Effects of continuous cucumber cropping and alternative rotations under protected cultivation on soil microbial community diversity

The diversity of soil microbial communities as affected by continuous cucumber cropping and alternative rotations under protected cultivation were evaluated using community level physiological profiles (CLPP) and random amplified polymorphic DNA (RAPD) analysis. The soils were selected from six cucumber cropping systems, which cover two cropping practices (rotation and continuous cropping) and a wide spectrum for cucumber cropping history under protected cultivation. Shannon–Weaver index and multivariate analysis were performed to characterize variations in soil microbial communities. Both CLPP and RAPD techniques demonstrated that cropping systems and plastic-greenhouse cultivation could considerably affect soil microbial functional diversity and DNA sequence diversity. The open-field soil had the highest Shannon–Weaver index (3.27 for CLPP and 1.50 for RAPD), whereas the lowest value occurred in the 7-year continuous protected cultivation soil (3.27 for CLPP and 1.50 for RAPD). The results demonstrated that continuous plastic-greenhouse cultivation and management can cause the reduction in the species diversity of the biota. Higher Shannon–Weaver index and coefficients of DNA sequence similarity were found in soils under rotation than those under continuous cropping. Cluster analysis also indicated that microbial community profiles of continuous cultivation soils were different from profiles of rotation soils. The reduction in diversity of microbial communities found in continuous cultivation soils as compared with rotation soils might be due to the differences in the quantity, quality and distribution of soil organic matter. Section Editor: D. E. Crowley     

农用化学品污染对土壤微生物群落DNA序列多样性影响研究

采用ＲＡＰＤ分子遗传标记技术研究了农用化学品不同使用环境下的４种土壤微生物群落ＤＮＡ序列多样性的变化。结果表明,４种土壤微生物群落ＤＮＡ序列在其丰富度、多样性指数、均匀度等方面均存在差异;农用化学品的使用会对土壤微生物群落在ＤＮＡ分子水平上的多样性产生影响;而冰同的农用化学品对土壤微生物群落ＤＮＡ序列多样性影响各不相同：化肥污染会引起某些土壤微生物的富集和一些微生物物种的丧失;农药杂会引起土壤微生     

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.     

不同森林恢复类型对土壤微生物群落的影响

为了评价不同森林恢复类型与方式对南方红壤丘陵区退化生态系统土壤微生物群落的影响,借助氯仿熏蒸法、平板涂抹法和BIOLOG检测法,比较研究了4种森林恢复类型土壤微生物的群落特征．结果表明,4种森林恢复类型土壤微生物生物量碳、细菌数量差异显著,2项指标均以天然次生林土壤最高,人工林次之,荒地最差;碳源平均颜色变化率(AWCD法)和微生物代谢多样性指数(丰富度和多样性)在5种植被类型的土壤中也有明显差异,其趋势与微生物量碳、细菌数量基本相同;天然次生林土壤微生物群落利用碳源的整体能力和功能多样性比人工林和荒地强．相关分析表明,0～20和20～40cm土壤微生物的代谢多样性与根系生物量紧密相关(r=0．933,P<0．05;r=0．925,P<0．05)．自然恢复更有利于改善土壤微生物的结构和功能．     

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.     

Differentiating between effects of invasion and diversity: impacts of aboveground plant communities on belowground fungal communities

Exotic plant species can affect soil microbial communities with the potential for community and ecosystem feedbacks. Yet, separating the effects of exotics from confounded changes in plant community diversity still remains a challenge. We focused on how plant diversity and native or exotic life history affected root fungi because of their significant roles in community and ecosystem processes. Specifically, we examined how fungi colonizing plant roots were affected by plant richness (one, two or four species) replicated across a range of plant community mixtures (natives, exotics, native-exotic mixtures). Fungal biomass inside roots was affected independently by plant richness and mixture, while root fungal community composition was affected only by plant richness. Extraradical networks also increased in size with plant richness. By contrast, plant biomass was a function of plant mixture, with natives consistently smaller than exotics and native-exotic mixtures intermediate. Plant invasions may have an impact on the belowground community primarily through their effects on diversity, at least in the short-term. Disentangling the effects of diversity and invasion on belowground microbial communities can help us to understand both the controllers of belowground resilience and mechanisms of successful colonization and spread of exotic plants.     

Does the Aboveground Herbivore Assemblage Influence Soil Bacterial Community Composition and Richness in Subalpine Grasslands?

