Belowground Microbial Communities Research Articles

Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes.

Plants serve as critical links between above- and below-ground microbial communitites, both influencing and being influenced by microbes in these two realms. Below-ground microbial communities are expected to respond to soil resource environments, which are mediated by the roots of plants that can, in turn, be influenced by the above-ground community of foliar endophytes. For instance, diverse plant communities deposit more, and more diverse, nutrients into the soil, and this deposition is often increased when foliar pathogens are removed. Differences in soil resources can alter soil microbial composition and phenotypes, including inhibitory capacity, resource use, and antibiotic resistance. In this work, we consider plots differing in plant richness and application of foliar fungicide, evaluating consequences on soil resource levels and root-associated Streptomyces phenotypes. Soil carbon, nitrogen, phosphorus, potassium, and organic matter were greater in samples from polyculture than monoculture, yet this increase was surprisingly offset when foliar fungal communities were disrupted. We find that Streptomyces phenotypes varied more between richness plots-with the Streptomyces from polyculture showing lower inhibitory capacity, altered resource-use profiles, and greater antibiotic resistance-than between subplots with/without foliar fungicide. Where foliar fungicide affected phenotypes, it did so differently in polyculture than in monoculture, for instance decreasing niche width and overlap in monoculture while increasing them in polyculture. No differences in phenotype were correlated with soil nutrient levels, suggesting the need for further research looking more closely at soil resource diversity and particular compounds that were found to differ between treatments.

Effects of fire and fire-induced changes in soil properties on post-burn soil respiration

Abstract Background Boreal forests cover vast areas of land in the northern hemisphere and store large amounts of carbon (C) both aboveground and belowground. Wildfires, which are a primary ecosystem disturbance of boreal forests, affect soil C via combustion and transformation of organic matter during the fire itself and via changes in plant growth and microbial activity post-fire. Wildfire regimes in many areas of the boreal forests of North America are shifting towards more frequent and severe fires driven by changing climate. As wildfire regimes shift and the effects of fire on belowground microbial community composition are becoming clearer, there is a need to link fire-induced changes in soil properties to changes in microbial functions, such as respiration, in order to better predict the impact of future fires on C cycling. Results We used laboratory burns to simulate boreal crown fires on both organic-rich and sandy soil cores collected from Wood Buffalo National Park, Alberta, Canada, to measure the effects of burning on soil properties including pH, total C, and total nitrogen (N). We used 70-day soil incubations and two-pool exponential decay models to characterize the impacts of burning and its resulting changes in soil properties on soil respiration. Laboratory burns successfully captured a range of soil temperatures that were realistic for natural wildfire events. We found that burning increased pH and caused small decreases in C:N in organic soil. Overall, respiration per gram total (post-burn) C in burned soil cores was 16% lower than in corresponding unburned control cores, indicating that soil C lost during a burn may be partially offset by burn-induced decreases in respiration rates. Simultaneously, burning altered how remaining C cycled, causing an increase in the proportion of C represented in the modeled slow-cycling vs. fast-cycling C pool as well as an increase in fast-cycling C decomposition rates. Conclusions Together, our findings imply that C storage in boreal forests following wildfires will be driven by the combination of C losses during the fire itself as well as fire-induced changes to the soil C pool that modulate post-fire respiration rates. Moving forward, we will pair these results with soil microbial community data to understand how fire-induced changes in microbial community composition may influence respiration.

Recovery of bacterial network complexity and stability after simulated extreme rainfall is mediated by K−/r-strategy dominance

