山地土壤微生物分布格局研究进展

土壤微生物在调控生物地球化学循环和维持生态系统功能方面起着重要作用。研究土壤微生物多样性分布格局具有重要生态学意义。本文概述了山地土壤微生物多样性分布格局的研究进展,讨论了土壤微生物多样性与影响因素的关系,并对以后的研究提出了展望。     

土壤线虫作为生态指示生物的研究进展

土壤线虫广布于各种类型的土壤中, 在维持土壤生态系统的稳定性、促进物质循环和能量流动等方面发挥着重要的作用, 同时也是理想的环境指示生物。简述了土壤线虫的生活史策略和营养类群的多样性、土壤线虫多样性的生态指数、影响土壤线虫群落多样性的环境因素, 以及线虫作为指示生物在农业生态系统、草地生态系统、森林生态系统的功能作用。提出了全球气候变化背景下对青藏高原高寒草地土壤线虫分类、群落结构特征以及土壤线虫的生物指示作用研究的必要性, 并对土壤线虫未来的发展趋势做了展望。     

土壤微生物多样性影响因素及研究方法的现状与展望

土壤微生物是土壤生态系统的重要组成部分, 在土壤有机物质分解和养分释放、能量转移等生物地化循环中起着重要作用。随着人们对生物多样性重要性认识的不断深入及研究方法的不断改进, 土壤微生物多样性, 尤其是功能多样性的研究工作逐渐受到生态学家的重视。本文从土壤微生物多样性的影响因素以及研究方法等方面阐述了目前国内外土壤微生物多样性的研究现状, 并对其未来研究方向进行了展望。     

环境DNA技术在地下生态学中的应用

地下生态过程是生态系统结构、功能和过程研究中最不确定的因素。由于技术和方法的限制,作为"黑箱"的地下生态系统已经成为限制生态学发展的瓶颈,也是未来生态学发展的主要方向。环境DNA技术,是指从土壤等环境样品中直接提取DNA片段,然后通过DNA测序技术来定性或定量化目标生物,以确定目标生物在生态系统中的分布及功能特征。环境DNA技术已成功用于地下生态过程的研究。目前,环境DNA技术在土壤微生物多样性及其功能方面的研究相对成熟,克服了土壤微生物研究中不能培养的问题,可以有效地分析土壤微生物的群落组成、多样性及空间分布,尤其是宏基因组学技术的发展,使得微生物生态功能方面的研究成为可能;而且,环境DNA技术已经在土壤动物生态学的研究中得到了初步应用,可快速分析土壤动物的多样性及其分布特征,更有效地鉴定出未知的或稀少的物种,鉴定土壤动物类群的幅度较宽;部分研究者通过提取分析土壤中DNA片段信息对生态系统植物多样性及植物分类进行了研究,其结果比传统的植物分类及物种多样性测定更精确,改变了以往对植物群落物种多样性模式的理解。同时,环境DNA技术克服传统根系研究方法中需要洗根、分根、只能测定单物种根系的局限,降低根系研究中细根区分的误差,并探索性地用于细根生物量的研究。主要综述了基于环境DNA技术的分子生物学方法在土壤微生物多样性及功能、土壤动物多样性、地下植物多样性及根系生态等地下生态过程研究中的应用进展。环境DNA技术对于以土壤微生物、土壤动物及地下植物根系为主体的地下生态学过程的研究具有革命性意义,并展现出良好的应用前景。可以预期,分子生物学技术与传统的生态学研究相结合将成为未来地下生态学研究的一个发展趋势。     

大数据时代土壤微生物地理学研究综述

土壤蕴含极为丰富的微生物多样性,它们在物质分解、元素生物地球化学循环、植物生产力和生物健康中扮演着关键角色。理解土壤微生物的生物地理分布格局、形成机制与群落构建规则,有助于预测在全球变化背景下土壤微生物组的功能演变及其对陆地生态系统的调控影响。自21世纪以来,土壤微生物生物地理学在各种大型国际微生物计划的推动下逐步形成了分子生物学技术耦合大数据分析的模式,实现了多种尺度上的关联研究。阐述了土壤微生物在分布格局和群落构建规则方面的研究进展,重点介绍了分子生物学技术和大数据分析在土壤微生物生物地理研究中的应用,对土壤微生物生物地理学未来在微生物分类分辨率、模型验证与构建和功能基因地理学的发展方向进行了展望。     

