青藏高原湖泊沉积物中有机碳组分构成及其对微生物群落结构的影响

【目的】探究湖泊沉积物中有机碳组分构成及其对湖泊微生物群落结构的影响。【方法】本研究采集了青藏高原29个湖泊共81个沉积物样品,通过硫酸水解法分析样品中易降解和难降解有机碳含量及其与环境变量之间的相关性;同时使用高通量测序技术分析样品中原核微生物和真菌群落的多样性和组成及其与易降解和难降解有机碳含量的相关关系。【结果】本研究的青藏高原湖泊沉积物中易降解有机碳Ⅰ(labile organic carbon Ⅰ, LOCⅠ)、易降解有机碳Ⅱ(labile organic carbon Ⅱ, LOCⅡ)和难降解有机碳(recalcitrant organic carbon, ROC)的含量分别为0.03–29.62 mg/g、0.02–23.38 mg/g和0.64–75.72 mg/g,ROC是沉积物有机碳的主要组分(占比为54.97%±19.50%)。LOCⅠ含量与海拔、总氮、总磷、钙离子、活性钙和活性铁含量显著相关(P<0.05);LOCⅡ含量与总氮、钙离子和活性钙含量显著相关;而ROC含量与海拔、总氮、总磷、钙离子和活性钙含量显著相关。其中,钙离子和活性钙的浓度与3种有机碳组分...     

微生物厌氧呼吸与有机污染水体沉积物修复

水体沉积物有机污染是当前全球关注的重要环境问题。微生物具有呼吸和代谢多样性,能以多种污染物作为厌氧呼吸的电子供体或受体,与周围环境中的生物和非生物因素组成代谢网络耦合有机污染物降解转化,是有机污染水体沉积物修复的重要驱动者。本文重点综述了微生物厌氧呼吸、电子传递网络及其对有机污染水体沉积物的修复机制研究进展,并对有机污染水体沉积物微生物修复理论和技术研究的问题和挑战进行了探讨。     

番茄青枯病发生对土壤真菌群落多样性的影响

土壤真菌群落对于维持土壤地力及作物健康有着重要的作用,但青枯病发生对土壤真菌群落影响的研究仍相对较少。应用实时荧光定量PCR及MiSeq高通量测序技术,研究了罹患青枯病与未患病番茄植株土体和根际的真菌群落组成。青枯病发生明显改变了番茄土体与根际土壤的真菌群落组成。与未患病根际土壤相比,患病番茄根际土壤的真菌丰度、Chao1值及Shannon值显著降低;潜在土著有益真菌如粘鞭霉属、被孢霉属、顶孢霉属和木霉属的相对丰度显著降低,而有害真菌镰刀菌属的相对丰度显著增加。综上,细菌性青枯病发生影响了土壤真菌群落的组成,其真菌丰度、多样性及土著有益真菌数量降低,而有害真菌数量增加,为阐明土传青枯病发生的微生态机制提供了一定的理论指导。     

橘皮表面真菌群落结构多样性分析

【目的】研究鲜橘皮表面真菌群落结构多样性,为探讨橘皮经贮藏陈化为陈皮真菌群落的变化奠定基础。【方法】在广东、四川、广西、江西、重庆5个柑橘主产地采集橘栽培变种茶枝柑、大红袍等的鲜橘皮,在Illumina Hi Seq平台上扩增橘皮表面真菌ITS区进行高通量测序,分析真菌物种注释及丰富度,并应用α与β多样性分析(AlphaBeta diversity)对真菌群落结构组成进行分析。【结果】8批橘皮样品的有效序列可分类至35个属,不同产地茶枝柑、大红袍等品种橘皮表面真菌群落由7类真菌群落组成,种类一致,其中担孢酵母属(Erythrobasidium)、青霉属(Penicillium)、曲霉属(Aspergillus)、红酵母属(Rhodotorula)、球腔菌属(Mycosphaerella)为最大相对丰度排名前5的属,首次在橘皮表面发现枝氯霉属和短梗霉属真菌。【结论】明确了橘皮表面真菌群落结构组成,为橘皮在贮藏过程中真菌群落变化与药材品质变化相关性研究奠定基础。     

