Microbial uncultured community of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea

Using methods of molecular biology (PCR and cloning), we studied the diversity of microorganisms in the surface layers of bottom sediments from the bays of Gydan and Yenisei of the Kara Sea, which have different component composition of the pore water and mineralization level. Representatives of the domains Bacteria and Archaea were identified based on the analysis of the 16S rRNA gene fragment nucleotide sequences. The composition of the community of microorganisms in the bottom sediments changed with the changing salinity gradient of the pore waters. The phylogenetic analysis of the nucleotide sequences showed that the composition of the microbial communities in the southern parts of these bays was affected by fresh-water flows from rivers and streams from the lakes within the catchment area, whereas that in the northern parts was influenced by sea waters. The results indicate the presence of bacteria in the bottom sediments that are capable of using a wide range of substrates as a carbon source including hydrocarbons and organochlorine and aromatic compounds. These data can also indicate the presence of different pollutants in the sediments of these areas and the potential ability of bacteria to degrade chemical compounds that enter the waters and bottom sediments of the Kara Sea.     

Profiling Planctomycetales diversity with reference to anammox‐related bacteria in a South China Sea,deep‐sea sediment

A systematic assessment of Planctomycetales diversity in a South China Sea, deep‐sea sediment (1657 m) was conducted using the 16S rRNA gene analysis approach. PCR amplification of the samples from seven sediment layers (0.1, 1, 3, 5, 7, 9 and 11 m below the surface sediment) using the primer set Pla‐46‐F/1392‐R showed that the Planctomycetales existed within a limited range of sediment depths (≤ 5 m), and had a decreasing trend in diversity with increasing depth. The majority of the retrieved Pla‐46‐F/1392‐R sequences belonged to Pirellula‐related Planctomycetales, and two sequences retrieved from the 0.1‐m layer (GenBank accession numbers: DQ996944 and DQ996945 ) shared the same anammox‐related signature oligonucleotides and were closely related to commonly recognized anammox organisms. To identify new anammox‐related biomarkers, three primer sets were designed for amplifying the fragments of hydroxylamine oxidoreductase and S‐adenosylmethionine radical enzyme genes, but no related sequences were found. Our multiple 16S rRNA gene primer sets (Journal of Rapid Methods and Automation in Microbiology, 2008, in press) revealed even an higher diversity of Planctomycetales in the 0.1‐m layer of the sediment, especially at genus level. Our data profiled the distribution pattern of Planctomycetales diversity along sediment depths, and provided molecular evidence for the existence of anammox‐related bacteria in a new location, which broadens our understanding of Planctomycetales diversity in deep sea sediments.     

Molecular phylogenetic analyses of threeSynechococcus strains isolated from seawater near the ieodo ocean research station

ThreeSynechococcus strains were isolated from seawater near the Ieodo Ocean Research Station (IORS), and their 16S rDNA genes and the internal transcribed spacer (ITS) between the 16S and 23S rRNA genes were sequenced to investigate their phylogenetic relationships. Phylogenetic trees based on the 16S rDNA and ITS sequences showed that they clustered in the main MC-ASynechococcus group (subcluster 5.1), but formed branches differentiating them from the described clades. As the IORS is located in an area affected by diverse water masses, highSynechococcus diversity is expected in the area. Therefore, the IORS might be a good site to study the diversity, physiology, and distribution of theSynechococcus group. Key words —Synechococcus, Phylogeney, 16S rRNA, ITS gene, Ieodo     

Regional and temporal changes in bivalve diversity off the south coast of Portugal

From 2000 to 2006, a total of 75 bivalve species were identified, varying from 29 (spring 2001) to 54 species (spring 2005) per year. Seasonal tendencies in diversity varied according the year, thus the interpretation of long-term and regional scales is essential before drawing any conclusions in other studies. Richness and diversity consistently decreased with depth and increased with sediment grain size (from low in very coarse sand to high in coarse silt). Diversity decreased progressively from 3 to 16 m depth, thus the harsher shallower environments (due to waves and tidal air exposure) showed greater diversity than the most stable areas. Communities in finer sediments were more diverse than those in coarser sand. Evenness showed patterns opposite to diversity, overall.Diversity and evenness maps (produced with multivariate universal kriging), showed that most geographic areas with greater diversity were farer from river outflows and wastewater treatment plants. Two types of geographic pattern were observed: areas with persistently greater bivalve diversity through time and areas that changed locally from year to year. This spatial analysis can be used to establish priority conservation areas for management purposes, and to analyse the persistency of regional diversity patterns. The area with most habitat heterogeneity (Sotavento) corresponded to greatest diversity.There was a positive relationship between Spisula solida and Chamelea gallina landings and bivalve diversity 2 years and 1 year later, respectively. Possibly, local fisheries, by selectively withdrawing the commercial numerically dominant species from the ecosystem, increased diversity 1 to 2 years later, as the ecological niches of the dominants are quickly filled by several other species thereby creating a more even community. On regional scales, no significant impact was found on long-term bivalve diversity in local fisheries,     

