Beyond microbial diversity for predicting soil functions: A mini review

Since the advent of sequencing technologies,the determination of microbial diversity to predict microbial functions,which are the major determinants of soil functions,has become a major topic of interest,as evidenced by the 900 publications dealing with soil metagenome published up to 2017.However,the detection of a gene in soil does not mean that the relative function is expressed,and the presence of a particular taxon does not mean that the relative functions determined in pure culture also occur in the studied soil.Another critical step is to link microbial community composition or function to the product analyzed to determine flux rates.Indeed,flux rates might not only be highly dynamic,but several metabolites can depend on different reactions,which makes the link to one process of interest difficult or even impossible.This review also discusses biases caused by sampling,storage of samples,DNA extraction and purification,sequencing(amplicon-vs.metagenome sequencing),and bioinformatic data analysis.Insights and the limits of predicting microbial interactions by network inference methods are critically discussed,and finally,future directions for a better understanding of soil functions by using measurements of microbial diversity are presented.     

Soil bacterial communities under slash and burn in Mozambique as revealed by a metataxonomic approach

The slash-and-burn system is a subsistence agronomical practice widespread in tropical areas worldwide. This system has been extensively studied,especially for its impacts on agronomical aspects and soil physicochemical properties; however, knowledge of soil microbial diversity under slash and bum is scarce. In this study, for the first time, soil bacterial diversity of three locations from Central Mozambique, where slash and burn has been practiced for different durations of the forest fallow p...     

农业土壤中频繁施用有机质提高土壤抑菌作用

Soil-borne plant pathogens are among the most important limiting factors for the productivity of agro-ecosystems.Fungistasis is the natural capability of soils to inhibit the germination and growth of soil-borne fungi in the presence of optimal abiotic conditions.The objective of this study was to assess the effects of different soil managements,in terms of soil amendment types and frequency of application,on fungistasis.For this purpose,a microcosm experiment was performed by conditioning a soil with frequent applications of organic matter with contrasting biochemical quality (i.e.,glucose,alfalfa straw and wheat straw).Thereafter,the fungistasis response was assessed on four fungi (Aspergillus niger,Botrytis cinerea,Pyrenochaeta lycopersici and Trichoderma harzianum).Conditioned soils were characterized by measuring microbial activity (soil respiration) and functional diversity using the BIOLOG EcoPlatesTM method.Results showed that irrespective of the fungal species and amendment types,frequent applications of organic matter reduced fungistasis relief and shortened the time required for fungistasis restoration.The frequent addition of easily decomposable organic compounds enhanced soil respiration and its specific catabolic capabilities.This study demonstrated that frequent applications of organic matter affected soil fungistasis likely as a result of higher microbial activity and functional diversity.     

Soil fungal and prokaryotic community structure exhibits differential short-term responses to timber harvest in the Pacific Northwest

Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest;however,information regarding how these practices impact soil microbial community structure at the regional scale is limited.With evidence of consistent and substantial impact of harvest on soil microbial functional profiles across the region(despite a range of environmental conditions),the objective of this study was to determine the extent to which harvest also influences the structure of prokaryotic and fungal soil microbial communities,and how generalized these trends are throughout the geographic region.Paired soil samples were collected one year before and after harvest across nine second-growth Douglas-fir forests in the Pacific Northwest.Total community DNA was extracted from the soils,and high-throughput targeted gene sequencing of the 16 S r RNA gene for prokaryotes and the internal transcribed spacer(ITS)gene for fungi was performed.Alpha diversity was consistently and significantly higher after harvest;it was moderately so for fungal communities(+14.6%),but only marginally so for prokaryotic communities(+2.0%).Similarly,on average,a greater proportion of the variation in the community structure of fungi(20.1%)at each site was associated with forest harvest compared to that of prokaryotes(13.2%).Overall,the greatest influence of timber harvest on soil microbial communities appeared to be a relative depletion of ectomycorrhizal fungi,with a concomitant enrichment of saprotrophic fungi.Understanding the short-term responses of soil microbial communities across the region,particularly those of tree root-associated symbionts,may aid our understanding of the role soil microbial communities play in ecological succession.     