不同施肥方式对酸性茶园土壤真菌群落的影响

为揭示不同施肥方式对茶园土壤真菌群落结构的影响,依托定位施肥试验,采集对照(CK)、纯化肥(N300)、有机肥配施(OM30) 3个处理的0—10 cm和10—20 cm两层土壤,通过高通量测序技术,分析不同施肥处理下,茶园土壤真菌群落结构特征及其与土壤理化性质的关系。结果表明0—10 cm土层中真菌Alpha多样性显著高于10—20 cm土层(P0.05);在同一土层中,Alpha多样性变化趋势为CK N300 OM30。子囊菌门、担子菌门、接合菌门是试验茶园土壤中三大优势真菌门类,Sordariomycetes纲,Tremellomycetes纲和Mortierellomycotina纲分别是子囊菌门、担子菌门和接合菌门下的优势种群。子囊菌门和担子菌门在0—10 cm土层中相对丰度较高,而接合菌门则在10—20 cm土层中具有较高丰度(P0.05)。施肥处理提高了土壤中接合菌门的相对丰度,降低了子囊菌门的相对丰度。不同深度土壤中真菌群落结构差异主要受土壤理化性质变化驱动,冗余分析和Monte Carlo置换检验结果显示,土壤有机碳、全氮、碳氮比、全钾、速效钾含量对土壤真菌群落结构影响显著(P0.05),而试验茶园土壤的pH变化对同一土层中真菌群落结构的影响并不显著(P0.05)。     

复合污染尾矿废水中真菌群落多样性及其驱动机制

金属尾矿废水中含有重金属以及多种有机和无机污染物, 然而在该极端生境中仍然有大量微生物存在。为了揭示碱性尾矿废水中真菌群落的组成模式和多样性格局及其维持机制, 本文利用ITS1区rDNA基因扩增子测序和qPCR技术对山西中条山十八河尾矿库废水中5个不同采样点真菌群落的组成、丰度和分布格局进行了研究。通过主坐标分析(PCoA)比较不同采样点间群落结构的差异性; 通过冗余分析(RDA)探讨了水体理化因子对真菌群落结构的影响; 通过零模型分析了影响群落结构的主要因素; 通过网络图分析了真菌类群之间的种间相互作用。结果表明, 布勒掷孢酵母属(Bullera)、Schizangiella、支顶孢属(Acremonium)和亚罗酵母属(Yarrowia)是主要的优势属, 真菌群落在不同采样地点从门到属水平的相对丰度均有明显变化。真菌群落丰度沿水流方向逐渐增加且与有机碳(TOC)浓度呈显著正相关。真菌群落的α-多样性与pH、重金属(As和Cu)、无机碳(IC)和铵态氮(NH₄⁺)浓度显著相关。真菌群落的空间结构在不同采样点具有明显差异, 这种差异性与理化因子没有显著关系; 不同采样点真菌群落的零偏差值均大于零, 且不同物种之间存在复杂的种间相互作用。以上结果说明, 在尾矿废水中环境因子只对真菌群落的α-多样性有显著影响, 而群落的β-多样性主要受种间相互作用关系的影响, 表明在碱性铜尾矿废水中存在比较复杂的真菌群落动态模式。     

白僵菌生物防治林中虫生真菌群落结构分析

对白僵菌生物防治林中虫生真菌群落的结构研究表明,长期接种式释放白僵菌的马尾松林中虫生真菌共有属7种.球孢白僵菌的数量占绝对优势,为总数的63.22%;拟青霉次之,占25.86%;绿僵菌占9.20%;轮枝孢仅占1.72%.从寄主昆虫的多样性来看,球孢白僵菌和环链拟青霉的Brillouin多样性指数分别为3.56和2.315,均匀度分别为0.81和0.865;粉拟青霉和蜡蚧轮枝孢的多样性指数分别为1.71和0.862,均匀度为0.963和1.000而黄绿绿僵菌、金龟子绿僵菌和玫烟色拟青霉多样性和均匀度指标均较低.不同季节中被白僵菌侵染的寄主昆虫多样性指数呈现出春秋高、夏季低的趋势,反映了白僵菌种群的季节性变化.     

