土壤细菌群落特征对高寒草甸退化的响应

为明确高寒草甸土壤细菌物种组成及功能结构对草地环境恶化的响应规律, 本文采用高通量基因测序技术对高寒草甸未退化、轻度退化、中度退化、重度退化和极重度退化草地土壤细菌的组成、格局和功能进行了研究。结果表明: 高寒草甸土壤优势细菌为酸杆菌门、放线菌门、浮霉菌门、变形菌门和疣微菌门, 在土壤细菌中占比分别为16%‒18%、9%‒12%、12%‒14%、23%‒29%和11%‒12%。退化草地中土壤细菌物种组成明显改变, 变形菌门细菌丰度降低, 酸杆菌门和浮霉菌门丰度增加, 不同草地科水平细菌丰度差异因土层而异。草地退化对细菌Chao1指数无影响, 轻度退化提高了细菌Simpson指数, 重度退化草地土壤细菌Shannon-Wiener指数最高。Faprotax细菌功能分组以化能异养、硝化作用、亚硝酸盐氧化及硫代谢作用为主, 草地退化改变了微生物介导的碳循环、氮循环、硫循环、铁循环和锰循环。重度及极重度退化提高了细菌氨氧化功能作用, 降低了硫化物、亚硝酸盐氧化及尿素水解作用; 草地退化过程中细菌化能异养、芳香族化合物降解及反硝化作用功能等均呈先降低后升高的变化趋势, 中度退化阶段是微生物群落生态功能结构转变的拐点。高寒草甸退化改变了土壤细菌的群落及功能结构, 土壤含水量、pH、总有机碳、全氮、全钾和有效氮磷比是土壤细菌群落及功能结构变化的主要驱动因子。     

鄂尔多斯台地盐沼滩涂湿地土壤细菌群落结构及特征

依据植被分类法将鄂尔多斯高原盐沼滩涂湿地划分为肉质耐盐草甸(B)、苔草草甸(C)、禾草草甸(D)和杂类草草甸(E)等4个植被亚型,并以盐沼裸地(A)为对照样地,共计5种盐沼滩涂湿地景观类型。运用高通量测序技术分别研究其土壤细菌群落结构特征、分布情况,以及土壤盐分与土壤细菌之间的关系。结果表明:(1) 5种盐沼滩涂湿地的土壤细菌样品共12213条OTUs,属于45个门,122个纲,365个目,663个科,1375个属,2882个种。(2)变形菌门(26.19%)是盐沼滩涂湿地平均相对丰度最高的门,其次为放线菌门(17.15%),绿弯菌门(12.62%),芽单胞菌门(Gemmatimonadetes,11.23%),拟杆菌门(Bacteroidetes,9.38%),酸杆菌门(Acidobacteria,8.83%)厚壁菌门(Firmicutes,2.96%);芽单胞菌纲中的未定细菌(norank＿c＿Gemmatimonadetes)是丰度最高的属,平均丰度为5.75%。(3)鄂尔多斯盐沼滩涂湿地自西南向东北,空间位置相近的土壤细菌群落结构具有更大的相似性,随着土壤盐分变化,变形菌门相对...     

土壤细菌类克隆群落及其结构的生态学特征

以16SrDNA分析方法为基础,获得来自不同土壤环境的细菌克隆群落（Cloning community),并分析了这些土壤细菌群落结构特征,在不同土壤环境中,细菌种类非常丰富,但其多样性将受到植被,土壤水分或土壤层次等因子的影响,表层土壤环境中细菌种类最丰富,多样性最高,且基因型中无明显的优势类群,不同土壤环境间细菌群落的相似性好低,表明群落结构以及空间隔离的复杂性。     

