Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

Background and Aims

Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover.

Methods

In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities.

Key Results

Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification.

Conclusions

The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.     

Microbial dynamics and soil physicochemical properties explain large‐scale variations in soil organic carbon

First‐order organic matter decomposition models are used within most Earth System Models (ESMs) to project future global carbon cycling; these models have been criticized for not accurately representing mechanisms of soil organic carbon (SOC) stabilization and SOC response to climate change. New soil biogeochemical models have been developed, but their evaluation is limited to observations from laboratory incubations or few field experiments. Given the global scope of ESMs, a comprehensive evaluation of such models is essential using in situ observations of a wide range of SOC stocks over large spatial scales before their introduction to ESMs. In this study, we collected a set of in situ observations of SOC, litterfall and soil properties from 206 sites covering different forest and soil types in Europe and China. These data were used to calibrate the model MIMICS (The MIcrobial‐MIneral Carbon Stabilization model), which we compared to the widely used first‐order model CENTURY. We show that, compared to CENTURY, MIMICS more accurately estimates forest SOC concentrations and the sensitivities of SOC to variation in soil temperature, clay content and litter input. The ratios of microbial biomass to total SOC predicted by MIMICS agree well with independent observations from globally distributed forest sites. By testing different hypotheses regarding (using alternative process representations) the physicochemical constraints on SOC deprotection and microbial turnover in MIMICS, the errors of simulated SOC concentrations across sites were further decreased. We show that MIMICS can resolve the dominant mechanisms of SOC decomposition and stabilization and that it can be a reliable tool for predictions of terrestrial SOC dynamics under future climate change. It also allows us to evaluate at large scale the rapidly evolving understanding of SOC formation and stabilization based on laboratory and limited filed observation.     

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.     

植物功能性状对土壤保持的影响研究述评

植被对土壤保持具有重要的影响,但是从植物功能性状的角度总结评述植被对土壤保持影响的研究并不多见。总结评述了植物地上功能性状、地下功能性状对土壤保持功能的影响以及植物地上、地下功能性状的关系,认为:(1)植被地上部分功能性状对土壤保持的作用主要体现在对溅蚀、面蚀的影响及间接改变土壤理化性质等方面,其功能性状指标主要包括叶面积、叶长、叶宽、枝数、植被高度等;(2)植被地下部分功能性状对土壤保持的作用主要体现在固持土壤、提高土壤抗剪切强度、提高土壤抗侵蚀能力、增强土壤渗透性,植物根系固持土壤与根系抗拉能力密切相关,植物根系土壤的物理和水文性质,与细根比例、根长密度、根表面积等性状密切相关;(3)可以通过植物地上部分功能性状间接反映地下部分功能性状,但是现有研究多为定性认识;(4)在植物功能性状对土壤保持的研究中亟待加强植被地上地下功能性状的长期定位监测,深化植被功能性状尤其是根系特征与土壤保持的作用机理,加强植被地上部分、地下部分功能性状的定量表达,建立植被功能性状与土壤保持功能的定量关系,实现植被功能性状与土壤保持功能特征的动态链接。     

Abiotic stress tolerance and competition‐related traits underlie phylogenetic clustering in soil bacterial communities

Soil bacteria typically coexist with close relatives generating widespread phylogenetic clustering. This has been ascribed to the abiotic filtering of organisms with shared ecological tolerances. Recent theoretical developments suggest that competition can also explain the phylogenetic similarity of coexisting organisms by excluding large low‐competitive clades. We propose that combining the environmental patterns of traits associated with abiotic stress tolerances or competitive abilities with phylogeny and abundance data, can help discern between abiotic and biotic mechanisms underlying the coexistence of phylogenetically related bacteria. We applied this framework in a model system composed of interspersed habitats of highly contrasted productivity and comparatively dominated by biotic and abiotic processes, i.e. the plant patch‐gap mosaic typical of drylands. We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. Conserved traits related to environmental stress tolerance (e.g. desiccation, formation of resistant structures) were differentially selected in either habitat, while competition related traits (e.g. organic C consumption, formation of nutrient‐scavenging structures) prevailed under high resource availability. Phylogenetic clustering was stronger in habitats dominated by biotic filtering, suggesting that competitive exclusion of large clades might underlie the ecological similarity of co‐occurring soil bacteria.     

