保护性耕作对土壤微生物群落及其介导的碳循环功能的影响

农田生态系统耕作方式显著影响土壤微生物群落结构和功能,进而影响土壤微生物介导的土壤碳循环过程。以免耕结合作物秸秆还田为核心的保护性耕作是提升土壤碳汇功能和肥力的重要措施,其中土壤微生物发挥了关键作用。尽管有较多关于保护性耕作下微生物群落结构与功能的研究,但由于土壤系统的复杂性、环境因素以及微生物群落评价方法的差异性,尚未形成对保护性耕作下土壤微生物群落响应规律的系统认知。此外,研究多关注土壤微生物作为分解者的作用以及植物源碳对土壤碳库形成的贡献,而忽略了微生物源碳对土壤碳库形成和稳定的贡献。本文在归纳土壤有机质形成和稳定理论体系演变的基础上,梳理了土壤微生物研究方法的进展,重点阐述了保护性耕作对土壤微生物生物量、群落多样性和组成、碳代谢活性以及微生物源有机碳截获的影响,并对未来该领域的研究方向进行展望,以期为探索农田生态系统土壤微生物群落响应规律及其介导的土壤碳循环功能提供参考。     

不同养殖场林麝肠道微生物组成和功能的差异

肠道疾病是养殖林麝(Moschus berezovskii)常见疾病。动物肠道微生物伴随宿主进化并与胃肠道构成了复杂的微生态系统。为探究不同饲养环境对圈养林麝肠道微生物组成和功能的影响,本研究对采自国内5个不同养殖场的215份粪便样品进行了16S rRNA基因高通量测序,对比分析不同养殖场林麝肠道微生物组成、多样性和功能的差异。结果显示,厚壁菌门和拟杆菌门是未喂食复合益生菌的祁连县养殖场林麝肠道菌群的绝对优势菌门,而喂食复合益生菌的甘肃两当县和陕西凤县的4家养殖场林麝肠道菌群的绝对优势菌门为厚壁菌门和变形菌门。不同养殖场林麝肠道菌群组成、优势菌门、优势菌属、潜在致病菌、代谢及疾病相关功能均有显著差异。祁连县养殖场林麝肠道微生物的α多样性和疾病相关功能表达量显著低于其他养殖场,并以肠型2为主,其主导菌为厚壁菌门、UCG-005和拟杆菌属;两当县和凤县的4家养殖场林麝肠道菌群潜在致病菌相对丰度较低。本研究推测食物组成差异可能是导致不同养殖场林麝肠道微生物差异的主要因素,复合益生菌的使用可能是导致α多样性和潜在致病菌下降的重要因素。该结果可为林麝的人工养殖和有效管理提供科学依据,也对人工饲养...     

人体肠道微生物多样性和功能研究进展

人体肠道中庞大而复杂的微生物群落对人体自身代谢表型有深远的影响.肠道微生物群落在亚种或菌株水平上表现出极大的多样性.利用微生物分子生态学、元基因组学和代谢组学研究方法,发现肠道微生物与宿主表现出共进化的特点,肠道微生物群落及其基因组为宿主提供了互补的遗传和代谢功能,表现出互惠共生关系.但是,肠道微生物群落中影响宿主代谢表型的关键功能菌鉴定及其作用模式问题仍然悬而未决,综合运用多种高通量研究方法和多维数据分析方法可能成为解决这个问题的突破口.     

中国林蛙蝌蚪肠道及皮肤微生物多样性分析

肠道及皮肤微生物群落对宿主的健康有着至关重要的影响。本研究使用16S rRNA基因测序技术研究中国林蛙(Rana chensinensis)Gosner38期蝌蚪肠道和皮肤共生微生物群落组成之间的差异。在门水平上,林蛙蝌蚪肠道中的优势门为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes),皮肤中的优势门为拟杆菌门、变形菌门和疣微菌门(Verrucomicrobia)。此外,显著性检验结果显示,肠道中厚壁菌门和放线菌门(Actinobacteria)的丰度显著偏高,皮肤中拟杆菌门的丰度显著偏高。肠道微生物群落多样性高于皮肤,而肠道和皮肤的物种丰富度之间无显著差异。在对KEGG通路的丰度进行比较时,结果显示肠道"环境信息处理"功能的丰度显著高于皮肤,而皮肤中"遗传信息处理"及"新陈代谢"功能显著偏高。本研究提示林蛙蝌蚪肠道及皮肤微生物群落组成之间存在显著差异。     