The complexity and stability of belowground microbial communities are among the core mechanisms that drive ecosystem functions. Disturbances, such as climate extremes, can exert a substantial influence on these microbial attributes. However, the role of the microbial life history strategy in determining the complexity and stability of desert soil microbial communities after extreme rainfall is poorly understood. Here, we explored the response patterns of bacterial network complexity and stability and characterized the bacterial life history strategy on the basis of the oligotroph (K-strategist)-to-copiotroph (r-strategist) ratio after three extreme rainfall treatments (11, 15, and 25 mm). Experimental results demonstrated that the bacterial communities immediately shifted from the K-strategy to the r-strategy one day after extreme rainfall and gradually recovered to the K-strategy over time, as verified by the increase (31.46 %–125.51 %) then decrease (41.51 % – 95.78 %) in the weighted rrn copy number. Meanwhile, bacterial network complexity and stability showed three-phase patterns [dramatic decline (decreased by 211.67 %–388.46 %)–gradual recovery (increased by 45.60 %–103.65 %)–insignificant change] after three extreme rainfall events. The decline/recovery of these bacterial attributes was highly pronounced/slow after the large extreme rainfall treatment. Specifically, the responses of bacterial network complexity and stability to extreme rainfall showed negative correlations with the response of the weighted rrn copy number (R = -0.55 – -0.74, P < 0.01). The mechanisms underlying the response patterns of bacterial network complexity and stability were related to the prevalence of the r-strategy of the bacterial communities (Phase 1) and the shifts from the r-strategy to the K-strategy due to the gradual reduction in soil moisture (Phase 2 and 3). These results emphasize the importance of the microbial life history strategy in maintaining network complexity and stability and help in understanding how belowground communities can withstand future disturbances.

Plant neighbors differentially alter a focal species' biotic interactions through changes to resource allocation.

Plant resource allocation strategies are thought to be largely a consequence of changing abiotic conditions and evolutionary history. However, biotic interactions also influence how a plant allocates resources. As a result, plants mediate indirect interactions between organisms above- and belowground through resource allocation. Neighboring plants can influence plant fitness directly through competition for resources, and indirectly by altering associated community interactions (associational effects), such as pollination, herbivory, and a suite of belowground interactions. Given the importance of community interactions for plant success, and the known ability for plant neighbors to change these interactions, the goal of this "pandemic project" was to understand how heterospecific plant neighbors alter plant resource allocation, whether this occurred through above- or belowground mechanisms, and whether this in turn alters biotic interactions and the relationship between a focal plant and its herbivore and soil community interactions. To do so, we established a common garden experiment, manipulating plant neighbor identity and the extent of interaction among neighbors (aboveground only, vs. above- and belowground interactions, using customized pot types), and measured changes to a focal plant and its biotic interactions over two growing seasons. We found evidence of both neighbor effects and pot type, showing that neighbor interactions affect a focal plant through both above- and belowground processes, and how the focal plant is affected depends on neighbor identity. Though neighbors did not directly alter herbivory or most soil microbial interactions, they did alter the relationship between belowground microbial communities and a plant response trait (specific leaf area). Plant resource allocation responses were reduced with time, showing the importance of extending experiments beyond a single growing season, and are an important consideration when making predictions about plant responses to changing conditions. This study contributes to a growing body of work showing how community contexts affect the above- and belowground interactions of a plant through plant resource allocation strategies.

Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard.

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.

Low impact of Carpobrotus edulis on soil microbiome after manual removal from a climate change field experiment

Synergic effects between climate change and invasive species may alter soil microbial diversity and functioning, as well as cause major shifts in physicochemical properties. Moreover, some of these ecological impacts may manifest even after the removal of the invasive species. We have conducted a field experiment to assess such effects on soil microbial communities (fungi and bacteria) and physicochemical properties seven months after the removal of Carpobrotus edulis (L.), an invasive plant of coastal dune ecosystems. C. edulis grew on the experimental plots for 14 months under current (“invasive species treatment”) and increased warming and drought conditions (“combined treatment”). Then, all plant parts (above and belowground biomass) were removed with a non-aggressive eradication method and soil samples were collected seven months later in the experimental and control plots (no invasive species and current climatic conditions). We predicted a general compositional shift in microbial communities in response to the presence of the invasive species. Moreover, given that water is the most limiting factor in this type of ecosystem, we also predicted a more pronounced compositional shift in the treatment combining invader presence and climate change. While species richness was similar amongst treatments, we observed some taxonomic and functional variation in soil microbial communities. Notably, fungal and bacterial communities exhibited contrasting responses. The species composition of bacteria differed significantly between the “invasive species” and “control” treatments, while, in the case of fungi, the most substantial difference occurred between the “invasive species” treatment and the combined treatment of “invasive species and climate change”. Some chemical properties, such as carbon and nitrogen content or pH, strongly differed amongst treatments, with the “invasive species” showing a different response compared to the other two treatments. Overall, our study suggests smaller short-term effects on the microbial community compared to soil chemical properties. Furthermore and contrary to our initial expectations, the potential impact on the soil microbiome seemed to be weaker in the face of rising temperatures and drought conditions predicted by climate change. This outcome highlights the remarkable complexity of the impact of invasive species and climate change on belowground microbial communities.