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.     

松嫩草地4种植物功能群土壤微生物碳源利用的差异

为了探讨草地不同植物功能群土壤微生物碳源利用差异,利用Biolog-ECO微平板检测法,研究了松嫩放牧草地禾草(Grass)、羊草(Leymus chinensis)、杂类草(Forb)和豆科牧草(Legume)4种植物功能群土壤微生物碳源代谢的多样性变化特征。结果表明,在培养的240h内,4种不同植物功能群的土壤微生物对碳源的利用程度均随着时间的延长而升高,表明微生物代谢活性随着时间而增强;不同植物功能群土壤微生物总体活性(AWCD)(P0.001)、Shannon-Wiener指数(H)(P0.001)、物种丰富度(R)(P=0.005)、Pielou均匀度指数(E)(P0.001)差异显著;其中禾草的各项指数明显高于其他3种(P0.01),杂类草的各指标均最低。禾草、羊草对糖类、氨基酸类、羧酸类、多聚物类有较好的利用,豆科牧草除羧酸类外对其他碳源都有更好的利用,杂类草只对酚类碳源利用率最高,而对其他碳源利用率极低。总体得出4种功能群土壤微生物的碳源利用率顺序为:禾草羊草豆科牧草杂类草。     

黄土高原不同土壤微生物量碳、氮与氮素矿化势的差异

以采自于黄土高原差异较大的25个农田石灰性耕层土壤为供试土样,对黄土高原主要类型土壤中微生物量碳(Bc)、微生物量氮(BN)和氮素矿化势(NO)的差异性进行了比较研究.结果表明,Bc、BN和NO在不同类型土壤间存在显著差异,由关中平原至陕北风沙区,BC、Bn和NO总体呈现下降趋势,其中以土垫旱耕人为土最高,简育干润均腐土最低,黄土正常新成土和干润砂质新成土居中:土垫旱耕人为土、简育干润均腐土、黄土正常新成土和干润砂质新成土等各土类平均BC分别为305.2μg·g-1,108.4μg·g-1,161.7μg·g-1和125.4μg·g-1,BN分别为43.8μg·g-1,20.3μg·g-1,26.0μg·g-1和30.6μg·g-1,NO分别为223μ·g-1,75μg·g-1,163μg·g-1和193μg·g-1.土壤氮素矿化速率(k)则以简育干润均腐土最大,干润砂质新成土最低,土垫旱耕人为土和黄土正常新成土居中:土垫旱耕人为土、简育干润均腐土、黄土正常新成土和干润砂质新成土的k分别为0.039w-1,0.044w-1,0.031w-1和0.019w-1.不同类型土壤BC、BN与NO的差异,主要与土壤形成过程、输入土壤的植物同化产物和土壤有机质的差异等有关,从较大尺度进一步证明了在黄土高原,土壤有机质是影响BC、BN的主要因子.研究结果对分析黄土高原土壤生产力形成过程具有一定参考价值.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

Similarity of plant functional traits and aggregation pattern in a subtropical forest

The distribution of species and communities in relation to environmental heterogeneity is a central focus in ecology. Co‐occurrence of species with similar functional traits is an indication that communities are determined in part by environmental filters. However, few studies have been designed to test how functional traits are selectively filtered by environmental conditions at local scales. Exploring the relationship between soil characteristics and plant traits is a step toward understanding the filtering hypothesis in determining plant distribution at local scale. Toward this end, we mapped all individual trees (diameter >1 cm) in a one‐ha subtropical forest of China in 2007 and 2015. We measured topographic and detailed soil properties within the field site, as well as plant leaf functional traits and demographic rates of the seven most common tree species. A second one‐ha study plot was established in 2015, to test and validate the general patterns that were drawn from first plot. We found that variation in species distribution at local scale can be explained by soil heterogeneity and plant functional traits. (From first plot). (1) Species dominant in habitats with high soil ammonium nitrogen and total phosphorus tended to have high specific leaf area (SLA) and relative growth rate (RGR). (2) Species dominant in low‐fertility habitats tended to have high leaf dry matter content (LDMC), ratio of chlorophyll a and b (ratioab), and leaf thickness (LT). The hypothesis that functional traits are selected in part by environmental filters and determine plant distribution at local scale was confirmed by the data of the first plot and a second regional site showed similar species distribution patterns.     