宿主肠道微生物群落多样性和演替分析技术的演变和发展

人或动物等宿主肠道内定植有大量微生物。但是,宿主肠道内微生物的多样性和演替一直被认为是人和动物营养研究中的黑箱（black box）。经过科学家几个世纪的研究已证实：正常微生物群是一个新的人体生理学系统;肠道微生物菌群参与宿主对营养素的消化、吸收与合成;刺激其免疫机制。近年又发现：微生物群影响宿主基因表达,可进行微生物与宿主之间的“分子对话”,例如：一个人肥胖或者苗条的倾向可能部分是由生活在肠道中的微生物群体的组成所决定的（戈登,2005）。可见,肠道微生物是未来微生态科学极其重要的研究领域。对于肠道微生物群落的分析方法主要有沿用已久的传统培养法和近年来兴起的基于基因序列的微生物分子生态学方法。     

戴云山南坡不同海拔森林土壤微生物功能多样性特征及影响因素

土壤微生物作为森林生态系统的主要分解者,参与土壤养分循环,在维持土壤生态系统功能和服务中发挥着重要作用。探讨不同海拔土壤微生物群落结构和功能多样性的季节变化,对维持土壤生态系统稳定具有重要研究价值。以戴云山南坡不同海拔土壤为研究对象(900-1500 m),采用Biolog-ECO微平板法,研究不同海拔土壤微生物群落结构和功能多样性的季节变化(夏季与冬季),揭示驱动戴云山不同海拔土壤微生物季节变化的主要因素。结果表明:(1)夏季海拔1400 m区域土壤微生物的碳源利用最强,微生物活性最高。冬季表现为海拔900 m处土壤微生物对碳源利用最强,活性最高。(2)土壤微生物群落对碳源利用特征的研究表明,夏季与冬季中氨基酸类和羧酸类碳源是7个海拔土壤微生物利用的主要碳源,且夏季碳源利用程度高于冬季。(3)冗余分析表明夏季和冬季戴云山南坡7个海拔土壤微生物群落功能多样性均受土壤环境因子驱动,解释量分别为72.63%和44.12%,均高于地形因子的解释量。(4)土壤温度和全钾含量等因子是驱动夏季土壤微生物群落功能多样性变化的主要因素;土壤全钾、全磷、有效磷含量和坡向是驱动冬季土壤微生物群落功能多样性变化的主要因素。海拔和季节变化通过调节土壤理化性质和土壤酶活性,进而影响森林土壤微生物群落结构和功能多样性。     

现代生物化学与分子生物学研究技术在植物微生物生态学中的应用

植物微生物生态学是研究植物微生态系统的一门学科,以植物组织细胞内微生物的组成、功能、演替,以及微生物之间和微生物与宿主之间的相互作用关系为研究对象。现代生物化学与分子生物学技术在植物微生物生态学研究领域的作用日益明显。介绍了上述技术及其在植物微生物生态学研究领域的应用进展,并对其在该领域的利用和发展进行了展望。     

低氧暴露对大鼠肠道微生物群落的影响

【背景】低氧暴露时机体会对物质的吸收和代谢作出调整,以维持自身的能量需求。肠道微生物参与了宿主众多生理过程,尤其在宿主消化、代谢、免疫等多方面发挥了重要作用。而目前对于低氧暴露过程中宿主肠道微生物群落结构和功能的动态变化,以及这些变化与宿主习服低氧之间的关系则少有报道。【目的】研究大鼠暴露于低氧环境后其肠道微生物群落的结构和多样性,探讨低氧暴露对宿主肠道微生物群落的影响,以及肠道微生物群落的变化与宿主代谢之间可能存在的关系。【方法】分别收集低氧暴露1、7、14、21和28 d的实验组(模拟海拔4 500 m)和对照组(43.5 m)的SD大鼠粪便样品,通过IlluminaHiSeq测序平台对样品进行16SrRNAV3-V4区测序,利用Uparse、Qiime、LEfSe和PICRUSt软件分析肠道微生物群落结构、丰度、多样性、组间差异,并利用KEGG数据库对肠道微生物的功能进行预测。【结果】不同低氧暴露时间组和对照组SD大鼠肠道微生物群落特征具有明显差异。低氧暴露组SD大鼠的肠道微生物群落中拟杆菌门(Bacteroidetes)、拟杆菌目(Bacteroidales)、拟杆菌科(Bacteroidaceae)、普氏菌科(Prevotellaceae)、普氏菌属(Prevotella)和普氏菌种(copri)的相对丰度较高且具有统计学意义。相应时间的对照组SD大鼠肠道微生物群落中瘤胃球菌科(Ruminococcaceae)、瘤胃球菌属(Ruminococcus)、梭菌纲(Clostridia)和梭菌目(Clostridiales)等相对丰度较高且具有统计学意义。功能预测发现遗传信息处理和代谢相关通路在低氧暴露组SD大鼠肠道微生物中明显富集。【结论】低氧暴露过程中SD大鼠肠道微生物群落结构和多样性呈动态变化,碳水化合物代谢相关菌群(普氏菌和拟杆菌)明显增加,可能参与了宿主能量代谢调整,有利于机体对低氧环境的习服。     

