Warming reshaped the microbial hierarchical interactions

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

Fungal community determines soil multifunctionality during vegetation restoration in metallic tailing reservoir

Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals.

Opposite effects of soil pH on bacteria and fungi β diversity in forests at a continental scale

Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial β diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal β diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with β diversity but not for fungal diversity. Soil fungi exhibited higher β diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal β diversity, and significant positive correlations were found between fungal β diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with β-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial β diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.

Cadmium contamination decreased bacterial network complexity and stability in coastal reclamation areas

Cadmium(Cd) contamination can exert significantly adverse effects on soil microbiota in reclaimed areas, however, its effects on bacterial network structure are still limitedly understood. Here we collected soil samples from typical reclaimed wetlands (RW) and ditch wetlands (DW) in coastal reclamation areas and examined the effects of Cd contamination on the bacterial network complexity and stability. The results showed that the bacterial networks were destabilized by the Cd contamination, while bacteria in DW soils showed robust invulnerability characterized by higher node constancy and compositional stability compared with RW soils. Soil bacteria resisted Cd stress by forming a network with intensive connections in the module but sparser connections among the modules. Especially, network modularity was higher in DW soils than in RW soils, but made it more vulnerable to nodes removal. In addition, Cd contamination promoted bacterial positive cohesion but decreased negative cohesion in RW soils. Flavobacteriaceae, Xanthomonadaceae, and Alcaligenaceae were identified as core phylotypes, which played pivotal roles in regulating interspecies interactions due to higher contributions to cohesion and significant correlations with soil nutrients. The findings of this work indicate the changes of bacterial network structure and the indispensable role of core phylotypes in regulating interactions and maintaining network sustainability under Cd contamination.

Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems

Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

The structure of bacteria-fungi bipartite networks along elevational gradients in contrasting climates

Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change.

Comparison of the coexistence pattern of mangrove macrobenthos between natural and artificial reforestation

The abandoned pond-to-mangrove restoration project provides greater advantages than tidal flats afforestation in restoring mangrove ecosystem services and will be the primary method for mangrove restoration in the future. The existing methods for abandoned pond-to-mangrove restoration include artificial restoration through 'dike-breaking, filling with imported soil and tree planting' and natural restoration through 'dike-breaking and natural succession'. However, little is known about which restoration strategy (natural or artificial restoration) provides more benefits to the biodiversity of mangrove macrobethos. Given a prevailing view suggested that artificial restoration should be the preferred approach for accelerating recovery of biodiversity and vegetation structure in tropical regions, we hypothesised higher macrobenthic biodiversity and more complex community structure in artificial restoration than in natural restoration. To test this hypothesis, macrobenthic biodiversity and ecological processes were monitored in a typical abandoned pond-to-mangrove area of Dongzhaigang Bay, China, where artificial and natural restoration methods were used concurrently. Differences in macrobenthic biodiversity, community structure and ecological processes were compared using diversity indices, complex network analysis and null models. Similar species composition and ecological niche overlap and width among macrobenthos were observed at artificial and natural restoration sites. The biotic heterogeneity and interaction among macrobenthos were higher at the natural restoration sites than at the artificial restoration sites. Macrobenthos community assembly at natural and artificial restoration sites was both determined by deterministic processes, with environmental filtering dominating, which explained 52% and 54% of the variations in macrobenthic community structures respectively. Although our findings did not validate the research hypothesis, higher biotic heterogeneity and species interaction among macrobenthos could support natural restoration as the primary method for abandoned pond-to-mangrove projects, because it is a nature-based solution for mangrove restoration.

