半滑舌鳎循环水养殖系统中生物滤池细菌多样性及功能预测分析

生物滤池中生物膜细菌群落是循环水养殖系统水处理的重要组成部分,目前关于半滑舌鳎海水循环水系统生物滤池生物膜细菌群落和功能研究鲜见报道。本研究于2019年4月对海水循环水养殖系统3级生物滤池中水体和生物膜进行采样,采用高通量测序技术对其群落组成进行了研究分析,结果表明生物滤池细菌群落主要由变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、浮霉菌门(Planctomycetes)、蓝藻细菌门(Cyanobacteria)等27个门组成,具有丰富的群落组成,生物膜和养殖水体样品细菌群落结构有所差异,不同生物滤池中生物膜细菌群落结构有较大差异;生物膜与水体中的浮霉菌门细菌存在显著差异,且在生物膜上发现有5.6%～11.7%的浮霉菌门细菌,推断其可能进行硝化作用。PICRUSt功能预测分析表明生物膜上细菌主要涉及代谢、遗传信息处理和环境信息处理等6类生物代谢通路,各级生物滤池生物膜细菌群落功能有所差异,所有样品均发现有氮代谢功能(Nitrotoluene degradation)的基因。本研究从细菌群落组成、细菌群落多样性及功能预测等角度初步分析了海水循环水系统3...     

基于高通量测序的表层水体纤毛虫多样性评估方法比较与优化

基于扩增子的高通量测序技术广泛应用于微型生物多样性的研究, 不同的测序手段和数据分析流程, 影响着微型生物多样性与群落结构的分析结果。本研究以易于形态鉴定的砂壳纤毛虫作为研究对象, 比较DNA测序、RNA测序和形态学方法检获的多样性和物种组成等, 探究序列分析流程中关键步骤: 嵌合体处理、可操作分类单元分析方法选择、合并相似分类单元以及去除稀有类群等对多样性结果的影响。研究结果显示无论基于DNA还是RNA的分子手段与形态学方法检获的主要物种基本一致, 与DNA测序相比, RNA测序检获的物种数少, 但差异不显著。基于97%以上相似度聚类和单核苷酸变异所得群落结构相似, 无显著差异; 且所有分析方法都能在一定程度上反映出自然界中不同类群的相对丰度。相较于单核苷酸变异和其他相似度阈值, 99%相似度下聚类所得多样性更为接近形态学结果。去除嵌合体和稀有类群(去除阈值: DNA测序0.05%; RNA测序0.07%), 可明显改善分子多样性虚高的问题。本研究为纤毛虫等真核微生物的分子多样性研究提供了科学的数据分析流程, 对未来真核微生物多样性研究具有指导意义。     

采水量对寡营养海域浮游真核微生物分子多样性评价的影响

真核微生物是海洋生态系统中生物多样性高且功能重要的组成部分,但因个体微小且形态特征不明显,传统的分类学方法很难全面评估其多样性。环境DNA结合高通量测序技术为真核微生物多样性研究提供了可靠技术支撑,然而采水量对于评估寡营养海域浮游真核微生物多样性的影响仍知之甚少。本研究在吕宋海峡及菲律宾海盆中设置5个采样点,每个站点各取4个10 L表层海水样品用于真核微生物高通量测序分析。对各站每个重复所获得的真核微生物多样性进行研究,并分析了采水量与真核微生物OTU数量、群落结构及优势种和稀有种之间的关系。研究发现,采水量和真核微生物OTU数量之间呈正相关关系, 10 L水所获得的平均OTU数量为40 L水的64%, 20 L水可获得82%, 30 L水为92%。10 L样品所获得的群落多样性指数显著低于30 L和40 L样品检获的群落,而20 L样品与30 L和40 L样品在多样性指数上无显著差异。随着采水量增加,更多的稀有OTUs被检获,而丰富OTUs数量变化不明显。但统计分析显示, 10 L与40 L组样品检获的真核微生物群落结构无显著差异。因此,综合考虑样品的可得性和现场处理时间,最低20L...     