Continental‐scale nitrogen pollution is shifting forest mycorrhizal associations and soil carbon stocks

Most tree roots on Earth form a symbiosis with either ecto‐ or arbuscular mycorrhizal fungi. Nitrogen fertilization is hypothesized to favor arbuscular mycorrhizal tree species at the expense of ectomycorrhizal species due to differences in fungal nitrogen acquisition strategies, and this may alter soil carbon balance, as differences in forest mycorrhizal associations are linked to differences in soil carbon pools. Combining nitrogen deposition data with continental‐scale US forest data, we show that nitrogen pollution is spatially associated with a decline in ectomycorrhizal vs. arbuscular mycorrhizal trees. Furthermore, nitrogen deposition has contrasting effects on arbuscular vs. ectomycorrhizal demographic processes, favoring arbuscular mycorrhizal trees at the expense of ectomycorrhizal trees, and is spatially correlated with reduced soil carbon stocks. This implies future changes in nitrogen deposition may alter the capacity of forests to sequester carbon and offset climate change via interactions with the forest microbiome.     

环丙沙星对土壤微生物量碳和土壤微生物 群落碳代谢多样性的影响

采用氯仿熏蒸浸提法和Biolog法,分析环丙沙星作用下的土壤微生物量碳和微生物群落碳代谢多样性,以揭示环丙沙星在环境中残留对土壤微生物学性状的影响.结果表明,环丙沙星(wCIP≥0.1 μg/g)对土壤微生物量碳含量影响显著(P＜0.05),土壤中环丙沙星浓度愈高,微生物量碳含量愈低,100μg/g的环丙沙星处理使土壤微生物量碳含量下降58.69％.环丙沙星对土壤微生物群落碳代谢功能影响显著,环丙沙星降低了土壤微生物对碳水化合物、羧酸、氨基酸、聚合物、酚类和胺类的碳源利用率;环丙沙星(wCIP≥0.1 μg/g)显著影响了土壤微生物群落碳源代谢强度和代谢多样性,但不同浓度的环丙沙星对土壤微生物群落碳代谢功能的影响不同,0.1、1、10 μg/g的环丙沙星处理对土壤微生物群落碳代谢功能的影响主要表现在处理前期(用药第7天、21天),这种影响在处理后期(用药第35天)表现不明显,100μg/g的环丙沙星在用药的前期和后期均显著影响土壤微生物群落碳代谢功能,土壤中环丙沙星积累到该浓度可能对土壤微生物群落碳代谢功能产生难以逆转的长期影响.     

青藏高原高寒草甸不同海拔梯度下土壤微生物群落碳代谢多样性

土壤微生物群落功能多样性对维持生态系统功能和稳定性具有非常重要的意义。为探究青藏高原高寒草甸不同海拔梯度下土壤微生物碳源利用差异以及影响机制,运用Biolog微平板技术,研究了西藏当雄县草原站4300—5100 m的6个不同海拔梯度下土壤微生物群落碳源代谢多样性。研究结果表明:(1)不同海拔下高寒草甸土壤微生物碳源的利用程度均随培养时间的延长而升高;微生物代谢活性和群落多样性指数均随海拔升高呈现先上升后下降的单峰变化趋势,整体表现4800 m4950 m4400 m4650 m5100 m4300 m;(2)主成分分析表明不同海拔显著影响了土壤微生物群落碳源代谢多样性,其中碳水化合物类、氨基酸类和胺类碳源是各海拔土壤微生物的偏好碳源;碳水化合物类、羧酸类、氨基酸类和胺类碳源的利用强度受海拔影响较大;(3)分类变异分析表明,土壤、植物和气候因素是影响不同海拔碳源利用变异的主要影响因子,可解释不同海拔的碳源利用差异的79.0%;排除环境因子之间的多重及交互作用,偏曼特尔检验表明土壤含水量、植被丰富度和年均降水量是影响不同海拔微生物碳源利用多样性的最重要的环境因子。综上,研究表明青藏高寒草甸不同海拔土壤微生物碳源代谢多样性呈现显著的海拔差异趋势,其海拔差异主要受到土壤含水量、植被丰富度和年均降水量的影响。     