Habitat changes due to glacial freezing and melting reshape microbial networks

The phenomenon of glacial freezing and thawing involves microbial sequestration, release, and colonization, which has the potential to impact ecosystem functioning through changes in microbial diversity and interactions. In this study, we examined the structural features of microbial communities of the Dongkemadi glacier, including bacteria, fungi, and archaea, in four distinct glacial environments (snow, ice, meltwater, and frontier soil). The sequestration, release, and colonization of glacial microbes have been found to significantly impact the diversity and structure of glacial microbial communities, as well as the complexity of microbial networks. Specifically, the complexity of bacterial networks has been observed to increase in a sequential manner during these processes. Utilizing the Inter-Domain Ecological Network approach, researchers have further explored the cross-trophic interactions among bacteria, fungi, and archaea. The complexity of the bacteria-fungi-archaea network exhibited a sequential increase due to the processes of sequestration, release, and colonization of glacial microbes. The release and colonization of glacial microbes led to a shift in the role of archaea as key species within the network. Additionally, our findings suggest that the hierarchical interactions among various microorganisms contributed to the heightened complexity of the bacteria-fungi-archaea network. The primary constituents of the glacial microbial ecosystem are unclassified species associated with the Polaromonas. It is noteworthy that various key species in glacial ecosystems are influenced by the distinct environmental factors. Moreover, our findings suggest that key species are not significantly depleted in response to abrupt alterations in individual environmental factors, shedding light on the dynamics of microbial cross-trophic interactions within glacial ecosystems.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Tobacco crop rotation enhances the stability and complexity of microbial networks

Introduction

The effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities.

Methods

In order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach.

Results

There was no significant difference in α diversity, but significant difference in β diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable.

Discussion

From this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil.

Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest

Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future.

IMPORTANCE

Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.

Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems

Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat.

IMPORTANCE

Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.

Unraveling the impact of climatic warming and wetting on eukaryotic microbial diversity and assembly mechanisms: A 10-year case study in Lake Bosten, NW China

Over the last six decades, northwest China has undergone a significant climatic shift from "warm-dry" to "warm-wet", profoundly impacting the structures and functions of lake ecosystem across the region. However, the influences of this climatic transition on the diversity patterns, co-occurrence network, and assembly processes of eukaryotic microbial communities in lake ecosystem, along with the underlying mechanisms, remain largely unexplored. To bridge this knowledge gap, our study focused on Lake Bosten, the largest inland freshwater body in China, conducting a comprehensive analysis. Firstly, we examined the dynamics of key water quality parameters in the lake based on long-term monitoring data (1992-2022). Subsequently, we collected 93 water samples spanning two distinctive periods: low water level (WL) and high total dissolved solids (TDS) (PerWLTDS; 2010-2011; attributed to "warm-dry" climate), and high WL and low TDS (PerTDSWL; 2021-2022; associated with "warm-wet" climate). Eukaryotic microorganisms were further investigated using 18S rRNA gene sequencing and various statistical methods. Our findings revealed that climatic warming and wetting significantly increased eukaryotic microbial α-diversity (all Wilcox. test: P<0.05), while simultaneously reducing β-diversity (all Wilcox. test: P<0.001) and network complexity. Through the two sampling periods, assembly mechanisms of eukaryotic microorganisms were predominantly influenced by dispersal limitation (DL) and drift (DR) within stochastic processes, alongside homogeneous selection (HoS) within deterministic processes. WL played a mediating role in eukaryotic microbial DL and HoS processes in the PerTDSWL, whereas water quality and α-diversity influenced the DL process in the PerWLTDS. Collectively, these results underscore the direct and indirect impacts of "warm-wet" conditions on the eukaryotic microorganisms within Lake Bosten. This study provides valuable insights into the evolutionary dynamics of lake ecosystems under such climatic conditions and aids in predicting the ecological ramifications of global climatic changes.

Sediment DNA Records the Critical Transition of Bacterial Communities in the Arid Lake

It is necessary to predict the critical transition of lake ecosystems due to their abrupt, non-linear effects on social-economic systems. Given the promising application of paleolimnological archives to tracking the historical changes of lake ecosystems, it is speculated that they can also record the lake's critical transition. We studied Lake Dali-Nor in the arid region of Inner Mongolia because of the profound shrinking the lake experienced between the 1300 s and the 1600 s. We reconstructed the succession of bacterial communities from a 140-cm-long sediment core at 4-cm intervals and detected the critical transition. Our results showed that the historical trajectory of bacterial communities from the 1200 s to the 2010s was divided into two alternative states: state1 from 1200 to 1300 s and state2 from 1400 to 2010s. Furthermore, in the late 1300 s, the appearance of a tipping point and critical slowing down implied the existence of a critical transition. By using a multi-decadal time series from the sedimentary core, with general Lotka-Volterra model simulations, local stability analysis found that bacterial communities were the most unstable as they approached the critical transition, suggesting that the collapse of stability triggers the community shift from an equilibrium state to another state. Furthermore, the most unstable community harbored the strongest antagonistic and mutualistic interactions, which may imply the detrimental role of interaction strength on community stability. Collectively, our study showed that sediment DNA can be used to detect the critical transition of lake ecosystems.

Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss

Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.

Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration

To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.

Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China

The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Polyethylene microplastic-induced microbial shifts affected greenhouse gas emissions during litter decomposition in coastal wetland sediments

Microplastic contamination has become increasingly aggravated in coastal environments, further affecting biogeochemical processes involved with microbial community shifts. As a key biogeochemical process mainly driven by microbiota in coastal wetland sediments, litter decomposition contributes greatly to the global greenhouse gas (GHG) budget. However, under microplastic pollution, the relationship between microbial alterations and GHG emissions during litter decomposition in coastal wetlands remains largely unknown. Here, we explored the microbial mechanism by which polyethylene microplastic (PE-MP) influenced greenhouse gas (i.e., CH4, CO2 and N2O) emissions during litter decomposition in coastal sediments through a 75-day microcosm experiment. During litter decomposition, PE-MP exposure significantly decreased cumulative CH4 and CO2 emissions by 41.07% and 25.79%, respectively. However, there was no significant change in cumulative N2O emissions under PE-MP exposure. The bacterial, archaeal, and fungal communities in sediments exhibited varied responses to PE-MP exposure over time, as reflected by the altered structure and changed functional groups of the microbiota. The altered microbial functional groups ascribed to PE-MP exposure and sediment property changes might contribute to suppressing CH4 and CO2 emissions during litter decomposition. This study yielded valuable information regarding the effects of PE-MP on GHG emissions during litter decomposition in coastal wetland sediments.

Responses of soil greenhouse gas emissions to soil mesofauna invasions and its driving mechanisms in the alpine tundra: A microcosm study

Climate change is resulting in significant modifications of the altitudinal patterns of soil fauna in mountains, leading to their upward invasion and alteration of soil ecological processes. However, the effects of soil greenhouse gas (GHG) emissions from soil mesofauna invasion and their driving mechanisms have not been clearly understood. To address this knowledge gap, we simulated a soil mesofauna invasion from an Erman's birch forest (EB) to the alpine tundra (AT) of the Changbai Mountain in Northeast China. Four treatments were established: no soil mesofauna (S0), native species (SN), invasive species (SI), and invasive species superposed native species (SS). We conducted a 79-day microcosm experiment, utilizing gas chromatography and high-throughput sequencing, to explore the variations in soil greenhouse gas emissions and their driving factors. Results showed that the cumulative CO2 emissions under SN, SI, and SS, compared with S0, increased by 34.13 %, 73.93 %, and 107.64 % and cumulative N2O emissions increased by 59.05 %, 101.18 %, and 183.88 %, respectively. Compared to SN, the cumulative emissions of CO2 and N2O increased by 29.89 % and 26.31 % under SI and by 54.91 % and 78.59 % under SS, respectively. The impacts of invasive species and native species on greenhouse gases were not a simple additive effect. Abiotic (soil variables) and biotic (soil mesofauna and microbial diversity) factors explained 37.76 % and 44.41 % of the total variations in CO2 and N2O emissions, respectively, in which NH4+-N and C: N ratios contributed the largest variations. The contribution of soil mesofauna diversity to the variations in CO2 and N2O emissions was higher than that of microbial diversity. The bacterial network graph density was correlated with soil CO2 and N2O emissions. Our findings highlight that soil mesofauna invasions increased GHG emissions, and these variations were predominantly explained by biotic rather than abiotic factors.

Different long-term fertilization regimes affect soil protists and their top-down control on bacterial and fungal communities in Mollisols

Soil protists represent a vastly diverse component of soil microbial communities and significantly contribute to biogeochemical cycling. However, how different fertilization regimes impact the protistan communities and their top-down control on bacteria and fungi remain largely unknown. Here, using high-throughput sequencing, we investigated the differences in protist communities and their relationships with bacterial and fungal communities in Mollisols of Northeast China that were subjected to chemical and organic fertilization over 30 years. The results showed that manure addition rather than chemical fertilization significantly increased protistan alpha diversity and changed protistan community structure. Manure amendments markedly increased the relative abundances of protistan consumers (such as Cercozoa) and reduced the proportion of phototrophic protists (such as Chlorophyta). Soil pH was the most influential factor driving microbial communities, and protists were less sensitive to environmental disturbances than bacteria and fungi. Protistan communities exhibited more stronger relationships with bacterial communities than fungal communities, and Chlorococcum was the most important contributor in regulation of microbial taxa and functional genes. Furthermore, manure addition slightly simplified the microbial network, and chemical plus manure fertilization improved network stability with the highest robustness. Manure addition specifically mitigated the negative interactions between protists and bacteria while reinforced the positive interactions between protists and fungi. This study advanced our knowledge about the roles of protistan groups in regulating microbial communities and ecosystem functions associated with chemical and organic fertilization.