南极菲尔德斯半岛土壤微生物在富集传代培养中对菲的响应

为揭示富集传代培养过程中南极多环芳烃降解菌群的演替规律,以菲为唯一碳源和能源对南极菲尔德斯半岛不同地理位置的6份土壤样品进行了富集和连续传代培养,并采用高通量测序技术分析了富集传代培养过程中菲降解菌群的群落结构及生物多样性.Alpha多样性分析结果表明,在富集培养阶段南极菲降解菌的物种丰富度显著高于传代培养阶段(P＜0...     

胶州湾浮游原生生物时空分布特征——丰度周年变化及与环境因子间的关系

为了解胶州湾浮游原生生物时空分布特征及与环境因子间的关系,自2007年6月～2008年5月,对青岛胶州湾内5个站点表层水的浮游原生生物丰度及环境因子进行了累计24次的周年采样调查及定性、定量分析.结果显示:(1) 浮游原生生物周年变动具有2个高峰,分别出现在4月和8月;(2) 浮游硅藻、鞭毛藻和纤毛虫的丰度周年变动均为双峰型:春节(4月)高峰、秋节(8月)高峰;(3) 浮游原生生物丰度与叶绿素a和溶解氧呈显著性相关,而其群落结构的变化与盐度、溶解氧、硝态氮和亚硝态氮的组合呈显著性相关.本工作为进一步探讨富营养化的内湾型近岸水体内原生生物生态学结构与功能提供了一份必要的基础资讯.     

中国亚热带-热带3个海区微型鞭毛虫群落优势种和稀有种的分布特征和建群机制

海洋微型鞭毛虫是海洋微型真核浮游生物中非常重要的一大类群,在构成和维持海洋生态系统的结构和功能中扮演着重要角色。微生物群落通常由少数优势种和大量稀有种组成,这种分布模式在海洋微型鞭毛虫群落中也极为常见,并且二者的内在特征可能对群落生物地理分布格局以及生态系统功能产生不同影响。然而在多数研究中并未将两种不同亚群落进行区分,对二者的分布特征、对环境和空间因子的响应以及在总体群落中的生态地位等的认识十分有限。本研究利用高通量测序技术,调查了中国近海亚热带-热带3个自然海区微型鞭毛虫群落中优势种和稀有种的分布特征,并探讨了环境因子和空间因子与不同亚群落之间的关系,利用中性模型揭示了中性过程在群落构建中的作用,最后通过共现网络分析解析了两种不同亚群落在总体群落中的生态地位。结果表明：3个海区微型鞭毛虫群落中的优势类群和稀有类群在多样性和物种组成上具有不同的特征,表现出一定的生物地理分布格局;这与它们受到不同程度环境因子和空间因子的驱动作用有关;中性模型的结果体现了随机过程在两种亚群落中的重要作用;最后,共现网络关系反映出不同丰富程度的生态类群具有重叠但又相异的生态位,从而在同一环境中形成物种的共...     

16SrDNA克隆文库解析仿刺参(Apostichopus japonicus)苗种培育池中生物絮团的细菌群落结构

通过采集东营和蓬莱地区采用生物絮团技术的仿刺参(Apostichopus japonicus)苗种培育池(DYt和PLt)及其对照池(DYc和PLc)海水样品,构建细菌16S r DNA克隆文库,对其中细菌群落的多样性和群落组成结构进行了分析。结果表明,四个文库Coverage值在34.7%—54.8%之间,文库丰富度指数(Chao)66.2—314.1,Shannon多样性指数从3.01—4.07变动,Pielou均匀度指数0.68—0.85,样品的细菌群落均具有很高的多样性,蓬莱仿刺参苗种培育池细菌多样性均高于东营;生物絮团文库中细菌包括拟杆菌门(Bacteroidetes)、变形细菌门(Proteobacteria)、厚壁菌门(Firmicutes)等八个菌门和未知类群,黄杆菌群(Flavobacteria)、α-变形菌群(Alphaproteobacteria)和芽孢杆菌群(Bacilli)为主要优势菌群;DYt和PLt处理组文库细菌多样性减少并出现特征菌群,生物絮团调控技术改变了仿刺参苗种培育环境的微生物群落结构。生物絮团的细菌群落结构研究,为揭示生物絮团的作用机制并进一步有效利用提供研究基础和依据。     