五大连池不同火山喷发沉积物的细菌群落多样性研究

【目的】揭示五大连池火山区的细菌多样性。【方法】运用Illumina Miseq高通量测序技术解析五大连池不同火山喷发沉积物中细菌的群落组成和分布规律。【结果】五大连池火山区沉积物中的细菌主要包含厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、疣微菌门(Verrucomicrobia)、酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)、放线菌门(Actinobacteria)等23个细菌门类,其中,厚壁菌门、变形菌门丰度较高,芽孢杆菌属(Bacillus)为绝对优势菌群。另外,由于火山物质的同源性,导致各沉积物中细菌的代谢通路多与C、N、S、Fe等元素的生化循环相关,群落结构及功能具有一定程度的相似性。但由于各研究区域在沉积组分、环境因素及地质演化进程上的差异,致使芽孢杆菌属、地杆菌属(Geobacter)、酸杆菌属(Acidobacterium)、嘉利翁氏菌属(Gallionella)、Blastocatella等部分种群在不同火山沉积物中呈现差异化分布,具有典型的地域适应特性。【结论】五大连池火山沉积物中含有较为丰富的细菌资源,...     

竹炭对三叶草生长及土壤细菌群落的影响

研究添加不同含量(0、3%和9%)和颗粒直径(0.05、0.05～1.0和1.0～2.0 mm)竹炭对三叶草生长及土壤微生物群落结构的影响.结果表明: 竹炭对三叶草生长的促进作用前期较明显,添加9%竹炭处理略好于添加3%竹炭处理,而不同颗粒直径对三叶草生长影响差异不显著;播种后0～120 d,竹炭对三叶草生长的促进作用随着时间推移而减弱,5个月后基本消失.16S rDNA V3区片段的DGGE分析表明,添加竹炭改变了土壤细菌群落结构特征,大部分种类土壤细菌数量和细菌群落多样性指数均高于对照.定量分析表明,添加9%、细粒(D<0.05 mm)竹炭处理土壤细菌数量显著高于其他处理.同一添加含量下,细粒径竹炭对土壤细菌数量的增加效应更明显.
     

贵州茂兰喀斯特森林不同小生境下土壤细菌群落特征

以贵州茂兰喀斯特森林小生境土壤(石洞、石缝、石沟、石槽、土面)为研究对象,利用高通量测序技术对其土壤细菌16S rRNA V3～V4可变区进行高通量测序,分析土壤细菌α多样性、物种组成及丰度差异情况,并应用数量生态学方法分析土壤理化因子对细菌群落结构的影响.结果表明: 5类小生境土壤共检测到27个门64个纲128个目242个科367个属704个种;主要优势菌门为变形菌门、放线菌门、酸杆菌门、绿弯菌门、硝化螺旋菌门;石洞表层(0～10 cm)、石洞下层(10～20 cm)、石缝及石槽等生境主要的优势菌门是放线菌门,土面表层(0～10 cm)、土面下层(10～20 cm)的是酸杆菌门,石沟表层(0～10 cm)、石沟下层(10～20 cm)的是变形菌门.石缝细菌Simpson多样性最高,土面下层(10～20 cm)最低.LEfSe分析表明,土面表层(0～10 cm)、土面下层(10～20 cm)、石洞下层(10～20 cm)以及石槽不同分类水平上的差异指示种数量高于石缝、石沟表层(0～10 cm)以及石沟下层(10～20 cm).例如,在门水平上,石洞下层(10～20 cm)差异指示种为放线菌门与绿弯菌门,石沟表层(0～10 cm)为变形菌门与Tectomicrobia门,土面表层(0～10 cm)为酸杆菌门、疣微菌门及Latescibacteria门,土面下层(10～20 cm)为硝化螺旋菌门,石槽、石缝以及石沟下层(10～20 cm)无差异指示种;但从门至属,石洞表层(0～10 cm)都无差异指示种.冗余分析(RDA)及集成推进树(ABT)分析表明,土壤有机质、pH及总磷较大程度上解释了细菌门类水平分布对土壤基本理化因子变化的响应机制.     

