若尔盖高原湿地泥炭沼泽土亚硝酸盐还原酶（nirK）反硝化细菌群落结构分析

若尔盖泥炭湿地是世界少有的低纬度永久冻土湿地,具有高海拔、高紫外辐射、高有机质的特点。该区域N2O的排放量对全球气候变暖有重要影响。对若尔盖高原湿地泥炭沼泽土中的亚硝酸盐还原酶(nir K)反硝化细菌群落结构多样性进行分析,以期揭示该区域N2O释放的微生物调控机制。基于若尔盖高原湿地泥炭沼泽土的理化性质和反硝化活性(PDA),结合限制性酶切片段长度多态性(Restriction fragment length polymorphism,RFLP)技术、克隆文库及分子测序对该生态系统中的nir K反硝化细菌群落结构及多样性进行分析。反硝化活性测定结果显示:阿西地区麦溪地区分区地区,反硝化活性与土壤有机碳、总氮和丰富度呈显著正相关(P0.05)。Shannon-wiener多样性指数以阿西最高、分区最低。3个样品中共测序15条nir K基因代表序列,系统发育表明若尔盖高原湿地优势nir K反硝化菌群为变形门菌群。其中,阿西地区主要为α-变形菌门,麦溪地区主要为β-变形菌门,分区地区无法确定优势种群。冗余分析(Redundancy analysis,RDA)显示:有效钾和有效磷是影响nir K反硝化细菌群落结构的关键环境因子。本论文显示,若尔盖高原湿地存在着明显的反硝化作用,调控这些反硝化作用的nir K反硝化细菌多样性较高,且与土壤有效钾和有效磷密切相关。     

黄河三角洲滨海湿地微生物多样性及其驱动因子

微生物在湿地的生物地球化学循环和生态功能调节中发挥着重要作用,对全球气候变化具有重大影响,对维持全球生态系统的健康至关重要。以黄河三角洲滨海湿地为研究对象,通过采集代表性植被群落的土壤表层和部分植物根系,探究土壤微生物群落组成、根际微生物、环境因子及其内在的关联性和影响机制。研究结果表明不同植被覆盖地区微生物多样性存在差异,芦苇区和柽柳区微生物丰度高于泥滩区、碱蓬区和棉田,海漫滩微生物丰度高于河漫滩地和泥滩。土壤微生物菌群结构和多样性显著高于根际：土壤细菌的香农指数约为4-5.5,根际微生物的香农指数约为0-4。土壤细菌主要为厚壁菌门、变形菌门、拟杆菌门和放线菌门,占样品总数的90%以上;而根际细菌主要是蓝藻门、变形菌门和放线菌门,二者在属水平上的菌群结构差异更加明显。环境因子的含量与生境类型有关,SO₄^2-和NO₃^-的相关性最高,植被覆盖区土壤中Mn⁴⁺、Fe³⁺和水解氮的含量低于滩涂裸地。冗余分析（RDA）表明,pH值在小空间尺度上对湿地土壤中细菌群落的影响较小,环境因子在门和属水平的解释率分别为89.7%和86.8%,其中K（23.4%）、NO₂^-（11.8%）、Mn⁴⁺（9.8%）和Na（8.0%）是解释门水平微生物区系结构变化和组成的主要因子。研究为理解湿地微生物多样性与湿地生态系统功能之间的影响机制提供了一个生态学视角,有助于了解黄河三角洲滨海湿地土壤和植物根际的细菌分布特征,对黄河三角洲退化滨海湿地的生物修复具有重要的指导意义。     

冰川生态系统固碳微生物研究进展

[目的] 海南海口含有丰富的温泉资源,对温泉微生物多样性进行研究,有助于进一步开发和利用海南温泉微生物资源。[方法] 本文采用Illumina HiSeq高通量测序技术对海口3个温泉[海甸岛荣域温泉（S1）、火山口开心农场温泉（S2）和西海岸海长流温泉（S3）] 水样中微生物ITS序列和16S rRNA基因V3-V4区进行测序及生物信息学分析,探究海口市3个不同区域的温泉真菌多样性与细菌多样性。[结果] （1）α多样性分析表明,真菌群落中,S3 > S1 > S2,而在细菌群落中,S2 > S1 > S3。β多样性分析表明,3个温泉真菌群落和细菌群落组成差异皆显著。（2）分类分析表明,温泉真菌群落优势菌门为子囊菌门（Ascomycota）和担子菌门（Basidiomycota）,细菌群落优势菌门为变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）、Thermi、硝化螺旋菌门（Nitrospirae）、绿菌门（Chlorobi）、厚壁菌门（Firmicutes）、绿弯菌门（Chloroflexi）、放线菌门（Actinobacteria）。（3）CCA（Canonical correspondence analysis）分析表明,3个温泉的真菌群落主要影响因子是温度,细菌群落主要影响因子是总磷。[结论] 海南省海口市温泉中含有丰富的微生物资源,其微生物群落组成受多种环境因子影响,且影响真菌和细菌的主要环境因子不同。     