Ultimate fate of halosulfuron methyl and its effects on enzymatic and microbial activities in three differently textured soils

Halosulfuron methyl is a sulfonylurea herbicide used worldwide for weed control in sugarcane, maize, wheat, and rice production. Considering its environmental impact, this study evaluated the effects of soil type, application rate, and temperature on the dynamics of halosulfuron methyl degradation.Additionally, as soil microbes and enzymes are reliable indicators of the impacts of anthropogenic activities on soil health, the effects of halosulfuron methyl on soil enzymatic and microbial activiti...     

通过纯培养蛋白质组学跟踪研究石油污染的土壤上微生物群落的变化

Hydrocarbon contamination may affect the soil microbial community, in terms of both diversity and function. A laboratory experiment was set-up, with a semi-arid control soil and the same soil but artificially contaminated with diesel oil, to follow changes in the dominant species of the microbial community in the hydrocarbon-polluted soil via proteomics. Analysis of the proteins extracted from enriched cultures growing in Luria-Bertani (LB) media showed a change in the microbial community. The majority of the proteins were related to glycolysis pathways, structural or protein synthesis. The results showed a relative increase in the complexity of the soil microbial community with hydrocarbon contamination, especially after 15 days of incubation. Species such as Ralstonia solanacearum, Synechococcus elongatus and different Clostridium sp. were adapted to contamination, not appearing in the control soil, although Bacillus sp. dominated the growing in LB in any of the treatments. We conclude that the identification of microbial species in soil extracts by culture-dependent proteomics is able to partially explain the changes in the diversity of the soil microbial community in hydrocarbon polluted semi-arid soils, but this information is much more limited than that provided by molecular methods.     

黄河三角洲退化湿地微生物群落特性研究

Five different sites with a soluble salt gradient of 3.0--17.7 g kg-1 dry soil from the coast to the inland were selected, and the microbial population size, activity and diversity in the rhizospheres of five common plant species and the adjacent bulk soils (non-rhizosphere) were compared in a degraded wetland of the Yellow River Delta, Shandong Province, China to study the effects of soil environment (salinity, seasonality, depth, and rhizosphere) on microbial communities and the wetland’s ecological function, thus providing basic data for the bioremediation of degraded wetlands. There was a significant negative linear relationship between the salinity and the total number of microorganisms, overall microbial activity, or culturable microbial diversity. Salinity adversely affected the microbial community, and higher salinity levels resulted in smaller and less active microbial communities. Seasonal changes were observed in microbial activity but did not occur in the size and diversity. The microbial size, activity and diversity decreased with increasing soil depth. The size, activity and diversity of culturable microorganisms increased in the rhizospheres. All rhizospheres had positive effects on the microbial communities, and common seepweed had the highest rhizosphere effect. Three halophilic bacteria (Pseudomonas mendocina, Burkholderia glumae, and Acinetobacter johnsonii) were separated through BIOLOG identification, and common seepweed could be recommended for bioremediation of degraded wetlands in the Yellow River Delta.     

Responses of soil microbial communities and functions associated with organic carbon mineralization to nitrogen addition in a Tibetan grassland

Alpine grasslands with a high soil organic carbon(SOC)storage on the Tibetan Plateau are experiencing rapid climate warming and anthropogenic nitrogen(N)deposition;this is expected to substantially increase the soil N availability,which may impact carbon(C)cycling.However,little is known regarding how N enrichment influences soil microbial communities and functions relative to C cycling in this region.We conducted a 4-year field experiment on an alpine grassland to evaluate the effects of four different rates of N addition(0,25,50,and 100 kg N ha^-1 year^-1)on the abundance and community structure(phospholipid fatty acids,PLFAs)of microbes,enzyme activities,and community level physiological profiles(CLPP)in soil.We found that N addition increased the microbial biomass C(MBC)and N(MBN),along with an increased abundance of bacterial PLFAs,especially Gram-negative bacterial PLFAs,with a decreasing ratio of Gram-positive to Gram-negative bacteria.The N addition also stimulated the growth of fungi,especially arbuscular mycorrhizal fungi,reducing the ratio of fungi to bacteria.Microbial functional diversity and activity of enzymes involved in C cycling(β-1,4-glucosidase and phenol oxidase)and N cycling(β-1,4-N-acetyl-glucosaminidase and leucine aminopeptidase)increased after N addition,resulting in a loss of SOC.A meta-analysis showed that the soil C/N ratio was a key factor in the response of oxidase activity to N amendment,suggesting that the responses of soil microbial functions,which are linked to C turnover relative to N input,primarily depended upon the soil C/N ratio.Overall,our findings highlight that N addition has a positive influence on microbial communities and their associated functions,which may reduce soil C storage in alpine grasslands under global change scenarios.     