甘肃小陇山油松与柴胡栽培土壤细菌群落特征

土壤细菌能够有效促进土壤中物质循环和能量流动,其群落组成、数量及多样性能够反映土壤质量状况。研究不同植被对土壤细菌群落结构和多样性的影响,有助于深入了解土壤健康状况,对实现植被管理和土地可持续利用具有重要意义。以甘肃小陇山移栽至耕地(耕地前期种植柴胡)后生长4年的人工油松苗(Pinus tabulaeformis Carr)土地和长期种植柴胡(Bupleurum chinense)土地的表层土壤(0—30 cm)为对象,采用Illumina Miseq高通量测序技术对2种人工植被下土壤细菌群落进行测定,分析了土壤细菌的Alpha多样性、群落组成和丰富度,并研究土壤化学性质对细菌群落结构的影响。结果表明:1)两种不同植被的土壤细菌群落丰度和多样性无明显差异,但油松地土壤细菌群落均匀度明显小于柴胡地土壤。2)所测土壤样品中共检测到细菌的37个门,84个纲,168个目;其中,主要的优势菌门为变形菌门(Proteobacteria),酸杆菌门(Acidobacteria),绿弯菌门(Chloroflexi),浮霉菌门(Planctomycetes),放线菌门(Actinobacteria),且油松地土壤中的变形菌门(Proteobacteria)的丰富度显著低于柴胡地土壤(P 0. 05),绿弯菌门(Chloroflexi)丰富度却显著高于柴胡地(P 0. 05);主要的优势菌纲为酸杆菌纲(Acidobacteria),β-变形菌纲(Betaproteobacteria),放线菌纲(Actinobacteria),变形菌纲(Alphaproteobacteria)和芽单胞菌纲(Gemmatimonadetes),但各优势菌纲的丰度在两个植被土壤之间差异不显著(P0.05)。3)变形菌门(Proteobacteria)丰富度与土壤的碱解氮含量呈显著负相关(P0.05),酸杆菌门(Acidobacteria)丰富度与全氮含量显著负相关(P0.01);通过RDA分析发现,碱解氮和全氮是影响细菌群落结构的最主要因子。可见,油松和柴胡植被土壤细菌群落结构及多样性差异不大,但油松地土壤细菌群落的物种分配较柴胡地集中,且优势细菌门中的变形菌门和绿弯菌门在两者之间的差异显著,同时,碱解氮和全氮含量是影响2种植被土壤细菌群落的主要因子。这些结论为了解小陇山不同植被土壤微生物群落组成及多样性提供理论,也为当地进行人工油松苗的种植、经营及土壤管理提供参考。     

青海湖主湖区与湖水淹没区的细菌群落结构差异分析

为对比青海湖与湖滨淹没区的微生物群落结构及多样性的差异, 利用16S rRNA高通量测序技术, 研究不同环境条件下水体的微生物群落组成的异同。结果表明: 青海湖主湖区及淹没区的细菌在分类门级水平上相对丰度最高的为变形菌门(Proteobacteria, 44.8%), 其次分别隶属于拟杆菌门[Bacteroidetes, (25.9%±7.8)%]、蓝细菌门[Cyanobacteria, (13.6%±5.4)%]、放线菌门[Actinobacteria, (7.54%±9)%]和柔壁菌门[Tenericutes, (3.32%±2)%]。淹没区整体微生物多样性显著高于主湖区水体。部分微生物分类属在两个湖区呈现显著的分布差异暗示这些细菌对于环境特征的适应性。节线藻在青海湖主湖的分布广泛显示其可能在高原咸水湖泊的碳氮循环过程中扮演着重要角色。研究对于深入了解栖居地如何塑造咸水水体微生物群落结构具有重要意义。     

连作对地黄根际土壤细菌群落多样性的影响

采用末端限制性片段长度多态性(T-RFLP)技术研究地黄连作下根际土壤细菌群落的动态变化.结果表明:地黄根际土壤细菌群落的香农多样性指数、丰富度指数和相似性指数均为对照(CK)1年2年,地黄连作下细菌优势种群的比例显著下降,种植1年土壤中厚壁菌门的芽孢杆菌纲在整个细菌群落中处于主导地位,而种植2年土壤中变形菌门ε-变形菌纲处于主导地位.地黄连作使其根际土壤细菌种类大量减少,群落结构趋于简单.连作后细菌群落多样性水平的变化导致根际土壤微生物群落功能的失调,可能是引发连作障碍的原因之一.     