芦苇克隆整合对石油污染湿地土壤微生物群落结构和生物量的影响

克隆植物形体相连的无性个体(分株)之间可以进行水分、养分和光合产物的传递和共享,并且这种克隆整合可以显著提高分株对环境胁迫的耐受能力,从而可能进一步影响分株周围的土壤微生物群落结构和生物量。尽管国内外已经开展了大量有关克隆整合对分株耐受胁迫能力影响的研究,但克隆整合对土壤微生物群落结构和生物量影响的研究却十分缺乏。以黄河三角洲芦苇(Phragmites australis)湿地生态系统为研究对象,将直径60 cm的圆形样方进行三个水平的石油添加处理(不添加石油或每年添加5 mm或10 mm厚的石油),同时通过切断或不切断样方内外芦苇根状茎的连接来控制克隆整合的有无。实验连续开展了两年(2014—2015年),每年8月份在样方内进行土壤样品取样,在实验室内采用磷酸脂肪酸(PLFA)法测定土壤微生物总量及主要微生物类群含量,并测定土壤微生物生物量碳和氮含量。取样时间显著影响土壤微生物PLFA总量、微生物碳和氮含量,这3个变量在2015年均显著高于2014年。石油添加在2015年显著增加了土壤微生物PLFA总量,但在2014年却无显著效应;同时,石油添加在2014年降低了土壤微生物碳和氮含量,而在2015年却增加了其含量。然而,无论在2014年还是2015年,芦苇的克隆整合对土壤微生物PLFA含量、微生物碳和氮含量均没有显著影响。土壤微生物PLFA总量与土壤微生物碳和氮含量呈正相关关系。这些结果表明,石油污染可以显著影响湿地土壤微生物动态,但克隆整合却无显著效应。     

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。     

Nitrogen deposition,vegetation burning and climate warming act independently on microbial community structure and enzyme activity associated with decomposing litter in low‐alpine heath

Low‐alpine heathlands are thought to be particularly sensitive to nitrogen (N) deposition, climate and land management change, yet little is known about how these factors regulate key belowground processes, like litter turnover, under field conditions. Here we use an in situ factorial field experiment to test the effects of increased atmospheric N deposition, climate manipulation and past vegetation burning, and their interactions, on litter decomposition and the activity and diversity of associated microorganisms. The use of litter from within (native) and outwith (standard) the experimental plots also enabled us to test whether decomposition and microbial functional diversity is driven primarily by soil conditions or litter chemistry. In general, extracellular enzyme activities of litter were driven by additions of simulated N deposition with phosphatase being the most responsive. We found that standard litter incubated in plots that had been burnt 8 years previously decomposed slower and lost less N and phosphorus than in unburnt plots. This material also had associated with it the greatest activity of glucosidase and the least diverse microbial community, as assessed by culture‐independent methods. Although all treatments significantly affected microbial diversity, burning explained most of the variability, indicating a close coupling between plant and microbial communities in these treatments. A striking feature of all the data relating to both standard and native litter was an almost complete lack of interactive effects between the treatments. The lack of interactions between the treatments indicates that each perturbation might affect different mechanisms in the decomposition process (including the composition of associated microbial communities) and nutrient cycling.     

The effects of some soil properties (soil nitrogen forms and moisture) on community structure in Mediterranean plant communities in the Black Sea region

Mediterranean ecosystems comprise the second biodiversity hotspot area after tropical rain forests and will be most affected by global climate change. Therefore, it is important to understand community dynamics for effective conservation in this region. We investigated the relationships between soil moisture, nitrogen forms and community structuring in Quercus ilexL., Erica arborea L. and Sarcopoterium spinosum (L.) Spach communities, representing different successional stages, distributed as Mediterranean enclaves on the Sinop Peninsula (Turkey). The soil moisture, ammonium, nitrate and nitrite content were measured seasonally. Differences in these abiotic parameters within and between communities over seasons were tested. Previously collected biotic data were then used to analyze the relationship between soil parameters and community structure. Significant differences in soil parameters within and between seasons were found within and between communities. Our results show that there are different relationships between soil moisture, nitrogen forms and community structure in Mediterranean plant communities representing different successional stages. Differentiation in vegetation structure during succession cause changes especially in the water and nitrate content of the soil, and these changes in turn affect the continuity of community structure in Mediterranean plant communities.