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。     

土壤微生物网络复杂性预测黄土高原造林恢复生态系统多功能性

人类活动导致黄土高原土地退化和生物多样性丧失,进而降低了生态系统功能。人工造林是该区域退化土地恢复的重要措施。现有的生态修复研究通常侧重于微生物群落物种多样性的恢复对单一生态系统功能的影响,而忽略了微生物间存在的相互作用与生态系统多功能性(Ecosystem multifunctionality, EMF)的关系。为探究造林恢复过程中土壤微生物多样性和网络复杂性与EMF的关系,本研究采用时空代换法(space-time substitution method),沿50年造林恢复时间序列,分析了黄土高原地区造林恢复对土壤微生物群落多样性、土壤微生物网络复杂性以及与土壤养分循环相关的10个生态系统功能指标的影响,明确了土壤微生物群落特征与EMF的关系。结果表明,随造林恢复时间序列的增加,土壤微生物群落的综合多样性、网络复杂性和EMF均呈现出显著增加后下降的趋势(P<0.05),其中土壤微生物综合多样性和网络复杂性在第8年达到最高值,EMF在第20年达到最大值。在未控制土壤环境因素时,细菌和古菌多样性与EMF无显著相关性,真菌多样性与EMF呈显著正相关(P<0.001);土壤微生...     

Microplastics reduce soil microbial network complexity and ecological deterministic selection

Microplastics have been proposed as emerging threats for terrestrial systems as they may potentially alter the physicochemical/biophysical soil environments. Due to the variety of properties of microplastics and soils, the microplastic-induced effects in soil ecosystems are greatly manifold. Here, we studied effects of three polymer microplastics (polyamide-6, polyethylene, and polyethylene terephthalate) on soil properties with four different soil types. The success patterns, interaction relationships, and assembly processes of soil bacterial communities were also studied. Microplastics have the potential to promote CO₂ emissions and enhance the soil humification. Even though microplastics did not significantly alter the diversity and composition of the soil microbial community, the application of microplastics decreased the network complexity and stability, including network size, connectivity, and the number of module and keystone species. The bacterial community assembly was governed by deterministic selection (77.3%–90.9%) in all treatments, while microplastics increased the contribution of stochastic processes from 9.1% in control to 13.6%–22.7%. The neutral model results also indicated most of the bacterial taxa were present in the predicted neutral region (approximately 98%), suggesting the importance of stochastic processes. These findings provided a fundamental insight in understanding the effects of microplastics on soil ecosystems.     

植物、土壤及土壤管理对土壤微生物群落结构的影响

土壤微生物是土壤生态系统的重要组成部分,对土壤微生物群落结构多样性的研究是近年来土壤生态学研究的热点。本文综述了有关植物、土壤类型以及土壤管理措施对土壤微生物群落结构影响的最新研究结果,指出植物的作用因植物群落结构多样性、植物种类、同种植物不同的基因型,甚至同一植物不同根的区域而异;而土壤的作用与土壤质地和有机质含量等因素有关;植物和土壤类型在对土壤微生物群落结构影响上的作用存在互作关系。不同的土壤管理措施对土壤微生物群落结构影响较大,长期连作、大量的外援化学物质的应用降低了土壤微生物的多样性;而施用有机肥、免耕可以增加土壤微生物群落结构多样性,有利于维持土壤生态系统的功能。     

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity–ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.     

Methods of studying soil microbial diversity

Soil microorganisms, such as bacteria and fungi, play central roles in soil fertility and promoting plant health. This review examines and compares the various methods used to study microbial diversity in soil.     