秸秆覆盖免耕对土壤细菌群落区系的影响

多年连续秸秆覆盖免耕对土壤细菌群落影响很大,免耕可提高０－１０ｃｍ土层土壤细菌总数、放线菌数、棒状细菌数和贫营养细菌数量,特别是免耕土壤能使芽孢杆菌数量增多几倍。     

Total bacterial diversity in soil and sediment communities—A review

Advances in microbial methods have demonstrated that microorganisms globally are the dominating organisms both concerning biomass and diversity. Their functional and genetic potential may exceed that of higher organisms. Studies of bacterial diversity have been hampered by their dependence on phenotypic characterization of bacterial isolates. Molecular techniques have provided the tools for analyzing the entire bacterial community including those which we are not able to grow in the laboratory. Reassociation analysis of DNA isolated directly from the bacteria in pristine soil and marine sediment samples revealed that such environments contained in the order of 10 000 bacterial types. The diversity of the total bacterial community was approximately 170 times higher than the diversity of the collection of bacterial isolates from the same soil. The culturing conditions therefore select for a small and probably skewed fraction of the organisms present in the environment. Environmental stress and agricultural management reduce the bacterial diversity. With the reassociation technique it was demonstrated that in heavily polluted fish farm sediments the diversity was reduced by a factor of 200 as compared to pristine sediments. Here we discuss some molecular mechanisms and environmental factors controlling the bacterial diversity in soil and sediments.     

青海湖区针茅草原植物群落特征及群落多样性研究

根据样方调查资料,采用聚类分析法,研究了青海湖区针茅草原围栏封育后植物群落特征及群落多样性变化。结果表明,草原经过长期围栏后,群落内优势种发生了不同程度的分异,由围栏外的紫花针茅(Stipa purpurea) 青海苔草(Carex ivanovae)草原演变成围栏内的冷地早熟禾(Poa crymophila) 猪毛蒿(Artemisia scoparia)草原群落,导致了群落结构特征的变化;长期的围栏活动对提高草原群落的盖度和生产能力是有益的,但却降低了群落的物种丰富度和多样性;草原开垦后,对周围草原有明显的影响,所形成土垄的群落特征和多样性变化都发生了极大的差异,成为赖草(Leymus secalinus) 大籽蒿(Artemisia sieversiana)群落类型,群落的物种丰富度和多样性均降低。     

南京玄武湖底泥微生物群落结构研究

采用变性梯度凝胶电泳(DGGE)的方法研究了南京玄武湖底泥中的微生物群落结构分布。此外,我们还采用了典范对应分析(CCA)的方法研究了底泥中一些环境因子对微生物群落结构的影响。在玄武湖三个不同湖区共选取八个采样点采集底泥样品,测定不同底泥样品中的总氮(TN)、总磷(TP)、有机质(OM)、pH和氧化还原电位(Eh),发现不同采样点的环境参数存在差异。其中,采样点S2底泥样品的总氮和有机质含量最高,氧化还原电位水平最低。对DGGE分离的DNA条带进行测序,测序结果利用BLAST与GenBank数据库中的菌种进行对比,运用MEGA 3.0软件构建了系统进化树。结果表明:玄武湖底泥中分离出的微生物属于Proteobacteria, Actinobacteria, Verrucomicrobia 和 Nitrospira,它们都属于富营养化湖泊中常见的微生物类群。典范对应分析(CCA)的结果表明: 底泥样品的pH值和氧化还原电位水平对底泥当中的微生物群落结构有显著影响。     