药用植物刺山柑不同部位细菌群落结构及其多样性

【目的】研究传统药用植物刺山柑（Capparis spinosa L.）不同部位细菌群落结构、物种组成和多样性特征,为药用植物微生物资源的开发及微生物与宿主互作提供理论依据。【方法】本研究以刺山柑地上部植物组织（果实、茎）和地下部土壤（根际土壤、非根际土壤）为研究材料,采用高通量测序技术分析刺山柑不同部位细菌的16S rRNA基因多样性,比较其细菌群落结构和物种组成特征。【结果】刺山柑4种样本共获得的3 649个操作分类单元（operational taxonomic unit,OTU）,属于34门、88纲、248目、464科和1 051属。土壤样本的细菌多样性大于植物组织,细菌群落多样性以根际土壤、非根际土壤、茎和果实的顺序逐渐降低,果实内生细菌群落多样性始终最低,显著低于根际土壤。不同部位相对丰度较高的细菌门如下：植物组织中以变形菌门为主,根际土壤中为变形菌门和放线菌门,非根际土中为厚壁菌门和放线菌门。无色杆菌属（Achromobacter）、欧文氏菌属（Erwinia）、肠球菌属（Enterococcus）、微小杆菌属（Exiguobacterium）、乳杆菌属（Lactobacillus）和克雷伯氏菌属（Klebsiella）主要存在于刺山柑植物组织中。游动球菌属（Planomicrobium）、库克菌属（Kocuria）、类芽孢杆菌属（Paenibacillus）、链霉菌属（Streptomyces）、微枝形杆菌属（Microvirga）和节杆菌属（Arthrobacter）主要分布于土壤中。β多样性分析结果表明,刺山柑植物组织和土壤的细菌群落结构具有显著差异,同类型样本的细菌群落结构相似。【结论】刺山柑土壤样本中细菌群落的多样性和丰富度均高于植物组织,刺山柑不同部位的细菌群落组成不同。本研究对刺山柑不同部位细菌群落结构进行了初步分析,鉴定了各部位细菌群落中的核心菌群,为以后挖掘刺山柑的功能研究和利用提供了准确的微生物信息。     

祁连山中部4种典型植被类型土壤细菌群落结构差异

土壤微生物参与土壤生态过程,在土壤生态系统的结构和功能中发挥着重要作用。2013年7月采集了祁连山中段4种典型植被群落(垫状植被、高寒草甸、沼泽草甸和高寒灌丛)的表层土壤,分析了表层土壤微生物生物量碳氮和采用Illumina高通量测序技术研究了土壤细菌群落结构及多样性,并结合土壤因子对土壤细菌群落结构和多样性进行了相关性分析。结果表明:(1)土壤微生物生物量碳氮的大小排序为:沼泽草甸高寒草甸高寒灌丛垫状植被;(2)土壤细菌群落相对丰度在5%以上的优势类群是放线菌门、酸杆菌门、α-变形菌、厚壁菌门和芽单胞菌门5大门类;(3)沼泽草甸土壤细菌α多样性(物种丰富度和系统发育多样性)显著高于其它3种植被类型(P0.05),而垫状植被土壤细菌α多样性最低;(4)冗余分析和Pearson相关性分析表明,土壤pH、土壤含水量、土壤有机碳和总氮是土壤细菌群落结构和α多样性的主要影响因子。研究结果可为祁连山高寒生态系统稳定和保护提供理论依据。     