Nematode species distribution patterns at the Håkon Mosby Mud Volcano (Norwegian Sea)

The Håkon Mosby Mud Volcano (HMMV) is a methane seep that is densely populated by the bacteria Beggiatoa spp. as well as by tubeworms of the Family Siboglinidae. Analyses of samples from seven stations located in five different habitats (bare sediments, bacterial mats, siboglinid fields, sediments with small patches of siboglinids and areas of ‘normal’ sea floor) revealed differences in the density and species‐level diversity of nematode communities. Total densities increased from stations inside the mud volcano and on its rim towards the ‘normal’ areas outside the volcano. Nematode species diversity was similar in samples from the siboglinid fields and the bare HMMV sediments. However, the sediment with patches of siboglinids collected outside the volcano was characterised by a diverse nematode community comprising 47 species, whereas the control sediments without siboglinids yielded only 27 species. The nematode assemblage at the bacterial mat site included only two identified species, Halomonhystera disjuncta and Sabatieria ornata, with H. disjuncta being strongly dominant. Terschellingia distlamphida, S. ornata and Aponema ninae dominated nematode communities at the siboglinid fields and in bare HMMV sediments. Species dominating at stations inside the caldera were found in comparable low densities in the sediment with siboglinid patches collected outside the volcano, but were missing in the background samples, where species of Endeolophos, Acantholaimus and Desmoscolex were dominant. Species diversity generally decreased with sediment depth. A subsurface‐dwelling nematode community was observed in the siboglinid fields and the bare sediments. Background sediments showed a sharp decline with 18–20 species at 0–2 cm versus three species at 3–5 cm sediment depth. The trophic composition of the nematode fauna at the HMMV showed a prevalence of deposit feeders at almost all stations, whereas background sediments exhibited a uniform distribution of non‐selective and selective deposit feeders and epistrate feeders. The high percentage of deposit feeders inside the mud volcano could be related to the grain‐size distribution and the significantly higher bacterial biomass compared to the control sediments.     

基于线粒体COI 基因的毛蚶群体遗传多样性

采用PCR技术,扩增了大连、乳山、烟台、舟山4个毛蚶(Scapharca subcrenata)地理群体共38个个体的线粒体COI基因部分序列,并分析了4个毛蚶群体的遗传多样性和系统发育关系。研究结果显示:38个毛蚶COI部分序列经处理得到长度均为625bp的基因片段,共分为30种单倍型;基于COI部分序列的分析结果,毛蚶4个地理群体总的变异位点为301个,多样性指数Pi为0.15048,平均核苷酸差异数为92.242,单倍型多样性指数S为241。聚类分析显示毛蚶大连群体、乳山群体和烟台群体具有高度的遗传多样性,3个群体交叉聚在一起,没有明显的群体分化;舟山群体单独聚为一支,与其他3个群体分化明显。研究表明,线粒体COI基因不能单独做为毛蚶大连、乳山和烟台群体的遗传标记,但可以作为毛蚶舟山群体的有效群体遗传标记,为线粒体COI基因在群体遗传学的应用提供了基础资料。     

Molecular phylogenetic analysis of sulfate-reducing bacteria from deep sediment layers of the tropical West Pacific warm pool

1IntroductionThe tropical West Pacific warm pool(TWP-WP),which spans an area roughly between10°Nto10°S of the equator from Indonesia to the dateline,has the world’s warmest sea surface temperature ofbeing greater than29℃.With the increase of recog-niz…     

