Research in the area of soil ecology focuses on biodiversity and ecological functions of soil organisms,as well as the interactions of soil organisms with the environment.Here we summarize the main research directions and contents in soil ecology,introduce concurrent hot topics and research progress,and discuss research prospects.The research of soil ecology may help recognition and utilization of soil biological resources and provide scientific theories and technological support to cope with environmental changes,restore degraded ecosystems,and develop sustainable agriculture.

Being a typical negative plant-soil feedback effect,soil sickness severely constrains the sustainable development of agriculture.This article reviews the brief history and main mechanism of plant-soil feedback and the relationship between plantsoil feedback and agricultural production.We propose that more efforts should be made to elucidate the mechanism for plant diversity to enhance crop health and increse yield by referring to the mechanisms of plant-soil feedback in natural ecosystems.Moreover,positive feedback in agricultural fields can be promoted by designing diversified cropping systems and enhancing the functioning of rhizosphere microbiota,so as to enhance crop health,alleviate soil sickness and promote sustainable agriculture.

Fencing is a major measure for restoration of degraded grassland and has been widely adopted all over the word.However,with the increase of fencing duration the adverse effects of fencing have become increasingly prominent.Soil microorganism is a key parameter for evaluating soil quality.The present paper summarizes the effects of fencing on soil physicochemical properties,bacteria,fungi and functional microorganism groups.Two key questions are addressed,namely responses of soil properties and microbial community to the fencing activity,and how to use indicators to evaluate the effect of soil restoration and propose a reasonable fencing duration for sustainable improvment and restoration of ecological functions of degraded grasslands.

Precision manipulation of soil food web is a critical point for exploring and enhancing the ecological functions of soil biota.In this study,we outline the current approaches to soil food web manipulation,discuss the present status and challenges of studies on the ecological functions of soil food web.The direct manipulation methods are limited in field application.Alternatively,soil food web could be indirectly manipulated but the manipulation consequences are likely not consistent due to the complexity of interactions.The figure of soil food web is still vague;the key stone taxa of soil food web and their contribution weights are difficult to be recognized;and finally the material cycling and energy flow in soil food web are not fully quantified.We suggest to explore the solutions from four dimensions:1) developing field technique systems for monitoring both soil food web and related ecological processes;2) developing simple and practicable techniques for field manipulation of soil food web;3) focusing on the soil food web-sphere;4) performing soil food web-related integrated studies of multiple scales,multiple factors and multiple processes.

Soil is a heterogeneous habitat and serves as the major reservoir and sink of antibiotic resistance.In this review,we summarize the sources and driving factors in shaping soil resistome,and the mechanisms underlying the transfer of antibiotic resistance genes (ARGs) amongst soil bacteria.We also present current knowledge on dissemination of ARG among soil,water,plant and soil fauna,and propose the future perspectives in this filed.This review will help illustrate mechanisms underpinning the dissemination of ARGs in soil.

Viruses are the most abundant biological entities on the planet and have important roles in microbial community composition,host evolution and nutrient biogeochemical cycles.Firstly,this article summarizes the research history and development status of environmental viruses and reveals the development process of virus ecology,with focuses on comparative approaches to study soil viral ecology including phenotype,gene diversity,metagenomic,bioinformatics analysis,etc.Then based on these approaches,soil viruses diversity is expounded and the ecological function of soil viruses is further explored.Finally,the application and development prospects of environmental phages (phage therapy) are reviewed and prospected.

Arbuscular mycorrhizal (AM) fungi are ubiquitous soil fungi in natural and agricultural ecosystems and can form symbiotic associations with most crops.AM symbiosis can assist plant uptake of mineral nutrients,enhance plant tolerance to various environmental stresses,and improve crop production and product quality.In this review,we overview the potential role and application of AM fungi in agricultural production,and summarize the influences of cropping system and field management on AM functions.Challenges and opportunities for future research to develop AM fungal technology are also briefly discussed.Comprehensive investigation on multifunction of AM fungi and optimization of their application scenarios will promote the development and wide practice of mycorrhizal technology,which will further support the development of sustainable agriculture and construction of ecological civilization in China.