土壤微生物群落构建理论与时空演变特征

土壤微生物作为陆地生态系统的重要组成部分,直接或间接地参与几乎所有的土壤生态过程,在物质循环、能量转换以及污染物降解等过程中都发挥着重要作用。对土壤微生物时空演变规律及其形成机制的研究,不仅是微生物演变和进化的基础科学问题,也是预测微生物及其所介导的生态功能对环境条件变化响应、适应和反馈的理论依据。讨论了土壤微生物群落的定义、测度方法和指标,认为群落是联系动植物宏观生态学与微生物生态学的基础,群落构建机制是宏观和微观生态学都需要研究的核心科学问题;从生态学的群落构建理论出发,阐述了包括生态位理论/中性理论、过程理论和多样性-稳定性理论在土壤微生物时空演变研究中的应用,以及微生物群落在时间和空间上的分布特征及其尺度效应;确立了以微生物群落构建理论为基础、不同时空尺度下土壤微生物群落演变特征为主要内容的微生物演变研究的基本框架。     

群落生态学中的植物-土壤反馈研究

植物-土壤反馈是指植物改变了其生长环境中土壤的生物和非生物属性,改变后的土壤进而影响植物适合度的过程。植物-土壤反馈的一个根本前提是:植物在根际周围产生由专化病原菌和共生菌构成的特异性微生物群落,专化微生物对宿主植物种群有很大的影响,对非宿主植物没有或者有微弱影响。自从20世纪90年代被明确提出后,植物-土壤反馈被广泛用于揭示不同尺度的生态学过程,诸如演替、竞争、生物入侵、全球变化对生态系统的影响等。近年来,植物-土壤反馈与群落生态学主要研究领域之间的整合取得了实质性进展。该文主要关注的是土壤微生物介导的植物-土壤反馈及其对植物物种共存、群落结构和生态系统功能的影响。土壤微生物不仅可以产生稳定化力量促进物种共存,也可以改变均一化力量或者种间适合度差异,从而影响植物种间共存。在群落生态学中通常假设稀有种受土壤负反馈的影响更弱,从而预测植物局域丰富度与土壤反馈强度具有负相关关系。然而实验证据却揭示了不同的模式,加强对植物与土壤病原菌之间的进化动态的关注是调和这些不一致模式的关键。土壤微生物也是驱动植物群落演替的关键因子。土壤微生物通过稀释效应影响植物多样性-群落生产力关系。专化土壤病原菌或...     

Climate change is not just global warming: Multidimensional impacts on animal gut microbiota

Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.     

Inferring dynamic signatures of microbes in complex host ecosystems

The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point, or measures of dissimilarity between pairs of time-points. Although these approaches, which treat data as static snapshots of microbial communities, can identify shifts in overall community structure, they fail to capture the dynamic properties of individual members of the microbiota and their contributions to the underlying time-varying behavior of host ecosystems. To address the limitations of current methods, we present a computational framework that uses continuous-time dynamical models coupled with Bayesian dimensionality adaptation methods to identify time-dependent signatures of individual microbial taxa within a host as well as across multiple hosts. We apply our framework to a publicly available dataset of 16S rRNA gene sequences from stool samples collected over ten months from multiple human subjects, each of whom received repeated courses of oral antibiotics. Using new diversity measures enabled by our framework, we discover groups of both phylogenetically close and distant bacterial taxa that exhibit consensus responses to antibiotic exposure across multiple human subjects. These consensus responses reveal a timeline for equilibration of sub-communities of micro-organisms with distinct physiologies, yielding insights into the successive changes that occur in microbial populations in the human gut after antibiotic treatments. Additionally, our framework leverages microbial signatures shared among human subjects to automatically design optimal experiments to interrogate dynamic properties of the microbiota in new studies. Overall, our approach provides a powerful, general-purpose framework for understanding the dynamic behaviors of complex microbial ecosystems, which we believe will prove instrumental for future studies in this field.     