青藏高原高寒草地地下生物多样性: 进展、问题与展望

栖息于土壤中的微生物和微型动物种类繁多、数量巨大, 在对地上生物多样性的调控和在生态系统功能与服务的维系中, 具有举足轻重的作用。虽然对土壤微生物以及土壤动物已经开展了广泛的调查, 但是整体上对于地下生物多样性的分布格局、驱动机制及其对全球变化的响应与适应过程, 仍缺乏深刻的认识。青藏高原是全球变化的敏感区域, 其中高寒草地是高原最主要的植被类型, 占高原面积的60%左右, 在高寒生态系统生物多样性维持中具有重要意义。近年来, 已有大量研究关注于高寒草地地下生物多样性, 但是缺乏系统的总结与论述。基于此, 本文从细菌、真菌、古菌、线虫、节肢动物五大土壤生物类群出发, 阐述了青藏高原高寒草地的地下物种丰富度、分布格局及其影响因素, 重点探讨了它们对气候变化和人类活动的响应, 并就未来高寒草地地下生物多样性亟需关注的关键问题进行了展望, 包括: (1)地下各个生物类群的分布格局、各类群之间的联系及驱动机制; (2)地上与地下生物多样性耦联的机制; (3)地下生物多样性对生态系统功能和健康的影响; (4)地下生物多样性的调控实验研究。     

河岸带生态系统植被与土壤对水文变化的响应研究进展

河岸带的植被与土壤是生态系统重要组成部分,对于维持河岸带的生态健康、生态系统服务与可持续性具有至关重要的作用。水文变化是河岸带生态系统的首要干扰因子,系统总结了水文变化对河岸带植被的特征以及植被形态、群落分布、繁殖、生存策略的影响,并阐述了河岸带水文和植被对土壤氮磷迁移转化的影响机制。根系作为土壤与植物地上部分之间物质、能量流动与信号传导的关键纽带,目前对根系的研究还较欠缺,需要加强水文变化对河岸带湿地植物根系形态、结构、功能特征的影响机理研究,以及湿地植物对水文变化的适应机制和耐受阈值方面的探究。在微观方面,应加强水文变化与植被等多因素耦合对土壤氮磷迁移转化过程的机理研究。河流形态和土壤的多样性决定着河岸带水文作用特征的复杂性,今后需注重河岸带个性特征与水文响应的关系研究。河岸带是横向的水陆生态过渡带和河流上下游的纵向生态廊道,亟需综合考虑和模拟流域土壤、植被与水文、人类活动之间的耦合关系,预测未来气候与社会经济情境下的河岸带生态系统演变规律,为河岸带生态系统的生态调节、生物多样性保护与生态恢复等提供理论依据与技术支撑。     

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。     

生物多样性与森林生态系统健康的几个关键问题

生物多样性和生态系统健康问的关系,是生态学领域的一个重大科学问题,近年来已成为关注的热点.首先,生物多样性在复杂的时空尺度上维持着生态系统过程的运行,是生态系统功能得以维持的生物基础;其次,生物多样性是生态系统抗干扰能力、恢复能力及适应环境变化能力的物质基础.生态系统健康的维持取决于系统的生物多样性、可再生能力和生产力,维护生物多样性是生态系统管理计划中不可缺少的部分;第三,对生态系统健康程度的评价,很大程度上依赖于对生态过程的认识,而生物多样性及其生态系统功能又是认识和了解生态过程的基础.本文通过对森林生态系统异质性、种间关系及关键种、外来物种入侵、"绿色沙漠"等问题的论述,阐述了生物多样性与森林生态系统健康之间的关系,提出了我国所面临的问题和相应的对策.     

土壤微生物生物地理学研究进展

生物地理学是研究生物（包括种群、群落等不同层次）地理分布格局及成因的一门交叉学科。微生物生物地理学的研究长期滞后于宏生物地理学。鉴于土壤微生物在调控生物地球化学过程和维持生态系统功能方面的重要作用,对其空间分布格局及形成机制的认识具有十分重要的理论和实际意义。随着分子生物学技术的发展,对微生物多样性的认知日益深入。越来越多的证据表明,土壤微生物群落结构和多样性具有一定的时空分布格局,从而对微生物全球性随机分布的传统观点提出了挑战。对当前土壤微生物生物地理学研究中的一些概念性问题,如微生物物种的定义、微生物多样性的定量测度、对微生物全球性随机分布的争论等,进行了系统评述;以微生物种-面积关系和距离-衰减关系为例对当前最新的土壤微生物生物地理学研究成果进行总结,并初步探讨了土壤微生物群落的地带性分布问题;在传统生物地理学理论的指导下,提出了一个可用于验证土壤微生物空间分布格局形成和机制维持的简单研究框架。这些对今后土壤微生物生物地理学的研究有一定借鉴和指导意义。     

Fertilization alters protistan consumers and parasites in crop-associated microbiomes

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant–soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.     

Coupling between taxonomic and functional diversity in protistan coastal communities

The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the operational taxonomic units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade-offs) in order to build the best functional groups. Based on the annotated OTUs and our functional groups, we demonstrated that the functional diversity of marine protist communities varied in parallel with their taxonomic diversity. The coupling between functional and taxonomic diversity was conserved across different protist size classes. However, the smallest size-fraction was characterized by wider taxonomic and functional groups diversity, corroborating the idea that nanoplankton and picoplankton are part of a more stable ecological background on which larger protists and metazoans might develop.     

