Soil microbial diversity and network complexity drive the ecosystem multifunctionality of temperate grasslands under changing precipitation

Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities

Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.

The type and degree of salinized soils together shape the composition of phoD-harboring bacterial communities, thereby altering the effectiveness of soil phosphorus cycling

Limitations in soil nutrient content, particularly phosphorus (P), are key factors constraining saline soil ecosystems. Soil phosphorus-cycling functional microorganisms contribute to the conversion of insoluble phosphorus and increase available phosphorus (AP) levels in phosphorus-deficient soils. However, there is limited knowledge on how soil phoD-harboring bacterial communities regulate AP availability across varying salinization types and degrees. This work evaluated the diversity, composition, assembly, and co-occurrence network properties of phoD-harboring bacteria, and explored their relationship with AP in salinized soils of Ningxia. First, TP, APi, and Ca10P levels were high in all salinized soils, whereas bioavailable fractions (AP, MBP, Ca2P, and Ca8P) were significantly low, limiting plant phosphorus uptake. Notably, the phoD gene, which is the most abundant functional gene involved in phosphorus cycling in saline soils, exhibits a pronounced salt-stress attenuation pattern along with the Shannon and Chao1 indices of the phoD-harboring bacterial community. Consistent with this pattern, the network complexity and stability of these bacteria were overall negatively affected by saline stress pressure when compared to non-saline soils. Furthermore, as evidenced by the distribution variations among bacteria such as Bradyrhizobium, Skermanella, Pseudomonas, Streptomyces, and Mesorhizobium, the type and degree of salinization jointly shape the composition of soil phoD-harboring bacterial communities. Importantly, the composition of these bacteria communities significantly regulates alkaline phosphatase ALP activity, thereby increasing soil AP levels. Consequently, the type and degree of salinized soil can indirectly regulate AP levels by influencing the composition of the phoD-harboring bacterial community. The research findings highlight that the composition of the phoD-harboring bacteria community is critical for the regulation of phosphorus efficiency in saline-affected soils, which holds significant theoretical and practical implications for the management of phosphorus in salinized soils and sustainable agricultural practices.

The community dynamic alterations mechanisms of traveling plastics in the Pearl River estuary with the salinity influence

Most ocean plastics originate from terrestrial emissions, and the plastisphere on the plastics would alter during the traveling due to the significant differences in biological communities between freshwater and marine ecosystems. Microorganisms are influenced by the increasing salinity during traveling. To understand the contribution of plastic on the alteration in biological communities of plastisphere during traveling, this study investigated the alterations in microbial communities on plastics during the migration from freshwater to brackish water and saltwater. The results revealed that the migrated plastics can form unique microhabitats with high bacterial and eukaryotic diversity. Compared with the natural carrier (stone), the communities in plastisphere had fewer variations with salinity, indicating that plastisphere can offer stronger protection for freshwater organisms. The hydrophobicity of plastics promoted algal colonization, providing a stable nutrient source for the community during salinity fluctuations. This reduced material exchange between the plastisphere and the surrounding high-salinity environment, facilitating greater community stability. Additionally, the abundant Ochrophyta and Bryozoa of eukaryotes on migrated plastics can facilitate further colonization and promote species diversity. Plastisphere microbial networks revealed that the reduction of salt-intolerant organisms during traveling had fewer effects on the abundance of associated organisms. A more stable community on migrated plastics led to the proliferation of pathogens and carbon cycle-degrading microorganisms. And the increasing relative abundance of carbon cycling functions indicated that the traveling plastics could pose higher environmental risks and exhibit enhanced carbon metabolic capabilities. The study highlighted the biofilms on migrated plastics as a unique ecological niche in estuarine environments, offering a crucial reference for evaluating the ecological risks linked to plastic travel from rivers to the ocean.

Maize associated bacterial and fungal microbiomes show contrasting conformation patterns dependent on plant compartment and water availability

