Diversity of protists and bacteria determines predation performance and stability

Predation influences prey diversity and productivity while it effectuates the flux and reallocation of organic nutrients into biomass at higher trophic levels. However, it is unknown how bacterivorous protists are influenced by the diversity of their bacterial prey. Using 456 microcosms, in which different bacterial mixtures with equal initial cell numbers were exposed to single or multiple predators (Tetrahymena sp., Poterioochromonas sp. and Acanthamoeba sp.), we showed that increasing prey richness enhanced production of single predators. The extent of the response depended, however, on predator identity. Bacterial prey richness had a stabilizing effect on predator performance in that it reduced variability in predator production. Further, prey richness tended to enhance predator evenness in the predation experiment including all three protists predators (multiple predation experiment). However, we also observed a negative relationship between prey richness and predator production in multiple predation experiments. Mathematical analysis of potential ecological mechanisms of positive predator diversity—functioning relationships revealed predator complementarity as a factor responsible for both enhanced predator production and prey reduction. We suggest that the diversity at both trophic levels interactively determines protistan performance and might have implications in microbial ecosystem processes and services.     

峡谷型喀斯特不同生态系统的土壤微生物数量及生物量特征

采用样地调查与室内分析相结合的方法,研究了峡谷型喀斯特水田、旱地、草地、灌丛、人工林、次生林6种生态系统不同深度土壤微生物数量、微生物生物量特征及其分形关系。结果表明:峡谷型喀斯特不同生态系统的土壤微生物数量及组成不同,微生物数量均以次生林最高,旱地最低,其组成数量均为细菌放线菌真菌,细菌是土壤微生物的主要类群,数量多达26.66×105—71.64×105cfu/g,占全部微生物比例为87.00%—95.50%,其次为放线菌数量,为1.45×105—3.78×105cfu/g,所占比例为4.21%—12.39%,真菌数量最小,为0.07×105—0.23×105cfu/g,所占比例仅为0.24%—0.61%,不足1%。不同生态系统土壤微生物生物量碳(MBC)、氮(MBN)、磷(MBP)的含量不同,次生林MBC与MBN最高,人工林MBP最高,旱地MBC最低,草地MBN与MBP最低;各生态系统均为MBCMBNMBP。不同生态系统的MBC/SOC、MBN/TN、MBP/TP分别为0.44%—0.97%、2.13%—3.13%、1.46%—2.13%,差异不显著;MBC/MBN在3.06—6.54之间,其中次生林极显著高于其他生态系统,其他生态系统差异不显著。不同生态系统土壤微生物数量及生物量均随土层加深而减少,且具有良好分形关系,均达到了极显著水平(P0.01)。探讨土壤微生物活性为提高石灰土土壤肥力、促进喀斯特植被迅速恢复提供依据。     

A stressed stream ecosystem: macroinvertebrate community integrity and microbial trophic response

A year-long study of a second-order stream in Southwestern Virginia was carried out from 1979–80. One of the objectives of the study was to evaluate the effects of sewage and electroplating plant effluent stress on the trophic response of aquatic invertebrate assemblages and microbial communities in the stream. Quantitative benthic samples were collected periodically at three reference stations and four stressed stations below the outfalls. Invertebrates were counted, identified taxonomically, and classified into functional groups based on their feeding strategies. Ash-free dry weights were obtained for each functional group by date and station, and the number and density of different taxa were calculated as well. Reference stations had diverse invertebrate assemblages; scrapers were well represented and all functional groups were present in reasonably equivalent proportions. Stressed stations were dominated by collector gatherers and filterers to the virtual exclusion of scrapers. The trophic status of the microbial community was determined by suspending artificial substrates in the stream for 1-week periods. The community that colonized the substrates was assayed for ATP and chlorophyll a, and an autotrophy index (AI) was calculated using these values. The autotrophic component of the microbial community was greatest at the reference stations, and the community became primarily heterotrophic below the outfalls. The AI correlated well with the proportion of scrapers. Aquatic invertebrate assemblages and microbial communities responded to stress by changing their trophic structure to fit best the available energy sources. Where heterotrophic microbes dominated, gathering and filtering invertebrates utilized the abundant organic matter. In areas where a mainly autotrophic microbial community existed, scrapers, gatherers, and filterers were all present in balanced proportions.     

