O）代谢

土壤生物是重要的基因库,土壤生物多样性是全球生物多样性的重要组成部分。土壤生物是C、N地球化学过程（土壤库）的驱动者,调控微量气体代谢。在微量气体代谢中,土壤微生物具有直接的作用。真菌、CH₄生成菌、CH₄氧化菌、硝化菌以及反硝化菌等是调控微量气体代谢的关键生态功能类群。由于相对大的体积和强大的酶化学分解作用,真菌通常主导枯枝落叶的分解活动。“通气—厌气”界面是微生物群落的活跃区域,易发生微量气体代谢。“有机—无机”过渡层、水生植物根际区、土壤动物肠道系统是典型的微量气体代谢界面。土壤动物对微量气体代谢的作用通常为前期的和间接的,并且又是重要的。节肢动物（白蚁）和环节动物（蚯蚓）是分别代谢CH₄和N₂O的两个关键性生态功能类群。在研究土壤生物多样性及其对微量气体代谢的作用方面,由于土壤生态系统的复杂性,需综合传统微生物实验技术与现代同位素技术和分子生物学技术。我国缺乏研究土壤生物多样性及其对微量气体代谢影响的实质性工作,有必要开展这方面的研究。     

释放后的转抗病虫基因作物对土壤生物群落的影响

土壤生物,尤其是土壤微生物多样性与活性的保持是农业生态系统健康稳定的基础,农业活动尤其是农作物植被类型的改变对土壤生物的群落结构和活性具有显著的影响。释放后的转基因作物作为生态系统的一种新的生物组分,被引入农田生态系统之间后所引发的农田生物群落（包括土壤微生物群落）的变化及其对农业生态系统的健康与稳定产生的影响,已成为研究热点,本文对转抗虫Bt基因作物、转T4-溶菌酶基因作物,转蛋白酶抑制剂I基因作物的基因产物、作物残体在土壤中的行为（如降解产物的存留形态与生物活性）及其对根际或残体周围土壤中各类生物,尤其是微生物群落结构与功能的影响进行了简要综合评述,指出基因表达产物的后效肯定是存在的且长远的,由其引发的土壤生物群落结构的变化是复杂的,因而有必要对不同类型的转基因作物释放后的生态效应做长期的跟踪研究,建议未来的研究工作应集中在以下3个方面：（1）不同的转基因表达产物在环境中的迁移、结构变化、消长动态及其对生物保持毒杀性的时间;（2）不同类型转基因的植物对土壤生物群落结构的影响趋势;（3）在实验条件下,研究分离纯化的各种转基因表达产物对土壤各生物功能类群的影响。     

城市土壤微生物多样性研究进展

城市化对生物多样性的影响是当前生态学研究的热点之一, 引起了人们的广泛关注。土壤微生物多样性是城市生物多样性的重要组成部分, 对维持城市生态系统的健康稳定具有重要意义和作用。近年来, 已有研究关注城市土壤微生物群落结构及多样性, 回答了一些关键问题, 但缺乏系统的总结与论述。基于此, 本文分析了城市化对土壤微生物特性、群落组成、功能和多样性的影响, 总结了影响城市土壤微生物多样性的主要因素, 发现城市化改变了土壤微生物组成和功能, 并且对细菌和真菌多样性的影响存在差异, 城市环境因子通过直接和间接作用共同影响土壤微生物多样性。进一步探讨了城市土壤微生物多样性的维持与保护, 并对今后城市土壤微生物研究需要关注的问题进行了展望, 包括: (1)城市化对城市绿地土壤微生物多样性的影响机制; (2)城市土壤微生物多样性变化对生态系统多功能性的影响; (3)土壤微生物多样性与人类健康的关系。以期为城市土壤生物多样性保护研究提供参考。     