Plant-associated microorganisms can help crops to alleviate stress and increase the resilience of agricultural ecosystems to climate change. However, we still lack knowledge on the dynamics of soil and plant microbiomes and their response to changing conditions. This information is essential for the development of microbiome-based solutions to improve crop resilience to stressors associated with climate change. In this work, we explored: (i) the conformation of the bacterial and fungal assemblages of different soil and plant compartments (bulk soil, rhizosphere, roots, leaves and grains) along the crop cycle of maize in an open field trial; and (ii) the effect of water restriction on the maize microbiome, comparing optimal irrigation with a 30% reduction of water supply. Our results show a dynamic compartment-driven recruitment of microorganisms with contrasting patterns for bacteria and fungi that were intensified towards the end of the plant cycle. Roots showed the most differentiated bacterial assemblage while fungi conformed a very distinct community in the leaves, suggesting a relevant contribution of aerial fungal propagules to the microbiome of this plant organ. Regarding the grain, bacterial communities looked closer to those in the leaves, while fungal communities were more like those in the root. Despite the reductions in plant growth and yield, the microbiome of limited-watered plants did not show severe alterations. Still, significant impacts were observed within compartments, being fungi more responsive to limited watering than bacteria, with hallmark fungal ASVs for each compartment and irrigation regime. Network analysis suggests that bacteria and fungi may play different roles in the shifts observed under water limitation. Our study highlights the importance of conducting multikingdom analyses for a holistic understanding of the dynamics and evolution of the microbial assemblages in the whole plant and their roles in plant response to environmental stressors.

Response of dissolved organic matter and bacterial community to anthropogenic disturbances in a plateau lake

Introduction

Dissolved organic matter (DOM) and bacterial communities play essential roles in lake ecosystem biogeochemical cycles. However, the effects of anthropogenic disturbances on their interactions are not fully understood.

Methods

This study used UV-vis techniques, excitation-emission matrix parallel factor analysis, and 16S rRNA sequencing to reveal the differences in the structures of fluorescent DOM (FDOM) and bacterial communities in lake sediments and water under different levels of anthropogenic disturbances. Methods such as Spearman correlation analysis, null model, neutral community model and random forest analysis were explored how FDOM composition and bacterial communities respond to anthropogenic disturbances in the sediments and water of the Caohai Lake.

Results

The results indicated that sediment FDOM was sensitive to anthropogenic disturbances, with protein-like substances dominating heavily disturbed areas (69%) and humic-like substances dominating less disturbed areas (63%). However, no significant difference in FDOM composition was found in the water. Similarly, α and β diversity indices for bacterial communities showed no marked variation (P > 0.05) between highly and lightly disturbed areas in both water and sediment samples. Nevertheless, co-occurrence network analysis revealed more negatively correlated links and longer average path length with stronger disturbances. This suggests that while the intensity of anthropogenic disturbance has not yet reached a threshold sufficient to alter the structure of the bacterial community, it might have influenced the types and quantities of resources accessible to the community. Consequently, bacteria might have responded to these changes through competitive interactions, enabling them to resist environmental fluctuations. We found that anthropogenic disturbances were positively linked stochastic processes in the bacterial community assembly and influenced groups that degraded terrestrial humic-like substances. Moreover, the sources and fluorescence components of DOM could have shaped bacterial diversity and community assembly.

Discussion

Overall, these findings illustrate that anthropogenic disturbance affects FDOM composition and its relationship with bacteria, providing valuable insights for managing shallow lake ecosystems.

Precipitation changes reshape desert soil microbial community assembly and potential functions

Understanding the responses of desert microbial communities to escalating precipitation changes is a significant knowledge gap in predicting future soil health and ecological function. Through a five-year precipitation manipulation experiment, we investigated the contrasting eco-evolutionary processes of desert bacteria and fungi that manifested in changes to the assembly and potential functions of the soil microbiome. Elevated precipitation increased the alpha diversity and network complexity of bacteria and fungi, proportion of non-dominant phyla, and abundance of carbon- and nitrogen-fixing bacteria and saprophytic, symbiotic, and pathogenic fungi. Conversely, decreased precipitation reduced the alpha diversity and network complexity of bacteria and fungi while increasing the proportion of non-dominant phyla, stability of the network, and abundance of functional genes related to carbon and nitrogen degradation, nitrification, and ammonification. This suggests that soil microbes may attenuate the negative effects of reduced precipitation by streamlining communities, enhancing carbon and nitrogen acquisition, and promoting nitrogen cycling. Furthermore, we revealed that soil properties and vegetation attributes explained approximately 27.86%-37.75% and 17.76%-22.84% of the variation in bacterial and fungal communities, respectively. Finally, we demonstrated that precipitation-driven soil nutrient content and vegetation attributes are the potentially critical factors in shaping the soil microbial assembly and functions. These findings provide a foundation for understanding the response of desert soil microbes to escalating climate change.