冰川微生物菌群分布的研究概况及其前景

冰川中以耐冷的生物为主,形成一个以微生物为主要生命形式的相对简单的生态系统.冰川中的微生物包括病毒、细菌、放线菌、丝状真菌、酵母菌和藻类.其中一些病毒对人类健康具有潜在的危害性.着重论述了不同区域和不同海拔高度的冰川微生物类群和数量分布特征以及冰芯（深冰川）细菌菌群分布与气候环境的关系.综述结果表明：一些微生物类群广泛存在于各地的冰川上,具有全球分布特性;另一些类群只出现在个别冰川上,为一些地方性冰川微生物.随着海拔高度的增加,冰川上呈现出冰、雪冰和雪环境明显不同的生态条件;微生物类群分布也具有明显的差异性,与冰川上的生态条件和盛行的风向有关.优势类群对冰、雪冰和雪环境具有一定的指示意义.冰川微生物数量分布不仅受到冰川上的水热、光照和营养状况的影响,还与降雪的沉积作用有关.冰芯中的细菌数量与矿物微粒含量具有密切的对应关系.最后指出了冰川微生物研究在基因多样性、气候环境变化、生物地球化学循环、微生物对环境变化的响应机制和星际生命探索中的重要性及其生态学和社会经济意义.     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.     

Functional stability of stream-dwelling microbial decomposers exposed to copper and zinc stress

1. We investigated the resistance of aquatic microbial decomposers to Cu and Zn stress and their ability to recover after release from metal exposure, by examining leaf mass loss, fungal reproduction and microbial biomass and diversity.
2. Alder leaves, colonised in a reference stream, were exposed in microcosms to copper (Cu) or zinc (Zn), alone or in mixtures, with metals added together or sequentially (at day 0 or after 10 days). After 20 days, half of the microcosms were released from metals.
3. Leaf mass loss and fungal reproduction were reduced in most metal treatments, and the structure of fungal and bacterial communities was altered as indicated by identification of conidia and DNA fingerprinting based on denaturing gradient gel electrophoresis. Metals reduced the biomass of bacteria, but not that of fungi.
4. After release from metal stress, the structure of fungal communities became similar to that of control, and a recovery of microbial activity seemed to occur as shown by the lack of differences in leaf mass loss, bacterial biomass and fungal reproduction between control and metal treatments.     

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Microbes are the unseen majority in soil and comprise a large portion of life's genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogen-fixing bacteria are responsible for c. 5–20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.     

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the ‘active'' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population''s growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.     

Impact of elevated atmospheric CO2 concentration on soil microbial biomass and activity in a complex, weedy field model ecosystem

Although soil organisms play an essential role in the cycling of elements in terrestrial ecosystems, little is known of the impact of increasing atmospheric CO₂ concentrations on soil microbial processes. We determined microbial biomass and activity in the soil of multitrophic model ecosystems housed in the Ecotron (NERC Centre for Population Biology, Ascot, UK) under two atmospheric CO₂ concentrations (ambient vs. ambient + 200 ppm). The model communities consist of four annual plant species which naturally co-occur in weedy fields and disturbed ground throughout southern England, together with their herbivores, parasitoids and soil biota. At the end of two experimental runs lasting 9 and 4.5 months, respectively, root dry weight and quality showed contradictory responses to elevated CO₂ concentrations, probably as a consequence of the different time-periods (and hence number of plant generations) in the two experiments. Despite significant root responses no differences in microbial biomass could be detected. Effects of CO₂ concentration on microbial activity were also negligible. Specific enzymes (protease and xylanase) showed a significant decrease in activity in one of the experimental runs. This could be related to the higher C:N ratio of root tissue. We compare the results with data from the literature and conclude that the response of complex communities cannot be predicted on the basis of oversimplified experimental set-ups.     

