Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents

The effects of short‐term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought‐induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant–microbial interactions and a greater incidence of certain soil‐borne diseases.     

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.     

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species‐rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short‐term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community‐weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon‐to‐nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long‐term climate change effects, especially in nutrient‐poor systems with slow‐growing vegetation.     

Late Quaternary climate change explains soil fungal community composition rather than fungal richness in forest ecosystems

The dramatic climate fluctuations of the late Quaternary have influenced the diversity and composition of macroorganism communities, but how they structure belowground microbial communities is less well known. Fungi constitute an important component of soil microorganism communities. They play an important role in biodiversity maintenance, community assembly, and ecosystem functioning, and differ from many macroorganisms in many traits. Here, we examined soil fungal communities in Chinese temperate, subtropical, and tropic forests using Illumina MiSeq sequencing of the fungal ITS1 region. The relative effect of late Quaternary climate change and contemporary environment (plant, soil, current climate, and geographic distance) on the soil fungal community was analyzed. The richness of the total fungal community, along with saprotrophic, ectomycorrhizal (EM), and pathogenic fungal communities, was influenced primarily by the contemporary environment (plant and/or soil) but not by late Quaternary climate change. Late Quaternary climate change acted in concert with the contemporary environment to shape total, saprotrophic, EM, and pathogenic fungal community compositions and with a stronger effect in temperate forest than in tropic–subtropical forest ecosystems. Some contemporary environmental factors influencing total, saprotrophic, EM, and pathogenic fungal communities in temperate and tropic–subtropical forests were different. We demonstrate that late Quaternary climate change can help to explain current soil fungal community composition and argue that climatic legacies can help to predict soil fungal responses to climate change.     

Warming and drying suppress microbial activity and carbon cycling in boreal forest soils

Climate warming is expected to have particularly strong effects on tundra and boreal ecosystems, yet relatively few studies have examined soil responses to temperature change in these systems. We used closed‐top greenhouses to examine the response of soil respiration, nutrient availability, microbial abundance, and active fungal communities to soil warming in an Alaskan boreal forest dominated by mature black spruce. This treatment raised soil temperature by 0.5 °C and also resulted in a 22% decline in soil water content. We hypothesized that microbial abundance and activity would increase with the greenhouse treatment. Instead, we found that bacterial and fungal abundance declined by over 50%, and there was a trend toward lower activity of the chitin‐degrading enzyme N‐acetyl‐glucosaminidase. Soil respiration also declined by up to 50%, but only late in the growing season. These changes were accompanied by significant shifts in the community structure of active fungi, with decreased relative abundance of a dominant Thelephoroid fungus and increased relative abundance of Ascomycetes and Zygomycetes in response to warming. In line with our hypothesis, we found that warming marginally increased soil ammonium and nitrate availability as well as the overall diversity of active fungi. Our results indicate that rising temperatures in northern‐latitude ecosystems may not always cause a positive feedback to the soil carbon cycle, particularly in boreal forests with drier soils. Models of carbon cycle‐climate feedbacks could increase their predictive power by incorporating heterogeneity in soil properties and microbial communities across the boreal zone.     

Differential sensitivity of total and active soil microbial communities to drought and forest management

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning—that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 60 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community‐based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought‐plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.     

Moderate Warming in Microcosm Experiment Does Not Affect Microbial Communities in Temperate Vineyard Soils

Changes in the soil microbial community structure can lead to dramatic changes in the soil ecosystem. Temperature, which is projected to increase with climate change, is commonly assumed to affect microbial communities, but its effects on agricultural soils are not fully understood. We collected soil samples from six vineyards characterised by a difference of about 2 °C in daily soil temperature over the year and simulated in a microcosm experiment different temperature regimes over a period of 1 year: seasonal fluctuations in soil temperature based on the average daily soil temperature measured in the field; soil temperature warming (2 °C above the normal seasonal temperatures); and constant temperatures normally registered in these temperate soils in winter (3 °C) and in summer (20 °C). Changes in the soil bacterial and fungal community structures were analysed by automated ribosomal intergenic spacer analysis (ARISA). We did not find any effect of warming on soil bacterial and fungal communities, while stable temperatures affected the fungal more than the bacterial communities, although this effect was soil dependent. The soil bacterial community exhibited soil-dependent seasonal fluctuations, while the fungal community was mainly stable. Each soil harbours different microbial communities that respond differently to seasonal temperature fluctuations; therefore, any generalization regarding the effect of climate change on soil communities should be made carefully.     

Effects of land use on the structure and function of leaf‐litter microbial communities in boreal streams

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Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land‐cover change affects belowground carbon storage and nutrient availability. We measured intra‐ and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well‐replicated, long‐term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter‐ and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land‐use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities.     

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.     

土壤微生物群落对麻栎-刺槐混交林凋落物分解的影响

以麻栎-刺槐混交林和麻栎纯林为研究对象,采用野外定点采样、室内分析与高通量测序的方法,对凋落物分解过程中土壤微生物菌群多样性特征及其对凋落物分解速率的影响进行了研究。结果表明:(1)麻栎-刺槐混交林凋落物的分解速率高于麻栎纯林。两种林分凋落物有机碳(TOC)、全氮(TN)发生释放,全磷(TP)发生积累-释放的过程。(2)两种林分土壤细菌优势类群为放线菌门(Acidobacteria)、变形菌门(Proteobacteria)、酸杆菌门(Actinobacteria)和疣微菌门(Verrucomicrobia),土壤真菌优势类群为担子菌门(Basidiomycota)、子囊菌门(Ascomycota)和被孢霉门(Moritierellomycota)。(3)凋落物分解过程中,麻栎-刺槐混交林土壤微生物菌群丰富度指数和菌群多样性指数变化范围小于麻栎纯林。(4)凋落物分解速率与土壤细菌菌群丰富度指数和菌群多样性指数呈显著正相关,与土壤真菌菌群丰富度指数呈显著正相关。土壤微生物群落对麻栎-刺槐混交林和麻栎纯林凋落物分解速率具有重要影响,研究结果为深入开展混交林土壤微生物多样性对凋落物分解的影响研究提供理论依据。     