分子生物学方法在微生物多样性研究中的应用

微生物多样性是生物多样性的重要组成部分。由于微生物和大生物（动、植物）相比,存在着多种显著差异,因此其多样性,保护及利用也有所不同,尤其是研究方法亟待完善,提高。近年来,分子生物学方法广泛用于微生物多样性的研究并取得了一系列研究成果。本文从四个方面加以介绍：１）微生物总ＤＮＡ制备及其遗传多样性检测方法;２）１６ＳｒＲＮＡ基因序列研究;３）核酸杂交分析技术;４）ＤＮＡ动力学的研究。今后的发展趋势是加     

土壤生物多样性对植物利用营养物质和水分的影响

土壤生物多样性影响土壤营养物质和水等自然资源的有效利用是农业生态系统的重要功能.有证据表明土壤微生物多样性可提高土壤营养物质和水的利用率.土壤动物对土壤营养物质和水的有效利用也产生了明显的影响,它主要是通过促进营养物质的转化和改善土壤水渗透率而间接实现的.从已有文献的报道来看,单从某一个方面来研究土壤生物多样性对土壤营养物质和水的有效利用的影响并不能全面地反应它们之间相互作用的规律.因此未来的研究应当把土壤生物多样性、土壤营养物质和水的供给与植物生物多样性、植物营养物质和水的利用率结合起来,这样才有可能从理论上对土壤生物多样性与营养物质和水的利用之间的关系有更加深刻的认识并运用到实践中.     

植物-土壤反馈与草地群落演替:菌根真菌和土壤病原菌的调控作用

由植物引起的根际土壤生物或非生物环境的改变能够反馈影响群落中不同植物的生长,直接改变共存植物的相对竞争关系,推动群落结构的动态变化。作为土壤生物群落的重要组成部分,土壤微生物在植物-土壤反馈关系中起到重要的调控作用,对解释植物群落的演替进程和方向有着重要的意义。在草地植物群落演替的早期阶段和外来物种入侵的过程中,宿主植物对丛枝菌根真菌（AMF）的依赖性较低,受本地病原菌的影响较小,一般不存在负反馈。在演替后期,植物对AMF更具依赖性,而积累的病原菌则产生较强的负反馈效应,从而促进群落物种共存和植物多样性,提高草地生产力和稳定性。研究微生物-植物反馈机制不仅有助于完善草地退化与恢复理论,还对退化草地恢复治理的实践有着指导意义。未来关于根际微生物-植物反馈在草地群落演替中的作用应该加强以下几方面的研究：（1）在实验方法上,开展专性微生物-植物反馈研究;（2）在测定指标上,进一步量化不同微生物在反馈关系中的功能差异;（3）在研究对象上,加强土壤微生物在植物群落水平的反馈研究;（4）在应用上,明晰植物-土壤反馈在退化草地恢复过程中的作用,指导草地管理实践。     

土壤生物工程在河道坡岸生态修复中应用与效果

土壤生物工程是一项采用存活植物构筑边坡结构,稳定河道（流）坡岸和生态修复的工程技术.本文简要讨论了土壤生物工程的原理和活枝扦插、柴笼、灌丛垫以及复合工程等基本种植技术;介绍了我国第一个采用土壤生物工程修复河道坡岸的示范工程,对比了工程实施后河道坡岸10个月来的坡岸土壤剪切力、生境条件和生物多样性变化.研究和示范工程表明,采用土壤生物工程方法可以稳定坡岸、改善坡岸的栖息地质量、修复河道的生态环境.土壤生物工程方法可以在我国各类岸（边）坡的生态修复中广泛运用.     