漳江口红树林沉积物真菌多样性分析及抗茶叶致病真菌生物活性筛选

以福建漳江口红树林国家级自然保护区红树林沉积物分离的真菌为对象,研究红树林沉积物真菌的多样性和筛选抗茶叶病原真菌活性的菌株。将分离纯化的135株真菌通过形态学和Ribosomal DNA-Internal Transcribed Spacer(rDNAITS)序列测定进行鉴定及多样性分析,归为40个种类型,分别属于17个属,其中青霉属(25%)为优势菌,木霉属(15%)、曲霉属(10%)和镰刀属(10%)次之,表明红树林沉积物真菌具有丰富的多样性;利用平板对峙法对真菌的发酵粗提物抗茶叶病原真菌生物活性研究,结果发现,共有17株(占42.5%)真菌具有抗茶叶病原真菌活性,其中15株能够抑制茶叶轮斑病(Pestalotiopsis theae)LH13,12株能够抑制茶叶炭疽病(Colletotrichum gloeosporioides)LH30,8株能够抑制茶叶溃疡病(Neofusicoccumsp.)LH107,有两株对这三种茶叶致病菌均有较强活性。这些活性菌株分布在6个属中,分别是青霉属(7株)、木霉属(3株)、镰孢属(2株)、枝孢属(2株)、白地霉属(2株)和球腔菌属(1株)。由此可见,红树林沉积物真菌抗菌活性菌株的种属分布具有多样性。     

水产养殖不同物种对水体和沉积物中细菌群落的影响

为探究水产养殖中养殖不同物种对水体和沉积物中细菌群落的影响,以养殖克氏原螯虾(Procambarus clarkii, PC)和中华鳖(Pelodiscus sinensis, PS)的水体和沉积物样品为研究对象,利用基于16S rRNA基因的高通量测序技术,对细菌群落多样性和群落组成进行分析,并结合环境因子,探究水产养殖对细菌群落的影响。结果显示,水体和沉积物中细菌群落的α多样性均呈现PS>PC的显著差异(P<0.05)。非度量多维尺度分析的结果显示,PC和PS区的水体和沉积物细菌群落结构均呈现明显差异。冗余分析(RDA)的结果表明,水体氨氮(NH~+₄-N)和硝酸盐氮(NO~-₃-N)是影响水体细菌群落结构的最主要环境因子,沉积物总氮(TN)、总磷(TP)和有机碳(OC)均对沉积物细菌群落结构有显著影响(P<0.05)。PC和PS区中的细菌隶属于34门、114纲、258目、504科和955属,水体中共筛选出了11个优势菌门(相对丰度>0.5%),沉积物中筛选出了13个。2个养殖区域的水体样品中共筛选出了15个优势(...     

树栖真菌群落多样性研究I.：红松芽,叶及短枝栖真菌群落组成分析

文章提出了树栖真菌的概念，并且以红松为例，对芽栖真菌、叶栖真菌和短枝栖真菌在不同树龄与叶龄以及不同树冠层次的情况下，进行了树栖真菌的群落组成和数量分析。共分离获得芽、叶、短枝栖真菌５９种。     