16S rDNA克隆文库解析刺参(Apostichopus japonicas)苗种培育池中生物絮团的细菌群落结构*

提要 通过采集东营和蓬莱地区采用生物絮团技术的刺参(Apostichopus japonicas)苗种培育池(DYt和PLt)及其对照池(DYc和PLc)海水样品,构建细菌16S rDNA 克隆文库,对其中细菌群落的多样性和群落组成结构进行了分析。结果表明,四个文库Coverage值在34.7%～54.8%之间,文库丰富度指数(Chao)66.2～314.1,shannon多样性指数从3.01～4.07变动,Pielou均匀度指数0.68～0.85,样品的细菌群落均具有很高的多样性,蓬莱刺参苗种培育池细菌多样性均高于东营;生物絮团文库中细菌包括拟杆菌门(Bacteroidetes)、变形细菌门(Proteobacteria)、厚壁菌门(Firmicutes)等八个菌门和未知类群,黄杆菌群(Flavobacteria)、α-变形菌群(Alphaproteobacteria)芽孢杆菌纲(Bacilli)为主要优势菌群;DYt和PLt处理组文库细菌多样性减少并出现特征菌群,生物絮团调控技术改变了刺参苗种培育环境的微生物群落结构。生物絮团的细菌群落结构研究,为揭示生物絮团的作用机制并进一步有效利用提供研究基础和依据。     

基于形态学与核糖体DNA及其cDNA高通量测序的海洋沉积物中纤毛虫多样性比较

高通量测序技术广泛应用于环境真核微生物多样性的研究,可检获较之传统形态学方法更高的多样性。然而,检获的高分子多样性与基于形态的物种多样性在构成上的差异仍然不明。本研究首次对比分析了基于形态学的南黄海沉积物中的纤毛虫物种多样性与基于核糖体18S DNA和c DNA高通量测序的多样性异同。结果表明:形态鉴定获得8纲、20目、30科、36属共97种纤毛虫;DNA测序检获10纲、28目、55科、76属共174个OTUs;而通过c DNA测序获取的纤毛虫多样性最高,获10纲、31目、68科、99属共284个OTUs。研究发现,形态学方法检获的纤毛虫均为底栖生纤毛虫;两种分子手段检获的多样性更高,群落结构更为近似,覆盖了形态鉴定所获的绝大部分类群。但DNA测序还检获了序列比例高达90%的浮游类群,可能源于包囊或死亡沉降的物种;而c DNA测序检获了约7%的浮游纤毛虫序列。较之DNA测序,c DNA法检获的底栖纤毛虫在群落结构上与形态学结果更为接近。本研究表明,分子手段有助于更全面地揭示沉积物中的纤毛虫多样性,DNA测序可同时揭示休眠包囊、胞外DNA及过去群落的信息,而c DNA测序在研究活动纤毛虫多样性上更有优势。     

浮游病毒遗传多样性的研究进展

浮游病毒是指游离在水体中的各类病毒,被认为是水体微生物群落中的重要成分.浮游病毒在微食物环、生物地球化学循环、群落结构及多样性等方面起着重要作用.浮游病毒的遗传多样性极其丰富,如何对其进行检测和分析是近几年国际上的研究热点.本文综述了浮游病毒主要类群藻病毒、噬藻体和噬菌体的遗传多样性;分析了宿主、水层、季节等对浮游病毒遗传多样性的影响;介绍了浮游病毒遗传多样性研究中常用的DNA聚合酶基因、结构蛋白基因等靶标基因及PFGE、RFLP、DGGE、DNA微阵列和宏基因组等分子生物学分析技术.     

