Achievements and new knowledge unraveled by metagenomic approaches

Metagenomics has paved the way for cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. In recent years, significant progress has been made in this research area. A major breakthrough was the improvement and development of high-throughput next-generation sequencing technologies. The application of these technologies resulted in the generation of large datasets derived from various environments such as soil and ocean water. The analyses of these datasets opened a window into the enormous phylogenetic and metabolic diversity of microbial communities living in a variety of ecosystems. In this way, structure, functions, and interactions of microbial communities were elucidated. Metagenomics has proven to be a powerful tool for the recovery of novel biomolecules. In most cases, functional metagenomics comprising construction and screening of complex metagenomic DNA libraries has been applied to isolate new enzymes and drugs of industrial importance. For this purpose, several novel and improved screening strategies that allow efficient screening of large collections of clones harboring metagenomes have been introduced.     

土壤宏基因组学技术及其应用

传统的基于培养的研究方法只能反映土壤中少数(0.1%～10 %)微生物的信息,而大部分微生物目前还不能培养,因而这部分微生物资源尚难以被有效地开发利用.宏基因组学是分子生物学技术应用于环境微生物生态学研究而形成的一个新概念,主要技术包括土壤DNA的提取、文库的构建和目标基因克隆的筛选.它可为揭示微生物生态功能及其分子基础提供更全面的遗传信息,并已在微生物新功能基因筛选、活性物质开发和微生物多样性研究等方面取得了显著成果.本文对土壤宏基因组学技术的方法和应用作了详细介绍.     

Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development

The origins of the biological complexity and the factors that regulate the development of community composition, diversity and richness in soil remain largely unknown. To gain a better understanding of how bacterial communities change during soil ecosystem development, their composition and diversity in soils that developed over c. 77 000 years of intermittent aeolian deposition were studied. 16S rRNA gene clone libraries and fatty acid methyl ester (FAME) analyses were used to assess the diversity and composition of the communities. The bacterial community composition changed with soil age, and the overall diversity, richness and evenness of the communities increased as the soil habitat matured. When analysed using a multivariate Bray-Curtis ordination technique, the distribution of ribotypes showed an orderly pattern of bacterial community development that was clearly associated with soil and ecosystem development. Similarly, changes in the composition of the FAMEs across the chronosequence were associated with biomarkers for fungi, actinomycetes and Gram-positive bacteria. The development of the soil ecosystem promoted the development of distinctive microbial communities that were reminiscent of successional processes often evoked to describe change during the development of plant communities in terrestrial ecosystems.     

Proportion of mycorrhiza-associated trees mediates community assemblages of soil fungi but not of bacteria

Recent studies have shown that mycorrhizal trees can greatly influence soil microbial communities, which in turn play important roles in the function offorest ecosystems. However, there is lack of understanding how the composition of trees with different mycorrhizal types affects soil microbial communities. Here, we collected 1606 soil samples from a 25-ha subtropical forest plot to investigate how the proportion of arbuscular mycorrhizal (AM) versus ectomycorrhizal (EcM) trees mediated soil microbial assemblages. Results showed the alpha diversities of both soil fungal and bacterial communities were significantly positively correlated with the ratio of AM/EcM trees. The AM/EcM tree ratio was important to the fungal community assembly, whereas soil pH was key to the bacterial communities. The increase in the AM/EcM tree ratio decreased the importance of stochastic forces in assembling fungal communities, while it had no significant effect on the bacterial communities. The differential importance of the AM/EcM tree ratio to fungal and bacterial communities highlights the role of mycorrhiza-associated tree composition in regulating soil microbial communities. This finding suggests that forests with different AM/EcM tree ratios would have different soil microbial communities, potentially leading to differences in soil nutrient cycling and in return different tree diversity and forest productivity.     

Microbial diversity and function in soil: from genes to ecosystems

Soils sustain an immense diversity of microbes, which, to a large extent, remains unexplored. A range of novel methods, most of which are based on rRNA and rDNA analyses, have uncovered part of the soil microbial diversity. The next step in the era of microbial ecology is to extract genomic, evolutionary and functional information from bacterial artificial chromosome libraries of the soil community genomes (the metagenome). Sophisticated analyses that apply molecular phylogenetics, DNA microarrays, functional genomics and in situ activity measurements will provide huge amounts of new data, potentially increasing our understanding of the structure and function of soil microbial ecosystems, and the interactions that occur within them. This review summarizes the recent progress in studies of soil microbial communities with focus on novel methods and approaches that provide new insight into the relationship between phylogenetic and functional diversity.     