Soil carbon stability regulate carbon dynamics following large-scale afforestation

Large-scale afforestation is considered an effective measure to mitigate climate change. However, due to the differences in the properties of soil organic carbon (SOC), the dynamic response of SOC to large-scale afforestation remained unclear. Therefore, we conducted paired sampling (farmland and afforestation) in plantation areas across northern China to evaluate the relationship between SOC stability and SOC increments (ΔSOC) resulting from afforestation. Our findings indicated that SOC-unstable soil supported greater carbon increments through afforestation, but at the expense of reduced SOC stability after afforestation. Additionally, we observed that this relationship exhibited geographical characteristics, with SOC-unstable soil demonstrating a stronger capacity to enhance ΔSOC at higher latitudes, particularly in the topsoil. This is primarily attributed to the fact that higher latitudes and colder climates enhance the contribution of particulate organic carbon to ΔSOC and weaken the regulatory effect of SOC chemical composition (carboxyl and aromatic carbon) on SOC stability after afforestation. These findings underscore the importance of incorporating pre-afforestation SOC stability to accurately predict soil carbon-afforestation feedback.

Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: Emphasis on antibiotic and metal resistance genes, and mobile genetic elements

The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.

Plant-microbiome interactions and their impacts on plant adaptation to climate change

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

The long-term straw return resulted in significant differences in soil microbial community composition and community assembly processes between wheat and rice

Introduction

Straw return is widely promoted as an environmentally sustainable practice to enhance soil health and agricultural productivity. However, the impact of varying straw return durations on soil microbial community composition and development remains insufficiently understood within a rice-wheat cropping system.

Methods

In this study, soil samples were collected during the wheat and rice harvesting periods following seven straw return durations: no straw return (NR) or 1, 3, 5, 7, 9, 11 years of straw return (SR1, 3, 5, 7, 9, 11), and microbial sequencing was performed.

Results

The results revealed a biphasic pattern in alpha diversity (Chao1 and Shannon) of soil microbial communities with increasing straw return duration, characterized by an initial increase followed by a subsequent decrease. Specifically, SR9 in the rice group exhibited the highest Chao1 and Shannon values, while SR3 in the wheat group showed the highest values. PCoA indicated significant shifts in microbial communities due to straw return, particularly in the wheat group compared to NR. Straw return obvious changed six bacterial phyla (Verrucomicrobiota, Proteobacteria, Desulfobacterota, MBNT15, Actinobacteriota, and Gemmatimonadota) during the rice and wheat harvesting periods, especially Proteobacteria. Correlation analysis between environmental factors and bacterial communities demonstrated a significant impact on these factors, particularly pH and total organic carbon (TOC) (p < 0.05), on the soil bacterial community during rice harvest, indicating the microbial enrichment after straw return may be related to the accumulation of TOC. Furthermore, the bacterial community network in the rice harvesting period was found to be more complex, with lower network stability compared to the wheat harvesting period. This complexity is closely associated with TOC accumulation in rice fields. Deterministic processes, including homogeneous and heterogeneous selection, were found to play a crucial role in shaping the soil bacterial communities in both rice and wheat systems. Environmental factors significantly influenced microbial community assembly during straw return and recycling.

Discussion

Our study enhances understanding of the impact of straw return on the diversity and assembly of soil microbial communities in the rice-wheat cropping system, which provide valuable insights for studying the mechanisms by which managing microbial communities after straw return can promote soil fertility restoration.

Deciphering bioprocess responses in organic phosphorus mineralization to different antibiotic stresses: Interaction mechanisms mediated by microbial succession and extracellular polymeric substances and regulatory patterns

Understanding the impacts and mechanisms of different antibiotics on organic phosphorus (OP) mineralization is crucial for promoting the rational utilization of resources and protecting the ecological environment. In this study, the effects of four commonly used antibiotics (sulfadiazine, ciprofloxacin, erythromycin, and ampicillin) on the mineralization of OP were explored using16S rRNA gene sequencing technology. The results showed that ciprofloxacin, erythromycin, and ampicillin negatively affected the mineralization capacity of OP, whereas sulfadiazine positively influenced OP mineralization. The content and composition of extracellular polymeric substances (EPS) and microbial phenotypes (biofilm formation and stress tolerance) were directly correlated with differences in OP mineralization capacity. Microbial diversity, network complexity and stability, and key microorganisms indirectly influenced OP mineralization by regulating EPS content and composition and microbial phenotypes. In summary, this study reveals specific impacts of different antibiotics on OP mineralization, offering valuable insights for addressing "phosphorus limitation" and "phosphorus load" amid various antibiotic stresses.