Diversity analysis of protistan microplankton in Sagami Bay by 18S rRNA gene clone analysis using newly designed PCR primers

The diversity of protistan microplankton in Sagami Bay was revealed by 18S rRNA gene clone analysis using newly designed PCR primers. PCR amplification consisted of a first reaction targeting the V3–V5 region of the 18S rRNA gene, followed by a nested reaction targeting the V3–V4 region. In total, 629 clones consisting of 108 phylotypes were affiliated with a variety of protistan groups including dinoflagellates, diatoms, prymnesiomonada, chlorophyta, ciliophora, cercozoa, and heterokonta. The dinoflagellate group was detected most frequently and shared approximately 74?% of the total clones. Within this group, approximately half of the clones belonged to the parasitic dinoflagellate Syndiniales group I, which was first reported from Sagami Bay. The genera Woloszynskia, Gonyaulax, Neoceratium, and Karlodinium have not been reported from this bay until now. The second most frequent group was diatoms, which shared approximately 22?% of the total clones. Within this group, highly diverse Thalassiosira phylotypes were detected, and they shared approximately 70?% of the diatom clones. Therefore, highly diverse protists including some candidate groups were successfully detected, indicating that the designed primers and PCR protocol will be useful for molecular diversity analyses of protistan microplankton communities in aquatic environments.     

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.     

Growth,feeding and ecological roles of the mixotrophic and heterotrophic dinoflagellates in marine planktonic food webs

Planktonic mixotrophic and heterotrophic dinoflagellates are ubiquitous protists and often abundant in marine environments. Recently many phototrophic dinoflagellate species have been revealed to be mixotrophic organisms and also it is suggested that most dinoflagellates may be mixotrophic or heterotrophic protists. The mixotrophic and heterotrophic dinoflagellates are able to feed on diverse prey items including bacteria, picoeukaryotes, nanoflagellates, diatoms, other dinoflagellates, heterotrophic protists, and metazoans due to their diverse feeding mechanisms. In turn they are ingested by many kinds of predators. Thus, the roles of the dinoflagellates in marine planktonic food webs are very diverse. The present paper reviewed the kind of prey which mixotrophic and heterotrophic dinoflagellates are able to feed on, feeding mechanisms, growth and ingestion rates of dinoflagellates, grazing impact by dinoflagellate predators on natural prey populations, predators on dinoflagellates, and red tides dominated by dinoflagellates. Based on this information, we suggested a new marine planktonic food web focusing on mixotrophic and heterotrophic dinoflagellates and provided an insight on the roles of dinoflagellates in the food web.     

Arctic summer sea ice phenology including ponding from 1982 to 2017

Information on the Arctic sea ice climate indicators is crucial to business strategic planning and climate monitoring. Data on the evolvement of the Arctic sea ice and decadal trends of phenology factors during melt season are necessary for climate prediction under global warming. Previous studies on Arctic sea ice phenology did not involve melt ponds that dramatically lower the ice surface albedo and tremendously affect the process of sea ice surface melt. Temporal means and trends of the Arctic sea ice phenology from 1982 to 2017 were examined based on satellite-derived sea ice concentration and albedo measurements. Moreover, the timing of ice ponding and two periods corresponding to it were newly proposed as key stages in the melt season. Therefore, four timings, i.e., date of snow and ice surface melt onset (MO), date of pond onset (PO), date of sea ice opening (DOO), and date of sea ice retreat (DOR); and three durations, i.e., melt pond formation period (MPFP, i.e., MO–PO), melt pond extension period (MPEP, i.e., PO–DOR), and seasonal loss of ice period (SLIP, i.e., DOO–DOR), were used. PO ranged from late April in the peripheral seas to late June in the central Arctic Ocean in Bootstrap results, whereas the pan-Arctic was observed nearly 4 days later in NASA Team results. Significant negative trends were presented in the MPEP in the Hudson Bay, the Baffin Bay, the Greenland Sea, the Kara and Barents seas in both results, indicating that the Arctic sea ice undergoes a quick transition from ice to open water, thereby extending the melt season year to year. The high correlation coefficient between MO and PO, MPFP illustrated that MO predominates the process of pond formation.     