Relationships among protozoa, bacteria and fungi in polycyclic aromatic hydrocarbon-contaminated soils

Soil bacterial and fungal communities play key roles in the degradation of organic contaminants, and their structure and function are regulated by bottom-up and top-down factors. Microbial ecological effects of polycyclic aromatic hydrocarbons (PAHs) and trophic interactions among protozoa and bacteria/fungi in PAH-polluted soils have yet to be determined. We investigated the trophic interactions and structure of the microbiome in PAH-contaminated wasteland and farmland soils. The results indicated that the total concentration of the 16 PAHs (∑PAHs) was significantly correlated with the Shannon index, NMDS1 and the relative abundances of bacteria, fungi and protozoa (e.g., Pseudofungi) in the microbiome. Structural equation modelling and linear fitting demonstrated cascading relationships among PAHs, protozoan and bacterial/fungal communities in terms of abundance and diversity. Notably, individual PAHs were significantly correlated with microbe-grazing protozoa at the genus level, and the abundances of these organisms were significantly correlated with those of PAH-degrading bacteria and fungi. Bipartite networks and linear fitting indicated that protozoa indirectly modulate PAH degradation by regulating PAH-degrading bacterial and fungal communities. Therefore, protozoa might be involved in regulating the microbial degradation of PAHs by predation in contaminated soil.

Differences in soil microbial community structure and assembly processes under warming and cooling conditions in an alpine forest ecosystem

Global climate change affects the soil microbial community assemblages of many ecosystems. However, little is known about the effects of climate warming on the structure of soil microbial communities or the underlying mechanisms that influence microbial community composition in alpine forest ecosystems. Thus, our ability to predict the future consequences of climate change is limited. In this study, with the use of PVC pipes, the in situ soils of the rush-tip long-bud Abies georgei var. smithii forest at 3500 and 4300 m above sea level (MASL) of the Sygera Mountains were incubated in pairs for 1 year to simulate climate cooling and warming. This shift corresponds to a change in soil temperature of ±4.7 °C. Findings showed that climate warming increased the complexity of bacterial networks but decreased the complexity of fungal networks. Climate cooling also increased the complexity of bacterial networks. However, in fungal communities, climate cooling increased the number of nodes but decreased the total number of edges. Stochastic processes acted as the drivers of bacterial community composition, with climate warming leading the shift from deterministic to stochastic drivers. Fungal communities were more sensitive to climate change than bacterial communities, with soil temperature (ST) and soil water content (SWC) acting as the main drivers of change. By contrast, soil bacterial communities were more closely related to soil conditions than fungal communities and remained stable after a year of soil transplantation. In conclusion, fungi and bacteria had different response patterns, and their responses to climate cooling and warming were asymmetric. This work is expected to contribute to our understanding of the response to climate change of soil microbial communities in alpine forests and our prediction of the functions of soil microbial ecosystems in alpine forests.

Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.

Microbial responses to long-term warming differ across soil microenvironments

Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.

Protists regulate microbially mediated organic carbon turnover in soil aggregates

Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems.

Warming reduces microeukaryotic diversity, network complexity and stability

Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P＜0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P＞0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.

Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field

Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.

Transformation of Biofilm to Carbon Sinks after Prolonged Droughts Linked with Algal Biodiversity Change

Global climate change significantly increased the duration of droughts in intermittent rivers, impacting benthic microbial-mediated biogeochemical processes. However, the impact of prolonged droughts on the carbon contribution of intermittent rivers remains poorly understood. In this study, we investigated the potential effects of varying drought gradients (ranging from 20 to 130 days) on benthic biofilms community structure (algae, bacteria, and fungi) and their carbon metabolism functions (ecosystem metabolism and carbon dioxide (CO2) emission fluxes) using mesocosm experiments. Our findings indicate that longer drought durations lead to reduced alpha diversity and community heterogeneity, tighter interdomain networks, and an increased role of stochastic processes in community assembly, with a discernible threshold at around 60 days. Concurrently, the biofilm transforms into a carbon sink following a drought period of 60 days, as evidenced by the transformation of CO2 emission fluxes from 633.25 ± 194.69 to -349.61 ± 277.79 mg m-2 h-1. Additionally, the partial least-squares path model revealed that the resilience of algal communities and network stability may drive biofilm's transformation into a carbon sink, primarily through the heightened resilience of autotrophic metabolism. This study underscores the significance of the carbon contribution from intermittent rivers, as the shift in carbon metabolism functions with increasing droughts could lead to skewed estimations of current riverine carbon fluxes.

Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau

Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.

Interkingdom network analyses reveal microalgae and protostomes as keystone taxa involved in nutrient cycling in large freshwater lake sediment

Few studies have explored the role of interkingdom interactions between bacteria and microeukaryotes in nutrient cycling in lake ecosystems. We conducted sediment sampling from 40 locations covering Hongze Lake and analyzed their chemical properties. Intra- and interkingdom networks were constructed using 16S and 18S rRNA gene amplicon sequencing. Microeukaryotic intranetworks were more complex in spring than in autumn, while no clear variation in the complexity of bacterial intranetworks was found between autumn and spring. Larger and more complex bacterial-microeukaryotic bipartite networks emerged in spring than in autumn, correlated with lower carbon, nitrogen, and phosphorus levels in spring, likely resulting in intense microbial competition. Bacteria and microeukaryotes played different topological roles in interkingdom networks, with microeukaryotes contributing to the networks' greater complexity. Seven keystone modules were identified in spring and autumn nutrient cycling. Importantly, keystone taxa in these modules belonged to photoautotrophic microalgae or predatory protostomes, indicating that these organisms are key drivers in lake sediment nutrient cycling. Our results suggested that nutrient content variation in autumn and spring changes interkingdom networks' topological structure between bacteria and microeukaryotes. Microalgae and protostomes are essential in freshwater lake nutrient cycling and may be targeted to modulate nutrient cycling in large freshwater ecosystems.

Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot

Introduction

Root rot caused by the fungal pathogen Fusarium sp. poses significant challenges to tobacco cultivation in China, leading to major economic setbacks. The interplay between this pathogen and the wider soil microbial community remains poorly understood.

Methods

High-throughput sequencing technology was utilized to evaluate soil prokaryotic, fungal, and protistan communities. We compared microbial communities in infected soils to those in healthy soils from the same field. Additionally, the influence of pH on the microbial communities was assessed.

Results

Infected soils displayed elevated levels of soil nutrients but diminished observed richness across prokaryotic, fungal, and protistan groups. The pathogenic fungi Fusarium solani f sp. eumartii's abundance was notably increased in infected soils. Infection with F. solani significantly altered the soil's microbial community structure and interactions, manifested as a decrease in network scale and the number of keystone species. An evaluation of prokaryotes' role in F. solani's invasion revealed an increased number of connecting nodes in infected soils. Additionally, relationships between predatory protists and fungi were augmented, whereas predation on F. solani declined.

Discussion

The study underscores the significance of comprehending the interactions among soil microorganisms and brings to light the susceptibility of soil microbial communities to pathogen invasion. It offers insights into the multifaceted relationships and potential vulnerabilities within the soil ecosystem in the context of Fusarium sp. invasion.

Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation

Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress is thought to promote microbial mutualism, there is a paucity of research in this area. Here, we monitor microbial communities in a quasi-natural composting system, where temperature variation (20 °C-70 °C) is the main abiotic stress. Genomic analyses and culturing experiments provide evidence that temperature selects for slow-growing and stress-tolerant strains (i.e., Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and the remaining strains through the sharing of cobalamin. Comparison of 3000 bacterial pairings reveals that mutualism is common (~39.1%) and competition is rare (~13.9%) in pairs involving T. fusca and S. viridis. Overall, our work provides insights into how high temperature can favour mutualism and reduce competition at both the community and species levels.

Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality

Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.