非培养手段分析珠江口淇澳岛海岸带沉积物中的古菌多样性

利用古菌16SrDNA特异引物对珠江口淇澳岛海岸带沉积物中古菌的多样性及垂直分布特征进行研究。结果表明珠江口淇澳岛海岸带沉积物中古菌多样性丰富,大部分为新的不可培养古菌;泉古菌在整个沉积物柱中是优势菌群,约占81%;古菌多样性随沉积物深度增加而增加,区系结构也随深度变化而呈现出明显的不同,在表层沉积物中,88%的序列属于Ⅰ型海洋泉古菌(MGⅠ),而在中层和底层检测到的古菌序列大部分与不可培养的富含甲烷的环境序列有最高的同源性,并且有15%的克隆子序列属于甲烷八叠球菌目(Methanosarcinales)和甲烷微菌目(Methanomicrobiales)。QC-PCR结果表明珠江口淇澳岛海岸带沉积物中古菌含量丰富[(1.93±0.60)×106~6.45±0.25×10716S rDNA拷贝/g],呈现随深度增加含量增加的趋势。     

中国南海一株固氮类芽孢杆菌的筛选和分离鉴定

为了解中国南海海洋自生固氮菌的种类,作者对采集的南海海底淤泥样品进行了固氮微生物的分离、筛选及鉴定。经过土样沸水加热处理,无氮培养基平板初筛后,对分离获得的细菌固氮酶结构基因nif H进行扩增,并对其固氮酶活性进行检测,最终获得一株能够产芽孢的固氮细菌。对该菌株进行生理生化性状测定、16S r DNA序列分析(Gen Bank登录号KJ627376),并基于nif H、16S r DNA系统进化树分析,确定该菌为一株固氮类芽孢菌(Paenibacillus sp.)NH-1。本研究表明固氮类芽孢杆菌在海洋中确有分布,海洋自生固氮菌的多样性远远超出人们之前的认识。     

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.     

Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin

A giant 800-m-diameter pockmark named REGAB was discovered on the Gabon continental margin actively emitting methane at a water depth of 3200 m. The microbial diversity in sediments from four different assemblages of chemosynthetic organisms, Mytilidae, Vesicomyidae, Siboglinidae and a bacterial mat, was investigated using comparative 16S rRNA gene sequence analysis. Aggregates of anaerobic methanotrophic archaea (ANME-2) and bacteria of the Desulfosarcina/Desulfococcus cluster were found in all four chemosynthetic habitats. Fluorescence in situ hybridization targeting the ANME-2/Desulfosarcina/Desulfococcus aggregates showed their presence few centimeters (3–5 cm) below the surface of sediment. 16S rRNA gene sequences from all known marine ANME groups were detected in the pockmark sediments, as well as from both known bacterial partners. The archaeal diversity was limited to the ANME cluster for all investigated samples. The bacterial diversity included members of the Proteobacteria, Bacilliales, Cytophaga/Flavobacteria, Verrucomicrobia, JS1 and Actinobacteria clusters. Bacterial 16S rRNA gene sequences related to those of known sulphide-oxidizing symbionts were recovered from tissues of several invertebrates including vesicomyid clams and siboglinid tubeworms of REGAB.     

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...     

8种石首鱼类线粒体基因组特征及分子系统进化分析

为探讨石首鱼科(Sciaenidae)鱼类分子系统进化关系,采用生物信息学方法分析了黑鳃梅童鱼(Collichthys niveatus)、棘头梅童鱼(C.lucidus)、大黄鱼(Larimichthys crocea)、小黄鱼(L.polyactis)、鮸鱼(Miichthys miiuy)、白姑鱼(Pennahia argentata)、黄姑鱼(Nibea albiflora)和皮氏叫姑鱼(Johnius belangerii)共8种石首鱼类线粒体基因组全序列的基本特征。结果显示,除皮氏叫姑鱼外,其余7种石首鱼类编码的37个基因排列顺序与脊椎动物线粒体基因组相同。基因组碱基分布存在不均衡现象,A+T含量高于G+C含量。线粒体基因组的基因变异位点分析结果表明,ND4和ND5基因可作为COI基因的辅助分子标记,应用于石首鱼类群体遗传学的研究中。黄鱼亚科5种鱼类13个蛋白质编码基因的Ka/Ks比值远低于1,显示出较强的纯化选择。皮氏叫姑鱼与其他石首鱼间的遗传距离均较大且亲缘关系较远,暗示叫姑鱼属或为石首鱼类中较为原始的类群。基于线粒体基因组全序列构建NJ系统树支持黄鱼亚科和白姑鱼亚科亲缘关系较近的形态学结论。而基于去除控制区后序列和13个蛋白质编码基因序列构建的系统树则表明两亚科鱼类间的差别在非编码区更为明显。     

