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.     

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.     

Historical forest disturbance mediates soil microbial community responses to drought

Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed ‘reference’ site and a ‘disturbed’ site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.     

Soil microbes alter plant fitness under competition and drought

Plants exist across varying biotic and abiotic environments, including variation in the composition of soil microbial communities. The ecological effects of soil microbes on plant communities are well known, whereas less is known about their importance for plant evolutionary processes. In particular, the net effects of soil microbes on plant fitness may vary across environmental contexts and among plant genotypes, setting the stage for microbially mediated plant evolution. Here, we assess the effects of soil microbes on plant fitness and natural selection on flowering time in different environments. We performed two experiments in which we grew Arabidopsis thaliana genotypes replicated in either live or sterilized soil microbial treatments, and across varying levels of either competition (isolation, intraspecific competition or interspecific competition) or watering (well‐watered or drought). We found large effects of competition and watering on plant fitness as well as the expression and natural selection of flowering time. Soil microbes increased average plant fitness under interspecific competition and drought and shaped the response of individual plant genotypes to drought. Finally, plant tolerance to either competition or drought was uncorrelated between soil microbial treatments suggesting that the plant traits favoured under environmental stress may depend on the presence of soil microbes. In summary, our experiments demonstrate that soil microbes can have large effects on plant fitness, which depend on both the environment and individual plant genotype. Future work in natural systems is needed for a complete understanding of the evolutionary importance of interactions between plants and soil microorganisms.     

Response of the Soil Microbial Community to Changes in Precipitation in a Semiarid Ecosystem

Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the structure and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation (+18%, −50%, or ambient) in a piñon-juniper woodland (Pinus edulis-Juniperus monosperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath piñon pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynamics, background climatic variability, and the composition of the associated aboveground community.     

The Pinyon Rhizosphere,Plant Stress,and Herbivory Affect the Abundance of Microbial Decomposers in Soils

In terrestrial ecosystems, changes in environmental conditions that affect plant performance cause a cascade of effects through many trophic levels. In a 2-year field study, seasonal abundance measurements were conducted for fast-growing bacterial heterotrophs, humate-degrading actinomycetes, fungal heterotrophs, and fluorescent pseudomonads that represent the decomposers in soil. Links between plant health and soil microbiota abundance in pinyon rhizospheres were documented across two soil types: a dry, nutrient-poor volcanic cinder field and a sandy-loam soil. On the stressful cinder fields, we identified relationships between soil decomposer abundance, pinyon age, and stress due to insect herbivory. Across seasonal variation, consistent differences in microbial decomposer abundance were identified between the cinders and sandy-loam soil. Abundance of bacterial heterotrophs and humate-degrading actinomycetes was affected by both soil nutritional status and the pinyon rhizosphere. In contrast, abundance of the fungal heterotrophs and fluorescent pseudomonads was affected primarily by the pinyon rhizosphere. On the cinder field, the three bacterial groups were more abundant on 150-year-old trees than on 60-year-old trees, whereas fungal heterotrophs were unaffected by tree age. Fungal heterotrophs and actinomycetes were more abundant on insect-resistant trees than on susceptible trees, but the opposite was true for the fluorescent pseudomonads. Although all four groups were present in all the environments, the four microbial groups were affected differently by the pinyon rhizosphere, by tree age, and by tree stress caused by the cinder soil and insect herbivory.     

内蒙草原不同植物功能群及物种对土壤微生物组成的影响

为了分析不同植物群落组成对内蒙古典型草原土壤微生物群落组成的影响,本研究利用植物功能群剔除处理实验平台,采用荧光定量PCR(real-timePCR)和自动核糖体间隔区基因分析(automated ribosomal intergenic spacer analysis,ARISA)技术,对不同植物功能群组成的非根际土壤和常见物种的根际土壤中细菌和真菌的数量及群落结构进行了分析。结果表明,在非根际土壤中,不同植物功能群组成对细菌数量有显著影响,而对真菌数量及细菌和真菌的群落结构影响不明显;在根际土壤中,不同植物物种对细菌、真菌的数量都有显著影响。此外,聚类分析表明,不同物种的根际土中细菌和真菌的群落结构也有所不同,尤其以细菌的群落结构变化较为明显。研究结果表明不同植物物种可以通过根系影响土壤微生物群落组成。     

Organic Matter Stimulates Bacteria and Arbuscular Mycorrhizal Fungi in Bauhinia purpurea and Leucaena diversifolia Plantations on Eroded Slopes in Nepal