Movement of protistan trophic groups in soil–plant continuums

Protists, functionally divided into consumers, phototrophs, and parasites act as integral components and vital regulators of microbiomes in soil–plant continuums. However, the drivers of community structure, assembly mechanisms, co-occurrence patterns, and the associations with human pathogens and different protistan trophic groups remain unknown. Here, we characterized the phyllosphere and soil protistan communities associated with three vegetables under different fertilization treatments (none and organic fertilization) at five growth stages. In this study, consumers were the most diverse soil protist group, had the role of inter-kingdom connector, and were the primary biomarker for rhizosphere soils which were subjected to decreasing deterministic processes during plant growth. In contrast, phototrophs had the greatest niche breadth and formed soil protistan hubs, and were the primary biomarkers for both bulk soils and the phyllosphere. Parasites had minimal input to microbial co-occurrence networks. Organic fertilization increased the relative abundance (RA) of pathogenic protists and the number of pathogen–consumer connections in rhizosphere soils but decreased protistan richness and the number of internal protistan links. This study advances our understanding of the ecological roles and potential links between human pathogens and protistan trophic groups associated with soil–plant continuums, which is fundamental to the regulation of soil–plant microbiomes and maintenance of environmental and human health.     

植物化感物质及化感潜力与土壤养分的相互影响

植物化感作用与许多生态因子有关.土壤养分缺乏,影响着许多植物化感物质的产生,从而影响植物的化感潜力;反过来,植物化感物质也通过络合、吸附、酸溶解、竞争、抑制等方式影响土壤的养分形态和水平.本文总结了植物化感物质及化感潜力与土壤养分的相互影响,并提出了今后该领域值得进一步研究的问题.包括以下几方面：加强植物化感研究与土壤 植物营养学研究的结合,以更深入地阐明植物化感物质、化感作用与土壤养分变化的关系;加强植物化感研究与生态系统养分循环研究的结合,以类似自然（nature-like）的方式模拟自然界植物所受的养分干,使养分干扰的化感研究结果更加逼真、可靠;加强对养分过量及受污染时植物化感作用的研究,为揭示农业和林业生产中植物的相互作用机制和生物量变化机制提供新的思路,为生态保护提供科学依据.     

Characterization of protistan assemblages in the Ross Sea, Antarctica, by denaturing gradient gel electrophoresis

The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.     

Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis

The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.     

Impact of protists on the activity and structure of the bacterial community in a rice field soil

Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a gamma-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G + C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO4(2-) was higher without protists, indicating that nitrogen mineralization and SO4(2-) reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major control, and O2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.     

Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem

The soils of the McMurdo Dry Valleys (MDV) of Antarctica are established models for understanding fundamental processes in soil ecosystem functioning (e.g. ecological tipping points, community structuring and nutrient cycling) because the extreme physical environment drastically reduces biodiversity and ecological complexity. Understanding the functioning of MDV soils requires in-depth knowledge of the diversity of MDV soil species. Protists, which contribute significantly to soil ecosystem functioning worldwide, remain poorly characterized in the MDV. To better assess the diversity of MDV protists, we performed shotgun metagenomics on 18 sites representing a variety of landscape features and edaphic variables. Our results show MDV soil protists are diverse at both the genus (155 of 281 eukaryote genera) and family (120) levels, but comprise only 6% of eukaryotic reads. Protists are structured by moisture, total N and distance from the local coast and possess limited richness in arid (< 5% moisture) and at high elevation sites, known drivers of communities in the MDV. High relative diversity and broad distribution of protists in our study promotes these organisms as key members of MDV soil microbiomes and the MDV as a useful system for understanding the contribution of soil protists to the structure of soil microbiomes.     

Global biogeography of highly diverse protistan communities in soil

Protists are ubiquitous members of soil microbial communities, but the structure of these communities, and the factors that influence their diversity, are poorly understood. We used barcoded pyrosequencing to survey comprehensively the diversity of soil protists from 40 sites across a broad geographic range that represent a variety of biome types, from tropical forests to deserts. In addition to taxa known to be dominant in soil, including Cercozoa and Ciliophora, we found high relative abundances of groups such as Apicomplexa and Dinophyceae that have not previously been recognized as being important components of soil microbial communities. Soil protistan communities were highly diverse, approaching the extreme diversity of their bacterial counterparts across the same sites. Like bacterial taxa, protistan taxa were not globally distributed, and the composition of these communities diverged considerably across large geographic distances. However, soil protistan and bacterial communities exhibit very different global-scale biogeographical patterns, with protistan communities strongly structured by climatic conditions that regulate annual soil moisture availability.     

Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment

Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.Subject terms: Microbial ecology, Microbial ecology, Biogeochemistry