peptide synthetase (NRPS) enzyme complex, and formed a new branch. These results reveal a high diversity and novelty of PKS genes in antarctic sediments.     

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.     

东太平洋海隆深海热液区沉积物古菌多样性分析

采用PCR-RFLP方法对东太平洋海隆深海热液区3个站位沉积物中的古菌多样性进行了初步研究.结果显示,从古菌16S rRNA基因文库中随机挑取的296个阳性克隆分属奇古菌门（Thaumarchaeota,47.64%）、广古菌门（Euryarchaeota,44.93%）、泉古菌门（Crenarchaeota,6.77%）和未分类古菌（0.68%）,其中优势菌群为奇古菌门的亚硝化侏儒菌属（Nitrosopumilus,35.47%）和广古菌门的热原体纲（Thermoplasmata,27.03%）,DHVE3、DHVE5、DHVE6、MBGB和MBGE类群在沉积物样品中也均有发现.另外,3个站位沉积物中古菌类群组成存在差异,S5-TVG1站位样品文库的97个古菌克隆分属奇古菌门（49.48%）、广古菌门（49.48%）和泉古菌门（1.03%）,S14-TVG10站位样品文库的103个古菌克隆由奇古菌门（84.47%）和广古菌门（15.53%）组成,S16-TVG12站位样品文库的96个古菌克隆包括广古菌门（71.88%）、泉古菌门（19.79%）、奇古菌门（6.25%）和未分类古菌（2.08%）.研究结果表明,东太平洋海隆深海热液区沉积物中古菌多样性丰富,存在着许多新的古菌菌群;不同站位古菌菌群结构以及多样性存在差异,这与其所处环境的热液活动密切相关.     

东太平洋中国多金属结核区锰结核样品中微生物群落结构的研究

通过非培养手段研究了东太平洋中国多金属结核区ES0303站点锰结核样品中的微生物群落结构.细菌16S rRNA基因克隆文库的研究结果表明：结核内细菌种群结构复杂,微生物种类丰富且各种群丰度不一（61个OTUs）,其中变形杆菌类群为优势种群,占所有细菌克隆子比例的64%,且主要分布于β/γ-、α-和δ-等3类变形杆菌（Proteobacteria）亚群之中,占比分别为34%、18%和12%.此外还存在包括酸杆菌（Acidobacteria）,放线菌纲（Actinobacteria）,绿弯菌门（Chloroflexi）,厚壁菌门（Firmicutes）,浮霉菌门（Planctomycetes）等在内的细菌类群的分布,克隆子比例依次为9%、7%、8%、2%和5%.古菌16S rRNA基因克隆文库的研究结果表明：古菌的群落结构单一（仅12个OTUs）,全部是由泉古菌海洋类群I（crenarchaeote marine group I,MGI）组成;其中MGI-η类群最为丰富,达到44%,而MGI-α、MGI-ζ和MGI-ε类群的克隆子比例分别为25%、18%和9%,另外还发现2个新的MGI分类类群.相关克隆子的数据库比对和系统发育树分析表明,并未发现已报道的直接参与铁锰氧化还原相关类群的存在,但它们大多数与来自多金属结核来源或深海来源的不可培养微生物具有较高的同源性.进一步的分析表明,锰结核内存在相当数量的氨氧化菌、硫酸盐还原菌、酸杆菌等能够改变pH值的细菌和古菌类群的存在,意味着它们可能在锰结核的形成过程中起到重要的作用.     

辽河口沉积物中古菌和细菌群落结构分析

本研究旨在了解辽河口表层沉积物中古菌和细菌的群落结构组成、多样性及其与环境因子之间的相关性。采用构建古菌和细菌16S rRNA基因文库的方法，应用Illumina Miseq测序技术进行序列分析。结果表明:辽河口表层沉积物中细菌多样性高于古菌多样性，近岸细菌和古菌多样性高于远岸，即河相区（0.8~7.04）细菌多样性高于混合区（13.1~20.7）和海相区（24.2~31.5）；主要古菌群落为奇古菌门（Thaumarchaeota，72.73%）和广古菌门（Euryarchaeota，25.05%），其中泉古菌门（Crenarchaeota，0.001%）只在河相区站位被发现；细菌群落组成中变形菌门（Proteobacteria，61.94%）为该河口的优势菌群，其次为拟杆菌门（Bacteroidetes，11.21%）和酸杆菌门（Acidobacteria，5.59%），其他门类如蓝藻门（Cyanobacteria，3.03%）等比例较小。与环境因子的冗余度分析表明:影响表层沉积物中古菌群落分布的主要环境因子依次为氨盐、泥、酸碱度、盐度、电导率和砂，而细菌群落的分布主要受到溶氧、泥、砂、黏土和总磷的影响。由此可见，不同环境条件下微生物的群落结构存在空间异质性，不同微生物对同一环境条件的响应亦不同。     