Unveiling sedimentary microbial communities: Restored mangrove wetlands show higher heterogeneity and network stability than natural ones

Mangrove wetlands, characterized by high biodiversity and crucial ecological functions, have witnessed extensive restoration efforts in China in recent decades. Despite the successful recovery of standing vegetation, the alterations in below-ground microbial communities, vital engines for completing biogeochemical cycles in wetlands, remain poorly understood. Here, the prokaryotic and microeukaryotic communities in restored mangrove forests (RMF) and natural mangrove forests (NMF) in Shenzhen, the world’s first International Mangrove Center in China were investigated and compared. This work aimed to explore an appropriate sampling strategy for sedimentary microbial community biodiversity study and evaluate their heterogeneity and network stability in RMF and NMF. The results revealed that a “broad-coverage and sparse-spot” sampling strategy was conducive to ensuring a sufficient representation of microbial diversity in mangrove wetlands. Significant differences were found in microbial community structures of RMF and NMF, with the relative abundances of Myxococcales and Cerozoa as potential biomarkers, respectively. RMF displayed higher prokaryotic richness, microbial community dissimilarity, and spatial turnover rate compared to those of NMF, indicating greater microbial diversity and spatial heterogeneity in RMF. Meanwhile, the RMF microbial network was characterized by lower complexity but higher modularity, robustness, and the ratio of negative to positive cohesion. These demonstrated that microbiomes were shaped by stability constraints and the RMF microbial network was more stable and resistant to environmental variations than that of NMF. Interestingly, the stability of these microbial networks appeared to depend on the topological roles of key species rather than on their abundance. Overall, this study disclosed a kind of relationship between the aboveground elements of restored and natural mangrove forests and their belowground microbial communities. These findings provide references for comprehensive assessments of biodiversity, stability, and ecological restoration in mangrove ecosystems.

Altering plant carbon allocation to stems has distinct effects on rhizosphere soil microbiome assembly, interactions, and potential functions in sorghum

AbstractAltering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk (D) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green (dd) sorghum but reduced carbon allocation in that of dry white (DD) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability.

Soil cover shapes organic matter pools and microbial communities in soils of maritime Antarctica

Bryophytes and biological soil crusts (biocrusts) are the two major biological soil cover types of maritime Antarctica and play a crucial role for key ecosystem functions in the barely vegetated and little developed soils. Besides their profound impacts on nutrient cycling, they also provide habitats and activity hotspots for unique soil microbial communities. Yet, the effects of biological soil cover on the physical and chemical soil environment and belowground microbial communities have not been comprehensively studied in this fragile ecosystem.We here address the research question how biocrusts and mosses shape the quantity and structure of the soil organic matter pool, and the activity and composition of subjacent microbial communities. Towards this end, we sampled soils under two common, but physiologically distinct moss species, Polytrichastrum alpinum and Sanionia unicinata, and adjacent biological soil crusts at two sites on Deception Island, South Shetland Islands.We found that biocrusts and mosses differentially influenced central soil properties and subjacent soil microbial communities. All major SOM compound groups (carbohydrates, aromatics and phenols, lipids, N-containing polymers) as well as microbial biomass were more abundant in soil under biocrusts. However, microbial mass-specific growth rates were higher in soil under mosses. Our results showed moss-species-specific effects in addition to effects of soil cover type, as P. alpinum affected the activity and structure of soil microbial communities and the composition of soil organic matter stronger than S. unicinata.Our study highlights the interconnectedness between soil cover and soil biogeochemistry, which is crucial for deepening our understanding of belowground functioning in Antarctic soils. This linkage is of particular importance in the context of ongoing rapid climate change on the Antarctic Peninsula, as future shifts in the distribution and abundance of soil cover may substantially impact multiple soil processes in this vulnerable ecosystem.

Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects.

Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by ‘Candidatus Phytoplasma pini’ as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, ‘Ca. Phytoplasma pini’ is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

Micronutrients modulate the structure and function of soil bacterial communities

Soil micronutrients are increasingly recognized as critical regulators of biogeochemical cycling and terrestrial ecosystem processes. Despite substantial efforts establishing how belowground microbial communities respond to macronutrients such as N and P, responses to micronutrients remain poorly understood. This is of particular interest in tropical soils, where micronutrients are heterogeneously distributed and often deficient. Using nearly 300 soil samples that span broad gradients in soil micronutrients, we aimed to determine how differences in micronutrients (Ca, Mg, S) and secondary macronutrients (Mn, Fe, Zn) shape soil bacterial communities and their metabolic capabilities. Along with key soil parameters including pH and climatic predictors, we found that Ca, Mg, and Mn were important in shaping the composition and function of soil microbiomes. We also identified lineages that were consistently responsive to specific micronutrients, with those taxa found in low micronutrient conditions often associated with oligotrophic life history strategies. We detected a subset of metabolic attributes related to nutrient cycling that were strongly associated with specific micronutrients. Notably, Mn was important in predicting the abundance of gene systems related to P metabolism including control of Pho regulon and alkylphosphonate utilization, suggesting that it may be important mediators of these responses. Taken together, our results begin to establish a broader understanding of the extent to which belowground systems are shaped by micronutrients and the strategies that soil microbes employ in variable micronutrient environments.

Nitrogen enrichment stimulates rhizosphere multi-element cycling genes via mediating plant biomass and root exudates

Global nitrogen (N) deposition has a significant impact on the structure and function of above-ground plant communities; however, the impact of N enrichment on below-ground microbial communities remains insufficiently elucidated, especially regarding the functional gene structure. An 18-month pot experiment was conducted to examine the effects of N addition rate (0, 5, 10, and 15 g N m−2 yr−1) on the functional gene composition of rhizosphere microorganisms of Bothriochloa ischaemum, a native grass species of the semiarid area, and to evaluate the soil and plant variables connected with the observed variation. Using microarray GeoChip analysis, 2676, 744, 308, and 515 gene probes involved in carbon (C), N, phosphorus (P) and sulfur (S) cycling, respectively, were detected. Compared with the weak response of genes in the bulk soil, N addition significantly increased the abundance of genes involved in C fixation (tkta, rubisco, TIM), C degradation (amyA, ara, chitinase), methanogenesis (mcra), N2-fixation (nifH), denitrification (narG, nirK/S, nosZ), polyphosphate degradation (ppx), and sulfite reduction (dsrA, dsrB, cysJ) in the rhizosphere. The abundance of genes responsible for C-, N-, P-, and S-cycling increased with the N addition rate and was mainly regulated by variations in plant biomass and root exudates. The quantity of soil dissolved organic C played a crucial role in determining the abundance of genes related to the cycling of C, N, P, and S. Plant biomass indirectly affected gene abundance by increasing organic acids in root exudates and dissolved organic C. These findings facilitate our understanding of microbial function to elevated N levels and highlight the key role of root exudates and plant biomass in regulating microbial functions under future N-enrichment scenarios.

Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils

An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0–9) on soil functions and bacterial communities in both topsoils (0–20 cm) and subsoils (20–40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.

Wetland soil microbial responses to upland agricultural intensification and snail invasion

Wetland soils harbor diverse microorganisms including bacteria, archaea, and fungi, all of which play significant roles in maintaining soil health and ecosystem functions but are susceptible to influences from multiple environmental changes. Agricultural intensification and biological invasion are two fundamental drivers of environmental change for wetlands, but their interactive effects on soil microbial communities remain less well understood, particularly for seasonal subtropical wetlands. Yet such understanding is vital for wetland conservation and management. In this study, we conducted a 14-week field mesocosm experiment to investigate how agricultural intensification and invasive apple snail (Pomacea maculata) – an emerging and increasingly concerning threat to natural and agricultural systems in southeastern U.S. – altered wetland soil microbial communities and structures. We found that invasive P. maculata showed selective effects on relative abundance of specific microbial taxa (e.g., Proteobacteria, Nitrospirota), and interactive effects with upland intensification on Spirochaetota and Mortierellomycota. Upland agricultural intensification also exerted significant and consistent effects on microbial composition and diversity across microbial domains. Changes in microbial composition were partly manifested through modifications in water chemistry, such as dissolved oxygen, which acted as environmental regulators. In addition, upland intensification led to more complex but sparsely connected microbial networks, while invasive snail presence decreased network complexity and resulted in greater modularity, less edge density, and longer path length, indicative of lower molecular information exchange efficiency. Our research emphasizes the need for a comprehensive evaluation of microbial responses (i.e., composition, diversity, and co-occurrence patterns) to better understand multi-stressor impacts from human activities on wetland belowground microbial communities. By holistically characterizing microbial responses, our findings show how global change drivers may impact wetland microorganisms in subtropical biomes and infer their functional consequences. Our results have important implications for sustainable landscape management and conservation of wetlands that are experiencing escalating human-induced environmental changes.