Gut microbiomes and their metabolites shape human and animal health

The host genetic background, complex surrounding environments, and gut microbiome are very closely linked to human and animal health and disease. Although significant correlations between gut microbiota and human and animal health have been revealed, the specific roles of each gut bacterium in shaping human and animal health and disease remain unclear. However, recent omics-based studies using experimental animals and surveys of gut microbiota from unhealthy humans have provided insights into the relationships among microbial community, their metabolites, and human and animal health. This editorial introduces six review papers that provide new discoveries of disease-associated microbiomes and suggest possible microbiome-based therapeutic approaches to human disease.     

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota

The use of lactobacilli as probiotics in swine has been gaining attention due to their ability to improve growth performance and carcass quality, prevent gastrointestinal infection and most importantly, their ‘generally recognized as safe’ status. Previous studies support the potential of lactobacilli to regulate host immune systems, enhance gut metabolic capacities and maintain balance in the gut microbiota. Research on swine gut microbiota has revealed complex gut microbial community structure and showed the importance of Lactobacillus to the host's health. However, the species‐ and strain‐specific characteristics of lactobacilli that confer probiotic benefits are still not well understood. The diversity of probiotic traits in a complex gut ecosystem makes it challenging to infer the relationships between specific functions of Lactobacillus sp. and host health. In this review, we provide an overview of how lactobacilli play a pivotal role in the swine gut ecosystem and identify key characteristics that influence gut microbial community structure and the health of pigs. In addition, based on recent and ongoing meta‐omics and omics research on the gut microbiota of pigs, we suggest a workflow combining culture‐dependent and culture‐independent approaches for more effective selection of probiotic lactobacilli.     

海洋鱼类肠道微生物研究进展及应用前景

肠道微生物在动物体内数量庞大、结构复杂,在宿主生长发育过程中发挥着重要作用。淡水鱼类肠道微生物的研究主要集中于其对鱼类生长代谢、营养吸收及免疫调节等方面的影响,海洋鱼类则研究相对较少,且多集中于肠道微生物多样性及其变动影响因素分析。本文在归纳总结鱼类肠道微生物功能及其研究方法的基础上,着重分析肠道微生物在海洋鱼类生长发育调控、食性、环境适应性及污染物指示等研究中的应用现状和发展前景,以期为今后利用海洋鱼类肠道微生物开展多学科交叉研究提供启发和参考。     

Research progress on the regulation mechanism of probiotics on the microecological flora of infected intestines in livestock and poultry

The animal intestine is a complex ecosystem composed of host cells, gut microbiota and available nutrients. Gut microbiota can prevent the occurrence of intestinal diseases in animals by regulating the homeostasis of the intestinal environment. The intestinal microbiota is a complex and stable microbial community, and the homeostasis of the intestinal environment is closely related to the invasion of intestinal pathogens, which plays an important role in protecting the host from pathogen infections. Probiotics are strains of microorganisms that are beneficial to health, and their potential has recently led to a significant increase in studies on the regulation of intestinal flora. Various potential mechanisms of action have been proposed on probiotics, especially mediating the regulation mechanism of the intestinal flora on the host, mainly including competitive inhibition of pathogens, stimulation of the host's adaptive immune system and regulation of the intestinal flora. The advent of high-throughput sequencing technology has given us a clearer understanding and has facilitated the development of research methods to investigate the intestinal microecological flora. This review will focus on the regulation of probiotics on the microbial flora of intestinal infections in livestock and poultry and will depict future research directions.     