Soil microbial community and influencing factors of different vegetation restoration types in a typical agricultural pastoral ecotone

Microbial network complexity is an important indicator for assessing the effectiveness of vegetation restoration. However, the response of the microbial network complexity of bacteria and fungi to different vegetation restoration types is unclear. Therefore, in this study, we selected four vegetation restoration types (Pinus sylvestris var. mongholica, Larix principis- rupprechtii, Populus tomentosa, and Ulmus pumila), while selected the nature grassland as a control, in the Zhangjiakou Tunken Forest Farm, which is a typical agricultural pastoral ecotone in northern China, to investigate the response of soil microbial diversity and network complexity to different vegetation restoration types. Our result showed that the bacterial Shannon and Chao indices of P. sylvestris var. mongholica were significantly 7.77 and 22.39% higher than those of grassland in the 20-40 cm soil layer, respectively. The fungal Chao indices of U. pumila were significantly 85.70 and 146.86% higher than those of grassland in the 20-40 cm and 40-60 cm soil layer, respectively. Compared to natural grassland, soil microbial networks became more complex in plantation forests restoration types (P. sylvestris var. mongholica, L. principis- rupprechtii, P. tomentosa, and U. pumila). Microbial network complexity increased with soil carbon and nitrogen. P. tomentosa is suitable for planting in the agricultural pastoral ecotone of Zhangjiakou, because of its high soil carbon, nitrogen and microbial network complexity. Bacterial community composition was found to be closely related to soil organic carbon (SOC), total nitrogen (TN), while that of fungi was closely related to SOC, clay and silt content. This improvement in microbial complexity enhances the ecological service function of the agricultural pastoral ecotone. These findings offer theoretical basis and technical support for the vegetation restoration of ecologically fragile areas in agricultural pastoral ecotone.

Legacy effects of precipitation change: Theories, dynamics, and applications

The intensification of climate-induced precipitation change poses a dual challenge to terrestrial ecosystems: immediate effects on their structure and function, coupled with legacy effects that persist beyond the cessation of precipitation change. Quantifying these legacy effects accurately can greatly assist in assessing the long-term impact of precipitation change. However, their broader understanding is just beginning. Therefore, this review endeavors to synthesize the existing knowledge concerning the legacy effects of precipitation change, elucidating their nature, characteristics, driving factors, and implications, thereby fostering further advancements in this research domain. To begin, we define that precipitation legacies are carried by the information and/or material remnants arising from previous precipitation change, with the enduring impacts of these remnants (precipitation legacy carriers) on the current ecosystem being termed the precipitation legacy effects. To comprehensively investigate the performances of precipitation legacy effects, we introduce a multi-faceted characterization framework, encompassing magnitude, direction, duration, and spatial-temporal variability. This framework is complemented by a proposed sequential analysis approach, spanning the pre-, during, and post-precipitation change phases. Next, we emphasize that the nature of precipitation legacy carriers and the pattern of precipitation change jointly determine the characteristics of precipitation legacy effect. Subsequently, we elucidate the possible carriers of precipitation legacies across species, community, and ecosystem levels, as well as the linkages among these carriers and levels, thereby introducing the underlying formation mechanism of precipitation legacy effects. Lastly, from the perspective of ecosystem stability debt, we propose potential applications of precipitation legacy effects in future climate change research. The viewpoints and methodologies outlined in this review can deepen our comprehension of precipitation legacy effects, contributing to the comprehensive assessment of precipitation impact on soil-vegetation systems and providing guidance for formulating effective strategies to address future climate change.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e. multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

Extreme soil salinity reduces N and P metabolism and related microbial network complexity and community immigration rate

