土壤微生物群落抵抗力和恢复力研究进展

人类活动的不断加剧使得土壤生态系统承受着环境干扰压力。土壤微生物受到环境干扰的响应程度（抵抗力）及恢复至原来状态的能力（恢复力）决定着土壤生态系统的可持续性。梳理和总结了土壤微生物群落对环境干扰的抵抗力和恢复力方面的研究进展。首先,在介绍土壤微生物群落抵抗力和恢复力概念的基础上,阐述了通过评估微生物群落的结构和功能的变化来系统表征抵抗力和恢复力;随后,分析了最近十年（2012-2021年）有关文献,发现土壤微生物群落的结构和（或）功能在环境干扰后的恢复力总体较弱,但耕作、有机物料添加和轮作等农田管理措施下的响应趋势表现出一定的规律性;继而,从个体水平的休眠和胁迫忍耐、种群水平的生存策略、群落水平的多样性和相互作用以及生态系统水平的历史遗留效应等方面分析了土壤微生物群落抵抗力和恢复力的维持机制;最后,从功能性状、多功能性和植物-土壤微生物整体性对未来研究做出了展望,以期为构建土壤健康评价体系及预测环境干扰对土壤功能的影响提供科学依据。     

Application of multivariate statistical techniques in microbial ecology

Recent advances in high‐throughput methods of molecular analyses have led to an explosion of studies generating large‐scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in‐depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high‐throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure.     

复合微生物菌剂对重茬苹果园土壤细菌群落的影响

【目的】了解抗重茬复合微生物菌剂对重茬苹果园土壤细菌数量及多样性的影响。【方法】对重茬苹果园土壤进行复合微生物菌剂处理后,采用自动核糖体内转录间隔区序列分析方法(Automated ribosomal intergenic spacer analysis,ARISA)对新茬苹果园、重茬苹果园土壤细菌群落多样性进行分析。【结果】经复合微生物菌剂处理2年后,重茬果园土壤OTUs总数和Shannon-Weiner指数分别为250和4.44,新茬果园OTUs总数和Shannon-Weiner指数分别为234和3.81,经One-Way ANOSIM法分析得到二者差异系数P分别为0.108 3和0.084 3。另外,重茬园和新茬园共享核心OTUs有89个,二者的Jaccard群落相似性系数为0.47,相似程度中等。【结论】复合微生物菌剂具有提高重茬果园土壤微生物多样性,促进重茬苹果园土壤微生物生态系统恢复的作用。     

微塑料对稻田土壤温室气体排放和微生物群落的影响

微塑料因在土壤环境中广泛存在及其潜在的生态风险而受到越来越多的关注。微塑料的赋存会改变土壤理化性质,并对土壤微生物群落及其驱动的生物地球化学过程产生影响,而相关研究尚处于起步阶段。可生物降解塑料作为传统塑料的替代品,越来越多地应用于农业活动,并释放到土壤中。然而,可生物降解微塑料对土壤微生物特性产生影响的研究鲜有报道。基于此,本试验以我国三江平原水稻田土壤为研究对象,选取了2种常见的微塑料为试验材料,分别为传统型微塑料聚丙烯(Polypropylene,PP)和可降解微塑料聚乳酸(Polylactic acid,PLA),进行了为期41d的微宇宙培养实验,旨在分析不同浓度与类型的微塑料对土壤可溶性有机碳(Dissolved Organic Carbon,DOC)含量及官能团特征、温室气体排放以及微生物群落结构的差异性影响。结果表明,传统型微塑料PP与可降解微塑料PLA添加均对土壤理化性质与微生物群落产生显著影响。其中,微塑料添加大体上增加了土壤DOC含量,PLA的促进作用较为明显,且增加含量与微塑料添加量呈正相关;PP和PLA均影响土壤DOC分子结构,削弱了土壤团聚化程度并促进了大分子量DOC化合物的生成;微塑料的添加促进土壤CH₄排放,而有效抑制了土壤CO₂排放;微塑料显著改变了土壤细菌和真菌群落的丰富度与多样性。相关分析结果表明,土壤CO₂累计排放量与芳香族化合物结构及疏水性等官能团特征、变形菌门(Proteobacteria)与放线菌门(Actinobacteria)均呈显著正相关关系。以上结果表明,微塑料添加改变了土壤DOC含量及官能团特征与微生物环境,进而影响土壤温室气体排放。本研究为今后微塑料对土壤地球化学和微生物特性的影响研究提供了科学的思路,同时也有助于评估微塑料对土壤生态系统的生态风险。     

