Biodiversity and community composition of sediment macrofauna associated with deep-sea Lophelia pertusa habitats in the Gulf of Mexico

Scleractinian corals create three-dimensional reefs that provide sheltered refuges, facilitate sediment accumulation, and enhance colonization of encrusting fauna. While heterogeneous coral habitats can harbor high levels of biodiversity, their effect on the community composition within nearby sediments remains unclear, particularly in the deep sea. Sediment macrofauna from deep-sea coral habitats (Lophelia pertusa) and non-coral, background sediments were examined at three sites in the northern Gulf of Mexico (VK826, VK906, MC751, 350–500 m depth) to determine whether macrofaunal abundance, diversity, and community composition near corals differed from background soft-sediments. Macrofaunal densities ranged from 26 to 125 individuals 32 cm⁻² and were significantly greater near coral versus background sediments only at VK826. Of the 86 benthic invertebrate taxa identified, 16 were exclusive to near-coral habitats, while 14 were found only in background sediments. Diversity (Fisher’s α) and evenness were significantly higher within near-coral sediments only at MC751 while taxon richness was similar among all habitats. Community composition was significantly different both between near-coral and background sediments and among the three primary sites. Polychaetes numerically dominated all samples, accounting for up to 70% of the total individuals near coral, whereas peracarid crustaceans were proportionally more abundant in background sediments (18%) than in those near coral (10%). The reef effect differed among sites, with community patterns potentially influenced by the size of reef habitat. Taxon turnover occurred with distance from the reef, suggesting that reef extent may represent an important factor in structuring sediment communities near L. pertusa. Polychaete communities in both habitats differed from other Gulf of Mexico (GOM) soft sediments based on data from previous studies, and we hypothesize that local environmental conditions found near L. pertusa may influence the macrofaunal community structure beyond the edges of the reef. This study represents the first assessment of L. pertusa-associated sediment communities in the GOM and provides baseline data that can help define the role of transition zones, from deep reefs to soft sediments, in shaping macrofaunal community structure and maintaining biodiversity; this information can help guide future conservation and management activities.     

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.     

东太平洋深海沉积物中DNA的提取及细菌多样性初步分析

以东太平洋海隆附近深海柱状沉积物为材料,通过化学裂解和酶消化相结合的方法提取了沉积物微生物的总基因组DNA,并进行了纯化。结果表明所得到的DNA分子片段大小在21kb左右,纯化后的DNA可直接用于PCR等分子生物学操作。细菌16SrDNAV3可变区的PCR—DGGE图谱展示出15条以上条带,表明深海沉积物中细菌多样性较高,群落结构比较复杂。对其中9条主要条带进行回收、测序和系统发育分析,结果表明所获得的序列分属放线菌门（Actinobacteria）,绿弯菌门（Chloroflexi）,γ-变形细菌亚门（Gamma—proteobacteria）,α-变形细菌亚门（Alpha—proteobacteria）和嗜酸菌门（Acidobacteria）5个大类群。     

深海热液环境中脂肪酸组成的研究进展

1977年科学家们在东太平洋拉帕戈斯裂谷发现了深海热液喷口,揭示了以化能合成为基础的一个新的生命世界。围绕喷口的热液环境不同于一般深海环境,具有异常的化学特征:高温、高压且硫化物含量丰富,因此,接近热液的生物,     

Abundance and distribution of fatty acids within the walls of an active deep-sea sulfide chimney

Abundance and distribution of total fatty acids (TFAs) were examined along the physicochemical gradient within an active hydrothermal chimney collected from the Main Endeavour segment of Juan de Fuca Ridge. Approximately 27 fatty acids are identified with a chain-length ranging from C12 to C22. From the exterior to the interior of the chimney walls, the total concentrations of TFAs (∑ TFAs) show a trend of evident decrease. The observed compositions of TFAs are rich in bacterial biomarkers especially monounsaturated fatty acids (MUFAs) and minor branched and cyclopropyl FAs. On the basis of the species-specific FAs and bacterial 16SrRNA gene analysis (Li et al., unpublished data), sulfur-based metabolism appears to be the essential metabolic process in the chimney. Furthermore, the sulfur oxidizing bacteria (SOB) are identified as a basic component of microbial communities at the exterior of the hydrothermal chimney, and its proportion shows an inward decrease while the sulfate reducing bacteria (SRB) have an inverse distribution.     

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.     