土壤细菌网络互作调控线虫肠道细菌群落

动物肠道细菌群落在联系宿主与生态系统功能中发挥着至关重要的作用。【目的】本研究旨在评估绿肥翻压和水稻生长不同时期对土壤细菌和线虫肠道细菌群落组成和结构的影响,并探究土壤细菌和线虫肠道细菌群落间的潜在关联关系。【方法】基于盆栽试验,结合16S rRNA基因高通量测序技术,分析黑麦草翻压和对照处理下水稻生长的前期(返青期)和后期(收获期)土壤细菌和线虫肠道细菌群落,结合网络分析研究土壤细菌网络互作对线虫肠道细菌群落的潜在影响。【结果】黑麦草翻压对土壤细菌和线虫肠道细菌群落组成和结构没有显著影响(P>0.05);水稻生长后期样品比前期样品具有更高的α多样性。基于随机森林机器学习法获得的土壤细菌和线虫肠道细菌生物标志物之间存在广泛的显著相关关系,为土壤细菌群落变化调控线虫肠道细菌群落组成提供了有力的证据。共现网络分析表明土壤细菌之间的正相互作用显著促进了土壤细菌和线虫肠道细菌之间的正相互作用(P<0.01),进而影响了线虫肠道细菌之间的网络互作。结构方程模型进一步表明土壤养分含量的降低主要通过降低土壤细菌之间正相互作用,从而间接影响线虫肠道细菌之间的互作。【结论】土壤细菌互作可能在...     

模式动物在共生微生物研究中的作用

共生微生物是一类定殖于宿主体表或体内, 可执行宿主本身无法完成的功能, 并依赖于宿主所提供的生长环境的微生物。众多研究表明, 人体肠道共生微生物与免疫、营养、代谢, 甚至精神健康等生理功能密切相关, 是重要的“微生物器官”。在早期的肠道微生物研究中, 模式动物就已经作为研究工具被使用。随着肠道微生物研究的不断深入, 模式动物作为不可替代的研究对象发挥了越来越重要的作用。本综述主要对几种重要的模式动物如斑马鱼(Danio rerio)、小鼠(Mus musculus)、猪(Sus scrofa domesticus)和猕猴(Macaca mulatta)在肠道微生物研究中的应用进行了总结, 介绍了各种模式动物的发展过程及特点, 各自在应用于研究时的优缺点, 以及利用这些动物模型在共生微生物领域所取得的一些标志性的科研成果。同时, 也就近年来在共生微生物领域新兴的一些模式生物如蜜蜂(Apis)、果蝇(Drosophila)、秀丽隐杆线虫(Caenorhabditis elegans)等进行了一些探讨。旨在让该领域的研究者们了解模式动物与人体在共生微生物方面的异同, 为更好地利用这一研究工具提供参考。     

Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts

The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 10¹³ microbial cells, NGS read counts are given in multiples of 10⁶, making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as ‘keystone species’, which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.     

Influence of Changing Plant Food Sources on the Gut Microbiota of Saltmarsh Detritivores

Changes in agricultural land-use of saltmarshes along the German North Sea coast have favoured the succession of the marsh grass Elytrigia atherica over the long-established Spartina anglica. Consequently, E. atherica represents a potential food source of increasing importance for plant-feeding soil detritivores. Considering the importance of this ecological guild for decomposition processes and nutrient cycling, we focussed on two sympatric saltmarsh soil macrodetritivores and their associated gut microbiota to investigate how the digestive processes of these species may be affected by changing plant food sources. Using genetic fingerprints of partial 16S rRNA gene sequences, we analysed composition and diversity of the bacterial gut community in a diplopod and an amphipod crustacean in relation to different feeding regimes representing the natural vegetation changes. Effects of syntopy on the host-specific gut microbiota were also taken into account by feeding the two detritivore species either independently or on the same plant sample. Bacterial community composition was influenced by both the host species and the available plant food sources, but the latter had a stronger effect on microbial community structure. Furthermore, bacterial diversity was highest after feeding on a mixture of both plant species, regardless of the host species. The gut microbiota of these two detritivores can thus be expected to change along with the on-going succession at the plant community level in this environment. Cloning and sequencing of bacterial 16S rRNA gene fragments further indicated a host-related effect since the two detritivores differed in terms of predominant bacterial taxa: diplopods harboured mainly representatives of the phyla Bacteroidetes and Gammaproteobacteria. In contrast, the genus Vibrio was found for the amphipod host across all feeding conditions.