Plant species and soil depth differentially affect microbial diversity and function in grasslands

AbstractIntroductionGrassland ecosystems are a major store of terrestrial carbon (C), yet little is known about their capacity to cycle and store C in deeper soil horizons. Further, it is unclear how plant community composition within agricultural grasslands mediates this capacity and influences microbial community composition. We investigated whether the aboveground community composition in intensively managed agricultural grasslands influenced belowground microbial community composition, abundance, respiration and enzyme activities with depth.Materials and MethodsSoil was sampled in four soil layers: A (0–15 cm), B (15–30 cm), C (30–60 cm) and D (60–90 cm) in monocultures of six grassland species and a mixture of all six. Functional capacity was measured through enzymatic and substrate‐induced respiration assays, and microbial abundance and diversity were assessed via quantitative polymerase chain reaction and sequencing (16S, Internal transcribed spacer), respectively.ResultsMicrobial abundance and C cycling enzyme activity decreased and community composition changed, along the soil depth gradient, regardless of the plant community. Microbial abundance was not significantly influenced by plant community type across the entire soil depth profile. However, prokaryotic community composition was significantly influenced by plant community in the top 15 cm of soil, and fungal community composition was significantly influenced between 15 and 30 cm in depth. Plant community types mediated the rate at which C cycling enzyme activity decreased along the soil depth gradient, and selected C cycling enzymes were significantly more active at 15–60 cm depth when Cichorium intybus (a deep rooting species) was present.ConclusionThis study provides an improved understanding of how agricultural grassland communities affect the soil microbiome with depth; this has potential implications for the management of these systems for enhanced soil health. Our work indicates the potential for multispecies mixtures with deep rooting species to be a practical strategy to increase C cycling capacity in deeper soil layers within grasslands, which may have implications for policy goals related to C storage.

Heterogeneous landscape promotes distinct microbial communities in an imperiled scrub ecosystem

ABSTRACT Habitat heterogeneity is a key driver of biodiversity of macroorganisms, yet how heterogeneity structures belowground microbial communities is not well understood. Importantly, belowground microbial communities may respond to any number of abiotic, biotic, and spatial drivers found in heterogeneous environments. Here, we examine potential drivers of prokaryotic and fungal communities in soils across the heterogenous landscape of the imperiled Florida scrub, a pyrogenic ecosystem where slight differences in elevation lead to large changes in water and nutrient availability and vegetation composition. We employ a comprehensive, large-scale sampling design to characterize the communities of prokaryotes and fungi associated with three habitat types and two soil depths (crust and subterranean) to evaluate (i) differences in microbial communities across these heterogeneous habitats, (ii) the relative roles of abiotic, biotic, and spatial drivers in shaping community structure, and (iii) the distribution of fungal guilds across these habitats. We sequenced soils from 40 complete replicates of habitat × soil depth combinations and sequenced the prokaryotic 16S and fungal internal transcribed spacer (ITS) regions using Illumina MiSeq. Habitat heterogeneity generated distinct communities of soil prokaryotes and fungi. Spatial distance played a role in structuring crust communities, whereas subterranean microbial communities were primarily structured by the shrub community, whose roots they presumably interacted with. This result helps to explain the unexpected transition we observed between arbuscular mycorrhiza–dominated soils at low-elevation habitats to ectomycorrhiza-dominated soils at high-elevation habitats. Our results challenge previous notions of environmental determinism of microbial communities and generate new hypotheses regarding symbiotic relationships across heterogeneous environments.