The effect of long-term mercury pollution on the soil microbial community

The effect of long-term exposure to mercury on the soil microbial community was investigated in soil from three different sites along a pollution gradient. The amount of total and bioavailable mercury was negatively correlated to the distance from the center of contamination. The size of the bacterial and protozoan populations was reduced in the most contaminated soil, whereas there was no significant difference in fungal biomass measured as chitinase activity. Based on the number of colony morphotypes, moreover, the culturable bacterial population was structurally less diverse and contained a higher proportion of resistant and fast-growing forms. The profiles of amplified 16S rDNA sequences obtained from community DNA by denaturating gradient gel electrophoresis (DGGE) also reflected the altered community structure and decreased diversity along the mercury gradient as expressed in terms of the number and abundance of bands. The functional potential of the microbial population measured as sole carbon source utilization by Ecoplates((R)) differed between the soils, but there was no change in the number of substrates utilized. The observed changes in the different soil microbial populations are probably a combination of both direct and indirect effects of the mercury contamination.     

Analysis of fungal community structure in the soil of Zoige Alpine Wetland

To understand the soil fungal community diversity in different zones of the Zoige Alpine Wetland, BIOLOG analysis and traditional culture method were employed in our research. Three sample sites namely the Conservatory Station up-hill slope (CSUS), the Flower Lake side (FLS) and the Conservatory Station down slope (CSDS) with increasing by water content were investigated. The results of BIOLOG showed that fungal catabolic richness index (S) and Shannon diversity index (H) increasingly rose with water content augmented from CSUS to CSDS, while different from the former tendency, the fungal catabolic activity was highest at CSDS and lowest at FLS. Principal component analysis (PCA) results demonstrated the functional diversity of fungal community varied among the three sample sites, showing us more similarity between CSDS and FLS, and considerable difference between CSUS and the former two sites. The outcome of traditional culture method illustrated the number of soil fungi increased from CSUS to CSDS, while the sort of fungal species that could be cultured did not show much difference among the three sample sites.     

Analysis of fungal community structure in the soil of Zoige Alpine Wetland

To understand the soil fungal community diversity in different zones of the Zoige Alpine Wetland, BIOLOG analysis and traditional culture method were employed in our research. Three sample sites namely the Conservatory Station up-hill slope (CSUS), the Flower Lake side (FLS) and the Conservatory Station down slope (CSDS) with increasing by water content were investigated. The results of BIOLOG showed that fungal catabolic richness index (S) and Shannon diversity index (H) increasingly rose with water content augmented from CSUS to CSDS, while different from the former tendency, the fungal catabolic activity was highest at CSDS and lowest at FLS. Principal component analysis (PCA) results demonstrated the functional diversity of fungal community varied among the three sample sites, showing us more similarity between CSDS and FLS, and considerable difference between CSUS and the former two sites. The outcome of traditional culture method illustrated the number of soil fungi increased from CSUS to CSDS, while the sort of fungal species that could be cultured did not show much difference among the three sample sites.     

Community action on water pollution

Actions to improve local water or air quality are likely to combine collective benefits with specific costs. This suggests that the variations among communities in their actions to improve water quality will involve opposition from industries bearing the specific costs. The use of Environmental Protection Agency (EPA)-funded matching grants for sewerage construction by large U.S. cities varies inversely with the imputed opposition from polluting industries. Use also increases with assessed need and with the extent of certain resources, including the credit rating. Matching grants funded by the Department of Housing and Urban Development (HUD) are not likely to have such specific costs, and imputed opposition does not affect their distribution. When location and the growth rate are controlled, use of restrictions and surcharges on industrial wastes increases with imputed opposition. It is possible that industries influence the specific regulations. Alternative explanations of the statistical relationship between opposition and EPA grant use are discussed.This research was partially supported by Department of Commerce Grants 2-35227 and 04-3-158-45 to the University of Southern California Sea Grant Program.     