南海北部陆坡深水区沉积物细菌多样性调查

采用分子生物学手段,调查南海北部陆坡深水区沉积物细菌多样性.分析表明其细菌分成5个类群,变形细菌门(Proteotmcteria),厚壁菌门(Firmicutes),浮霉菌门(Planctomycetes),拟杆菌门(Cytophaga/Flexi-bacteria/Bacteroides,简称CFB)及脱铁杆菌门(Deferribacteres).分别占总体的34%,38%,18%,4%,6%.其中60%以上的克隆子与硫代谢相关,20%克隆子最相近序列来自于油污染环境,说明硫代谢是该区域物质代谢的重要组成,同时该区域有油气渗透的烃类物质存在并影响着该区域的微生物群落结构.     

Spatial distribution, diversity and composition of bacterial communities in sub-seafloor fluids at a deep-sea hydrothermal field of the Suiyo Seamount

Spatial distribution, diversity, and composition of bacterial communities within the shallow sub-seafloor at the deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean, were investigated. Fluids were sampled from four boreholes in this area. Each borehole was located near or away from active vents, the distance ranging 2–40 m from active vents. In addition, fluids discharging from a natural vent and ambient seawater were sampled in this area. We extracted DNA from each sample, amplified bacterial 16S rRNA genes by PCR, cloned the PCR products and sequenced. The total number of clones analyzed was 348. Most of the detected phylotypes were affiliated with the phylum Proteobacteria, of which the detection frequency in each clone library ranged from 84.6% to 100%. The bacterial community diversity and composition were different between hydrothermal fluids and seawater, between fluids from the boreholes and the vent, and even among fluids from each borehole. The relative abundances of the phylotypes related to Thiomicrospira, Methylobacterium and Sphingomonas were significantly different among fluids from each borehole. The phylotypes related to Thiomicrospira and Alcanivorax were detected in all of the boreholes and vent samples. Our findings provide insights into bacterial communities in the shallow sub-seafloor environments at active deep-sea hydrothermal vent fields.     

西南印度洋深海热液硫化物区沉积物微生物群落结构和固氮基因多样性

A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.     

海南岛东部501站位沉积物古细菌多样性研究

从海南岛东部501站位沉积物中扩增古菌16S rRNA基因构建文库,并对得到的OTU(Operation taxonomic units)进行系统发育学分析.古菌文库由泉古生菌(Crenarchaeota)和广古生菌(Euryarchaeota)构成,其中泉古生菌占总克隆文库的96.8%,由I型海洋泉古生菌(Mrain...     

Novel active kinetoplastids associated with hypersaline anoxic basins in the Eastern Mediterranean deep-sea

The combination of nearly saturated salt concentration and corresponding high density, high hydrostatic pressure, absence of light, anoxia, and a sharp chemocline make the deep hypersaline anoxic basins in the Eastern Mediterranean Sea some of the most polyextreme habitats on Earth. Using kinetoplastid-specific primers, we detected kinetoplastid flagellates in some of the harshest deep-sea environments known to date, including some whose small subunit ribosomal RNA gene sequences are not closely related to cultured representatives. Kinetoplastids, including presumably novel representatives appear to be specialists of halocline environments in the Eastern Mediterranean, and to comprise a significant fraction of the protist communities in the brines and haloclines of several basins. Fluorescent in situ hybridization data indicate a novel ‘unidentified’ sequence clade of kinetoplastids related to bodonids represents as much as 10% of the total protist community in the Discovery Basin halocline. Different kinetoplastid groups are unevenly represented in the different basins and habitats we sampled, which we discuss as a result of environmental selection.     

印度洋深海沉积物样品纯培养细菌的分离鉴定

为探索印度洋深海沉积物中纯培养细菌的多样性,本文对采自印度洋12个沉积物样品进行细菌纯培养分离,共获得343株细菌。所有细菌采用16S rRNA 基因进行比对分析,鉴定为4个门：厚壁菌门（Firmicutes）、变形菌门（Proteobacteria）、放线菌门（Actinobacteria）和拟杆菌门（Bacteroidetes）,5个纲,13个目,26个科,39个属下的121个种。分离出的优势类群为链霉菌属（Streptomyces,分离率为16.53%）和芽孢杆菌属（Bacillus,分离率为8.26%）,其中可能有12个潜在的新分类单元。研究结果表明,印度洋深海沉积环境中纯培养细菌资源丰富,潜在新物种较多;其次,分离培养方法与从海洋沉积物中获得的细菌物种多样性直接相关。     

High gray whale relative abundances associated with an oceanographic front in the south-central Chukchi Sea