Grassland ecosystems support large communities of aboveground herbivores that are known to directly and indirectly affect belowground properties such as the microbial community composition, richness, or biomass. Even though multiple species of functionally different herbivores coexist in grassland ecosystems, most studies have only considered the impact of a single group, i.e., large ungulates (mostly domestic livestock) on microbial communities. Thus, we investigated how the exclusion of four groups of functionally different herbivores affects bacterial community composition, richness, and biomass in two vegetation types with different grazing histories. We progressively excluded large, medium, and small mammals as well as invertebrate herbivores using exclosures at 18 subalpine grassland sites (9 per vegetation type). We assessed the bacterial community composition using terminal restriction fragment length polymorphism (T-RFLP) at each site and exclosure type during three consecutive growing seasons (2009–2011) for rhizosphere and mineral soil separately. In addition, we determined microbial biomass carbon (MBC), root biomass, plant carbon:nitrogen ratio, soil temperature, and soil moisture. Even though several of these variables were affected by herbivore exclusion and vegetation type, against our expectations, bacterial community composition, richness, or MBC were not. Yet, bacterial communities strongly differed between the three growing seasons as well as to some extent between our study sites. Thus, our study indicates that the spatiotemporal variability in soil microclimate has much stronger effects on the soil bacterial communities than the grazing regime or the composition of the vegetation in this high-elevation ecosystem.     

镜泊湖岩溶台地不同植被类型土壤微生物群落特征

为了探讨不同演替阶段植被类型土壤微生物群落特征,分别选取镜泊湖岩溶台地草本、矮灌木、高灌木、小乔木与灌木混生(简称混生)群落、落叶阔叶林及针阔混交林6种典型植被类型,进行植物群落调查和对土壤微生物生物量、群落结构和多样性指标、土壤物理化学性质的测定。结果表明：从土壤微生物量、土壤微生物群落组成、土壤微生物代谢动力学过程和代谢功能多样性的角度来看,各种植被类型土壤微生物群落具有明显的差异。演替前期的草本群落土壤微生物量碳氮、细菌生物量、真菌生物量,代谢活性及丰富度指数均最低,但Shannon-Wiener多样性指数和均匀度指数显著(P<0.05)高于其他植被类型。矮灌木土壤微生物群落组成显著受植被类型的影响。高灌木群落和混生(小乔木与灌木混生)群落具有极强的相似性, 但在碳源利用类型上两者表现出一定的差异。落叶阔叶林代谢活性最高,碳源利用能力最强,能利用BIOLOG微孔板中的所有31种碳源,这与其具有较高的微生物量碳氮和细菌生物量一致,其代谢功能丰富度最高。演替后期的针阔混交林下的土壤pH最低,真菌比例升高,在碳源丰富的条件下具有极强的竞争优势(仅次于落叶阔叶林),但在碳源贫瘠的条件下其利用碳源能力较弱(仅高于草本)。植被可能主要通过土壤全磷和有机质影响土壤微生物代谢功能多样性。     

Effects of plant species richness and evenness on soil microbial community diversity and function

Understanding the links between plant diversity and soil communities is critical to disentangling the mechanisms by which plant communities modulate ecosystem function. Experimental plant communities varying in species richness, evenness, and density were established using a response surface design and soil community properties including bacterial and archaeal abundance, richness, and evenness were measured. The potential to perform a representative soil ecosystem function, oxidation of ammonium to nitrite, was measured via archaeal and bacterial amoA genes. Structural equation modeling was used to explore the direct and indirect effects of the plant community on soil diversity and potential function. Plant communities influenced archaea and bacteria via different pathways. Species richness and evenness had significant direct effects on soil microbial community structure, but the mechanisms driving these effects did not include either root biomass or the pools of carbon and nitrogen available to the soil microbial community. Species richness had direct positive effects on archaeal amoA prevalence, but only indirect impacts on bacterial communities through modulation of plant evenness. Increased plant evenness increased bacterial abundance which in turn increased bacterial amoA abundance. These results suggest that plant community evenness may have a strong impact on some aspects of soil ecosystem function. We show that a more even plant community increased bacterial abundance, which then increased the potential for bacterial nitrification. A more even plant community also increased total dissolved nitrogen in the soil, which decreased the potential for archaeal nitrification. The role of plant evenness in structuring the soil community suggests mechanisms including complementarity in root exudate profiles or root foraging patterns.