A new perspective on functional redundancy and phylogenetic niche conservatism in soil microbial communities

Functional redundancy in soil microbial communities seems to contradict the notion that individual species have distinct metabolic niches in multi-species communities.All soil microbiota have the metabolic capacity for"basic"functions(e.g.,respiration and nitrogen and phosphorus cycling),but only a few soil microbiota participate in"rare"functions(e.g.,methanogenesis and mineralization of recalcitrant organic pollutants).The objective of this perspective paper is to use the phylogenetic niche conservatism theory as an explanation for the functional redundancy of soil microbiota.Phylogenetic niche conservatism is defined as the tendency for lineages to retain ancestral functional characteristics through evolutionary time-scales.The present-day soil microbiota is the result of a community assembly process that started when prokaryotes first appeared on Earth.For billions of years,microbiota have retained a highly conserved set of core genes that control the essential redox and biogeochemical reactions for life on Earth.These genes are passed from microbe to microbe,which contributes to functional redundancy in soil microbiota at the planetary scale.The assembly of microbial communities during soil formation is consistent with phylogenetic niche conservatism.Within a specific soil,the heterogeneous matrix provides an infinite number of sets of diverse environmental conditions,i.e.,niches that lead to the divergence of microbial species.The phylogenetic niche conservatism theory predicts that two or more microbial species diverging from the same clade will have an overlap in their niches,implying that they are functionally redundant in some of their metabolic processes.The endogenous genetic factors that constrain the adaptation of individuals and,thus,populations to changing environmental conditions constitute the core process of phylogenetic niche conservatism.Furthermore,the degree of functional redundancy in a particular soil is proportional to the complexity of the considered function.We conclude with a conceptual model that identifies six patterns of functional redundancy in soil microbial communities,consistent with the phylogenetic niche conservatism theory.     

等温微量热技术在土壤与环境科学中的应用

Isothermal microcalorimetry provides thermodynamic and kinetic information on various reactions and processes and is thereby a powerful tool to elucidate their mechanisms. Certain improvement in isothermal microcalorimetry with regard to the studies on soil and environmental sciences is briefly described. This review mainly focuses on the use of microcalorimetry in the determination of soil microbial activity, monitoring the toxicity and biodegradation of soil organic pollutants, the risk evaluation of metals and metalloids, the heat effect of ion exchange and adsorption in soil, and environmental researches. Promising prospects for the applications of the technique in the field are also discussed.     

有机无机肥长期配合施用对江苏小麦玉米两熟制作物产量和土壤肥力的影响

Winter wheat-maize rotations are dominant cropping systems on the North China Plain, where recently the use of organic manure with grain crops has almost disappeared. This could reduce soil fertility and crop productivity in the long run. A 20-year field experiment was conducted to 1) assess the effect of inorganic and organic nutrient sources on yield and yield trends of both winter wheat and maize, 2) monitor the changes in soil organic matter content under continuous wheat-maize cropping with different soil fertility management schemes, and 3) identify reasons for yield trends observed in Xuzhou City, Jiangsu Province, over a 20-year period. There were eight treatments applied to both wheat and maize seasons: a control treatment (C); three inorganic fertilizers, that is, nitrogen (N), nitrogen and phosphorus (NP), and nitrogen, phosphorus and potassium (NPK); and addition of farmyard manure (FYM) to these four treatments, that is, M, MN, MNP, and MNPK. At the end of the experiment the MN, MNP, and MNPK treatments had the highest yields, about 7 t wheat ha^-1 and 7.5 t maize ha^-1, with each about 1 t ha^-1 more than the NPK treatments. Over 20 years with FYM soil organic matter increased by 80% compared to only 10% with NPK, which explained yield increases. However, from an environmental and agronomic perspective, manure application was not a superior strategy to NPK fertilizers. If manure was to be applied, though, it would be best applied to the wheat crop, which showed a better response than maize.     