土壤微生物多样性研究方法

概述了研究土壤微生物多样性的主要方法．传统上,土壤微生物群落的分析依赖于培养技术,使用各种培养基最大限度地培养各种微生物群体,但仍只能培养和分离出一小部分土壤微生物群落．使用Biolog分析、磷脂脂肪酸分析和核酸分析等方法,可研究和表征那些现在还不能够被培养的土壤微生物。从而获取关于土壤微生物群落多样性的更多和更完整的信息．     

Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat

We applied nucleic acid-based molecular methods, combined with estimates of biomass (ATP), pigments, and microelectrode measurements of chemical gradients, to map microbial diversity vertically on a millimeter scale in a hypersaline microbial mat from Guerrero Negro, Baja California Sur, Mexico. To identify the constituents of the mat, small-subunit rRNA genes were amplified by PCR from community genomic DNA extracted from layers, cloned, and sequenced. Bacteria dominated the mat and displayed unexpected and unprecedented diversity. The majority (1,336) of the 1,586 bacterial 16S rRNA sequences generated were unique, representing 752 species (> or =97% rRNA sequence identity) in 42 of the main bacterial phyla, including 15 novel candidate phyla. The diversity of the mat samples differentiated according to the chemical milieu defined by concentrations of O(2) and H(2)S. Bacteria of the phylum Chloroflexi formed the majority of the biomass by percentage of bulk rRNA and of clones in rRNA gene libraries. This result contradicts the general belief that cyanobacteria dominate these communities. Although cyanobacteria constituted a large fraction of the biomass in the upper few millimeters (>80% of the total rRNA and photosynthetic pigments), Chloroflexi sequences were conspicuous throughout the mat. Filamentous Chloroflexi bacteria were identified by fluorescence in situ hybridization within the polysaccharide sheaths of the prominent cyanobacterium Microcoleus chthonoplastes, in addition to free living in the mat. The biological complexity of the mat far exceeds that observed in other polysaccharide-rich microbial ecosystems, such as the human and mouse distal guts, and suggests that positive feedbacks exist between chemical complexity and biological diversity. The sequences determined in this study have been submitted to the GenBank database and assigned accession numbers DQ 329539 to DQ 331020, and DQ 397339 to DQ 397511.     

微生物多样性对土壤氮磷钾转化、酶活性及油菜生长的影响

采用灭菌土壤分别接种不同稀释倍数(1、10~(-2)、10~(-4)和10~(-6))未灭菌土壤悬浊液的方法,研究了土壤微生物多样性降低对油菜生长和养分吸收、土壤养分有效性和酶活性的影响。结果表明:(1)随着接种土壤悬浊液稀释倍数增加,油菜生物量逐渐降低,10-4的油菜生物量显著低于1和10~(-2),10~(-6)仅为1的26%;(2)油菜氮、磷和钾的吸收量与油菜生物量呈现相同的变化规律;(3)土壤铵态氮浓度随接种土壤悬浊液稀释倍数增加而降低;而土壤硝态氮则以10~(-4)为最高,其它处理间没有显著差异;土壤有效磷未发生显著变化;有效钾反而有上升趋势;(4)土壤多酚氧化酶(PhO X)活性随接种土壤悬浊液稀释倍数增加逐渐升高;β-1,4-葡萄糖苷酶(βG)活性以10~(-6)为最高,而其它处理差异不显著;土壤亮氨酸酶氨肽酶(LAP)活性和酸性磷酸酶(AP)活性变化不显著;(5)相关分析表明,油菜生物量与土壤铵态氮浓度的对数显著正相关;与多酚氧化酶、葡萄糖苷酶和亮氨酸氨肽酶活性显著负相关。研究表明,微生物多样性降低主要通过抑制土壤氮素释放影响植物生长。     