山口红树林根际土壤可培养细菌多样性及其活性筛选

为探讨广西山口红树林土壤可培养细菌的多样性,采用纯培养分离技术对采集的25个红树林样品进行可培养细菌多样性分析,挑选117株菌株进行16S rRNA基因测序并构建系统发育树分析。结果表明117株菌株分别属于9个纲20个目27个科35个属,9个纲包括α-变形菌纲（21.37%）、β-变形菌纲（1.71%）、γ-变形菌纲（12.82%）、δ-变形菌纲（0.85%）、噬纤维菌纲（0.85%）、鞘脂杆菌纲（0.85%）、黄杆菌纲（2.56%）、放线菌纲（27.35%）、芽孢杆菌纲（31.62%）。优势属为芽孢杆菌属,占所有菌株的28.20%,此外α-变形菌纲、γ-变形菌纲、黄杆菌纲和放线菌纲中发现了7株潜在的新物种。分离菌株的产酶活性检测表明,山口红树林根际土壤蕴含丰富的产淀粉酶、蛋白酶、葡聚糖、纤维素酶和几丁质酶等生物活性酶的菌株,其中芽孢杆菌纲的产酶菌株数最为丰富。初步研究结果表明广西山口红树林土壤可培养细菌资源丰富,新物种资源多样,是农业微生物开发应用的重要资源库。     

合浦珠母贝iPS细胞相关的转录因子的克隆及分析

转录因子Sox2、Oct4、c-Myc和KLF4在iPS细胞研究中具有重要作用,将它们加入体外培养的细胞中,可以诱导体细胞去分化成为多能干细胞。作者通过RACE-PCR技术从合浦珠母贝(Pinctada fucata)的外套膜组织中克隆获得了3个转录因子——c-Myc、Sox2及KLF4的cDNA。c-Myc全长1585bp,开放阅读框的长度为1131bp,编码376个氨基酸,蛋白结构分析表明它具有保守的HLH和Myc-N结构域。Sox2全长1908bp,开放阅读框长度为990bp,编码329个氨基酸,蛋白结构分析它具有保守的HMG-box和Soxp结构域。KLF4全长2268bp,开放阅读框长624bp,编码207个氨基酸,预测该蛋白具有两个zf-H2C2_2结构域。BLAST分析它们均与太平洋牡蛎的相关蛋白具有较高同源性,说明其与太平洋牡蛎亲缘关系更近。RT-PCR实验发现这3个基因在合浦珠母贝外套膜、足、生殖腺、内脏团、闭壳肌和鳃6种组织中均有表达,表明它们是非常保守的转录因子。本研究对于合浦珠母贝细胞系建立和研究具有启发意义。     

高通量测序分析北仑河口红树林潮间带底栖真核生物分布

为了解红树林不同潮位沉积物中底栖真核生物群落分布,基于18S rRNA基因采用高通量测序方法分析了广西北仑河口陆缘、林中和海缘3个潮位红树林沉积物中底栖生物群落结构。结果表明,北仑河口潮间带红树林沉积物中底栖生物多样性丰富,Shannon-Wiener指数变化范围在6. 08～6. 73之间; PCA分析表明潮间带中底栖生物群落差异较大,陆缘红树林中扁形动物、节肢动物和软体动物相对丰度较高,林中区域中纤毛虫、环节动物和轮虫相对丰度较高,海缘红树林中硅藻相对丰度较高;红树林中主要OTUs有桡足类的太平洋纺锤水蚤(Acartia pacifica)、硅藻类的海链藻(Thalassiosira sp.)、纤毛虫类的前管虫(Prorodon teres)、多毛类的小头虫(Capitella sp.)。高通量测序方法能较全面反映红树林区微型/小型底栖生物群落,研究结果为丰富红树林底栖生物群落研究和解析底栖生物在红树林生态系统发挥的作用提供基础数据。     