川西亚高山三种天然次生林土壤微生物多样性变化特征

开展川西亚高山相似土壤母质背景下天然次生林土壤微生物群落结构及其多样性探究,可加深次生林更新过程中土壤微生物群落结构变化的认知。选取川西米亚罗林区20世纪60年代采伐后经自然更新恢复形成的3种天然次生林（槭-桦阔叶林,ABB;桦-槭-冷杉针阔混交林,BAA;岷江冷杉林,AFF）,分析林下表层（0-20 cm）土壤微生物群落结构变化及其影响因素,结果显示：（1）3种林型土壤细菌Chao1和Shannon指数均极显著高于真菌,但仅真菌群落的Shannon指数差异显著,表现为BAA > ABB > AFF;（2）细菌群落优势门主要为变形杆菌门、酸杆菌门、疣微菌门、拟杆菌门、绿弯菌门,相对丰度占比超过82%;真菌群落则为子囊菌门和担子菌门,占比超过85%,AFF担子菌门相对丰度最高而子囊菌门最低。（3） RDA分析显示,土壤pH和乔木物种多样性（Shannon指数）是影响微生物群落结构变化的主导因子;土壤养分元素对细菌群落影响不显著,真菌群落主要受TN、TP含量显著影响。总体上,林型间乔木层物种多样性、土壤酸碱度及其氮磷含量是导致微生物群落结构变化的关键因素。     

呼伦贝尔沙地樟子松人工林土壤细菌群落结构与功能预测

为揭示呼伦贝尔沙地樟子松人工林土壤细菌群落结构和功能特征,以3种林龄（25 a、34 a和43 a）沙地樟子松人工林为研究对象,沙质草地为对照,采用野外调查、Illumina Miseq高通量测序和PICRUSt功能预测相结合的研究方法,鉴定分析土壤细菌群落结构,阐明土壤理化因子对土壤细菌群落结构的影响,预测土壤细菌功能特征。研究结果显示：（1）呼伦贝尔沙地樟子松人工林共获得土壤细菌35门92纲109目210科267属,主要细菌优势门为变形菌门（Proteobacteria）（24.29%±3.39%）、放线菌门（Actinobacteria）（23.72%±4.10%）和酸杆菌门（Acidobacteria）（23.40%±2.55%）。人工林与沙质草地的变形菌门和酸杆菌门相对丰度存在显著差异（P<0.05）,人工林间土壤细菌多样性指数不存在显著差异（P>0.05）。（2）研究区土壤细菌群落的主要影响因子是速效钾、全磷和全氮。（3）PICRUSt功能预测共获得5个一级功能层和31个二级功能层,主要涉及环境信息处理、代谢和遗传信息处理等功能。43 a人工林土壤细菌代谢功能活跃,有利于植物对养分的吸收和利用。在呼伦贝尔沙地种植樟子松人工林有助于改善土壤细菌群落结构,促进土壤细菌代谢功能,且表层土壤细菌群落对土壤环境变化更为敏感。     

五台山亚高山土壤真菌海拔分布格局与构建机制

生物多样性的海拔分布格局与维持机制是生物多样性与生态系统功能研究的热点领域。尽管微生物驱动着地球上许多重要的生物地球化学循环,但与大型生物体相比,对微生物多样性海拔梯度分布格局知之甚少。运用Illumina Miseq高通量测序技术,全面分析了五台山亚高山生态系统（海拔2000-3058 m范围内）土壤真菌群落组成和多样性变化特征。结果表明,子囊菌门（Ascomycota）、担子菌门（Basidiomycota）、接合菌门（Zygomycota）、壶菌门（Chytridimycota）为主要的优势菌门。非度量多维尺度分析（NMDS）和相似性分析（ANOSIM）表明真菌群落组成和结构在海拔梯度上存在显著的差异（P<0.05）。典范对应分析（CCA）显示pH、植物丰富度、总碳含量与土壤真菌群落结构存在显著相关性（P<0.05）。局域海拔尺度上,土壤真菌多样性与植物多样性（α和β多样性）呈显著正相关关系（P<0.05）。方差分解分析（VPA）和偏Mantel分析表明土壤真菌群落构建过程中,环境因子和空间变量都起作用,并且环境因子占绝对的优势。土壤真菌群落之间的Bray-Curtis距离与海拔距离呈显著正相关关系（P<0.05）,说明环境选择是亚高山土壤真菌海拔分布格局的决定因素。总之,五台山亚高山沿海拔梯度土壤真菌群落结构和多样性产生明显的变化,群落构建主要由确定性过程和随机过程驱动,但确定性过程占主导地位。土壤pH、植物丰富度、总碳含量是影响土壤真菌群落结构的重要因素。     