水热条件变化对黑土细菌群落结构的影响及其演替特征

全球气候变化导致的水热条件变化,对土壤微生物群落结构及功能产生重要影响。深入理解这些变化如何影响微生物群落的结构及其随时间的演替,对于有效预测和适应未来的气候变化至关重要。【目的】在气候变化背景下,本研究旨在探索黑土细菌群落的多样性、组成和结构,以及群落演替特征的变化情况。【方法】利用中国科学院海伦、封丘、鹰潭农田生态系统国家野外科学观测研究站长期土壤置换实验平台,选择寒温带地区(中国海伦)的黑土作为研究对象,并将其移置于暖温带地区(封丘)和中亚热带地区(鹰潭)以模拟水热条件增加。通过采集2005年至2011年的63个黑土样本(包括原位、移置封丘县和移置鹰潭市),利用16S rRNA基因高通量测序技术,研究了水热条件变化对黑土细菌群落多样性、组成和结构的影响;同时结合土壤理化性质,分析环境因素与微生物群落特征间的关系,并计算物种周转率(w)。【结果】经过6年的移置,将寒温带黑土移至暖温带和中亚热带后,土壤的理化性质发生了显著改变。土壤有机质和全氮含量显著降低,地上部生物量显著减少。土壤细菌群落的多样性下降,群落组成和结构发生了显著变化。主要细菌类群包括疣微菌门(Verrucomicrobia)、变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)和放线菌门(Actinobacteria)等,其中疣微菌门在移置鹰潭地区后的相对丰度显著增加。此外,气候因子与微生物群落特征高度相关。非度量多维尺度分析显示,群落结构随水热条件和时间的变化而演替,这与微生物时间周转率的增加相关。在不同水热条件下,细菌群落的时间周转率差异显著,依次为0.030 (海伦)<0.033 (封丘)<0.045 (鹰潭)。【结论】6年的水热条件增加显著降低了细菌群落的多样性,显著改变了其组成和结构,并加快了细菌群落时间周转率的响应。     

基于高通量测序的鄱阳湖典型湿地土壤细菌群落特征分析

采用高通量测序技术分析了鄱阳湖典型湿地土壤细菌群落特征。测序结果表明,不同植被土壤细菌群落丰度与多样性的排序相同:苔草带苔草-虉草带芦苇带泥滩带藜蒿带。沿湖面至坡地,空间位置相近的土壤细菌群落结构具有更大的相似性,苔草-虉草带、苔草带和芦苇带的细菌群落结构相近,泥滩带和藜蒿带的细菌群落结构差异较大。变形菌门(30.0%)是湿地土壤平均相对丰度最高的门,其次为酸杆菌门(16.7%)和绿弯菌门(16.5%);多数门分类细菌相对丰度沿湖面至坡地存在一定变化趋势。硝化螺菌属是第一大属分类水平细菌群落。在土壤化学指标中,与鄱阳湖湿地细菌群落相关性较大的是总磷、铵态氮和有机质含量。以上研究结果表明,鄱阳湖湿地不同植被土壤细菌群落具有结构性差异,但沿湖面至坡地存在规律性变化。     

Response of bacterial communities to cyanobacterial harmful algal blooms in Lake Taihu,China

Cyanobacterial harmful algal blooms are prevalent around the world, influencing aquatic organisms and altering the physico-chemical properties in freshwater systems. However, the response of bacterial communities to toxic cyanobacterial blooms and associated microcystins (MC) remain poorly understood even though global concentrations of MC have increased dramatically in the past few decades. To address this issue, the dynamics of bacterial community composition (BCC) in the water column and how BCC is influenced by both harmful cyanobacterial blooms and environmental factors were investigated on a monthly basis from August 2013 to July 2014 in Lake Taihu, China. Non-metric multidimensional scaling (NMDS) revealed that seasonal variation in BCC was significant, and that the succession of BCC greatly depends on changes in environmental conditions. Redundancy analysis (RDA) results showed that the overall variation of BCC was explained mainly by dissolved oxygen (DO), nitrate nitrogen (NO₃⁻-N), and Microcystis. The alpha biodiversity of the bacterial community was different among months with the highest diversity in February and the lowest diversity in October. Furthermore, significant negative relationships were found between alpha biodiversity indices and Microcystis abundance as well as with intracellular MC concentrations, indicating that Microcystis and associated MC may influence the bacterial community structure by reducing its biodiversity. This study shows that potential associations exist between toxic cyanobacterial blooms and bacterial communities but more investigations are needed to obtain a mechanistic understanding of their complex relationships.     