Quantitative assessment of microbial necromass contribution to soil organic matter

Soil carbon transformation and sequestration have received significant interest in recent years due to a growing need for quantitating its role in mitigating climate change. Even though our understanding of the nature of soil organic matter has recently been substantially revised, fundamental uncertainty remains about the quantitative importance of microbial necromass as part of persistent organic matter. Addressing this uncertainty has been hampered by the absence of quantitative assessments whether microbial matter makes up the majority of the persistent carbon in soil. Direct quantitation of microbial necromass in soil is very challenging because of an overlapping molecular signature with nonmicrobial organic carbon. Here, we use a comprehensive analysis of existing biomarker amino sugar data published between 1996 and 2018, combined with novel appropriation using an ecological systems approach, elemental carbon–nitrogen stoichiometry, and biomarker scaling, to demonstrate a suit of strategies for quantitating the contribution of microbe‐derived carbon to the topsoil organic carbon reservoir in global temperate agricultural, grassland, and forest ecosystems. We show that microbial necromass can make up more than half of soil organic carbon. Hence, we suggest that next‐generation field management requires promoting microbial biomass formation and necromass preservation to maintain healthy soils, ecosystems, and climate. Our analyses have important implications for improving current climate and carbon models, and helping develop management practices and policies.     

An experimental analysis of species sorting and mass effects in freshwater bacterioplankton

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Bacteria—A link among ecosystem constituents

Microbial ecology has undergone a revolution over the past two decades due to the numerous innovations in techniques, allowing bacteria to be detected more accurately by direct means. Thus, bacterial life can be distinguishedin situ by direct counting under epifluorescence microscopy; automatically counting and sizing by image analyzer equipped with epifluorescence microscopy or by use of flow cytometry; specific radioisotope techniques; and molecular techniques to detect specific taxa. All of these approaches do not require cultivation, which provides a biased view of bacterial communities in nature. Bacteria are abundant in aquatic environments and play important roles as links between dissolved nutrients and the grazers in the food web. The new techniques allow an evaluation of bacterial population dynamics and function in relation to other organisms of higher trophic levels. This mini review aims to show briefly the state-of-the-art in microbial ecology for ecologists concerned with organisms other than microbes, in order to develop further intensive study together with microbial ecologists.     

长期不同施肥下太湖地区黄泥土表土微生物碳氮量及基因多样性变化

农业管理措施影响下土壤微生物群落结构的变化是农业土壤质量研究的前沿问题。运用化学分析方法和 PCR- DGGE技术从土壤微生物碳氮量及基因多样性角度研究了长期不同施肥措施下太湖地区代表性水稻土 -黄泥土的表土微生物活性与分子多样性的变化。结果表明 ,施用化肥以及化肥和有机肥配施在提高土壤有机碳含量的同时 ,不仅提高了水稻土的微生物碳氮量 ,而且改变了微生物的群落结构 ;与长期单施化肥相比 ,长期化肥配施有机肥不仅显著提高了土壤微生物碳氮量 ,而且提高了土壤微生物的分子多样性 ;就土壤的微生物分子群落相似性来说 ,单施化肥下与未施肥下相近 ,而化肥配施秸秆下与化肥配施猪粪下接近 ,说明土壤的有机培肥对土壤微生物群落结构有重要影响。长期单施化肥下水稻产量的年际波动性显著大于化肥配施有机肥下 ,这进一步佐证了化肥配施有机肥显著促进了水稻土的生态系统初级生产力与较高的土壤生态系统稳定性。应用PCR- DGGE技术所揭示的微生物分子群落结构特点可以指示水稻土 10 a尺度的不同农业管理措施下的土壤质量变化     

关于草鱼肠炎微生态调节的研究

对健康草鱼肠道菌、患肺炎病草鱼肠道菌进行菌群分析,发现正常草鱼肠道中有气单胞菌(Aeromonas)、哈夫尼亚菌(Hafnia)、黄杆菌属(Flavobacterium)等多种菌,肠炎病鱼肠道中一般仅有气单胞菌的单一菌群。拮抗试验表明哈夫尼亚菌与气单胞菌之间有一定的拮抗性。回归试验表明哈夫尼亚菌无致病性,3种气单胞菌有致病性。微生态治疗试验表明哈夫尼亚菌对患肠炎病的草鱼肠道有促进肠道微生态平衡作用。     

Spatial and halophyte-associated microbial communities in intertidal coastal region of India