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.Subject terms: Metagenomics, Climate-change ecology, Microbial ecology, Biogeochemistry, Soil microbiology     

The effect of fire on microbial biomass: a meta-analysis of field studies

Soil microbes regulate the transfer of carbon (C) from ecosystems to the atmosphere and in doing so influence feedbacks between terrestrial ecosystems and global climate change. Fire is one element of global change that may influence soil microbial communities and, in turn, their contribution to the C dynamics of ecosystems. In order to improve our understanding of how fire influences belowground communities, we conducted a meta-analysis of 42 published microbial responses to fire. We hypothesized that microbial biomass as a whole, and fungal biomass specifically, would be altered following fires. Across all studies, fire reduced microbial abundance by an average of 33.2% and fungal abundance by an average of 47.6%. However, microbial responses to fire differed significantly among biomes and fire types. For example, microbial biomass declined following fires in boreal and temperate forests but not following grasslands fires. In addition, wildfires lead to a greater reduction in microbial biomass than prescribed burns. These differences are likely attributable to differences in fire severity among biomes and fire types. Changes in microbial abundance were significantly correlated with changes in soil CO₂ emissions. Altogether, these results suggest that fires may significantly decrease microbial abundance, with corresponding consequences for soil CO₂ emissions.     

Microbial community composition in soils of Northern Victoria Land, Antarctica

Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme systems are highly diverse with patchy distributions. Investigating the physical and biological controls over the distribution and activity of microbial biodiversity in Victoria Land is essential to understanding ecological functioning in this region. Currently, little information on the distribution, structure and activity of soil communities anywhere in Victoria Land are available, and their sensitivity to potential climate change remains largely unknown. We investigated soil microbial communities from low- and high-productivity habitats in an isolated Antarctic location to determine how the soil environment impacts microbial community composition and structure. The microbial communities in Luther Vale, Northern Victoria Land were analysed using bacterial 16S rRNA gene clone libraries and were related to soil geochemical parameters and classical morphological analysis of soil metazoan invertebrate communities. A total of 323 16S rRNA gene sequences analysed from four soils spanning a productivity gradient indicated a high diversity (Shannon-Weaver values > 3) of phylotypes within the clone libraries and distinct differences in community structure between the two soil productivity habitats linked to water and nutrient availability. In particular, members of the Deinococcus/Thermus lineage were found exclusively in the drier, low-productivity soils, while Gammaproteobacteria of the genus Xanthomonas were found exclusively in high-productivity soils. However, rarefaction curves indicated that these microbial habitats remain under-sampled. Our results add to the recent literature suggesting that there is a higher biodiversity within Antarctic soils than previously expected.     

岷江干旱河谷优势灌丛对土壤微生物群落组成的影响

通过调查岷江干旱河谷两河口、飞虹、撮箕和牟托4个样地优势灌丛及其灌丛间空地的表土土壤物理化学性质和微生物群落组成,探讨植物灌丛群落对土壤微生物群落组成的影响。研究发现不同灌丛种类对土壤微生物群落组成以及土壤物理化学性质并没有显著影响,而同一样地灌丛与空地间的差异却较为显著。灌丛下比空地土壤中具有更高的有机质、养分含量,更高的土壤含水量和更低的容重,而灌丛下相对富集的养分资源是造成灌丛与空地间微生物群落组成差异的主要原因。不同样地影响微生物群落的主要因子存在一定差异,但与氮相关的因子(总氮、有效氮、碳/氮比)对土壤微生物群落着非常重要的影响,特别是对土壤微生物群落总生物量和细菌类群(革兰氏阳性菌、革兰氏阴性菌、细菌等)。虽然不同灌丛和空地下土壤中细菌群落都没有显著地变化,但真菌和菌根真菌却明显的在灌丛下富集。在飞虹和牟托样地,总磷和碳/磷比与真菌类群,主要指真菌和菌根真菌,表现出显著正相关性,这或许反映了真菌类群对于该区域磷循环的重要作用。研究结果揭示了灌丛植被在干旱河谷地区地下生态系统中的重要作用,以及氮、磷这两种养分元素对土壤微生物群落的重要影响。同时,未来对于干旱河谷地区植物-土壤关系的研究应该关注真菌和菌根真菌类群的作用。     

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

It is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, with Proteobacteria as the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, with Proteobacteria, Bacteroidetes, and Verrucomicrobia as the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.     

Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils

Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.     

Native soil microbial amendments generate trade‐offs in plant productivity,diversity, and soil stability in coastal dune restorations

Given the important role that soil microbes play in structuring plant communities and mediating ecosystem functions, there is growing interest in harnessing microbial communities to restore degraded ecosystems. Dune restorations, in particular, may benefit from native soil amendments because microbial diversity and abundance are very low in unvegetated areas. In an outdoor mesocosm experiment simulating Texas Gulf Coast dune restorations, we tested how native soil microbial amendments and restored diversity of foundational grasses influenced three key restoration responses: plant performance, plant diversity (including the colonization of native forbs), and soil stability. We found that native microbial amendments increased plant diversity and have the potential to increase soil stability, but this came at the cost of decreased plant biomass. Our results suggest that soil enemies in the native microbial amendments increased plant diversity by decreasing the performance of the dominant grass species and that arbuscular mycorrhizal fungi in the native microbial amendments increased the density of fungal hyphae in the soil, which can increase soil stability. Depending on the goals of the restoration, native soil microbial amendments may be a simple and inexpensive method to provide restoration benefits.     

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.     

Microclimate is a strong predictor of the native and invasive plant-associated soil microbiome on San Cristóbal Island,Galápagos archipelago

Understanding the drivers that affect soil bacterial and fungal communities is essential to understanding and mitigating the impacts of human activity on vulnerable ecosystems like those on the Galápagos Islands. The volcanic slopes of these Islands lead to steep elevation gradients that generate distinct microclimates across small spatial scales. Although much is known about the impacts of invasive plant species on the above-ground biodiversity of the Galápagos Islands, little is known about their resident soil microbial communities and the factors shaping them. Here, we investigate the bacterial and fungal soil communities associated with invasive and native plant species across three distinct microclimates on San Cristóbal Island (arid, transition zone and humid). At each site, we collected soil at three depths (rhizosphere, 5 cm and 15 cm) from multiple plants. Sampling location was the strongest driver of both bacterial and fungal communities, explaining 73% and 43% of variation in the bacterial and fungal community structure, respectively, with additional minor but significant impacts from soil depth and plant type (invasive vs. native). This study highlights the continued need to explore microbial communities across diverse environments and demonstrates how both abiotic and biotic factors impact soil microbial communities in the Galápagos archipelago.     

Microbial dynamics in glacier forefield soils show succession is not just skin deep

All over the world, glaciers are receding. One key consequence of glacier area loss is the creation of new terrestrial habitats. This presents an experimental opportunity to study both community formation and the implications of glacier loss for terrestrial ecosystems. In this issue of Molecular Ecology, Rime et al. ( 2015 ) describe how microbial communities are structured according to soil depth and development in the forefield of Damma glacier in Switzerland. The study provides insights into the contrasting structures of microbial communities at different stages of soil development. An important strength of the study is the integration of soil depth into the paradigm of primary succession, a feature which has rarely been considered by other studies. These findings underscore the importance of studying the interactions between microbial communities and glaciers at a time when Earth's glacial systems are experiencing profound change.     