Relic DNA obscures DNA-based profiling of multiple microbial taxonomic groups in a river-reservoir ecosystem

Numerous studies have investigated the spatiotemporal variability in water microbial communities, yet the effects of relic DNA on microbial community profiles, especially microeukaryotes, remain far from fully understood. Here, total and active bacterial and microeukaryotic community compositions were characterized using propidium monoazide (PMA) treatment coupled with high-throughput sequencing in a river-reservoir ecosystem. Beta diversity analysis showed a significant difference in community composition between both the PMA untreated and treated bacteria and microeukaryotes; however, the differentiating effect was much stronger for microeukaryotes. Relic DNA only resulted in underestimation of the relative abundances of Bacteroidota and Nitrospirota, while other bacterial taxa exhibited no significant changes. As for microeukaryotes, the relative abundances of some phytoplankton (e.g. Chlorophyta, Dinoflagellata and Ochrophyta) and fungi were greater after relic DNA removal, whereas Cercozoa and Ciliophora showed the opposite trend. Moreover, relic DNA removal weakened the size and complexity of cross-trophic microbial networks and significantly changed the relationships between environmental factors and microeukaryotic community composition. However, there was no significant difference in the rates of temporal community turnover between the PMA untreated and treated samples for either bacteria or microeukaryotes. Overall, our results imply that the presence of relic DNA in waters can give misleading information of the active microbial community composition, co-occurrence networks and their relationships with environmental conditions. More studies of the abundance, decay rate and functioning of nonviable DNA in freshwater ecosystems are highly recommended in the future.

Temperature-mediated microbial carbon utilization in China's lakes

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands

Introduction

Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions.

Methods

To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China.

Results and Discussion

We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Untangling microbiota diversity and assembly patterns in the world's longest underground culvert water diversion canal

The long-distance underground box culvert water transport system (LUBWT) is a crucial link between the source of drinking water and the consumers. It must ensure the stability of water quality during transportation. However, uncontrollable microbial growth can develop in the water delivery system during the long delivery process, posing a risk to health and safety. Therefore, we applied 16 s and 18 s gene sequence analysis in order to study microbial communities in box culvert waters sampled in 2021, as well as a molecular ecological network-based approach to decipher microbial interactions and stability. Our findings revealed that, in contrast to natural freshwater ecosystems, micro-eukaryotes in LUBWT have complex interactions such as predation, parasitism, and symbiosis due to their semi-enclosed box culvert environment. Total nitrogen may be the primary factor affecting bacterial community interactions in addition to temperature. Moreover, employing stability indicators such as robustness and vulnerability, we also found that microbial stability varied significantly from season to season, with summer having the higher stability of microbial communities. Not only that but also the stability of the micronuclei also varied greatly during water transport, which might also be related to the complex interactions among the micro-eukaryotes. To summarize, our study reveals the microbial interactions and stability in LUBWT, providing essential ecological knowledge to ensure the safety of LUBWT's water quality.

The effects of climate warming on microbe-mediated mechanisms of sediment carbon emission

Due to significant differences in biotic and abiotic properties of soils compared to those of sediments, the predicted underlying microbe-mediated mechanisms of soil carbon emissions in response to warming may not be applicable for estimating similar emissions from inland water sediments. We addressed this issue by incubating different types of sediments, (including lake, small river, and pond sediments) collected from 36 sites across the Yangtze River basin, under short-term experimental warming to explore the effects of climate warming on sediment carbon emission and the underlying microbe-mediated mechanisms. Our results indicated that under climate warming CO₂ emissions were affected more than CH₄ emissions, and that pond sediments may yield a greater relative contribution of CO₂ to total carbon emissions than lake and river sediments. Warming-induced CO₂ and CH₄ increases involve different microbe-mediated mechanisms; Warming-induced sediment CO₂ emissions were predicted to be directly positively driven by microbial community network modularity, which was significantly negatively affected by the quality and quantity of organic carbon and warming-induced variations in dissolved oxygen, Conversely, warming-induced sediment CH₄ emissions were predicted to be directly positively driven by microbial community network complexity, which was significantly negatively affected by warming-induced variations in pH. Our findings suggest that biotic and abiotic drivers for sediment CO₂ and CH₄ emissions in response to climate warming should be considered separately when predicting sediment organic carbon decomposition dynamics resulting from climate change.

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival

BACKGROUND

Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.

CONCLUSION

The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.