三江平原沼泽湿地垦殖及自然恢复对土壤细菌群落多样性的影响

为量化垦殖对我国东北沼泽湿地的影响程度,于2015年6月基于Illumina Miseq PE300第二代高通量测序平台,对黑龙江省洪河国家级自然保护区的原始沼泽、耕地、退耕湿地的土壤细菌16S r RNA基因高变区域进行测序,并分析沼泽湿地土壤细菌群落多样性和结构组成与垦殖的关系。结果表明:共获得358737条修剪序列且被划分为36个已知的菌门,在11个主要的土壤细菌门类中(相对丰度1%),芽单胞菌门(P0.01)、拟杆菌门(P0.01)、厚壁菌门(P0.01)和绿菌门(P0.01)在不同生境类型样地差异显著,土壤细菌群落alpha多样性由高到低排序依次是:耕地、退耕湿地、原始沼泽。结合相关性分析和冗余分析可以证明,长期的耕作,特别是旱田耕作对沼泽湿地土壤细菌群落组成产生显著的影响,土壤p H、含水量、全碳、有机碳、可溶有机碳、碱解氮、微生物量碳、微生物量氮对土壤细菌的多样性和群落组成产生影响。总之,研究结果发现自然恢复可以显著促进土壤细菌群落多样性的恢复,但是沼泽湿地土壤细菌群落结构一旦被垦殖干扰改变将很难恢复到原始状态,强调了有效地利用土壤细菌群落对维护土壤生态系统平衡具有重要的意义。     

尖峰岭热带天然林不同土层细菌群落多样性和组成的海拔变异规律

土壤微生物群落结构沿海拔梯度的变异是微生物生物地理学分异和群落空间分布的重要内容,然而,热带森林土壤微生物多样性及其群落特征的海拔模式尚不明确。研究海南省尖峰岭自然保护区0—20cm和20—40cm土壤细菌多样性和群落组成沿海拔梯度(400—1410m)的变化及其与环境因子的关系。结果表明：在0—20cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高(峰顶降低)而增加,20—40cm土壤微生物生物量碳、生物量氮和生物量磷随海拔升高呈先升高后降低趋势;整体上,变形菌门、放线菌门、酸杆菌门、拟杆菌门、厚壁菌门在0—20cm中占优势,丰度总和占该层细菌总量的88.17%;变形菌门、放线菌门、酸杆菌门、厚壁菌门、绿弯菌门在20—40cm中占优势,丰度总和占该层细菌总量的90.82%;随海拔增加,0—20cm细菌多样性线性减少,20—40cm细菌多样性变化不显著;沿海拔梯度,0—20cm细菌群落组成可分为低(409—1018m),中(1018—1357m)和高(1410m)三个海拔聚集群落,20—40cm细菌群落组成随海拔无显著性变化;两土层细菌多样性与土壤pH显著正相关,土壤细菌群落组成在0...     

Global biogeography of highly diverse protistan communities in soil

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.     

植物群落和土壤理化性质对碧塔海湿地土壤细菌群落的影响

土壤微生物是湿地生态系统中土壤-植物系统生源要素迁移转化的引擎。探究湿地生态系统地上植物群落、土壤理化性质和空间结构与土壤细菌间的相互关系是维护湿地生态系统健康和稳定的关键。本研究运用双向指示种分析法(TWINSPAN)对碧塔海湿地采集的35个样方中的植物群落进行分类,并采用高通量测序技术对样方的表层土壤细菌进行测序,分析植物群落、土壤理化性质和空间结构与细菌群落间的关系。结果表明: 双向指示种分析将样方的植物群落划分为3种群落类型,相同类型的植物群落在外貌和结构上相似,说明基于双向指示种分析的数量分类方法在高原湿地生态系统植物群落分类中有较好的适用性;细菌相对丰度统计结果表明,酸杆菌门(21.0%)、绿弯菌门(15.5%)、变形菌门(15.3%)和拟杆菌门 (10.1%)是碧塔海湿地总丰度高于10%的门类,相似性分析(ANOSIM)显示,不同植物群落类型对应的土壤细菌群落存在显著差异,说明植物群落对土壤细菌组成有一定的影响;典范对应分析(CCA)结果显示,植物群落的多样性、含水率、pH、铁和空间结构是影响土壤细菌群落的重要因素。方差分解结果显示,细菌群落既受单一环境变量的影响,也受环境变量间复合作用的影响。综上,地上植物群落、土壤理化环境和空间结构共同塑造细菌群落,地上植物群落-细菌-土壤理化性质是不可分割的整体。     

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.     