Preliminary study on community structures of meiofauna in the middle and eastern Chukchi Sea

Sediment core samples were collected from 17 stations in the middle and eastern Chukchi Sea during the sixth Chinese National Arctic Research Expedition(CHINARE-Arctic) in summer 2014.The samples were analyzed for composition,abundance,biomass,vertical distribution,size spectra,and ecological indexes of meiofauna.A total of 14 meiofauna taxa were detected,and the free-living marine nematodes comprised the most dominant taxon,accounting for 97.21% of the average abundance.The abundance and biomass of meiofauna were within ranges of(218.12±85.83)-(7 239.38±1 557.15) ind./(10 cm~2) and(130.28±52.17)-(3 309.56±1 751.80) μg/(10 cm~2),with average values of(2 391.90±1 966.19) ind./(10 cm~2) and(1 549.73±2 042.85) μg/(10 cm~2)(according to dry weight)respectively.Furthermore,91.26% of the individuals were distributed in the top layer of 0-5 cm of surface sediment,and 90.84% had sizes of 32-250 μm.Group diversity index of meiofauna in the survey area was low,and the variation of abundance was the main difference in meiofauna communities among all stations.Abundance and biomass of meiofauna were not significantly correlated with environmental factors except concentration of nutrient Si in bottom seawater.Abundance of meiofauna in shallow water of marginal seas in the Pacific sector of the Arctic Ocean is likely at a same level and higher than that in most of China sea areas,suggesting that the shallow water of the summer Chukchi Sea is a continental shelf area with rich resources of meiofauna.The Chukchi Sea is important for studying the ecosystem of the Arctic Ocean and environmental responses.However,studies on meiofauna in the Chukchi Sea are still not enough,and in the future,natural and human disturbances may increase due to global warming,the Arctic channel opening,and other factors.Thus,more studies on meiofauna should be required,in order to know more about how the Arctic benthic community would alter.     

气候变化背景下北极航线综合评估模型研究

在全球持续变暖的影响下,北极部分地区夏季出现无冰期,北极航线具有更短的航运距离和相对稳定的地缘政治人文环境。文章从气候变化角度出发,构建包含航行环境模块、航迹规划模块和航线经济效益模块在内的综合评估模型,评估北极地区海冰、风、浪、流等气象水文地理要素对船舶航速的影响,确定北极地区的可航行天数;在此基础上,利用A-Star算法寻找北极航线的最优路径,并分析该路径上的航运经济效益;采用该评估模型对比在RCP4.5情景下2050年船舶往返欧亚大陆之间经东北航线与经苏伊士运河航线的经济效益,结果表明,苏伊士运河航线的经济效益更高,北极航线可作为替补航线。     

北欧海海面高度上升减缓及其机理研究

A slowdown of sea surface height(SSH) rise occurred in the Nordic(GIN) seas around 2004.In this study,SSH satellite data and constructed steric height data for the decades before and after 2004(i.e.,May 1994 to April 2014)were used for comparative analysis.The findings indicate that the rate of slowdown of SSH rises in the GIN seas(3.0 mm/a) far exceeded that of the global mean(0.6 mm/a).In particular,the mean steric height of the GIN seas increased at a rate of 4.5 mm/a and then decreased at a slower pace.This was the main factor responsible for the stagnation of the SSH rises,while the mass factor only increased slightly.The Norwegian Sea particularly experienced the most prominent slowdown in SSH rises,mainly due to decreased warming of the 0–600 m layer.The controlling factors of this decreased warming were cessation in the increase of volume of the Atlantic inflow and stagnation of warming of the inflow.However,variations in air-sea thermal flux were not a major factor.In the recent two decades,mean halosteric components of the GIN seas decreased steadily and remained at a rate of 2 mm/a or more because of increased flow and salinity of the Atlantic inflow during the first decade,and reduction in freshwater inputs from the Arctic Ocean in the second decade.     