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。     

氮沉降对森林生物多样性的影响

从3个方面论述了氮沉降对森林生物多样性影响：（1）森林植物多样性,包括乔木层植物、林下层植物和隐花植物;（2）土壤微生物多样性,主要是细菌和真菌;（3）森林动物多样性：主要包括地下土壤动物和地上草食动物。综合来看,氮沉降改变了物种组成,过量氮沉降降低了生物多样性。同时,也对氮沉降影响生物多样性的机理进行了分析。最后,还探讨了当前在氮沉降对森林生物多样性影响的研究方面存在的问题以及今后研究的方向。     

土壤生物多样性与微量气体(CO2、CH4、N2O)代谢

土壤生物是重要的基因库 ,土壤生物多样性是全球生物多样性的重要组成部分。土壤生物是C、N地球化学过程 (土壤库 )的驱动者 ,调控微量气体代谢。在微量气体代谢中 ,土壤微生物具有直接的作用。真菌、CH4 生成菌、CH4 氧化菌、硝化菌以及反硝化菌等是调控微量气体代谢的关键生态功能类群。由于相对大的体积和强大的酶化学分解作用 ,真菌通常主导枯枝落叶的分解活动。“通气—厌气”界面是微生物群落的活跃区域 ,易发生微量气体代谢。“有机—无机”过渡层、水生植物根际区、土壤动物肠道系统是典型的微量气体代谢界面。土壤动物对微量气体代谢的作用通常为前期的和间接的 ,并且又是重要的。节肢动物 (白蚁 )和环节动物 (蚯蚓 )是分别代谢CH4 和N2 O的两个关键性生态功能类群。在研究土壤生物多样性及其对微量气体代谢的作用方面 ,由于土壤生态系统的复杂性 ,需综合传统微生物实验技术与现代同位素技术和分子生物学技术。我国缺乏研究土壤生物多样性及其对微量气体代谢影响的实质性工作 ,有必要开展这方面的研究。     

Buried treasure: soil biodiversity and conservation

Soils are incredibly biodiverse habitats, yet soil-dwelling organisms have received little attention within the field of conservation biology. Due to difficulties involved in studying soil biota, and to taxonomic biases in conservation research, the full extent of soil biodiversity is not well understood, and soil-dwelling organisms are rarely candidates for conservation. The biogeography of soil biota differs significantly from that of plants or animals aboveground, and the taxonomic and functional diversity of soil-dwellers allows them to have a multitude of ecological effects on aboveground organisms. Soil organisms exhibit levels of biodiversity several orders of magnitude greater than those found in their aboveground counterparts on a per-area basis. The biodiversity of soils underpins many crucial ecosystem services which support the plants and animals typically targeted by conservation efforts. Strategies detailed in this paper provide practitioners with the ability to address many of the challenges related to incorporating soils and soil organisms into conservation planning.     

Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity–ecosystem function relationship

A technique based on progressive fumigation was used to reduce soil microbial biodiversity, and the effects of such reductions upon the stability of key soil processes were measured. Mineral soil samples from a grassland were fumigated with chloroform for up to 24 h and then incubated for 5 months to allow recolonisation by surviving organisms. The diversity of cultivable and non‐cultivable bacteria, protozoa and nematodes was progressively reduced by increasing fumigation times, as was the number of trophic groups, phyla within trophic groups, and taxa within phyla. Total microbial biomass was similar within fumigated soils, but lower than for unfumigated soil. There was no direct relationship between biodiversity and function. Some broad‐scale functional parameters increased as biodiversity decreased, e.g. thymidine incorporation, growth on added nutrients, and the decomposition rate of plant residues. Other more specific parameters decreased as biodiversity decreased, e.g. nitrification, denitrification and methane oxidation. Thus specific functional parameters may be a more sensitive indicator of environmental change than general parameters. Although fumigation reduced soil microbial biodiversity, there was evidence to suggest that it selected for organisms with particular physiological characteristics. The consequences of this for interpreting biodiversity – function relationships are discussed. The stability of the resulting communities to perturbation was further examined by imposing a transient (brief heating to 40°C) or a persistent (addition of CuSO₄) stress. Decomposition of grass residues was determined on three occasions after such perturbations. The soils clearly demonstrated resilience to the transient stress; decomposition rates were initially depressed by the stress and recovered over time. Resilience was reduced in the soils with decreasing biodiversity. Soils were not resilient to the persistent stress, there was no recovery in decomposition rate over time, but the soils with the highest biodiversity were more resistant to the stress than soils with impaired biodiversity. The study of functional stability under applied perturbation is a powerful means of examining the effects of biodiversity.     