Microbial communities in intertidal coastal soils respond to a variety of environmental factors related to resources availability, habitat characteristics, and vegetation. These intertidal soils of India are dominated with Salicornia brachiata, Aeluropus lagopoides, and Suaeda maritima halophytes, which play a significant role in carbon sequestration, nutrient cycling, and improving microenvironment. However, the relative contribution of edaphic factors, halophytes, rhizosphere, and bulk sediments on microbial community composition is poorly understood in the intertidal sediments. Here, we sampled rhizosphere and bulk sediments of three dominant halophytes (Salicornia, Aeluropus, and Suaeda) from five geographical locations of intertidal region of Gujarat, India. Sediment microbial community structure was characterized using phospholipid fatty acid (PLFA) profiling. Microbial biomass was significantly influenced by the pH, electrical conductivity, organic carbon, nitrogen, and sodium and potassium concentrations. Multivariate analysis of PLFA profiles had significantly separated the sediment microbial community composition of regional sampling sites, halophytes, rhizosphere, and bulk sediments. Sediments from Suaeda plants were characterized by higher abundance of PLFA biomarkers of Gram-negative, total bacteria, and actinomycetes than other halophytes. Significantly highest abundance of Gram-positive and fungal PLFAs was observed in sediments of Aeluropus and Salicornia, respectively than in those of Suaeda. The rhizospheric sediment had significantly higher abundance of Gram-negative and fungal PLFAs biomarkers compared to bulk sediment. The results of the present study contribute to our understanding of the relative importance of different edaphic and spatial factors and halophyte vegetation on sediment microbial community of intertidal sediments of coastal ecosystem.     

种植Bt玉米对土壤微生物活性和肥力的影响

在温室种植比较了美国Bt玉米(34B2 4 (Mon810 ) )与同源常规玉米(34B2 3)、中国Bt玉米(12 4 6×14 82 (Cry1A) )与常规玉米(农大3138)对土壤微生物活性和肥力的影响。结果表明,两个Bt玉米品种5次取样(2 5、39、5 3、6 7、82 d)的根际土壤中都能检测到Bt蛋白,含量在2 0～80 ng·g- 1 dry soil之间。4个处理土壤硝化作用和精氨酸氨化作用强度在所有取样时期均没有显著差异;土壤蔗糖酶、土壤蛋白酶和酸性磷酸酶活性则分别只在2 5 d(农大3138<34B2 4与12 4 6×14 82 )、6 7d(34B2 4 >12 4 6×14 82和农大3138)和6 7d(34B2 4 >其它3个处理)存在显著差异;土壤脱氢酶、土壤脲酶和土壤呼吸强度则在多数取样时期多个处理间存在显著差异,说明其与玉米品种特性关系密切,其中,土壤脱氢酶和脲酶活性的差异在两个Bt玉米品种、Bt与同源常规品种(34B2 4与34B2 3)、Bt与常规品种(12 4 6×14 82与农大3138)以及常规与常规品种(34B2 3与农大3138)之间均没有一致的规律,但34B2 4与34B2 3处理的土壤呼吸作用强度高于12 4 6×14 82与农大3138,说明种植该系列品种的土壤中微生物总活性较高、土壤代谢旺盛。82 d后4个处理土壤有机质、NPK全量与速效养分含量均没有显著差异。本试验观测期种植Bt玉米并没有导致土壤微生物活性和土     