不同土壤采样设计下土壤表层微生物α多样性的差异分析

【背景】土壤采样是土壤研究的基础,采样方案的不同可能会对土壤微生物多样性的研究结果产生一定影响。【目的】研究不同的土壤采样设计方案对土壤样品16S rRNA基因高通量测序结果的影响。【方法】对2个不同生境样地的土壤进行网格化采样,对采集的18个土壤样品进行16S rRNA基因测序分析,通过模拟5种常见土壤采样方法,对比不同采样方式所获得的测序结果。【结果】不同采样方式会产生不同的测序结果。在测序深度有效的情况下,细菌总物种数随着采样数的增加而逐渐增长,增长速度在采样数大于5以后趋于平缓;样品中的优势物种(序列数200以上)只需很少的采样数(1-3)即可观察到全部物种;Shannon-Wiener指数与Simpson指数的变化较相似,当采样数由1到3时两指数均有较大增长,之后变化放缓。【结论】土壤细菌微生物测序研究中,土壤样地采样数量低于3个会影响测序结果的可靠性,采样方案选择梅花形采样法或蛇形采样法较为适宜。     

土壤微生物群落多样性解析法:从培养到非培养

土壤微生物群落多样性是土壤微生物生态学和环境科学的重点研究内容之一.传统的土壤微生物群落多样性解析技术是指纯培养分离法(平板分离和形态分析法以及群落水平生理学指纹法).后来,研究者们建立了多样性评价较为客观的生物标记法(磷脂脂肪酸法和呼吸醌指纹法).随着土壤基因组提取技术和基因片段扩增(PCR)技术的发展,大量的现代分子生物学技术不断地涌现并极大地推动了土壤微生物群落多样性的研究进程.这些技术主要包括:G+C％含量、DNA复性动力学、核酸杂交法(FISH和DNA芯片技术)、土壤宏基因组学以及DNA指纹图谱技术等.综述了这些技术的基本原理、比较了各种技术的优缺点并且介绍了他们在土壤微生物群落多样性研究中的应用,展望了这些技术的发展方向.     

Reclamation of abandoned saline-alkali soil increased soil microbial diversity and degradation potential

Plant and Soil - Reclamation of saline-alkali soils to grow cotton (Gossypium spp.) is very common in the arid Manas River Basin in Northwest China. However, little is known about the degradation...     

Termite mounds reduce soil microbial diversity by filtering rare microbial taxa

Termites are ubiquitous insects in tropical and subtropical habitats, and some of them construct massive nests (‘mounds’), which substantially promote substrate heterogeneity by altering soil properties. Yet, the role of termite nesting process in regulating the distribution and diversity of soil microbial communities remains poorly understood, which introduces uncertainty in predictions of ecosystem functions of termite mounds in a changing environment. Here, by using amplicon sequencing, we conducted a survey of 134 termite mounds across >1500 km in northern Australia and found that termite mounds significantly differed from bulk soils in the microbial diversity and community compositions. Compared with bulk soils, termite nesting process decreased the microbial diversity and the relative abundance of rare taxa. Rare taxa had a narrower habitat niche breadth than dominant taxa and might be easier to be filtered by the potential intensive microbial competition during the nesting processes. We further demonstrated that the shift in pH induced by termite nesting process was a major driver shaping the microbial community profiles in termite mounds. Together, our work provides novel evidence that termite nesting is an important process in regulating soil microbial diversity, which advances our understanding of the functioning of termite mounds.     

长期施肥土壤微生物群落的剖面变化及其与土壤性质的关系

摘要:【目的】认识不同施肥模式对土壤微生物群落的长期影响及其与土壤理化属性的联系。【方法】利用新一代高通量测序技术,研究绿洲农田20年单施化肥(N 300 kg/hm2、P2O5 150 kg/hm2与K2O 60 kg/hm2)与化肥配施秸秆(同量的N与P肥配施5.4 t秸秆)对土壤剖面(0－300 cm)微生物群落结构的影响。【结果】放线菌与α-变形菌为土壤表层(0－20 cm)的优势类群。随土壤剖面深度的增加,放线菌相对丰度减少,而变形菌,特别是γ-变形菌与β-变形菌相对丰度增加,逐渐成为深层(20－300 cm)土壤中的优势类群。长期施肥对整个土壤剖面的微生物群落结构均有显著影响,并且明显提高了0－40 cm土层中氨氧化古菌的相对丰度。此外,农田管理模式如灌溉可能是氨氧化细菌在土壤垂直剖面的重要驱动因素。统计分析表明土壤全氮含量对表层土壤中微生物群落结构的影响最大,而有机碳含量则是影响深层土壤微生物群落的最重要因子。【结论】长期施肥改变了土壤剖面碳源与氮源的可利用量,导致了施肥处理间土壤微生物群落结构的差异,特别在剖面深层更为明显。     