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.     

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale‐dependent nature of soil biodiversity.     

Terra incognita of soil biodiversity: unseen invasions under our feet

Whilst cartographers of the 19th century endeavoured to chart the last unknown lands, the great challenge for biologists in the 21st century is to fill the gaps on the biodiversity map of the Earth. And one of the largest gaps concerns the biodiversity of soils, a terra incognita right under our feet. The study of soil biodiversity, and particularly the complex communities of small invertebrates, has suffered from a severe ‘taxonomic impediment’ (Decaëns 2010 ) leading to great uncertainties about total species richness, phylogenetic diversity, geographical structure, temporal dynamics of soil organisms, and consequently about their role on ecosystem function (Bardgett & van der Putten 2014 ). However, the revolution in high‐throughput sequencing is now revealing the hidden biodiversity of the soil with unprecedented detail (e.g. Arribas et al. 2016 ). In a noteworthy from the Cover article in this issue of Molecular Ecology, Cicconardi et al. ( 2017 ) apply these new tools to study soil communities of Collembola in three distant oceanic islands of volcanic origin, obtaining a striking result: only 38 of 70 species (54%) are exclusively found in a single island, with the remaining shared among islands or with other distant regions, suggesting a massive recent introduction of soil species, whose impact is entirely unknown.     

Locality or habitat? Exploring predictors of biodiversity in Amazonia

Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diversity patterns of most other organisms remain elusive, although some of them, for instance microorganisms, constitute the overwhelming majority of taxa in any given location, both in terms of diversity and abundance. Here, we use DNA metabarcoding to estimate prokaryote and eukaryote diversity in environmental soil and litter samples from 39 survey plots in a longitudinal transect across Brazilian Amazonia using 16S and 18S gene sequences, respectively. We characterize richness and community composition based on operational taxonomic units (OTUs) and test their correlation with longitude and habitat. We find that prokaryote and eukaryote OTU richness and community composition differ significantly among localities and habitats, and that prokaryotes are more strongly structured by locality and habitat type than eukaryotes. Our results 1) provide a first large‐scale mapping of Amazonian soil biodiversity, suggesting that OTU richness patterns might follow substantially different patterns from those observed for macro‐organisms; and 2) indicate that locality and habitat factors interact in determining OTU richness patterns and community composition. This study shows the potential of DNA metabarcoding in unveiling Amazonia's outstanding diversity, despite the lack of complete reference sequence databases for the organisms sequenced.     

Putting soil invertebrate diversity on the map

Ecologists have had a very good foundational knowledge of the global distribution of plants and aboveground animals for many decades. But despite the immense diversity of soil organisms, our knowledge of the global distribution, drivers and threats to soil biodiversity is very limited. In this issue of Molecular Ecology, Bastida et al. (2020) produce the first global maps of soil invertebrate diversity that have been sampled at 83 locations, across six continents, using standardised methods and DNA sequencing. Using data from nematodes, arachnids and rotifers, and structural equation models, they find that diversity of these taxa is primarily driven by vegetation and climate. Given the anthropogenic changes that are occurring, and are projected to continue, this study provides important baseline information for future soil biodiversity and function monitoring, as well as exciting working hypotheses for targeted experiments.     