The effects of water pollution on the phylogenetic community structure of aquatic plants in the East Tiaoxi River,China

1. Water pollution is one of the most serious aquatic environmental problems worldwide. In China, recent agricultural and industrial development has resulted in rapid changes in aquatic ecosystems. Here, we reveal the effects of water pollution on the phylogenetic community structure of aquatic macrophytes in the Tiaoxi River, China.
2. We placed a rectangular plot at 47 sites within the Tiaoxi River from the mouth of the river to 88.5 km upstream, in which we recorded species abundance and measured 22 physico-chemical variables. Bayesian phylogeny using the rbcL and matK gene sequences was employed to quantify phylogenetic α- and β-diversity, and test the phylogenetic signal in four growth forms: emergent, floating-leaved, free-floating, and submerged.
3. Within communities, water contamination and phytoplankton abundance decreased species richness and phylogenetic diversity, which resulted in phylogenetic clustering; species within communities were more closely related to each other than expected. Between communities, differences in geographical distance and phytoplankton abundance resulted in phylogenetic dissimilarity among plots. Aquatic macrophytes showed phylogenetic signals in which related species responded more similarly to disturbance.
4. Thus, the observed patterns could be explained by environmental filtering and suggested that water pollution by human activity has added more filters to the existing environmental filters that drive the species assembly of macrophyte communities.

     

台州市路桥区重金属污染对土壤动物群落结构的影响

通过对台州市路桥区峰江再生园区及周围的8个样地采样调查,分析了重金属污染对土壤动物多样性的影响。对研究区域进行大量取样调查并测定土样中Cu、Zn、Pb、Cd 的含量。计算出重金属综合污染指数,运用地理信息系统(GIS)技术中的插值法根据重金属综合污染指数制作重金属综合污染趋势图。结合重金属综合污染趋势图与实地勘察,共设置8个采样地。研究方法为大型土壤动物采用野外分层手捡计数,中小型土壤动物用取土器分层取土,带回室内分别用干湿漏斗分离并镜检。结果表明:(1)8个样地共获得土壤动物844只,分属于4门9纲20个类群,其中优势类群为蜱螨目、弹尾目和线虫纲,其他为常见类群和稀有类群。(2)8个样地中土壤动物的个体数量存在极显著性差异(P<0.01),类群数存在极显著性差异(P<0.01)。在严重污染区,土壤动物的数量和类群数稀少,而轻度污染区土壤动物的密度大、群落多样性高,稀有类群大量出现。表明重金属污染能对土壤动物多样性构成严重影响,土壤动物群落的类群和个体数量随污染程度的加重而减少(3)用群落多样性指标DG衡量重金属污染对土壤动物多样性的影响,结果为随着综合污染指数的减小,DG指数逐渐增大。(4)用简单相关性分析表明土壤动物数量变化与综合污染指数具有极显著负相关性(相关系数-0.86),与有机质含量有一定相关性(相关系数0.42)。在轻度污染的样地中,土壤动物的数量随有机质含量的升高而上升,表明在严重的污染区,重金属的毒性对土壤动物的影响是主要的,而在轻度污染区,有机质含量可能成为影响土壤动物多样性的主要因素。(5)从弹尾目的等节跳科和球角跳科在8个样地中的分布特点可知,本地区的等节跳科对重金属污染的耐受力最强。球角跳科数量大、密度高,对重金属污染较敏感,可作为重金属污染的指示生物。     

New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi

Background

To date, biologists have discovered a large amount of valuable information from assembled genomes, but the abundant microbial data that is hidden in the raw genomic sequence data of plants and animals is usually ignored. In this study, the richness and composition of fungal community were determined in the raw genomic sequence data of Ceratosolen solmsi (RGSD-CS).

Results

To avoid the interference from sequences of C. solmsi, the unmapped raw data (about 17.1%) was obtained by excluding the assembled genome of C. solmsi from RGSD-CS. Comparing two fungal reference datasets, internal transcribed spacer (ITS) and large ribosomal subunit (LSU) of rRNA, the ITS dataset discovered a more diverse fungal community and was therefore selected as the reference dataset for evaluating the fungal community based on the unmapped raw data. The threshold of 95% sequence identity revealed many more matched fungal reads and fungal richness in the unmapped raw data than those by identities above 95%. Based on the threshold of 95% sequence identity, the fungal community of RGSD-CS was primarily composed of Saccharomycetes (88.4%) and two other classes (Agaricomycetes and Sordariomycetes, 8.3% in total). Compared with the fungal community of other reported fig wasps, Agaricomycetes and Eurotiomycetes were found to be unique to C. solmsi. In addition, the ratio of total fungal reads to RGSD-CS was estimated to be at least 4.8 × 10⁻³, which indicated that a large amount of fungal data was contained in RGSD-CS. However, rarefaction measure indicated that a deeper sequencing coverage with RGSD-CS was required to discover the entire fungal community of C. solmsi.

