南海三沙永乐龙洞古菌群落结构与多样性特征     

甄毓  贺惠  傅亮  刘乾  毕乃双  杨作升 《海洋与湖沼》2018,49(6):1259-1267

海洋蓝洞作为一种独特的海洋地貌单元,洞内的生物群落结构与生态系统特征一直是国内外同行学者关注的热点问题之一。南海三沙永乐龙洞是世界上最深的海洋蓝洞(300m),其独特的生态特征更为引入瞩目。本研究以古菌16S rRNA基因序列为目标,采用Illumina高通量测序技术对西沙永乐龙洞内水体与沉积物中的古菌群落结构进行了研究。结果表明,本研究所获得的古菌类群可归为4门、21纲、29目、42科、45属,广古菌和奇古菌是丰度最高的两种古菌。龙洞内表层水体中古菌群落多样性与洞外水体相差不大,但随深度增加,洞内古菌群落多样性显著降低,深水层古菌群落结构与浅水层差异显著。龙洞内沉积物中的古菌生存环境与水体差异巨大,为大量特殊物种提供了生存空间。侧壁沉积物中的古菌群落多样性随深度增加显著降低,而150m平台处古菌群落多样性则远高于侧壁沉积物。水温对龙洞内水体中的古菌群落结构具有显著影响(P0.01)。研究结果显示永乐龙洞古菌群落有很高的多样性,其垂向分布与洞内环境多要素的变化密切相关。本研究对认识三沙永乐龙洞内的生态系统特征有显著意义。  相似文献   

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     

黄平平  赵峰  徐奎栋 《海洋与湖沼》2020,51(3):602-612

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。  相似文献   

Genomic resources for the spotted ragged-tooth shark Carcharias taurus     

JD Klein  AE Bester-van der Merwe  ML Dicken  A Emami-Khoyi  KL Mmonwa 《African Journal of Marine Science》2019,41(1):115-118

Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark Carcharias taurus using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.  相似文献   

罗氏沼虾(Macrobrachium rosenbergii)卵巢发育不同时期转录组分析     

陈雪峰  王春琳  顾志敏  徐宾朋  张宇飞  慎佩晶  程海华  彭菲  李喜莲  黄振远 《海洋与湖沼》2019,50(2):398-408

为发掘罗氏沼虾(Macrobrachiumrosenbergii)卵巢发育过程中的重要功能基因,采用IlluminaHiSeqTM4000高通量测序平台对罗氏沼虾卵巢发育四个时期卵巢组织进行转录组测序。所测序列经质控、组装后比对到NR、String、Swiss-prot、Pfam、GO、KEGG数据库中注释,并进行差异基因聚类分析。结果显示,四个样品共产生221580604个Cleanreads,拼接获得95379个Unigenes。分别对四个样品测序文库进行两两比较,共检测到6605个差异表达基因,其中显著上调基因2410个,显著下调基因4195个。GO功能分类显示,共有6422条unigenes可分为分子功能、细胞组分、生物学过程3大类59分支,差异基因主要涉及糖类转运、氨基酸合成、酶活性、细胞膜组成等。通过KEGG通路注释,共有8423条unigenes被注释,涉及184种代谢途径,有7个代谢通路与卵巢发育相关,差异基因的KEGG富集结果显示,药物代谢细胞色素P450通路、氨基丁酸神经元突触、鞘糖脂生物合成、氮素代谢等通路富集显著。此外,对SSR与SNP分子标记进行了鉴定。研究结果为进一步探索罗氏沼虾卵巢发育机制提供了基础信息。  相似文献   

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems     

《Limnologica》2017

The majority of usable freshwater is stored as groundwater in the subsurface. Pristine groundwater ecosystems are characterised as oligotrophic environments which facilitate low energy yield, activity, growth, and reproduction for numerous and highly adapted organisms living in these environments. Degradation of groundwater quality and quantity are hence reflected in the structural changes of groundwater species communities. Despite an increasing awareness of this problem, current assessment methods for groundwater ecosystems are solely based on the analysis of abiotic parameters. However, this approach is insufficient to detect changes in microbial communities and their related metabolic functions. In recent years, the development of culture-independent molecular techniques to analyse microbes has vastly improved our knowledge concerning the diversity and composition of microbial communities in various environments. High-throughput sequencing (HTS) techniques enable the detection of single bacterial species in a sample and thus provide a high resolution of the composition and diversity of microbial communities in various environments. Furthermore, the taxonomic information obtained allows for the inference of metabolic functions of a given community. However, since the method is labour intensive and costly it is not necessarily the method of choice for analysing numerous samples. By comparison, DNA-fingerprinting is a less elaborate and inexpensive method that is able to detect changes in microbial communities, although identification of species present in a community is not possible, and therefore represents a valuable supplement to HTS. The present paper intends to render information about the applicability of this method as a monitoring tool against this background, by directly comparing results of DNA-fingerprinting with the results of HTS. Despite the fact that the analysis of bacterial communities using HTS captured significantly higher diversity estimates in our study, results of both methods were positively associated. And even though HTS produced more accurate and detailed results regarding composition and diversity of bacterial communities, patterns of community composition captured by DNA-fingerprinting were similar in comparison to HTS. We thus can suggest DNA-fingerprinting as a cost efficient alternative for community assessment and diversity estimation, specifically as a promising methodological approach in environmental assays.  相似文献   