Impact of soil leachate on microbial biomass and diversity affected by plant diversity

Plant and Soil - High plant diversity is usually linked with high soil microbial diversity, which is hypothesized to be attributed to a high diversity of components in the soil leachate, but...     

Distinct soil microbial diversity under long-term organic and conventional farming

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.     

Plant diversity loss reduces soil respiration across terrestrial ecosystems

The rapid global biodiversity loss has led to the decline in ecosystem function. Despite the critical importance of soil respiration (Rs) in the global carbon and nutrient cycles, how plant diversity loss affects Rs remains uncertain. Here we present a meta‐analysis using 446 paired observations from 95 published studies to evaluate the effects of plant and litter mixtures on Rs and its components. We found that total Rs and heterotrophic respiration (Rh) were, on average, greater in plant mixtures than expected from those of monocultures. These mixture effects increased with increasing species richness (SR) in both plant and litter mixtures. While the positive effects of species mixtures remained similar over time for total Rs, they increased over time for Rh in plant mixtures but decreased in litter mixtures. Despite the wide range of variations in mean annual temperature, annual aridity index, and ecosystem types, the plant mixture effects on total Rs and Rh did not change geographically, except for a more pronounced increase of total Rs in species mixtures with reduced water availability. Our structural equation models suggested that the positive effects of SR and stand age on total and Rh were driven by increased plant inputs and soil microbial biomass. Our results suggest that plant diversity loss has ubiquitous negative impacts on Rs, one of the fundamental carbon‐cycle processes sustaining terrestrial element cycling and ecosystem function.     

Relationship between Mikania micrantha invasion and soil microbial biomass, respiration and functional diversity

The aim of this study was to determine elemental composition of sap-feeding insects inhabiting various parts of the Ni hyperaccumulating plant Berkheya coddii Roessl., the endemic species of ultramafic outcrops in Mpumalanga, South Africa. Three species were examined: the aphid Protaphis pseudocardui (Aphididae), abundant on young leaves; the mealybug Orthesia sp. (Ortheziidae) colonizing underground parts of this plant, and the bug Norialsus berkheyae (Cixiidae) living on young shoots. Maps of Ni, K, Ca, Zn, and Fe for selected body areas of these species were generated using Dynamic Analysis method on the basis of particle-induced X-ray emission (micro-PIXE) and proton backscattering (BS) measurements. Atomic absorption spectrometry was used to determine Ni, Zn, Cu, Fe contents in the B. coddii organs, in some sap-feeding insect species including these mentioned above, and in the assassin bug hunting on Chrysolina pardalina, a monophagous beetle of B. coddii. Bioaccumulation factor for Ni in the examined species was below 0.05, and much higher for other metals (Zn ≥ 2; Fe ≤ 5). Ni distribution within body was species-dependent. It was the highest in the antennae of P. pseudocardui, in the head of Orthesia sp. and in the metathorax of N. berkheyae. Distribution patterns of other metals were different among examined species. Ca was recorded mainly in peripheral parts of the body in all species. Zn showed similar distribution to Ni. Fe distribution was similar to Ni only in the mealybugs. Uneven concentrations of metals within selected body regions indicated their relations with specific organs. Analysis of Ni transfer to higher trophic levels was done on the basis of two food nets: B. coddii—C. pardalina—Rhinocoris neavii and B. coddii—P. pseudocardui—Polyrhachis ant and led to the conclusion that the role of sap-feeding insects in Ni transfer was marginal.