珠江口表层水体颗粒物中古菌四醚类脂物的分布特征

类异戊二烯甘油二烷基甘油四醚类化合物（isoGDGTs）是古菌微生物的特征脂类标志物,由这组化合物构造出的TEX₈₆温标在海水古温度重建中得到了广泛应用。本文调查了珠江口及近岸海域（水深小于30 m）4个季节水体悬浮颗粒物（SPM）的isoGDGTs分布情况。结果显示:虎门上游河流水体中的isoGDGTs主要来自原地生产的甲烷古菌输入,进入河口水体后,主要来自原地奇古菌和广古菌的输入。陆源古菌的输入在5月份和8月份,对河流水体产生一定的影响,但对河口水体的影响相对较小。珠江口水体isoGDGTs中的GDGT-2与GDGT-3比值（GDGT-[2]/[3]）和GDGT-Cren'的丰度百分比（Cren'%）分别小于4和4%,与南海深水沉积物明显不同,表明珠江口与南海深水沉积物中isoGDGTs的古菌来源存在差异,这也可能是引起珠江口水体TEX₈₆温度（基于全球标定公式）偏离水体实际温度的原因。珠江口表层水体isoGDGTs中的GDGT-2和GDGT-3的丰度百分比与南海表层水体存在差异,这可能与GroupⅠ奇古菌和GroupⅡ广古菌相对比例空间变化有关。珠江口表层水体isoGDGTs的TEX₈₆温度在2月份明显高于原地表层水体温,而其他月份都低于原地表层水体温度,可能与Group Ⅰ奇古菌和Group Ⅱ广古菌相对比例的季节变化有关。几个月份中11月份isoGDGTs绝对含量最高,8月份较低,表明11月份和8月份分别是原地古菌生产量较大和较小时期。统计分析的结果显示,水体铵根离子含量、水体温度,以及溶解氧水平可能是控制珠江口水体isoGDGTs分布的主要环境因素。     

Abundance and distribution of meiofauna in the Chukchi Sea

The metazoan meiofauna in the Chukchi Sea were collected from seven shallow water stations(depths ranging 46 to 52 m) and five deep sea stations(depths ranging between 393 and 2 300 m) during the 4th Chinese National Arctic Research Expedition in 2010. The results showed that abundance of meiofauna was higher in shallow water sediments(average of 2 445 ind./(10 cm2)) than in deep sea sediments(407.06 ind./(10 cm2)). A UNIANOVA test for difference between the two different regions was highly significant(F=101.15, p0.01). Nematodes were numerically dominant, representing(96.6±4.6)% of the total meiofaunal abundance at the shallow water stations and(98.90±1.42)% at deep sea stations. The number of higher taxonomic groups and abundance of meiofauna were higher at Stas CC1, CC4, and R06 near the Bering Strait and the continent, than at the rest of the shallow water and deep sea stations. The primary factors causing the differences were concentrations of nutrients P and Si of bottom seawater(R=0.831, p0.003), followed by depth(R=-0.655, p0.05) and sand fractions of sediments(R=0.632, p 0.05). The numbers of meiofauna on the 65 μm and 32 μm sieves were significantly higher than those on the rest of the screens. Differences in numbers of meiofauna retained on screens with different mesh openings were highly significant among all sampling stations(F=31.60, p0.01). The highest numbers of individuals on screens with 32 μm mesh openings were found at deep sea stations. The number of meiofauna in the top 0–1, 1–2, and 2–4 cm segments constituted 84.4% of the total and was significantly higher than those in the bottom 4–6 and 6–10 cm segments(F=15, p0.01).     

青岛市雾天细菌气溶胶群落结构特征及健康风险

本文于2020年7—9月采集雾天和晴天生物气溶胶样品,利用高通量测序和BugBase基因功能预测,评估了雾天细菌气溶胶群落特征及潜在健康风险.结果表明,雾天可操作分类单元(OTUs)、物种多样性及丰富度均低于晴天,组内亲缘复杂度高于晴天.罗尔斯通氏菌、短杆菌、丙酸菌和短波单胞菌是雾天优势细菌属,雾天微生物几乎来源于本土...     

西菲律宾海比科尔陆架深海沉积物古菌多样性研究

通过构建16S rRNA 基因文库, 对西太平洋西菲律宾海东板比科尔陆架5 个不同层位沉积物样品中的古菌的多样性进行了研究, 并获得了465 个有效克隆63 个OTUs （Operational Taxonomic Units）。通过16S rRNA 序列与GenBank 已知序列的同源性比较及构建系统进化树的结果显示...     

近海水体环境DNA沉降对沉积物中纤毛虫分子多样性评估的影响

在陆架海区沉积物中, DNA高通量测序技术可检获大量浮游寡毛类和舞毛类等非底栖纤毛虫,这些源于水体的环境DNA(eDNA)如何影响对沉积物中纤毛虫分子多样性的评估,以及影响程度如何尚不明确。本研究选取了黄海冷水团中的两个站位,通过提取水体和沉积物中DNA和RNA,并采用直接提取法和洗脱法提取沉积物DNA,结合DNA和cDNA测序技术,探讨了水体和沉积物中纤毛虫分子多样性的关系。研究表明,基于洗脱DNA法、直接提取DNA法和cDNA法获得的沉积物中纤毛虫OTUs数分别为451、312和324个,其中211个OTUs同时由三种方法检获;而164个OTUs仅通过洗脱DNA法检获,其中89%为相对丰度低于0.1%的稀有类群。直接提取DNA法所获的寡毛类和舞毛类序列数占比达46%,而在洗脱DNA法和cDNA法中占比仅为12%和10%。沉积物中检获的43%—71%的舞毛类和寡毛类OTUs与浅层水(40m)共有,仅19%—29%与深层水(40m)共有,且这些共有的OTUs可同时在浅层水中检获。本研究发现,对沉积物中纤毛虫分子多样性评价造成影响的浮游类群主要来自浅层水,洗脱DNA与cDNA测序均可显著降低浮游类群eDNA的影响。鉴于洗脱DNA法较之cDNA法操作更简便,且避免了反转录过程导致的偏差,因此推荐用于对近海沉积物中纤毛虫等真核微生物的分子多样性研究。