Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (similar to 13 degrees N)

The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) similar to 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.

Perspectives on the origin of microfilaments, microtubules, the relevant chaperonin system and cytoskeletal motors - a commentary on the spirochaete origin of flagella

The origin of cytoskeleton and the origin of relevant intracellular transportation system are big problems for understanding the emergence of eukaryotic cells. The present article summarized relevant information of evidences and molecular traces on the origin of actin, tubulin, the chaperonin system for folding them, myosins, kinesins, axonemal dyneins and cytoplasmic dyneins. On this basis the authors proposed a series of works, which should be done in the future, and indicated the ways for reaching the targets. These targets are mainly: 1) the reconstruction of evolutionary path from MreB protein of archaeal ancestor of eukaryotic cells to typical actin; 2) the finding of the MreB or MreB-related proteins in crenarchaea and using them to examine J. A. Lake's hypothesis on the origin of eukaryote from "eocytes" (crenarchaea); 3) the examinations of the existence and distribution of cytoskeleton made of MreB-related protein within coccoid archaea, especially in amoeboid archaeon Thermoplasm acidophilum; 4) using Thermoplasma as a model of archaeal ancestor of eukaryotic cells; 5) the searching for the homolog of ancestral dynein in present-day living archaea. During the writing of this article, Margulis' famous spirochaete hypothesis on the origin of flagella and cilia was unexpectedly involved and analyzed from aspects of tubulins, dyneins and spirochaetes. Actually, spirochaete cannot be reasonably assumed as the ectosymbiotic ancestor of eukaryotic flagella and cilia, since their swing depends upon large amount of bacterial flagella beneath the flexible outer wall, but not depends upon their intracellular tubules and the assumed dyneins. In this case, if they had "evolved" into cilia and lost their bacterial flagella, they would immediately become immobile! In fact, tubulin and dynein-like proteins have not been found in any spirochaete.

Characterization of stable isotope fractionation during methane production in the sediment of a eutrophic lake,lake dagow,germany

We measured delta C-13 of CO2, CH4, and acetate-methyl in profundal sediment of eutrophic Lake Dagow by incubation experiments in the presence and absence of methanogenic inhibitors chloroform, bromoethane sulfonate (BES), and methyl fluoride, which have different specificities. Methyl fluoride predominantly inhibits acetoclastic methanogenesis and affects hydrogenotrophic methanogenesis relatively little. Optimization of methyl fluoride concentrations resulted in complete inhibition of acetoclastic methanogenesis. Methane was then exclusively produced by hydrogenotrophic methanogenesis and thus allowed determination of the fractionation factors specific for this methanogenic pathway. Acetate, which was then no longer consumed, accumulated and allowed determination of the isotopic signatures of the fermentatively produced acetate. BES and chloroform also inhibited CH4 production and resulted in accumulation of acetate. The fractionation factor for hydrogenotrophic methanogenesis exhibited variability, e. g., it changed with sediment depth. The delta C-13 of the methyl group of the accumulated acetate was similar to the delta C-13 of sedimentary organic carbon, while that of the carboxyl group was by about 12 parts per thousand higher. However, the delta C-13 of the acetate was by about 5 parts per thousand lower in samples with uninhibited compared with inhibited acetoclastic methanogenesis, indicating unusual isotopic fractionation. The isotope data were used for calculation of the relative contribution of hydrogenotrophic vs. acetoclastic methanogenesis to total CH4 production. Contribution of hydrogenotrophic methanogenesis increased with sediment depth from about 35% to 60%, indicating that organic matter was only partially oxidized in deeper sediment layers.

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

The authors would like to thank Jin Sun, Jian Sun, Liangliang Kong, Nianshuang Wang, Chunhui Wang, Linbao Zhang and Ying Zhang for their assistance in the project. This work was supported by China Ocean Mineral Resources R&D Association grants DYXM-115-02-2-20 and DYXM-115-02-2-6, Hi-Tech Research and Development Program of China grant 2007AA091903, China National Natural Science Foundation grant 40576069, National Basic Research Program of China grant 2009CB219506 and the Fundamental Research Funds for the Central Universities of China grant 09CX05005A. M. G. K. was funded by incentive funds provided by the UofL-EVPR office and the US National Science Foundation (EF-0412129).

Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin

The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved. Our aim was to study the diversity, structure and distribution of the AEA community in the sediments of the tropical West Pacific Continental Margin, to develop a general view of the AEA biogeography in the deep-sea extreme environment. Archaeal amoA clone libraries were constructed. Diverse and novel amoA sequences were identified, with the Bohol Sea, Bashi Strait and Sibuyan Sea harbouring the highest and the Bicol Shelf the lowest AEA diversity. Phylogenetic and statistical analyses illustrate a heterogeneous distribution of the AEA community, probably caused by the differential distribution of the terrestrial or estuarine AEA in the various sampling sites. The deep-sea sedimentary environments potentially harbour diverse and novel AEA in the tropical West Pacific Continental Margin. The stations in the Philippine inland seas (including station 3043) may represent AEA assemblages with various terrestrial influences and the stations connected directly to the open Philippine Sea may represent marine environment-dominant AEA assemblages. Our study indicates the potential importance of geological and climatic events in the transport of terrestrial micro-organisms to the deep-sea sedimentary environments, almost totally neglected previously.

Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea

Diverse nifH and nifH-like gene sequences were obtained from the deep-sea surface sediments of the methane hydrate-bearing Okhotsk Sea. Some sequences formed novel families of the NifH or NifH-like proteins, of currently unresolved bacterial or archaeal origin. Comparison with other marine environments indicates environmental specificity of some of the sequences, either unique to the methane seep sediments of the Okhotsk Sea or to the general deep-sea methane seep sedimentary environments.

Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea

Ammonia-oxidizing archaea (AOA) have recently been found to be potentially important in nitrogen cycling in a variety of environments, such as terrestrial soils, wastewater treatment reactors, marine waters and sediments, and especially in estuaries, where high input of anthropogenic nitrogen is often experienced. The sedimentary AOA diversity, community structure and spatial distribution in the Changjiang Estuary and the adjacent East China Sea were studied. Multivariate statistical analysis indicated that the archaeal amoA genotype communities could be clustered according to sampling transects, and the station located in an estuarine mixing zone harboured a distinct AOA community. The distribution of AOA communities correlated significantly with the gradients of surface-water salinity and sediment sorting coefficient. The spatial distribution of putative soil-related AOA in certain sampling stations indicated a strong impact of the Changjiang freshwater discharge on the marine benthic microbial ecosystem. Besides freshwater, nutrients, organic matter and suspended particles, the Changjiang Diluted Water might also contribute to the transport of terrestrial archaea into the seawater and sediments along its flow path.

鄂霍次克海天然气水合物区与东海内陆架泥质区沉积物古菌多样性研究

为研究鄂霍次克海天然气水合物区沉积物古菌、甲烷厌氧氧化古菌和硫酸盐还原细菌的多样性分布，我们以PCR技术为基础构建mcrA、dsrAB和古菌16S rRNA 基因文库。对所获得的序列进行系统进化和统计学分析发现：鄂霍次克海古菌类群主要为Marine Benthic Group D (MBG-D)、Marine Benthic Group B (MBG-B)、Marine Crenarchaeotic Group I(MG- I)，另外少量古菌16S rRNA基因序列为Anaerobic Methanotrophs 2c（ANME-2c），主要分布在LV39-25H岩心的表层沉积物中。LV39-40H岩心表层的古菌群落结构与其他六个层位古菌群落结构相比有着显著的差异。mcrA基因序列主要为催化甲烷厌氧氧化的古菌ANME-2（c和d簇），在所研究的各个层位的沉积物中均广泛分布。少量的ANME-1（a簇）发现于LV39-40H岩心表层以下的沉积物中。产甲烷古菌数目不多，集中分布在LV39-25H岩心200cm和LV39-40H岩心180cm的沉积物中。dsrAB基因文库分析表明硫酸盐还原细菌种类丰富，表层沉积物中硫酸盐还原细菌多样性最高。在两个岩心所有层位的沉积物中都有一定数量的克隆属于DSS簇，它们可能与ANME共生催化甲烷的厌氧氧化作用。总之，所有数据表明在鄂霍次克海天然气水合物区存在着较活跃的甲烷厌氧氧化作用，揭示了参与甲烷厌氧氧化作用的微生物群落结构和多样性。 为研究东海内陆架闽浙沿岸泥质区不同深度沉积物中古菌群落垂向分布特征，通过古菌16S rRNA 基因文库共得到473个有效克隆50个OTUs (Operational Taxonomic Units)。16S rRNA基因序列系统进化和统计分析发现古菌分别归属于泉古生菌（Crenarchaeota）和广古生菌（Euryarchaeota），其中以Miscellaneous Crenarchaeotic Group（MCG）为主，仅含少量的MBG-B、South African Gold Mine Euryarchaeotic Group(SAGMEG)、 ANME-3、MG- I和MBG-D。该泥质区沉积物可能存在由ANME-3催化的甲烷厌氧氧化作用，同源序列分析表明其古菌群落分布与周边环境有较大联系。UniFrac与沉积物环境因子分析表明该泥质区古菌群落垂向分布与沉积物有机质含量和粒度变化密切相关。 通过对比发现，鄂霍次克海天然气水合物区甲烷厌氧氧化古菌主要为ANME-2和少量的ANME-1，而东海内陆架泥质区甲烷厌氧氧化古菌仅为极少量的ANME-3；鄂霍次克海天然气水合物区广古生菌和泉古生菌数量各占一半，主要为MBG-D、MBG-B、MG-I。东海内陆架泥质区沉积物古菌序列主要为泉古生菌（MCG）。海域类型的不同以及有机碳含量等环境因子的差异可能是这两个海域古菌群落结构差异的主要原因.