栉孔扇贝(Chlamys farreri)过氧化物酶体增殖物激活受体基因的鉴定与表达分析

过氧化物酶体增殖物激活受体(peroxisome-proliferator-activated receptors,PPARs)是核激素受体超家族成员,在脂肪代谢过程中发挥重要的调控作用,目前贝类过氧化物酶体增殖物激活受体仍未见报道。本文利用已发表的栉孔扇贝(Chlamys farreri)基因组和转录组,获得其PPAR基因,命名为CfPPAR-like,基因开放阅读框全长1572 bp,编码486个氨基酸,预测蛋白质分子量MW为54305.3 Da,等电点pI为8.3,二、三级结构以转角和卷曲为主,无信号肽和跨膜区域,属于胞内蛋白。与脊椎动物PPARs蛋白序列比对表明CfPPAR-like包含DBD和LDB结构域,其中DBD区域保守性较高,而LBD的保守性较低。进化分析显示,栉孔扇贝等软体动物的PPARs聚为单独一支,仿刺参等棘皮动物的PPARs聚为单独一支,果蝇和线虫的PPARs基因同源物在进化树的最外端,脊椎动物的三种PPARs亚型分别聚类后,再与无脊椎动物PPARs聚类,结果支持核激素受体超家族在脊椎动物进化早期出现了各亚型这一假说。CfPPAR-like在幼虫发育过程中呈现普遍性表达,暗示其参与扇贝幼虫早期的分裂,贝壳的形成以及幼贝的变态过程;在成体各组织中,CfPPAR-like在栉孔扇贝的性腺、肾脏以及消化腺中表达量较高,表明其参与扇贝性腺分化、脂肪代谢等过程的调控。研究结果对于揭示贝类脂质代谢调控机制以及优良扇贝品种的培育具有重要意义。     

杭州西溪湿地沉积物细菌的群落结构和多样性

采用Illumina Mi Seq高通量测序技术,对杭州西溪湿地4种不同植被下沉积物的细菌多样性进行了研究。通过提取样品基因组DNA,对16S r RNA V3、V4区测序,共获得有效序列67734条,产生2181个OTU,序列平均长度为441 bp,其中大于400bp的序列占99.74%。对97%相似水平的OTU代表序列进行分类学分析,结果表明,沉积物具有很高的细菌多样性,涵盖了30个门252个属的细菌。其中变形菌门(Proteobacteria)是各样品的优势类群,所占比例高达30.0%—64.7%。同时,β-变形菌纲、γ-变形菌纲和δ-变形菌纲在变形菌门中占主导地位,在这些类群中发现有大量与N、S等元素代谢相关的菌群,应该在湿地沉积物的元素循环中发挥着重要作用。此外,4个样品中约有10%—15%的序列属于无法确定分类位置(Unclassified)的类群,说明西溪湿地沉积物中蕴藏有较多的潜在新物种。本研究结果将为西溪湿地的保护和修复提供理论和实践依据。     

Molecular evidence for multiple UDP-glucuronosyltransferase gene familes in fish

The presence of multiple distinct UGT genes in fish was derived by analysis of DNA sequence data derived the zebrafish EST project, confirming indications from previous protein purification studies in another fish species, the plaice, for a diversity of isoforms in lower vertebrates. At least 10 different UGTs can be identified from nucleotide sequence data in zebrafish. Phylogenetic analysis of exon 1 sequences of the zebrafish, plaice and human UGTs indicates that six of these genes are related to the 1A, 1B and 2 families and that a further four genes were of more ancient lineage. Importantly data for the 3' sequences of the zebrafish clones, both from the database and our own sequences of the publicly available clones did not provide any evidence for elaboration of family 1A genes by alternative splicing in this lower vertebrate.     

莱州湾近岸海域浮游纤毛虫群落组成和季节变化

浮游纤毛虫是真核微型生物的重要类群,在浮游生态系统中发挥着重要作用。利用传统形态学与高通量测序技术相结合的方法,于2020年9月至2021年8月对莱州湾三山岛近岸浮游纤毛虫进行每月两次的调查。对环境DNA的18S rRNA基因的V4区进行高通量测序,结果显示无壳寡毛类(占纤毛虫序列丰度的40.14%)和砂壳纤毛虫(10.67%)是优势类群,并且具有明显的季节变化。无壳寡毛类在冬季序列相对丰度最高,主要由急游虫属(Strombidium)和急游虫科未定类群(Strombidiidae_X)组成;砂壳类在春夏季序列相对丰度最高,主要由砂壳目未定类群(Tintinnida_XX)和拟铃虫属(Tintinnopsis)组成。浮游纤毛虫群落的β多样性呈现显著的季节变化,而α和β多样性在站点间差异均不显著。与环境因子的RDA分析显示,总有机碳和溶解氧含量是影响纤毛虫群落结构的主要环境驱动因子。形态学方法共检获鉴定17种纤毛虫,分别隶属于7个属,其中砂壳类在多样性和检获频率上均为最优势类群。研究填补了莱州湾三山岛海域浮游纤毛虫的多样性、群落结构和季节动态研究的空白,同时为深入研究温带海湾近岸浮游纤毛虫群落的长期变化规律以及对环境因子的响应机制提供本底资料。