Temperature mediates microbial multitrophic communities assembly and soil-borne fungal pathogens in coastal ecosystems

A better understanding of assembly processes of multitrophic microbial communities and soil-borne fungal pathogens is important to predict changes in ecosystem functions. However, the drivers governing the microbial community assembly processes and soil-borne fungal pathogen distributions, particularly in the coastal ecosystem is unclear. Here, we examined the shifts in soil bacterial, fungal, protistan communities and soil-borne fungal pathogens across 2000 km in the coastal areas of eastern Australia. Determinism predominated the multitrophic microbial community assembly with mean annual temperature (MAT) differentially mediates deterministic and stochastic processes. Contrasting to protistan community, bacterial and fungal community assembly tended to be more deterministic in higher MAT regions. A total of 609 soil-borne fungal pathogens were identified with the total relative abundances ranged from 0.34 % to 52.29 % in a given soil sample. The profile of soil-borne fungal pathogens was significantly correlated with bacterial and protistan communities. Random forest indicated that MAT was the main driver of soil-borne fungal pathogens. Altogether, our work provided evidence that MAT is a critical factor driving the belowground microbial community assembly and soil-borne fungal pathogen patterns and highlighted the potential importance of trophic interactions in predicting dynamics of soil-borne fungal pathogens under the changing environment.

Mosses stimulate soil carbon and nitrogen accumulation during vegetation restoration in a humid subtropical area

Mosses form a ground layer with a thickness of nearly 1 cm during the first decade of vegetation restoration, but their effects on the belowground microbial community and soil properties and the associated soil carbon (C) and nitrogen (N) accumulation in subtropical areas are unclear. Here, we measured soil C and N variables (soil organic C [SOC], total N [TN], dissolved organic C, ammonium [NH4+-N] and nitrate [NO3−-N]), soil microbial community and soil properties (soil water content [SWC] and pH) under four treatments (bare soil [BS], bare soil with transplanted moss, moss-covered soil [MS] and moss-covered soil with moss removed) in three vegetation types (forest plantations, forage grasslands and mixed plantations and forage grasslands) in a subtropical climate. We analyzed the effects of native mosses, moss transplantation and removal using BS and MS as references. One year post-treatment, moss transplantation increased NO3−-N and NH4+-N in the 0–5 cm and 2–5 cm soil layers, respectively. Conversely, moss removal decreased SOC and TN in the 0–2 cm soil layer and SWC in the 0–5 cm soil layer. Compared to BS and MS, native moss presence, moss transplantation and removal decreased the total microbial, bacterial and fungal biomass and altered the soil microbial community composition (ratios of fungi and bacteria and Gram-positive bacteria to Gram-negative bacteria) to varying degrees. Moss properties (biomass, C and N concentrations, C:N ratio and saturated water absorption content), as well as SWC, soil microbial biomass and community composition regulated by mosses affected soil C and N. These findings underscore the crucial role of mosses in facilitating soil C and N accumulation during vegetation restoration.

Unravelling the dynamics of soil microbial communities under the environmental selection and range shift process in afforestation ecosystems

The process of forest range shift not only affects the vegetation aboveground but also influences the dynamics of belowground microbial communities. To investigate the changes in soil under forest range shift, we examined the natural forest soil microbiome along with its corresponding physicochemical properties, as well as the afforestation of natural forest by seedlings and sowing. By utilizing natural forests and employing different afforestation methods, we simulated the three stages of forest range shift: the staging stage, regeneration, and colonization. We employed network analysis and phylogenetic assemblages to examine the structure of soil microbial communities during these three stages in a macro-environmental change context. Ordination and regression analyses were also used to explore the correlation between microorganisms, environmental factors, and changes in their niches. The findings revealed that different afforestation (range shift) types led to distinct microbial compositions. Seedling afforestation exhibited similarities to mature forests, suggesting a significant influence on below-ground microorganisms. In contrast, sowing-based afforestation resulted in small changes in soil microbes, indicating a legacy effect on grassland soils. The impact of the rhizosphere on microbial composition remained consistent across the three forest types. Overall, this study underscores the significance of forest range shift in shaping soil microbial communities and emphasizes the need to consider these dynamics in forest management and restoration endeavours.