Erosion resulting from landslides is a serious problem in mountainous countries such as Nepal. To restore such sites it is essential to establish plant cover that protects the soil and reduces surface erosion. Mycorrhizal fungi growing in symbiosis with plants are essential in this respect because they improve both plant nutrient uptake and soil structure. We investigated the influence of organic matter and P amendment on recently produced biomass of bacteria and arbuscular mycorrhizal (AM) fungi in eroded slopes in Nepal. Eroded soil mixed with different types of organic matter or P was placed in mesh bags, which were buried around trees of Bauhinia purpurea and Leucaena diversifolia between June 2003 and December 2003 (the wet season) or between December 2003 and June 2004 (the dry season). Signature fatty acids were used to determine bacterial and AM fungal biomass after the 6‐month intervals. The amount and composition of AM fungal spores were analyzed in the mesh bags from the dry season. More microbial biomass was produced during the wet season than during the dry season. Furthermore, organic matter addition enhanced the production of AM fungal and bacterial biomass during both periods. The positive influence of organic matter addition on AM fungi could be an important contribution to plant survival in plantations on eroded slopes. Different AM spore communities and bacterial profiles were obtained with different organic amendments and this suggests a possible way of selecting for specific microbial communities in the management of eroded sites.     

Microbial community biogeographic patterns in the rhizosphere of two Brazilian semi-arid leguminous trees

Arid environments are regular and well distributed over all continents and display drought characteristics whether full-time or seasonal. This study aims to characterize how the microbial communities of the rhizosphere of two leguminous trees from the Brazilian semi-arid biome the Caatinga are geographically and seasonally shaped, as well as the factors driving this variation. With that purpose, the soil rhizosphere from two leguminous trees (Mimosa tenuiflora and Piptadenia stipulacea (Benth.) Ducke) were sampled in two different seasons: rainy and drought at five different sites. Assessment of bacterial and archaeal communities occurred by T-RFLP analysis of 16S rRNA and archaeal amoA genes. By these means, it was observed that the seasons (wet and dry periods) are the factors that most influence the composition of the microbial community from both analyzed plants, except for the results obtained from the CCA applied to Archaeas. Furthermore, soil physical–chemical factors also had a significant influence on the community and indicated a geographical pattern of the bacterial community. It was not possible to observe significant modifications in the composition in relation to the plant species. We have seen that soil characteristics and rainfall were the factors that most influenced the microbial composition. Also, the bacterial community had a significant correlation with soil characteristics that indicates that these rhizosphere communities might be selected by environmental characteristics. Furthermore, the data suggest that climate plays a key role in structuring the microbial community of this biome.     

Soil microbial communities in restored and unrestored coastal dune ecosystems in California

Most restoration projects involving invasive plant eradication tend to focus on plant removal with little consideration given to how these invasives change soil microbial communities. However, soil microorganisms can determine invasibility of habitats and, in turn, be altered by invasives once established, potentially inhibiting native plant establishment. We studied soil microbial communities in coastal dunes with varying invasion intensity and different restoration approaches (herbicide, mechanical excavation) at Point Reyes National Seashore. Overall, we found evidence of a strong link between bacterial and fungal soil communities and the presence of invasives and restoration approach. Heavily invaded sites were characterized by a lower abundance of putatively identified nitrifiers, fermentative bacteria, fungal parasites, and fungal dung saprotrophs and a higher abundance of cellulolytic bacteria and a class of arbuscular mycorrhizal fungi (Archaeosporomycetes). Changes in soil microbiota did not fully dissipate following removal of invasives using herbicide, with exception of reductions in cellulolytic bacteria and Archaeosporomycetes abundance. Mechanical restoration effectively removed both invasives and soil legacy effects by inverting or “flipping” rhizome‐contaminated surface soils with soils from below and may have inadvertently induced other adverse effects on soils that impeded reestablishment of native dune plants. Land managers should consider additional measures to counteract lingering legacy effects and/or focus restoration efforts in areas where legacy effects are less pronounced.     