Effects of nitrogen and phosphorus supply levels and ratios on soil microbial diversity-ecosystem multifunctionality relationships in a coastal nontidal wetland

Human activities have changed the levels and ratios of nitrogen (N) and phosphorus (P) in wetland ecosystems. However, the effects of N and P levels and ratios on wetland soil microbial community and ecosystem multifunctionality remain unclear, especially on the relationships between soil microbial diversity and ecosystem multifunctionality. In this study, the effects of a 7-year experimental nutrient addition on the soil microbial community and ecosystem multifunctionality (12 function variables related to carbon, N, and P cycling) were assessed by combining three N and P supply levels with three N:P supply ratios in a coastal nontidal wetland ecosystem. According to the obtained results, the N and P supply levels significantly affected soil bacterial community composition, as well as ecosystem multifunctionality, while no significant effects of N:P supply ratios were observed. Although N and P supply levels did not significantly affect bacterial and fungal diversity, they both changed the complexity of bacterial and fungal networks. Soil ecosystem multifunctionality was significantly and positively correlated with bacterial diversity rather than fungal diversity. Moreover, the correlation coefficient between bacterial diversity and ecosystem multifunctionality showed an increasing-decreasing trend with increasing N and P supply levels and an increasing trend with increasing N:P supply ratios. However, the correlation coefficient between bacterial diversity and ecosystem multifunctionality was not significantly correlated with bacterial network complexity. The current study provides new insights into the impacts of N and P levels and ratios on soil microbial community and ecosystem multifunctionality in a coastal nontidal wetland. In particular, the present study highlighted that changes in N and P supply levels and ratios lead to changes in the relationship between soil bacterial diversity and ecosystem multifunctionality, which should be considered in related studies to accurately predict the responses of ecosystem multifunctionality to N and P inputs in coastal nontidal wetlands.

Spatial distribution patterns across multiple microbial taxonomic groups

Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R² = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.

Mechanism of bacterial communities regulating litter decomposition under climate warming in temperate wetlands

Plant litter decomposition plays a crucial role in the flow of nutrients and energy in ecosystems. However, the mechanism of bacterial communities regulating litter decomposition under climate warming in temperate wetlands remains largely unknown. The objective of this study was to determine the influences of temperature on decomposition and the bacterial regulatory mechanism under climate warming in temperate wetlands. In this study, we conducted a 1.5-year litter decomposition warming experiment using dominant plant species in the temperate lake wetlands of the North China Plain. Our results showed that the decomposition rate (K) had a significant positive correlation with temperature, and the non-additive effects of litter decomposition could be clearly observed in the mixtures of Phragmites australis and Typha angustata, especially under warming conditions. Among the three types of litter, Phragmites australis had the highest temperature sensitivity (2.75), which meant that it would be most affected by climate change in the future. The concentrations of C and N showed a significant positive correlation with the decomposition rate and were mainly driven by Proteobacteria and Firmicutes, while the concentration of lignin and the lignin:N ratio had a highly significant negative correlation with the decomposition rate and were mainly driven by Bacteroidota and Actinobacteriota. Furthermore, the bacterial cooccurrence network revealed that the abundance of Firmicutes and Desulfobacterota increased significantly, and positive edges accounted for 67.81% ~ 71.14% under warming conditions. The bacterial networks of litter decomposition were mainly composed of symbiotic relationships, and warming was helpful for improving the positive correlations and symbiotic relationships of bacterial flora and sped up the litter decomposition process. These results will be helpful to further understand the mechanism of bacterial communities regulating litter decomposition under climate warming in temperate wetland ecosystems.

Electrostimulation triggers an increase in cross-niche microbial associations toward enhancing organic nitrogen wastewater treatment

As an efficient wastewater pretreatment biotechnology, electrostimulated hydrolysis acidification (eHA) has been used to accelerate the removal of refractory pollutants, which is closely related to the effects of electrostimulation on microbial interspecies associations. However, the ecological processes underpinning such linkages remain unresolved, especially for the microbial communities derived from different niches, such as the electrode surface and plankton. Herein, the principles of cross-niche microbial associations and community assembly were investigated using molecular ecological network and phylogenetic bin-based null model analysis (iCAMP) based on 16S rRNA gene sequences. The electrostimulated planktonic sludge and electrode biofilm displayed significantly (P < 0.05) 1.67 and 1.53 times higher organic nitrogen pollutant (azo dye Alizarin Yellow R) degradation efficiency than non-electrostimulation group, and the corresponding microbial community composition and structure were significantly (P < 0.05) changed. Electroactive bacteria and functional degraders were enriched in the electrode biofilm and planktonic sludge, respectively. Notably, electrostimulation strengthened the synergistic microbial associations (1.8 times more links) between sludge and biofilm members. Additionally, both electrostimulation and cross-niche microbial associations induced greater importance of deterministic assembly. Overall, this study highlights the specificity of cross-electrode surface microbial associations and ecological processes with electrostimulation and advances our understanding of the manipulation of sludge microbiomes in engineered wastewater treatment systems.