Soil fungal and bacterial responses to conversion of open land to short‐rotation woody biomass crops

Short‐rotation woody biomass crops (SRWCs) have been proposed as an alternative feedstock for biofuel production in the northeastern US that leads to the conversion of current open land to woody plantations, potentially altering the soil microbial community structures and hence functions. We used pyrosequencing of 16S and 28S rRNA genes in soil to assess bacterial and fungal populations when ‘marginal’ grasslands were converted into willow (Salix spp.) and hybrid poplar (Populus spp.) plantations at two sites with similar soils and climate history in northern Michigan (Escanaba; ES) and Wisconsin (Rhinelander; RH). In only three growing seasons, the conversion significantly altered both the bacterial and fungal communities, which were most influenced by site and then vegetation. The fungal community showed greater change than the bacterial community in response to land conversion at both sites with substantial enrichment of putative pathogenic, ectomycorrhizal, and endophytic fungi associated with poplar and willow. Conversely, the bacterial community structures shifted, but to a lesser degree, with the new communities dissimilar at the two sites and most correlated with soil nutrient status. The bacterial phylum Nitrospirae increased after conversion and was negatively correlated to total soil nitrogen, but positively correlated to soil nitrate, and may be responsible for nitrate accumulation and the increased N₂O emissions previously reported following conversion at these sites. The legacy effect of a much longer grassland history and a second dry summer at the ES site may have influenced the grassland (control) microbial community to remain stable while it varied at the RH site.     

Abiotic drivers and plant traits explain landscape‐scale patterns in soil microbial communities

The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape‐scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community‐weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial‐dominated microbial communities were associated with exploitative plant traits versus fungal‐dominated communities with resource‐conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.     

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.     

Soil Bacterial Community Response to Differences in Agricultural Management along with Seasonal Changes in a Mediterranean Region

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity.     

城市化对土壤生态环境的影响研究进展

城市土壤是城市生态系统中最重要的组成部分之一,发挥着重要的生态系统服务功能。在全球快速城市化的背景下,城市土壤受到人类活动的强烈干扰,土壤物理、化学性质发生改变,土壤退化与污染日益加重。城市土壤退化导致土壤动物生态特征与行为模式发生变化,城市景观格局与土地利用类型的变化强烈影响了土壤动物的栖息地,为土壤动物的生存与生物多样性带来潜在威胁;另一方面,城市化过程改变了土壤微生物群落组成与功能特征。城市化直接影响了城市土壤维持植物生长、土壤自然消减能力以及碳储存功能等重要的生态系统服务功能。针对城市化过程对土壤生态环境产生的一系列影响,需要采用科学的管理方式,改善土壤理化性质,提高土壤环境质量,保护和恢复土壤生物多样性,从而增强城市土壤的生态系统服务功能。     

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.     

古大湖湿地盐碱土壤微生物群落结构及多样性分析

以黑龙江省古大湖湿地原生、林地、耕地及湖岸盐碱土壤微生物为研究对象,基于高通量测序方法,分析4种生境类型条件下土壤细菌和真菌群落结构及多样性。结合土壤理化指标,进一步分析影响微生物群落多样性的环境因子。结果表明:细菌群落中变形菌门的相对丰度值最高,真菌群落中为子囊菌门。同一生境细菌群落多样性具有相似性,而真菌具有一定的差异;不同生境间两者均具有差异。耕地土壤和林地土壤的细菌群落多样性接近,但与湖岸土壤真菌的更相近。前两者中细菌群落多样性较高,其次为原生土壤,而湖岸土壤中的最低。耕地土壤与湖岸土壤真菌群落多样性较高,原生土壤较低,而林地土壤中最低。与真菌相比,细菌的群落多样性受土壤环境因子影响更大,其中pH值、含水量对土壤细菌和真菌群落多样性均具有显著影响。     

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting–drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide.     

Microbial communities and their responses to simulated global change fluctuate greatly over multiple years

We used microbial lipid analysis to analyze microbial biomass and community structure during 6 years of experimental treatment at the Jasper Ridge Global Change Experiment (JRGCE), a long‐term multi‐factor global change experiment in a California annual grassland. The microbial community fingerprint and specific biomarkers varied substantially from year to year, in both control and experimental treatment plots. Possible drivers of the variability included plant growth, soil moisture, and ambient temperature. Surprisingly, background variation in the microbial community was of a larger magnitude than even very significant treatment effects, and this variation appeared to constrain responses to treatment. Microbial communities were mostly not responsive or not consistently responsive to the experimental treatments. Both arbuscular mycorrhizal fungi biomarker abundance (16 : 1 ω5c) and the fungal to bacterial ratio were lower under nitrogen addition in most years. Bacterial lipid biomarker abundances (15 : 0 iso and 16 : 1 ω7c) were higher under nitrogen addition in 2002, the year of largest microbial biomass, suggesting that bacteria could respond more to nitrogen addition in years of better growth conditions. Nitrogen addition and warming led to an interactive effect on the Gram‐positive bacterial biomarker and the fungal to bacterial ratio. These patterns indicate that in California grassland ecosystems, microbial communities may not respond substantially to future changes in climate and that nitrogen deposition may be a determinant of the soil response to global change. Further, year‐to‐year variation in microbial growth or community composition may be important determinants of ecosystem response to global change.