不同施肥和耕作制度下土壤微生物多样性研究进展

本文主要介绍了运用Biolog GN、磷脂脂肪酸(PLFA)、核酸分析法进行土壤微生物群落分析的优缺点,综述了施肥、耕作两种农业措施对土壤微生物多样性影响的研究进展。指出不同施肥处理对微生物影响效果不同,合理施用有机肥有利于维持土壤微生物的多样性及活性;由于受其他环境因素(如土壤类型、农作制度、残茬量等)的影响,不同耕作措施对土壤微生物多样性影响有差异,但是大多试验结果显示免耕、少耕能增加微生物多样性和生物量,保持系统的稳定性。文章还指出了目前研究中存在的问题,并对今后的研究方向做了展望。     

核酸分析方法在土壤微生物多样性研究中的应用

土壤微生物多样性一般包括微生物分类群的多样性、遗传(基因)多样性、生态特征多样性和功能多样性。传统的分离培养方法和土壤微生物的生化研究手段具有一定的局限性,核酸分析方法为土壤微生物多样性研究注入了新活力。本文主要综述了近年来国内外研究土壤微生物多样性所采用的核酸提取方法及核酸分析方法。重点阐述了基于PCR的分子指纹技术、核酸杂交技术、基因芯片等核酸分析方法的原理、优缺点和应用。各种土壤微生物多样性研究方法的综合应用可扬长避短,起到相互补充的作用,从而能够提供更加丰富而准确的土壤微生物群落结构及种群丰度变化等方面的信息,也将成为这一领域今后的发展趋势。     

生物有机肥对土壤微生物活性的影响

通过两次连续温室玉米盆栽试验,研究了施用具有调节微生物功能的生物有机肥对土壤微生物数量与活性的影响,并利用传统平板计数法与BIOLOGECO方法相结合研究生物有机肥对土壤微生物生态的影响。结果表明,与化肥相比,施用生物有机肥可显著提高土壤微生物中3大菌群的数量;AWCD值及微生物对不同碳底物利用水平的测定结果表明,施用生物有机肥可明显提高土壤微生物对碳源的利用率,尤其土壤中的羧酸、胺类和其他类碳源等。表明生物有机肥的施用能增加土壤微生物利用碳源能力,改善微生物营养条件,使微生物保持较高活性,提高土壤微生物多样性。     

BIOLOG在土壤微生物群落功能多样性研究中的应用

微生物功能多样性信息对于明确不同环境中微生物群落的作用具有重要意义 ,而微生物群落的定量描述一直是微生物学家面临的最艰巨的任务之一。目前 ,以群落水平碳源利用类型为基础的BIOLOG氧化还原技术为研究土壤微生物群落功能多样性提供了一种简单、快速的方法 ,并得以广泛应用。但它仍然是一种以培养为基础的方法 ,显示的代谢多样性类型也不一定反映整个土壤微生物群落的功能多样性。因此 ,这种方法优点明显 ,缺陷也存在 ,并且在应用过程中还有很多关键的操作要点与技巧。本文综述了BIOLOG研究土壤微生物群落功能多样性的原理、BIOLOG研究土壤微生物群落功能多样性的方法与技巧、应用过程中容易产生的问题及可能克服的办法 ,同时还提出了值得进一步研究的问题。旨在促进对BIOLOG测定土壤微生物群落功能多样性的了解 ,为正确运用这种方法开展土壤微生物群落功能多样性研究提供科学依据和理论指导。     

Linkage between soil organic carbon and the utilization of soil microbial carbon under plastic film mulching in a semi-arid agroecosystem in China

ABSTRACT

Studying changes in soil organic carbon (SOC) pools and soil microbial C substrate utilization under plastic mulching in different seasons is of great significance for improving soil fertility and sustainable agricultural development. Based on a 2-year plastic film mulching experiment in northeastern China, we investigated the SOC, labile SOC fractions under three treatments: non-mulching (NM), autumn mulching (AM) and spring mulching (SM). The results showed that SOC decreased with soil depth under the AM and SM treatments compared with the NM treatment. The microbial biomass carbon (MBC) and dissolved organic carbon (DOC) under the AM treatment increased significantly in the 0–10 cm soil layer, by 31.2% and 27.2% (p < 0.05), respectively. The AM treatment significantly increased the utilization of amino acids and carbohydrate C sources. Redundancy analysis (RDA) indicated that MBC was the main factor influencing microbial metabolic functional diversity and accounted for the largest variation in the 0–10 cm layer. Pearson’s correlation analysis illustrated that MBC was strongly correlated with the utilization of the microbial C substrate. We suggest that AM may be an effective and sustainable management practice for improving soil quality and maintaining microbial functional diversity in semi-arid agroecosystems in this area.     