Termination of belowground C allocation by trees alters soil fungal and bacterial communities in a boreal forest

The introduction of photosynthates through plant roots is a major source of carbon (C) for soil microbial biota and shapes the composition of fungal and bacterial communities in the rhizosphere. Although the importance of this process, especially to ectomycorrhizal fungi, has been known for some time, the extent to which plant belowground C allocation controls the composition of the wider soil community is not understood. A tree-girdling experiment enabled studies of the relationship between plant C allocation and microbial community composition. Girdling involves cutting the phloem of trees to prevent photosynthates from entering the soil. Four years after girdling, fungal and bacterial communities were characterized using DNA-based profiles and cloning and sequencing. Data showed that girdling significantly altered fungal and bacterial communities compared with the control. The ratio of ectomycorrhizal to saprobic fungal sequences significantly decreased in girdled treatments, and this decline was found to correlate with the fungal phospholipid fatty acid biomarker 18:2ω6,9. Bacterial communities also varied in the abundance of the two dominant phyla Acidobacteria and Alphaproteobacteria . Concomitant changes in fungal and bacterial communities suggest linkages between these two groups and point toward plant belowground C allocation as a key determinant of microbial community composition.     

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.     

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.     

Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray–Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg⁻¹ hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities.     

Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe

Foraging intensity of large herbivores may exert an indirect top‐down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long‐term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β‐diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.     

Fungal community responses to precipitation

Understanding how fungal communities are affected by precipitation is an essential aspect of predicting soil functional responses to future climate change and the consequences of those responses for the soil carbon cycle. We tracked fungal abundance, fungal community composition, and soil carbon across 4 years in long‐term field manipulations of rainfall in northern California. Fungi responded directly to rainfall levels, with more abundant, diverse, and consistent communities predominating under drought conditions, and less abundant, less diverse, and more variable communities emerging during wetter periods and in rain‐addition treatments. Soil carbon storage itself did not vary with rainfall amendments, but increased decomposition rates foreshadow longer‐term losses of soil carbon under conditions of extended seasonal rainfall. The repeated recovery of fungal diversity and abundance during periodic drought events suggests that species with a wide range of environmental tolerances coexist in this community, consistent with a storage effect in soil fungi. Increased diversity during dry periods further suggests that drought stress moderates competition among fungal taxa. Based on the responses observed here, we suggest that there may be a relationship between the timescale at which soil microbial communities experience natural environmental fluctuations and their ability to respond to future environmental change.     

典型农田退耕后土壤真菌与细菌群落的演替

土壤真菌和细菌作为地下生态系统的重要组成部分,其群落的恢复状况是评价农田退耕还林生态效益的重要指标。以云南省维西县典型退耕还林农田为对象,利用高通量测序等方法比较了不同退耕年限的农田土壤中真菌和细菌群落随植被演替的变化特征。结果发现,农田撂荒后土壤细菌多样性先显著降低后缓慢上升,真菌多样性变化不明显;地上部植被由草本经灌丛再向林地演替的过程中,土壤真菌的群落组成随植被变化呈现明显的改变,主要体现在粪壳菌纲(Sordariomycetes)所占比例的减少(由30%减至10%左右)和伞菌纲(Agaricomycetes)所占比例的增加(由5%以下增至20%以上);而细菌的群落组成无明显变化。聚类分析的结果显示,真菌的群落组成变化与植物群落的演替规律更为同步。不同演替阶段的退耕农田土壤真菌和细菌群落均明显区别于未经扰动的天然林,表明人为扰动对土壤微生物群落的影响可能在较长时间内持续存在。研究揭示了云南典型农田退耕后地下土壤真菌和细菌群落随植被演替的变化特征,为全面评价该地区退耕还林的生态效益提供了数据支撑。     

内蒙古草原典型植物对土壤微生物群落的影响

为了分析内蒙古草原不同植物物种对土壤微生物群落的影响, 采用实时荧光定量PCR (real-time PCR)以及末端限制性片段长度多态性分析(terminal restriction fragment length polymorphism, T-RFLP)等分子生物学技术, 测定了退化-恢复样地上几种典型植物的根际土壤和非根际土壤中细菌和真菌的数量及群落结构。结果表明, 不同植物物种对根际和非根际细菌及根际真菌数量均有显著影响。根际土壤中的细菌和真菌数量普遍高于非根际土壤, 尤其以真菌更为明显。对T-RFLP数据进行多响应置换过程(multi-response permutation procedures, MRPP)分析和主成分分析(principal component analysis, PCA), 结果表明, 大多数物种的根际细菌及真菌的群落结构与非根际有明显差异, 并且所有物种的真菌群落可以按根际和非根际明显分为两大类群。此外, 细菌和真菌群落结构在一定程度上存在按物种聚类的现象, 以细菌较为明显。这些结果揭示了不同植物对土壤微生物群落的影响特征, 对理解内蒙古草原地区退化及恢复过程中植被演替引起的土壤性质和功能的变化有一定的帮助。