The in vitro effect of hydrogen peroxide on vaginal microbial communities

This study presents a series of experiments carried out in order to elucidate the role of H2O2 in antimicrobial activity of lactobacilli. Vaginal swabs were collected from 60 premenopausal women and checked for pH and Nugent score, and Lactobacillus species were cultured, phenotyped and genotyped. The main outcome measures involved: (1) species of vaginal lactobacilli most effective in liberating H2O2, (2) minimal microbicidal concentrations of added H2O2, (3) kinetics of H2O2 liberation in relation to oxygen tension, (4) antimicrobial activity of pure H2O2 versus one produced by selected vaginal lactobacilli and the total activity of their culture supernatants. Results showed that H2O2 was liberated especially by: Lactobacillus delbrueckii, Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus johnsonii and L. gasseri. Hydrogen peroxide reached concentrations from 0.05 to 1.0 mM, which under intensive aeration increased even up to 1.8 mM. Microorganisms related to vaginal pathologies show varied resistance to the action of pure H2O2. Most potent inhibitory activity against bacteria and yeasts was presented by Lactobacillus culture supernate producing H2O2, followed by the nonproducing strain and pure H2O2. To conclude - the antimicrobial activity of lactobacilli is a summation of various inhibitory mechanisms in which H2O2 plays some but not a crucial role, in addition to other substances.     

水稻化感品种对土壤微生物的影响

通过盆栽实验研究三叶期水稻化感品种对土壤微生物种群数量的影响。结果显示,土壤细菌、放线菌、真菌、氨化细菌和好气性自生固氮菌数量在水稻化感品种P1312777和水稻非化感品种“辽粳九”、“秋光”的土壤中存在显著差异,土壤中大多数微生物被水稻化感品种所抑制,但化感品种土壤中的放线菌和好气性纤维素分解菌数量则介于两种非化感品种之间。这一研究表明,水稻化感品种能显著地影响土壤微生物种群数量。     

Distinct microbial communities associated with buried soils in the Siberian tundra

Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.     

Spatial distribution of microbial communities in the cystic fibrosis lung

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.     

中亚热带几种针、阔叶树种凋落物混合分解对土壤微生物群落碳代谢多样性的影响

土壤微生物群落功能如何响应凋落物物种组成的改变,对于指导我国的人工林种植具有重要意义。通过小盆模拟试验,用BIOLOG微平板培养的方法研究了南方红壤丘陵区典型物种马尾松和湿地松的凋落物分别与白栎和青冈的凋落物混合,与单一针叶凋落物分解时相比,针阔混合凋落物分解过程中土壤微生物群落功能多样性的差异。结果表明：(1)针叶和阔叶混合分解提高了土壤微生物群落碳代谢的强度、丰富度以及多样性,针阔混合凋落物分解时土壤微生物群落的碳源代谢方式与单一针叶分解时差异显著;(2)凋落物分解前期土壤微生物群落碳代谢强度、丰富度和多样性与凋落物初始C/N呈显著负相关,分解后期土壤微生物群落碳代谢强度与凋落物初始木质素/N比呈显著负相关,碳代谢多样性与初始P含量呈显著正相关;(3)通过改变凋落物物种组成,进而改变凋落物元素组成(C/N、木质素/N和P),能显著影响土壤微生物群落的碳代谢强度和代谢多样性。在南方红壤丘陵区,针-阔叶混合的凋落物比单一针叶凋落物更有利于提高土壤微生物群落的功能。     