生草对渭北旱地苹果园土壤有机碳组分及微生物的影响

在渭北旱地苹果园行间播种毛苕子（Vicia villosa）、白三叶（Trifolium repens）、黑麦草（Lolium perenne）和早熟禾（Poa pratensis）,以清耕为对照,对0100 cm土层的土壤有机碳各组分及微生物群落功能多样性进行研究。结果表明,行间生草可显著增加040 cm土层土壤的总有机碳（TOC）、颗粒有机碳（POC）、轻质有机碳（LFOC）、易氧化有机碳（ROC）、可溶性有机碳（DOC）和微生物量碳（MBC）,豆科牧草毛苕子和白三叶的各有机碳含量总体上高于禾本科牧草黑麦草和早熟禾。其中在020 cm土层中,豆科牧草的TOC含量平均每年增加约1.2 g/kg,禾本科牧草每年增加约0.9 g/kg。生草处理的微生物群落碳源利用率（AWCD）、微生物群落Shannon 指数（H）和微生物群落丰富度指数（S）均高于清耕处理,其中豆科牧草的微生物活性更高。因此,生草可以提高土壤有机碳各组分的含量、土壤微生物群落碳源利用率、微生物群落的丰富度和功能多样性,豆科牧草毛苕子和白三叶提高效应更加明显。     

不同施肥措施对德州市农田土壤生物学性状的影响

[目的]探讨不同施肥措施对山东省德州市农田土壤生物学性状的作用效果,为农田土壤的培肥与农作物的合理种植提供理论依据。[方法]通过连续3a的大田试验,研究CK(对照,不施肥)、CF(尿素提供100%的氮)、CM(牛粪提供100%的氮)和CM+CF(牛粪和尿素各提供50%的氮)等处理对德州市农田土壤养分、微生物数量、微生物多样性、活性有机碳及碳库管理指数的影响。[结果]与CF处理相比,CM+CF处理显著提高了农田土壤碱解氮、速效磷、速效钾含量和部分微量元素的有效性,降低了pH值;明显增加了土壤微生物数量与微生物量碳、氮含量,其中细菌数分别较CK,CF和CM处理显著增加91.22%,65.47%和17.11%;同时,CM+CF处理的微生物多样性指数最高,并与微生物总量的变化趋势一致,而CF与CK处理的微生物多样性指数与微生物总量的变化趋势不一致。此外,CM+CF处理的低活性有机碳含量和碳库管理指数亦显著高于其他处理,其中碳库管理指数比CK,CF和CM处理高出69.52,67.84,38.61。与CM+CF处理相比,CM处理对农田土壤的影响效果较小。[结论]牛粪与化肥配施能显著改善德州市农田土壤的生物学性状,有利于提升土壤肥力和增强供肥性。     

土壤微生物多样性研究方法的进展

对土壤微生物的4类研究方法即:传统微生物培养法、微生物标记物法、BIOLOGGN微平板法和微生物分子生物技术方法及其应用特点进行了简要的评述和分析,旨在通过比较寻求能够揭示土壤微生物群落结构的最佳方法。分子生物技术方法与传统研究方法等相结合将是大力推动土壤微生物研究的有效方式。     

Pesticide effects on bacterial diversity in agricultural soils – a review

According to guidelines for the approval of pesticides, side-effects on soil microorganisms should be determined by studying functional parameters such as carbon or nitrogen mineralisation. However, the microbial diversity may have been markedly changed following pesticide use despite unaltered metabolism, and such changes may affect soil fertility. This review evaluates new methods for measuring pesticide effects on bacterial diversity, and discusses how sampling should take temporal and spatial heterogeneity into account. Future research on pesticide approval protocols should establish the relationships between mineralisation assays and new and rapid bacterial diversity profiling methods, and should include the possible ecological implications of altered bacterial diversity for soil fertility.