环境因素对东平湖沉积物细菌群落结构的影响

【目的】探讨环境因素对东平湖沉积物细菌群落结构的影响。【方法】应用T-RFLP(Terminal RestrictionFragment Length Polymorphism)技术分析和比较了6个不同位置的东平湖沉积物在丰水期和枯水期的细菌多样性,并结合不同样品环境因子的差异,采用主成分分析(PCA)和典型对应分析(CCA),探讨了环境因子对细菌多样性的影响。【结果】不同沉积物样品的T-RFLP图谱具有较高的相似性。除2号样品外,所有枯水期样品的细菌群落具有较高的丰富度、多样性、均匀度和较低的优势度。CCA结果表明,558bp T-RF的丰度与总磷、总氮、总有机碳、铵态氮和硝态氮含量呈负相关而与碳氮比和水深呈正相关;64.5、164、509和543bp T-RFs的丰度与总氮、总有机碳、铵态氮、硝态氮、碳氮比和水深呈正相关;而其它14种主要的T-RFs在不同样品间分布较为稳定受环境因子影响不大。90、136.5、138和488bp等T-RFs可能代表了东平湖沉积物中占优势地位的土著菌群。通过Phylogenetic Assignment Tool在线分析结果推测,东平湖沉积物中的优势菌群可能属于Firmicutes和Proteobacteria门。【结论】环境因素对东平湖沉积物的细菌多样性产生显著影响,但对其土著菌群的影响不大。     

Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil

In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.     

Bacterial communities in sediments of the shallow Lake Dongping in China

Aims: The purpose of this study was to discuss how the environmental inputs and anthropogenic activities impact bacterial communities in the sediments of a shallow, eutrophic and temperate freshwater lake. Methods and Results: Sediment cores were collected from Lake Dongping, located in Taian, Shandong, China. All samples were processed within 4 h of collection. Total nitrogen, total phosphorus (TP), total organic carbon, ammonium nitrogen and nitrate nitrogen content of samples were measured by Kjeldahl determination, sulphuric acid–perchloric acid digestion and molybdenum blue colorimetry, potassium dichromate titration, Nessler’s reagent colorimetric and the phenol disulphonic acid colorimetric method, respectively. Seasonal and temporal diversity of sediment bacterial communities at six stations in Lake Dongping were investigated using molecular approaches (terminal restriction fragment length polymorphism and 16S rDNA clone libraries). Noticeable seasonal and temporal variations were observed in bacterial diversity and composition at all six stations. Sediment bacterial communities in Lake Dongping belonged to 16 phyla: Proteobacteria (including α‐Proteobacteria, β‐Proteobacteria, δ‐Proteobacteria, ε‐Proteobacteria, γ‐Proteobacteria), Acidobacteria, Planctomycetes, Bacteroidetes, Firmicutes, Verrucomicrobia, Nitrospira, Chloroflexi, Gemmatimonadetes, Chlorobi, Cyanobacteria, Deferribacteres, Actinobacteria, OP8, Spirochaetes and OP11. Members of β‐, δ‐ and γ‐Proteobacterial sequences were predominant in 11 of 12 clone libraries derived from sediment samples. Sediment samples collected at stations 1 and 4 in July had the greatest bacterial diversity while those collected at station 2 in October had the least diversity. TP concentration was significantly correlated with the distribution of bacterial communities. Conclusions: Our results suggested that different environmental nutrient inputs contribute to seasonal and temporal variations of chemical features and bacterial communities in sediments of Lake Dongping. TP concentration was significantly correlated with the distribution of bacterial communities. Significance and Impact of the Study: This study has an important implication for the optimization of integrated ecosystem assessment of shallow temperate freshwater lake and provides interesting information for the subsequent of the ecosystem.