尿素肥斑扩散对土壤微生物群落结构的影响

磷脂脂肪酸 (PL FA)被认为是有效指示活体土壤微生物群落结构变化的标记物之一 ,该方法已在土壤微生物的研究中被大量应用。采用特制容器 ,模拟尿素肥斑在土壤中的扩散行为 ,观察距尿素肥斑不同距离微域中养分形态和浓度变化及其对土壤微生物群落结构的影响。试验结果表明 ,培养 7d后 ,No.7(距肥斑 7cm)和 No.8(距肥斑 8cm )微域的 NH 4、NO- 2 、NO- 3浓度最高 ,NO- 2 是尿素扩散区域的主要离子存在形态。对提取到的 2 5种 PL FA进行主成分分析 (PCA) ,发现 PL FA组成随不同微域养分浓度变化而变化 ,说明微生物群落结构发生了改变。就标记性 PL FA而言 ,尿素扩散导致真菌 PL FA在高浓度养分微域浓度增加 ,细菌 PL FA浓度下降 ,其中 ,No.7微域的真菌 PL FA18∶ 2ω6 ,9和 PL FA18∶ 1ω9浓度分别比对照 (No.2 0微域 )增加 173%和 4 7.2 %。然而 ,放线菌 PL FA 10 Me18∶ 0浓度变化不大     

地下水微生物功能群及生物地球化学循环

地下水系统是地球关键带的重要组成部分,为微生物提供了特殊的栖息环境和复杂的生存条件,进而演化出复杂的生物地球化学过程.随着多技术、多学科的交叉融合及发展,近几十年地下水微生物功能群及生物地球化学循环研究取得了引人瞩目的 重要进展.本文从地下水中的微生物群功能分区、微生物介导的地球化学元素循环、污染与修复中的生物地球化学...     

Biogenic amine-forming microbial communities in cheese

The aim of this study was to screen two cheese starter cultures and cheese-borne microbial communities with the potential to produce biogenic amines in cheese during ripening. Bacteria of the genera Enterococcus and Lactobacillus and coliform bacteria were isolated from Dutch-type semi-hard cheese at the beginning of the ripening period. Statistically significant counts of bacterial isolates were screened for the presence of specific DNA sequences coding for tyrosine decarboxylase (tyrDC) and histidine decarboxylase (hDC) enzymes. The PCR analysis of DNA from 14 Enterococcus and 3 Lactobacillus isolates confirmed the presence of the targetted DNA sequences. Simultaneously, 13 tyrDC- and 3 hDC-positive isolates were grown in decarboxylase screening medium and this was followed by HPLC analysis of the produced tyramine and histamine. Conventional and molecular taxonomic analyses of the above-mentioned isolates identified the following species: Enterococcus durans (7 strains), Enterococcus faecalis (3 strains), Enterococcus faecium (1 strain), Enterococcus casseliflavus (3 strains), Lactobacillus curvatus (1 strain), Lactobacillus lactis (1 strain) and Lactobacillus helveticus (1 strain). All of the above Enterococcus and two of the Lactobacillus strains originated from contaminating microbial communities. The L. helveticus strain, which was tyrosine decarboxylase-positive and exhibited tyramine production, originated from starter culture 1 used for cheese production. Comparison of partial tyrDC sequences of positive Enterococcus isolates revealed 89% sequence similarity, and that of hDC-positive Lactobacillus isolates revealed 99% sequence similarity.     

Genomic structure predicts metabolite dynamics in microbial communities

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The pattern of recovery of disturbed microbial communities inhabiting hard substrates

The recovery of microbial communities removed from hard substrates was studied in the laboratory and on microepiphyton in the White Sea, in St. Petersburg, and in Karelija. The removal of these communities from hard substrates destroyed their spatial structure. Recovery was allowed to proceed from the suspension on a horizontal substrate in stagnant water at low temperature. The sequence of colonization in the laboratory was the same as that in the field. Laboratory recovery was complete in 12–24 h and did not depend on the age of the natural community. From the comparison between laboratory and field data on such mechanical disturbance, a pattern of recovery, termed ‘self-assembly’, is proposed. This revised version was published online in September 2006 with corrections to the Cover Date.     