Eukaryotes contribute more than bacteria to the recovery of freshwater ecosystem functions under different drought durations

Global climate change mostly impacts river ecosystems by affecting microbial biodiversity and ecological functions. Considering the high functional redundancy of microorganisms, the unknown relationship between biodiversity and ecosystem functions obstructs river ecological research, especially under the influence of increasing weather extremes, such as in intermittent rivers and ephemeral streams (IRES). Herein, dry-wet alternation experiments were conducted in artificial stream channels for 25 and 90 days of drought, both followed by 20 days of rewetting. The dynamic recovery of microbial biodiversity and ecosystem functions (represented by ecosystem metabolism and denitrification rate) were determined to analyse biodiversity-ecosystem-function (BEF) relationships after different drought durations. There was a significant difference between bacterial and eukaryotic biodiversity recovery after drought. Eukaryotic biodiversity was more sensitive to drought duration than bacterial, and the eukaryotic network was more stable under dry-wet alternations. Based on the establishment of partial least squares path models, we found that eukaryotic biodiversity has a stronger effect on ecosystem functions than bacteria after long-term drought. Indeed, this work represents a significant step forward for further research on the ecosystem functions of IRES, especially emphasizing the importance of eukaryotic biodiversity in the BEF relationship.

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.

Soil bacterial communities associated with multi-nutrient cycling under long-term warming in the alpine meadow

Introduction

The functions of terrestrial ecosystems are mainly maintained by bacteria, as a key component of microorganisms, which actively participate in the nutrient cycling of ecosystems. Currently, there are few studies have been carried out on the bacteria contributing to the soil multi-nutrient cycling in responding to climate warming, which hampers our obtainment of a comprehensive understanding of the ecological function of ecosystems as a whole.

Methods

In this study, the main bacteria taxa contributing to the soil multi-nutrient cycling under the long-term warming in an alpine meadow was determined based onphysichemical properties measurement and high-throughput sequencing, and the potential reasons that warming altered the main bacteria contributing to the soil multi-nutrient cycling were further analyzed.

Results

The results confirmed that the bacterial β-diversity was crucial to the soil multi-nutrient cycling. Furthermore, Gemmatimonadetes, Actinobacteria, and Proteobacteria were the main contributors to the soil multi-nutrient cycling, and played pivotal roles as keystone nodes and biomarkers throughout the entire soil profile. This suggested that warming altered and shifted the main bacteria contributing to the soil multi-nutrient cycling toward keystone taxa.

Discussion

Meanwhile, their relative abundance was higher, which could make them have the advantage of seizing resources in the face of environmental pressures. In summary, the results demonstrated the crucial role of keystone bacteria in the multi-nutrient cycling under the climate warming in the alpine meadow. This has important implications for understanding and exploring the multi-nutrient cycling of alpine ecosystems under the global climate warming.

Responses of soil microbial diversity, network complexity and multifunctionality to three land-use changes

Land-use change is one of the greatest challenges for natural ecosystem services. Soil microbiomes are essential for modulating multiple ecosystem functions. However, little is known about the impact of land-use changes on soil microbial communities and their associated soil functions. In this study, 150 alpine soil samples representing conversion of forests to shrublands or grasslands, and of shrublands to grasslands were investigated for bacterial, fungal and protistan community diversity, co-occurrence network, as well as their relationships with soil multifunctionality via a sampling strategy of space-for-time substitution. The conversion of forest to grassland increased the diversity of fungi and bacteria, and altered the microbial community structures of bacteria, fungi and protists, resulting a greater impact on soil microbiome than other land-use conversions. Cross-trophic interaction analyses demonstrated this conversion increased microbial network complexity and robustness, whereas forest to shrubland had the opposite trend. The land-use induced changes in soil multifunctionality were related with microbial network modules, but were not always associated with variations of microbial diversity. Random forest modeling further suggested the significant role of microbial modules in explaining soil multifunctionality, together with environmental factors. These findings indicate divergent responses of belowground multitrophic organisms to land-use changes, and the potential role of microbial module in forecasting soil multifunctionality.