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.     

盐城滨海滩涂湿地典型植物群落土壤微生物组成与结构特征

土壤微生物是生态系统维持正常结构与功能的重要组成部分,为探究盐城滩涂典型湿地土壤微生物群落结构特征,以江苏盐城滩涂互花米草、藨草、盐地碱蓬、芦苇及淤泥质光滩5种典型群落为对象,采用16S rRNA高通量测序技术分析0—10 cm(表层)、10—30 cm(中层)、30—60 cm(深层)土壤微生物多样性及群落结构。结果表明：(1)几种植物群落间,土壤微生物群落结构差异较大,主要体现在细菌群落结构的差异性,古菌群落结构差异相对较小。光滩与植物群落间,在土壤细菌种类及相对丰度上差异相对较大,互花米草群落与本土植物群落间,在微生物群落的细菌种类组成上存在较大差异;藨草群落土壤表层微生物群落结构与互花米草群落相似,深层与盐地碱蓬、芦苇群落相似。(2)同一群落不同层次土壤微生物群落结构相似,差异小于不同群落间土壤微生物群落的结构差异性;不同群落对应层次间,表深层土壤中五种群落土壤微生物多样性存在显著差异,中层土壤中五种群落微生物多样性差异不显著。总体上,植物群落类型对土壤微生物群落结构的影响大于土壤深度;与本土植物群落相比,互花米草群落土壤主要优势门微生物种类差异较小,但部分优势门微生物相对丰度...     

Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

The extent to which the distribution of soil bacteria is controlled by local environment vs. spatial factors (e.g. dispersal, colonization limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here, we constrained environmental factors (soil chemistry, climate, above‐ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 10² km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilization) was also shown to be highly correlated with community structure, but not to abiotic factors, suggesting nonstochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio‐temporal patterns of microbial diversity, as well as life history of the groups being investigated, much as is the case for macro‐organisms.     

若尔盖高寒湿地干湿土壤条件下微生物群落结构特征

土壤水分含量的空间异质性是引起湿地生态系统结构和功能空间变异的关键因素。目前有关低纬度高寒湿地土壤水分对微生物群落结构影响的研究较少。于2007年4月(冷季)和8月(暖季)采集若尔盖高寒湿地常年淹水和无淹水两种水分条件的土壤样品,利用磷脂脂肪酸方法分析其微生物群落结构。结果表明,土壤微生物总生物量、细菌生物量、革兰氏阳性细菌及革兰氏阴性细菌生物量均表现为常年淹水土壤高于无淹水土壤,且4月份高于8月份;与土壤通气量关系密切的真菌、放线菌,其生物量表现为无淹水土壤显著高于常年淹水土壤;反映群落组成的真菌:细菌磷脂脂肪酸比值也表现为无淹水土壤显著高于常年淹水土壤。磷脂脂肪酸的主成分分析表明,水分条件不同的两种土壤中微生物群落结构显著不同,季节变化并未引起土壤微生物群落结构的改变。     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?

Uganda''s forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last.     

Salinity and Bacterial Diversity: To What Extent Does the Concentration of Salt Affect the Bacterial Community in a Saline Soil?

In this study, the evaluation of soil characteristics was coupled with a pyrosequencing analysis of the V2-V3 16S rRNA gene region in order to investigate the bacterial community structure and diversity in the A horizon of a natural saline soil located in Sicily (Italy). The main aim of the research was to assess the organisation and diversity of microbial taxa using a spatial scale that revealed physical and chemical heterogeneity of the habitat under investigation. The results provided information on the type of distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH. The analysis of bacterial 16S rRNA showed differences in bacterial composition and diversity due to a variable salt concentration in the soil. The bacterial community showed a statistically significant spatial variability. Some bacterial phyla appeared spread in the whole area, whatever the salinity gradient. It emerged therefore that a patchy saline soil can not contain just a single microbial community selected to withstand extreme osmotic phenomena, but many communities that can be variously correlated to one or more environmental parameters. Sequences have been deposited to the SRA database and can be accessed on ID Project PRJNA241061.