Macroecological patterns in soil communities

Aim To review published evidence regarding the factors that influence the geographic variation in diversity of soil organisms at different spatial scales. Location Global. Methods A search of the relevant literature was conducted using the Web of Science and the author's personal scientific database as the major sources. Special attention was paid to include seminal studies, highly cited papers and/or studies highlighting novel results. Results Despite their significant contribution to global biodiversity, our taxonomic knowledge of soil biota is still poor compared with that of most above‐ground organisms. This is particularly evident for small‐bodied taxa. Global patterns of soil biodiversity distribution have been poorly documented and are thought to differ significantly from what is reported above‐ground. Based on existing data, it appears that microorganisms do not respond to large‐scale environmental gradients in the same way as metazoans. Whereas soil microflora seem to be mainly represented by cosmopolitan species, soil animals respond to altitudinal, latitudinal or area gradients in the same way as described for above‐ground organisms. At local scales, there is less evidence that local factors regulate above‐ and below‐ground communities in the same way. Except for a few taxa, the humpbacked response to stress and disturbance gradients doesn't seem to apply underground. Soil communities thus appear weakly structured by competition, although competitive constraints may account for assembly rules within specific taxa. The main factor constraining local soil biodiversity is the compact and heterogeneous nature of soils, which provides unrivalled potential for niche partitioning, thus allowing high levels of local biodiversity. This heterogeneity is increased by the impact of ecosystem engineers that generate resource patchiness at a range of spatio‐temporal scales.     

Transgenic Bt cotton has no apparent effect on enzymatic activities or functional diversity of microbial communities in rhizosphere soil

A transgenic Bt cotton (Sukang-103) and its non-Bt cotton counterpart (Sumian-12) were investigated to evaluate the potential risk of transgenes on the soil ecosystem. The activities of urease, phosphatase, dehydrogenase, phenol oxidase, and protease in cotton rhizosphere were assayed during the vegetative, reproductive, and senescing stages of cotton growth and after harvest. A Biolog system was used to evaluate the functional diversity of microbial communities in soils after a complete cotton growth cycle. Enzymatic activities in soils amended with cotton biomass were also assayed. Results showed that there were few significant differences in enzyme activities between Bt and non-Bt cottons at any of the growth stages and after harvest; amendment with cotton biomass to soil enhanced soil enzyme activities, but there were no significant difference between Bt and non-Bt cotton; the richness of the microbial communities in rhizosphere soil did not differ between Bt and the non-Bt cotton, and close to that of control soil; the functional diversity of microbial communities were not different in rhizosphere soils between Bt and non-Bt cotton. All results suggested that there was no evidence to indicate any adverse effects of Bt cotton on the soil ecosystem in this study.     

Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities

The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.     

有机卤呼吸微生物菌群营养交互的作用机制

有机卤呼吸细菌(organohalide-respiringbacteria,OHRB)是污染场地土壤与地下水中厌氧降解及生物修复有机卤代污染物的主力军。微生物种群间的资源竞争、生长抑制、代谢交叉喂养(crossfeeding,即营养的动态交换,包括碳源、氮源、氨基酸、维生素、核苷酸、电子供体、电子受体和其他生长因子等)、水平基因转移及其他交互作用机制是群落结构稳定平衡的基础,有利于促进有机卤代污染物消减效率的最大化。本文围绕OHRB种群及与其他微生物种群间的互作机制(如交叉喂养机制、竞争机制及抑制机制等)进行了概述,并对未来互作机制的研究进行了探讨与展望,旨在为有机卤代物污染场地生物修复效率的提高提供科学理论和技术参考依据。