The rapid development of omics technology represented by metagenomics technology has greatly promoted our understanding of microbial diversity,composition,structure,and function in the natural ecosystem.However,the big data generated by the technology can be a great challenge to researchers'data analyzing and mining abilities.This review,based on two technical aspects,amplicon and whole-genome shotgun sequencing,summarizes the analysis workflow of metagenomics for discovering microbial community.Then,the concepts of microbial community diversity,the related principles of statistical analysis,and related interpretation of statistical tests are illustrated.Finally,the paper points out that to overcome the complexity of metagenomic data and huge amount information,using big data analysis so as to illuminate analytical results are the common challenge for environmental microbiologists,bioinformaticians,and statisticians.

Microbial biogeography mainly focuses on the distribution patterns of microorganisms and their driving mechanisms,and currently classical frequency mathematical and statistical methods are widely used in this field.In recent years,Bayesian inference has been continuously applied as an important random simulation mathematical statistics method for soil microbial biogeographical study.In this paper,we briefly introduce the differences between Bayesian inference and classical frequency mathematical statistics,and highlight the basic analytical process of Bayesian inference in soil microbial biogeographical study in terms of model construction,model fitting,and model improvement.We also evaluate the advantages,application potentials and development directions of Bayesian inference in this field and demonstrate the Bayesian inference process using simulated data with island biogeography theory as the research framework.Finally,we give an outlook on the application prospects of Bayesian inference in soil microbial biogeography.We believe that Bayesian inference will become one of the important tools for studying complex data and conducting model simulations in soil microbial biogeography.

At a large scale (China),climatic factors such as monsoon and precipitation probably provide significant contributions to spatial distribution of mercury (Hg) and selenium (Se) in soil considering their volatile properties.However,it is still unclear which factors influence Hg and Se accumulations in surface soil and what their contribution rates are.This study mainly analyzes the contributions of dry and wet depositions and volatilization to accumulations of Hg and Se in surface soil,and argues that the accumulation of Hg and Se in surface soil is a dynamic process.At a national scale,the contribution rates of wet deposition to surface soil Se and Hg are 91.5% and 49.4%,respectively.The contribution of normalized difference vegetation index (NDVI) to soil Hg is 23.4%.Since mercury and selenium exist in different ways in the atmosphere,Hg is dominated by insoluble Hg⁰,while Se is dominated by soluble methylated Se.The contributions of dry and wet depositions to Hg and Se are significantly different.This study systematically presents the climatic factors affecting the distributions of Hg and Se in surface soil,and has important guiding significance for comprehensive understanding of the biogeochemical cycles of Hg and Se.

Improper application of nitrogen fertilizers may lead to excessive emissions of soil nitrogen gases (N_r,including N₂O,HONO,NOx,NH₃,etc.),which may seriously threaten the ecological environment and human health.Emission of N_r from soil involves a variety of biotic and abiotic processes,which have complex mutual interactions.Soil physical and chemical properties,fertilization factors,climate,etc.will all affect the production and emission of soil N_r to a certain extent.This paper summarizes the current research status of soil N_r emission processes,regulatory factors,and soil N_r emission flux estimation.We further argue that future research should adopt a variety of methods,such as the combination of macro and micro studies,multi-disciplinary cross studies,combination of GIS technology and mechanic modelling,metagenomics sequencing,remote sensing observation and other techniques,and so on.More work should focus on in-depth exploration of key mechanisms,driving factors and spatial patterns of soil N_r emissions,as well as the response of soil N_r emissions to global change and carbon neutrality,and improving estimation models of soil N_r emission.This review provides a scientific basis and guidance for effectively controlling and reducing atmospheric N_r pollution,improving air quality and optimizing nitrogen fertilizer utilization.