Conclusion

This study investigated the richness and composition of fungal community in RGSD-CS and provided new insights into the efficient study of microbial diversity using raw genomic sequence data.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0370-3) contains supplementary material, which is available to authorized users.     

淮南市重金属污染对土壤动物群落和多样性影响研究

通过对淮南煤矿和发电厂及灰场污染地的土壤动物群落结构进行分析。结果表明,土壤动物群落的组成与数量随着污染的加重而减少,土壤动物的密度也有同样的变化趋势;在重污染土壤中,优势类群与常见类群的种类明显减少。随着污染的加重使土壤动物的种类和数量逐渐减少。重金属污染对土壤动物群落结构的影响是随着污染的加重,多样性指数、均匀性指数、密度类群指数都有减少的趋势,优势度指数在灰场外围是先增加后减少。在群落指标的相关性中,多样性指数和均匀性指数呈密切正相关,多样性指数与优势性指数呈负相关,有机质含量与土壤动物个体数量关系不密切。     

纳帕海高原湿地真菌群落多样性和组成的分布

【背景】位于滇西北的纳帕海高原湿地,是我国唯一的低纬度、高海拔、季节性半封闭型高原湿地。真菌在湿地生态系统的维持和稳定中发挥着特殊作用,然而关于纳帕海高原湿地真菌群落多样性和组成的研究目前仍无报道。【目的】对纳帕海高原湿地不同季节和土壤类型真菌群落多样性和组成及与环境因子的关系开展系统研究分析,促进对高原湿地微生物多样性的深入认识。【方法】采用荧光定量PCR和高通量测序技术,分析了纳帕海高原湿地不同季节和土壤类型中真菌的数量、群落多样性和组成及其与环境因子的关系。【结果】真菌数量级的变化对于人为干扰下的湿地土壤退化是敏感的响应指标。在真菌群落组成中,约有60%以上未确定的分类信息,40%有确定分类信息的包括6个门17个纲37个目53个科63个属,大部分分类信息集中在Ascomycota门,相对优势属为Gibberella。通过分类水平、OTU水平和β多样性分析比较,在纳帕海高原湿地整体真菌群落多样性和组成受季节变化影响不显著,但不同土壤类型的变化呈显著差异,推测是由于不同采样区植物根际效应和种类的影响。CCA (Canonical correlation analysis)分析表明,在不同采样区受不同土壤理化因子的影响。【结论】揭示了纳帕海高原湿地土壤真菌群落多样性和组成的区域特征,从微生物学角度进一步提出了对纳帕海高原湿地环境保护和恢复的重要性。     

A preliminary survey of organic pollution of shellfish in Tolo Harbour,Hong Kong

A preliminary survey on the contamination of clams and sea-waters in various towns in Tolo Harbour was carried out using bacteriological tests. The ‘percentage clean’ method and the ‘most probably number’ method were employed. The pH, salinity and temperature of the seawater were also tested in the field. It was discovered that the number of coliform bacteria obtained by the ‘percentage clean’ was zero in both seawater and clams from all sites including the control. The ‘most probable number’ indicated that the water and the clam tissue collected in the three sites in Tolo Harbour ranged from 15–1,100/100 ml in the water and 825–11,000/g in the clams compared with 0/100 ml and 115/g of the control site. Due to the high level of organic pollution in Tolo Harbour, improvement of the sanitary situation is urged. Cultivation of clams collected in this area in clean and sterilized water for a few days before consumption is recommended.