凡纳滨对虾(Litopenaeus vannamei)循环水养殖系统中养殖效果及菌群结构和功能研究     

唐亚鹏  董世瑞  田吉腾  周茜  王印庚  张天时 《海洋与湖沼》2022,53(2):466-474

循环水养殖可有效减少病原体的入侵,是我国水产养殖业发展的重要方向。为完善凡纳滨对虾(Litopenaeus vannamei)循环水养殖系统,采用生态调控、16S rRNA高通量测序、宏基因组学分析与数理统计等方法,系统分析了对虾循环水养殖系统中水质指标变化与菌群结构和基因功能的关系。结果显示,养殖池水质指标包括温度、溶解氧、盐度、pH以及氨氮0.11~1.16mg/L,亚硝酸氮0.10~0.66mg/L,硝酸氮0.84~35.40mg/L均在安全范围内;经过63d养殖,凡纳滨对虾平均体重达到11.78g左右,产量为3.28kg/m³左右,存活率为69.59%左右。菌群结构与功能分析结果显示:在开始运行期与水质变化平稳期生物滤池中菌群结构差异较大。在开始运行期海杆菌属(31.37%)占绝对优势,而在平稳期则以分枝杆菌属(6.65%)、分枝菌酸杆菌属(6.39%)、食烷菌属(5.21%)、海杆菌属(3.36%)、中慢生根瘤菌属(2.30%)、红杆菌属(1.34%)、副球菌属(1.29%)等反硝化细菌和硝化杆菌属(1.17%)占据优势。通过比对KEGG数据库发现涉及碳水化合物代谢和氨基酸代谢的蛋白数目最多,说明异养反硝化菌需要利用多种碳源来执行反硝化功能。  相似文献   

基于低压变频电场技术对带鱼(Trichiurus lepturus)保鲜过程中微生物群落影响分析          下载免费PDF全文

史恬恬  谢超  张家玮  李远慧  朱亚猛  吴玉婷  周卓颖  虞舟 《海洋与湖沼》2022,53(1):133-140

带鱼(Trichiurus lepturus)在低温条件运输和贮藏过程中,易受微生物和内源性蛋白酶的影响而产生胺类和醛类物质导致腐败。为了研究低压变频电场对微冻带鱼在贮藏过程中的微生物群落特征,采用Miseq基因组测序技术,对贮藏至40d的舟山带鱼的微生物群落进行碱基信息测序。将产生的碱基序列通过OTU聚类、多样性分析、相关性分析等手段分析了影响带鱼保鲜效果的微生物群落组成和发育信息。在此基础上,研究了不同强度电场(0,2,2.5,3 kV/m)处理对带鱼微生物群落组成的影响。根据菌属相对丰度结果,推测希瓦氏菌属(Shewanella)、假单胞菌属(Pseudomonas)、紫色杆菌属(Janthinobacterium)是带鱼微生物腐败主要致腐菌。结果表明,40 d后,经3 kV/m处理的样品其OTU6嗜冷菌属和OTU13假单胞菌属c的相对丰度均小于1%,而且OTU7、OTU14、OTU8、OTU9等菌属未被OTU聚类。结果表明,经3kV/m电场强度的低压静电场处理的抑菌保鲜效果最好,表现为在贮藏过程中杂菌种类最少,样本微生物群落物种丰度和多样性均最低,腐败程度最低。  相似文献   

Particle size shapes the prokaryotic microbial communities in mangrove sediments: A case study of Sanya,China     

Wu Qu  Michael Vicent Shija  Jie Wu  Min Jin  Jianxin Wang  Runying Zeng  Zhuhua Chan 《海洋学报(英文版)》2022,41(8):120-128

The prokaryotic microbial communities in the sediments play crucial roles in the ecological functions of mangrove ecosystems. Therefore, the environmental factors that affect the structures of these prokaryotic microbial communities could indirectly participate in the regulation of mangrove functions, which is of great value for mangrove studies. The particle size (PS) of soils is recently demonstrated as a key environmental factor for shaping the microbial communities; however, this hypothesis has rarely been tested for mangrove environments. A case study of three tropical mangroves from Sanya, China was performed in this work to assess the influence of PS on the prokaryotic microbial community structures of bacteria, archaea, diazotrophs, and denitrifiers in the sediments. Results showed the variability in the spatial scale and the stability in the temporal scale for the prokaryotic communities, indicating that the tropical mangrove sediments could be a versatile but stable environment. Among the collected environmental factors, PS, salinity, and humidity had the greatest impacts, and PS mostly affected the structures of these prokaryotic communities based on its highest R2 values of canonical correspondence analysis, Mental test, and linear fitting (p≤0.05). Furthermore, PS was positively correlated with the diversity and abundance of diazotrophic communities and negatively correlated with the abundances of methanogenic communities including Methanobacteriaceae, Methanospirillaceae, Methanoregulaceae, and Methanosaetaceae. Former studies show the increasing trend of PS caused by the rise of sea level and the intensification of human activities. Therefore, our findings indicate that PS could be a potential intermediate that links climate change and human activities with the possible ecological function migration of mangroves; meanwhile, the increase of PS could in turn release the stress of these environmental changes by increasing the abundance and diversity of the diazotrophic community and decreasing the abundances of methanogens.  相似文献   

De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis   总被引：1，自引：1，他引：0  

SONG Lipu  WU Shuangxiu  SUN Jing  WANG Liang  LIU Tao  CHI Shan  LIU Cui  LI Xingang  YIN Jinlong  WANG Xumin  YU Jun 《海洋学报(英文版)》2014,33(2):45-53

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Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene     

LIANG Xiayuan  WANG Xumin  CHI Shan  WU Shuangxiu  SUN Jing  LIU Cui  CHEN Shengping  YU Jun  LIU Tao 《海洋学报(英文版)》2014,33(2):27-36

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