Developing a set of simulation-based indicators to assess harmfulness and contribution to biodiversity of weed communities in cropping systems

Weeds are both harmful for agricultural production and an essential component of biodiversity in agricultural landscapes. Therefore, new cropping systems aiming at both maximising weed-related biodiversity and minimising weed harmfulness are needed. New cropping systems are now increasingly designed with weed dynamics models but these usually only consider weed densities or crop yield losses. The present paper proposed a set of indicators for assessing the impact on crop production and biodiversity of weed communities simulated with a cropping system model. Five harmfulness indicators were developed to take account of the criteria most frequently listed by farmers via an internet survey: (1) crop yield loss, (2) harvest pollution by weed seeds, stems and leaves, (3) harvesting problems due to green weed biomass blocking the combine, and (4) field infestation represented by weed biomass averaged over cropping seasons. A fifth indicator was added, i.e. (5) the increase in crop disease (i.e. take-all disease of cereals) in the presence of weeds. The biodiversity indicators were chosen in collaboration with ecologists. Two indicators reflect the weed contribution to vegetal biodiversity: (1) species richness and (2) Pielou's index for species equitability. Three other indicators were developed to assess weeds as a trophic resource for other organisms in the agro-ecosystems: (3) the number of weed seeds present on soil surface in autumn and winter to feed field birds, (4) lipid-rich seeds on soil surface in summer to feed insects such as carabids, and (5) weed flowers in spring and summer to feed domestic bees. These indicators were tested in a series of contrasted cropping systems identified in farm surveys and simulated with FlorSys. Analyses of variance showed that the cropping system and the crop sequence presented the highest impact on indicator values. Weather scenario and pedoclimate had little effect. Antagonisms and synergies between weed-related harmfulness and biodiversity were identified with Spearman correlations. Harmfulness indicators were all positively correlated, except for additional disease risk which was at best poorly correlated with other indicators. Most weed-related biodiversity indicators were also positively correlated, except species richness which was negatively correlated with species equitability, bird resource and insect resource. Weed harmfulness generally increased with increasing weed-related biodiversity. These correlations were though weak, and others were negative, showing that increased biodiversity could occur with decreased harmfulness (e.g. trophic resource for insects vs. yield loss or field infestation). Consequently, there are cropping systems that reconcile agricultural production and biodiversity.     

Contrasting diversity patterns of soil mites and nematodes in secondary succession

Soil biodiversity has been recognized as a key feature of ecosystem functioning and stability. However, soil biodiversity is strongly impaired by agriculture and relatively little is known on how and at what spatial and temporal scales soil biodiversity is restored after the human disturbances have come to an end. Here, a multi-scale approach was used to compare diversity patterns of soil mites and nematodes at four stages (early, mid, late, reference site) along a secondary succession chronosequence from abandoned arable land to heath land. In each field four soil samples were taken during four successive seasons. We determined soil diversity within samples (α-diversity), between samples (β-diversity) and within field sites (γ-diversity). The patterns of α- and γ-diversity developed similarly along the chronosequence for oribatid mites, but not for nematodes. Nematode α-diversity was highest in mid- and late-successional sites, while γ-diversity was constant along the chronosequence. Oribatid mite β-diversity was initially high, but decreased thereafter, whereas nematode β-diversity increased when succession proceeded; indicating that patterns of within-site heterogeneity diverged for oribatid mites and nematodes. The spatio-temporal diversity patterns after land abandonment suggest that oribatid mite community development depends predominantly on colonization of new taxa, whereas nematode community development depends on shifts in dominance patterns. This would imply that at old fields diversity patterns of oribatid mites are mainly controlled by dispersal, whereas diversity patterns of nematodes are mainly controlled by changing abiotic or biotic soil conditions. Our study shows that the restoration of soil biodiversity along secondary successional gradients can be both scale- and phylum-dependent.     

转基因植物对农业生物多样性的影响

论述了近年来转基因植物对农业生态系统生物多样性影响的研究进展．主要在遗传多样性、物种多样性和生态系统多样性3个层次上予以评述．包括转基因植物对作物遗传多样性的影响;转基因植物的外源基因向杂草和近缘野生种转移;转基因抗虫植物对目标害虫的影响。抗除草剂转基因植物对作物和杂草的影响,抗病毒转基因植物对病毒的影响;转基因植物对非目标生物的影响,对土壤生态系统的影响等．