Linking bacterial community structure to carbon fluxes in marine environments

Microbial oceanography is undergoing a dramatic revolution thanks to the rapid development of novel techniques that allow the examination of microbial diversity and functions via molecular methods, including genomic and metagenomic analyses. During the past decade, studies have revealed previously unknown and surprisingly diverse bacterial communities in marine waters. These studies have radically changed our understanding of spatiotemporal patterns in marine bacterial community composition and the distribution of specific genes. However, our knowledge of the role of individual bacterial subgroups in oceanic food webs and biogeochemical cycles remains limited. To embed the internal dynamics of bacterial communities into marine biogeochemistry models, the characteristic parameters of individual bacterial subgroups (i.e., growth, mortality, and utilization of dissolved organic matter) must be determined. Here, we survey the approaches used to assess variation in and factors controlling bacterial communities in marine environments, emphasizing the importance of quantitative studies that examine growth and grazing parameters of bacterial subgroups.     

全球变化背景下暖水珊瑚礁生态系统的适应性与修复研究

暖水珊瑚礁生态系统是热带海域最具生物多样性和代表性的生态系统之一。本研究分析了全球变化背景下暖水珊瑚礁生态系统的变化和风险,开展了受损暖水珊瑚礁生态系统退化和消失的致灾因子归因分析,综述了暖水珊瑚礁生态系统的适应性与修复技术研究。分析表明:①过去几十年来,暖水珊瑚礁生态系统快速退化,包括大面积白化和死亡、多样性明显减少和生态功能显著衰退,主要归因于海洋升温与人类活动等致灾因子的影响;②在温室气体高排放浓度情景下(RCP 8.5),相比工业革命前,到本世纪中叶,南海升温将可能远超过2℃,这表明南海暖水珊瑚礁生态系统正在逼近其气候临界点,即全球升温高于2℃时,90%~99%以上的暖水珊瑚将消失;③1980年代以来,海洋升温、海洋热浪和强热带气旋等海洋气候变化致灾因子对南海暖水珊瑚的危害性(影响的强度、范围和时间)明显增加,对暖水珊瑚礁生态系统产生了严重的影响;与此同时,近岸海域的过度或破坏性捕捞、采挖和潜水等人类活动,对暖水珊瑚造成了严重损害,增加了暖水珊瑚的气候脆弱性,而这种人类活动既是局部的,也是全球性的现象,使得暖水珊瑚更难以适应全球变暖的影响。分析还表明,为了增强暖水珊瑚适应气候与环境变化的恢复力(韧性),人们开展了诸多受损珊瑚礁生态系统的适应性与修复研究,但主要是采用无性繁殖或结合人工基质的修复方式,而应用有性繁殖技术恢复受损珊瑚礁的方式仍较少;最近,暖水珊瑚耐热的基因适应性研究取得了重要进展,为暖水珊瑚适应全球变暖提供了一种新的途径。本研究最后探讨了中国受损珊瑚礁生态系统的修复问题与对策。     

南、北极近岸海水中好氧不产氧光合基因pufM的多样性

好氧不产氧光合(AAP)细菌因其具有利用溶解性有机物及光能的能力,在海洋碳循环及能量流动中发挥着重要的作用。该类细菌广泛分布在海洋环境中,其在不同生境中的多样性已被调查。但到目前为止,人们对于高纬度地区好氧不产氧光合细菌的认识还较为缺乏。有鉴于此,本研究基于编码光反应复合物上一个色素结合蛋白亚基的pufM基因,对北极王湾及南极乔治王岛近岸水体中夏季好氧不产氧光合细菌的多样性进行了检测。针对2个王湾站位和2个南极麦克斯维尔湾站位构建了4个pufM基因克隆文库,获得674个阳性克隆子。北极克隆子全部由α-变形细菌组成,而南极克隆子则包括α-变形细菌及β-变形细菌。来源于类似红细菌科的pufM基因在所有样品中皆占据优势。此外,与一株滴状亚硫酸盐杆菌中质粒编码的pufM基因存在亲缘关系的序列,在南、北极样品中均占优势。结果表明海洋环境中的pufM基因存在跨极甚至是环球分布。与此同时,南、北极序列之间的差异,也表明了极地地方种的存在。这些结果显示,作为好氧不产氧光合细菌的红细菌科在两极的近岸水体中具有重要的地位。