We describe gray whale (Eschrichtius robustus) distribution in the south-central Chukchi Sea in relation to environmental factors during two 5-day surveys in June and September of 2003. Whale counts per 10-min scan (an index of relative abundance) ranged from 0 to 41 in June and from 0 to 28 in September. CTD data showed an ocean front around 67.8°N with strong horizontal gradients in temperature, salinity, chlorophyll-a concentration and water-column stability. Highest whale abundance indices occurred in or near the front in both periods. Preliminary qualitative assessment of biological communities in the study area suggests that infaunal clams, echinoderms, euphausids, chaetognaths and Arctic cod were common, while ampeliscid amphipods, the previously abundant infauna (and likely prey) in the nearby Chirikov Basin feeding area, were not dominant. Euphausids may be a prey for gray whales in this area. We suggest that frontal systems may play an important role in eastern North Pacific gray whale foraging grounds. Further study is needed to fully describe the role of frontal systems in gray whale foraging grounds.     

Morphology and downslope sediment displacement in a deep-sea valley,the Valencia Valley (Northwestern Mediterranean)

The Valencia Valley is a Quaternary, 200 km long deep-sea valley in the Valencia Trough, Western Mediterranean Sea. A swathmapping survey approximately mid-way along the valley length, where the floor has an average gradient of 1:250 (0.2°), shows valley walls that rise 200 to 350 m above the valley floor, with slopes of 2 to 18°. Sediment forming the walls is undergoing retrogressive, upslope-directed slumping with increasing bedding disruption along steeper walls. The valley exhibits a winding course with steep outer and gentler inner walls around bends, and bedforms on the valley floor. Lateral migration around bends is less than 5 km and the valley is deeply entrenched into Quaternary-bedded sediments.     

Composition and heterogeneity of the microbial community in a coastal microbial mat as revealed by the analysis of pigments and phospholipid-derived fatty acids

The beaches of the North Sea barrier island Schiermonnikoog (The Netherlands) are covered by microbial mats. Five types of microbial mats were distinguished based on a variety of characteristics, located along a transect perpendicular to the coast. Biomass abundance and composition of the microbial community were analyzed in these mats using pigments and phospholipid-derived fatty acids (PLFA) as biomarkers. Biomass per gram sediment increased more than six-fold from the mats at the low water mark to mats found at the edge of the dunes. Microscopic analysis revealed that the increase in biomass was accompanied by a change in species composition. Pigment- and PLFA composition reflected the changes in species composition. The PLFA data could be used to estimate the relative group abundance using the matrix factorization program CHEMTAX., whereas the pigment data were found not to be suitable for this purpose.     

Isotopic composition of fatty acids of extremely piezophilic bacteria from the Mariana Trench at 11,000 m

Two extremely piezophilic bacteria, DB21MT-2 and DB21MT-5, isolated from sediments of the Mariana Trench at 11,000 m, were grown in the laboratory under low-temperature (10 °C) and high-pressure (70 MPa) conditions. Phospholipid ester-linked fatty acids (PLFA) were analyzed by gas chromatography/mass spectrometry (GC/MS) and isotopic compositions of individual fatty acids were determined by gas chromatography isotope ratio mass spectrometry (GC-IRMS) in order to determine isotopic fractionation effects during biosynthesis. The piezophiles are characterized by fatty acids with carbon chains ranging from 14 to 22 carbons in length and by the presence of abundant polyunsaturated fatty acids (PUFA). Fatty acids from each culture exhibit a wide range of isotopic compositions (δ¹³C vs. Pee Dee Belemnite (PDB)). With two exceptions (C15:0 and C17:1 from DB21MT-2), all fatty acids are depleted in ¹³C relative to that of bulk carbon in the bacterial growth substrate. In addition, strain DB21MT-2 shows systematically higher (less negative) δ¹³C values than strain DB21MT-5. The implications for isotope fractionation in fatty acid biosynthesis and the interpretation of isotopic composition of sedimentary fatty acids are discussed. It is suggested that the same type of microorganisms could have rather different δ¹³C under the same growth conditions, and that sedimentary fatty acids with distinct δ¹³C values do not necessarily have to originate from different organisms. Interpretation of δ¹³C values of sedimentary biomarkers may be complicated by such large variations in δ¹³C of fatty acids given that they are biosynthesized by the same type of microorganisms grown under identical conditions.     

Inventory of nonvolatile fatty acids and hydrocarbons in the oceans

A survey of the distribution of nonvolatile fatty acids and hydrocarbons in the oceans is given. The results represent more a “feel” from the literature rather than a mathematical analysis and are given in Table III. Fatty acid concentration appears to show a greater variation, presumably because they are more prone to biological influences than the hydrocarbons.     

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.