胶州湾和东太平洋海隆(~13°N)沉积物微生物多样性研究

海洋是一个巨大的生态系统，多样的微生物是构成海洋生态系统的基本元素。海洋微生物的群落结构及演变深刻的反映着海洋生态系统的变迁。本文采用分子生物学技术，研究了近海沉积物生态系统——胶州湾沉积物中细菌的多样性、群落结构的时空演替规律以及远洋深海沉积物生态系统——东太平洋海隆北纬13o附近深海沉积物中细菌和古细菌群落结构沿沉积物断层的分布情况，结果表明在两处沉积物中，微生物群落的结构都与环境因子有显著的相关性，是反映海洋沉积物环境特征的重要（分子）标志物，并且可能在这些环境中参与生物地球化学循环等重要过程。 1.从胶州湾不同区域的8个代表性站点采集4个季度的沉积物样品。提取总基因组DNA，利用16S rDNA作为分子标记，采用克隆文库对胶州湾沉积物中细菌群落的组成、空间分布和季节演替规律进行了研究。结果显示沉积物中的细菌具有高度多样性，来自于13个细菌门，同时还有28%的未鉴定克隆，表明胶州湾沉积物中蕴藏着巨大的微生物资源。其中已鉴定的优势种群是α-、β-、γ-、δ-变形细菌、绿弯菌、厚壁菌、蓝细菌和放线菌。同时还包括酸杆菌、拟杆菌、浮霉菌、疣微菌、芽单胞菌、绿菌、梭杆菌、异常球菌-栖热菌等类群的存在。将各克隆库的组成与温度、总碳、总氮等环境因子结合分析，结果显示细菌群落结构更替的主要驱动力是季节变化所带来的温度等环境因子的演变。对数据库中与本研究所获得序列具有最近亲缘关系序列的来源环境进行分析表明，胶州湾中细菌群落受航运活动、水产养殖、重金属污染等人类活动的明显影响，同时这些活动表现出显著的空间特异性，比如C4和D6等站点明显受到航运活动的影响，而A3和Y1等站点则容易受到沿岸径流所带来的淡水和油污染的影响。 2.分别利用PCR-DGGE和克隆文库技术对东太平洋海隆北纬13o附近深海柱状沉积物样品中细菌和古菌群体进行研究，结果显示这些微生物群落沿四个分别代表不同沉积年代断层明显的成层分布，与环境因子结合分析表明这种成层分布与氧化还原性质等地球化学特征的成层分布相吻合，提示我们该生态系统中的微生物受到环境因子的巨大作用，同时也表明这些微生物可能参与该生态系统中硫、金属元素代谢等过程。通过系统发育分析，四个断层中的微生物群落中呈现出很多与热液活动相关的个体（其中34.7%的细菌序列和31%的古菌序列与来源于各种热液环境的序列具有最近的亲缘关系）。但总体群落结构分析表明该区域可能属于热液活动影响区域的边缘，处于从热液活动环境到普通的低温沉积物环境的过渡区域。 3.将在胶州湾和东太平洋海隆北纬13o附近海洋沉积物生态系统中都存在的优势细菌类群（α-、β-、γ-、δ-变形细菌和放线菌、绿弯菌、厚壁菌、酸杆菌、浮霉菌）进行系统发育分析和背景比较分析，结果显示两处沉积物中的细菌优势种群虽然在大类群上很多是相同的，但是可能由于两处沉积物中不同物理化学等环境因子的选择作用（如胶州湾的近海特征和人为活动，东太平洋深海特点和热液活动），而导致优势种群在系统发育关系上距离比较远。这表明独特的微生物群落结构，特别是优势种群的群落结构信息是描述特定环境生态系统的重要方面。本研究表明在全球环境变迁中,自然环境因子和人类活动都在深刻改变着微生物群落的结构和功能。本文阐述了在环境变迁特定时期两处沉积物生态系统中的微生物群落结构及时空差异，为研究大范围生态系统的演变提供了依据，同时也为在两处沉积物环境中进行微生物参与的生物地球化学研究奠定了基础。