森林土壤微生物对干旱和氮沉降的响应

干旱和氮沉降深刻影响着人类世森林生态系统的生命活动与物质循环,进而影响全球碳平衡、并反馈作用于气候变化。土壤微生物驱动元素的生物地球化学循环和关键土壤生态过程,在气候变化生物学研究方面具有核心地位和全球重要性。本文综述了干旱和氮沉降对森林土壤细菌和菌根真菌的影响。提出未来应加强全球变化多因子交互作用对土壤微生物多样性、活性与生态功能的研究;建立野外长期定位站,强化亚热带森林生态系统与全球变化研究;注重土壤生物之间互作及网络研究;利用微生物大数据建立相关的机理模型等。从认识微生物多样性和群落组成对全球变化的响应与适应,逐步发展为调控利用微生物群落服务于森林的优化管理、生态资源的合理保护与可持续利用,为充分发挥微生物减缓全球气候变化的作用提供理论基础。     

Bouncing Back: Plant-Associated Soil Microbes Respond Rapidly to Prairie Establishment

It is well established that soil microbial communities change in response to altered land use and land cover, but less is known about the timing of these changes. Understanding temporal patterns in recovering microbial communities is an important part of improving how we assess and manage reconstructed ecosystems. We assessed patterns of community-level microbial diversity and abundance in corn and prairie plots 2 to 4 years after establishment in agricultural fields, using phospholipid fatty acid biomarkers. Principal components analysis of the lipid biomarkers revealed differing composition between corn and prairie soil microbial communities. Despite no changes to the biomass of Gram-positive bacteria and actinomycetes, total biomass, arbuscular mycorrhizal fungi biomass, and Gram-negative bacteria biomass were significantly higher in restored prairie plots, approaching levels found in long-established prairies. These results indicate that plant-associated soil microbes in agricultural soils can shift in less than 2 years after establishment of perennial grasslands.     

Drought‐resistant fungi control soil organic matter decomposition and its response to temperature

Microbial‐mediated decomposition of soil organic matter (SOM) ultimately makes a considerable contribution to soil respiration, which is typically the main source of CO₂ arising from terrestrial ecosystems. Despite this central role in the decomposition of SOM, few studies have been conducted on how climate change may affect the soil microbial community and, furthermore, on how possible climate‐change induced alterations in the ecology of microbial communities may affect soil CO₂ emissions. Here we present the results of a seasonal study on soil microbial community structure, SOM decomposition and its temperature sensitivity in two representative Mediterranean ecosystems where precipitation/throughfall exclusion has taken place during the last 10 years. Bacterial and fungal diversity was estimated using the terminal restriction fragment length polymorphism technique. Our results show that fungal diversity was less sensitive to seasonal changes in moisture, temperature and plant activity than bacterial diversity. On the other hand, fungal communities showed the ability to dynamically adapt throughout the seasons. Fungi also coped better with the 10 years of precipitation/throughfall exclusion compared with bacteria. The high resistance of fungal diversity to changes with respect to bacteria may open the controversy as to whether future ‘drier conditions’ for Mediterranean regions might favor fungal dominated microbial communities. Finally, our results indicate that the fungal community exerted a strong influence over the temporal and spatial variability of SOM decomposition and its sensitivity to temperature. The results, therefore, highlight the important role of fungi in the decomposition of terrestrial SOM, especially under the harsh environmental conditions of Mediterranean ecosystems, for which models predict even drier conditions in the future.     

Contrasting Responses of Soil Microbial and Nematode Communities to Warming and Plant Functional Group Removal Across a Post-fire Boreal Forest Successional Gradient

Global warming is causing increases in surface temperatures and has the potential to influence the structure of soil microbial and faunal communities. However, little is known about how warming interacts with other ecosystem drivers, such as plant functional groups or changes associated with succession, to affect the soil community and thereby alter ecosystem functioning. We investigated how experimental warming and the removal of plant functional groups along a post-fire boreal forest successional gradient impacted soil microbial and nematode communities. Our results showed that warming altered soil microbial communities and favored bacterial-based microbial communities, but these effects were mediated by mosses and shrubs, and often varied with successional stage. Meanwhile, the nematode community was generally unaffected by warming and was positively affected by the presence of mosses and shrubs, with these effects mostly independent of successional stage. These results highlight that different groups of soil organisms may respond dissimilarly to interactions between warming and changes to plant functional groups, with likely consequences for ecosystem functioning that may vary with successional stage. Due to the ubiquitous presence of shrubs and mosses in boreal forests, the effects observed in this study are likely to be significant over a large proportion of the terrestrial land surface. Our results demonstrate that it is crucial to consider interactive effects between warming, plant functional groups, and successional stage when predicting soil community responses to global climate change in forested ecosystems.