土壤微生物多样性通过共现网络复杂性表征高寒草甸生态系统多功能性

土壤微生物多样性在生态系统功能的维持方面发挥着至关重要的作用,但是土壤生物多样性与生态系统功能（Biodiversity-ecosystem function,BEF）关系仍存在争议。以往的研究多基于简单多样性指标（如物种数、香浓多样性指数等）对BEF关系进行探究,忽略了物种间复杂的相互作用在BEF关系中的重要性。以青藏高原米拉山高寒草甸为研究对象,使用Illumina MiSeq高通量测序技术测定了6个海拔高度（3755 m、3994 m、4225 m、4534 m、4900 m、5120 m）土壤细菌和真菌群落特征,分析了简单微生物多样性指标（物种数）和共现网络复杂性与生态系统多功能性（Ecosystem multifunctionality,EMF）的关系,以期进一步揭示微生物多样性与EMF的关系。共现网络分析表明,表征土壤细菌和真菌网络复杂性的节点（Node）和边（Link）沿海拔高度的升高显著下降（P<0.05）。土壤细菌和真菌的多样性和网络复杂性均沿海拔的升高显著下降（P<0.05）,而且网络复杂性比相应的多样性下降明显。在未控制环境因素时,真菌和细菌的多样性和网络复杂性均与EMF显著正相关（P<0.05）;其中真菌和细菌网络复杂性对EMF的解释度高于相应多样性对EMF的解释度。通过偏回归分析（Partial least squares regression,PLSR）控制年降水、年均温、黏粒含量、盐基离子和酸性离子等气候及土壤环境因子影响后,土壤细菌和真菌物种多样性与EMF的显著正相关关系变为不相关（P>0.05）,而网络复杂性与EMF的显著正相关关系（P<0.05）仍然存在。利用方差分解分析（Variance partition analysis,VPA）将环境因子纳入对EMF的影响后发现,土壤微生物网络复杂性和环境因子对EMF变化的解释度可达80%,高于土壤微生物多样性与环境因子对EMF变化的解释度。结构方程模型（Structural equation model,SEM）分析进一步显示,土壤细菌多样性和真菌多样性通过促进对应共现网络的复杂性,间接对EMF产生正向影响。综上所述,相较于简单的多样性指标,土壤微生物网络复杂性对EMF具有更好的解释度和预测性,微生物多样性主要通过促进网络复杂性间接正向影响EMF。研究结果扩展了BEF关系的研究,证明微生物物种多样性主要通过促进对应的网络复杂性维持EMF。     

绿弯菌的研究现状及展望

绿弯菌是一个深度分支的门级别细菌类群,广泛分布于生物圈各种生境。现已生效发表的绿弯菌构成9个纲,但仅包含56个种;基于分子生态学的研究结果表明尚有大量绿弯菌类群仍是未培养状态。绿弯菌形态多样,营养方式和代谢途径十分丰富,参与了C、N、S等一系列重要生源元素的生物地球化学循环过程。研究该类群不仅有助于认识环境中微生物的多样性及其代谢特征,从而更好的理解微生物参与的生态学过程,还有助于揭示微生物对环境的适应及其进化。本文主要综述了绿弯菌的发现历史、营养、代谢及其在元素循环中的作用,并总结了其分离培养和潜在应用价值,最后展望了未来的研究方向,旨在为深入探究绿弯菌的进化、培养和驱动地球化学元素循环等研究提供参考。     

中国土壤微生物多样性监测的现状和思考

土壤微生物多样性研究是整个生态系统研究中最薄弱的环节之一。高通量测序技术和生物信息学方法的快速发展极大地促进了土壤微生物多样性监测研究的深度和广度。目前世界范围内已经开展了一些综合的微生物多样性研究计划, 如地球微生物计划。这些计划存在的主要问题是缺少动态的监测、研究方法不统一、数据整合困难等。中国土壤微生物多样性监测网(Soil Microbial Observation Network, SMON)是中国生物多样性监测与研究网络(Chinese Biodiversity Monitoring and Research Network, Sino BON)的重要组成部分, 本文中我们对该监测网的建设提出了一些思考。在监测布局上建议选择我国南北水热梯度下的森林生态系统、东西降雨梯度下的草原生态系统、典型湿地生态系统及重要农田生态系统, 同时依托现已建成的生物多样性监测网络观测点或大样地, 布设监测样点, 利用现代环境基因组学和生物信息学技术, 重点围绕土壤微生物群落和功能基因组的组成与多样性, 开展长期定点的动态监测。监测的结果将以名录、数据集或图鉴的形式发布, 包括中国典型生态系统中土壤细菌、古菌、真菌与地衣、土壤宏基因组和重要功能基因的组成和多样性等数据, 同时建设土壤生物大数据平台, 达到监测数据的储存、查询、分析、下载、成图的功能。通过土壤微生物多样性监测, 将阐明我国重要森林、草地、湿地、农田生态系统中土壤微生物组成、多样性、功能基因的时空变化特征和驱动机制, 建立土壤微生物多样性变化与生态系统功能的关系及相关的模型, 预测全球环境条件变化下土壤微生物的演变规律, 为土壤微生物多样性资源的保护和利用提供科学依据。