Soil microbiomes are well known to suffer from the effects of rising salinity. There are, however, no current understandings regarding its specific effects on microbial metabolic functions associated with nitrogen (N) and phosphorus (P) cycling, particularly in the Yellow River Delta (YRD), one of the largest estuaries in the world. This research examined soil microbiomes at 50 sites in the YRD region to analyze their co-occurrence networks and their relationship with N (nitrification, denitrification, dissimilatory, assimilatory, fixation, and mineralization) and P (solubilization, mineralization, transportation, and regulation) metabolism processes. Our findings indicate a notable reduction in soil multifunctionality as salinity levels increase, with Halofilum-ochraceum playing a significant role in nitrification, whereas Bacteroidetes-SB0662-bin-6 helps solubilize inorganic P in highly saline areas. High soil salinity negatively affected the amoA gene involved in nitrification and increased the nosZ gene involved in denitrification in extreme salinity soil with 8.2 g/kg salt content. Extreme salinity significantly reduced the expression of genes involved in inorganic P solubilization, such as ppa and ppx. Additionally, the alkaline P gene phoD exhibited significant decreases in extremely saline soils, thereby impeding the mineralization of organic P. The neutral community models indicated that microbial community immigration rate showed a linear negative relationship with soil EC in the six N and four P processes. Salinization, however, displayed a nonlinear pattern with clearly defined thresholds on the community of microbes involved in N and P cycling. Reduced microbial diversity and interactions are causing a decline in soil multifunctionality, and the soil multifunctionality and network edges jointly limited the microbial community immigration rate involved in N and P cycling. It is crucial to preserve soil microbial functions to support nutrient cycling and predict the ecological effects of soil salinization.

Soil microfauna mediate multifunctionality under multilevel warming in a primary forest

Soil microfauna play a crucial role in maintaining multiple functions associated with soil phosphorous, nitrogen and carbon cycling. Although both soil microfauna diversity and multifunctionality are strongly affected by climate warming, it remains unclear how their relationships respond to different levels of warming. We conducted a 3-year multilevel warming experiment with five warming treatments in a subtropical primary forest. Using infrared heating systems, the soil surface temperature in plots was maintained at 0.8, 1.5, 3.0 and 4.2°C above ambient temperature (control). Our findings indicated that low-level warming (+0.8-1.5°C) increased soil multifunctionality, as well as nematode and protist diversity, compared with the control. In contrast, high-level warming (+4.2°C) significantly reduced these variables. We also identified significant positive correlations between soil multifunctionality and nematode and protist diversity in the 0-10 cm soil layer. Notably, we found that soil multifunctionality and protist diversity did not change significantly under 3.0°C warming treatment. Our results imply that a temperature increase of around 3°C may represent a critical threshold in subtropical forests, which is of great importance for identifying response measures to global warming from the perspective of microfauna in the surface soil. Our findings provide new evidence on how soil microfauna regulate multifunctionality under varying degrees of warming in primary forests.

Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality

Global change has the potential to alter soil carbon (C) inputs from above- and below-ground sources, with subsequent influences on soil microbial communities and ecological functions. Using data from a 13-year field experiment in a semi-arid grassland, we investigated the effects of litter manipulations and plant removal on soil microbiomes and ecosystem multifunctionality (EMF). Litter addition did not affect soil microbial α-diversity whereas litter removal reduced bacterial and fungal α-diversity due to decreased C substrate supply and soil moisture. By contrast, plant removal led to larger declines in bacterial and fungal α-diversity, lower microbial network stability and complexity. EMF was enhanced by litter addition but largely reduced by plant removal, primarily attributed to the loss of fungal diversity. Our findings underscore the importance of C inputs in shaping soil microbiomes and highlight the dominant role of plant root-derived C inputs in maintaining ecological functions under global change scenarios.

Network and stoichiometry analysis revealed a fast magnesium and calcium deficiency of mulched Phyllostachys violascens

The imbalanced fertilization and the consequential deterioration on the rhizosphere microbial community (RMC) were two potential reasons for the quick yielding degradation of Phyllostachys violascens (Lei-bamboo), a high-value shoot-oriented bamboo. However, most research only focused on nitrogen, phosphorus, and potassium; the studies on the dynamics of other nutrients, such as calcium and magnesium; and their driving mechanisms, lags far behind. Thus, Lei-bamboo fields of different mulching and recovery ages were selected to investigate the dynamics of calcium and magnesium in both soil and bamboo tissue, and to explore their relationship to RMC composition and network patterns. The results showed that mulching increased the content of soil acidification, total organic carbon, alkali-hydrolysable nitrogen, available phosphorus, and available potassium but reduced soil exchangeable magnesium and calcium in soil as well as the magnesium and calcium content in rhizome, stem, and leaf of Lei-bamboo, which indicated an increased relative limitation on magnesium and calcium. Mulching also enhanced the α-diversity and reshaped the composition of RMC, which had a close link to Mg rather than nitrogen, phosphorus, and potassium. As the mulching years increased, the RMC network became bigger and more complex, and the magnesium and calcium gradually appeared in the network center, which further support the magnesium and calcium deficiency to RMC. Nearly all the variation mentioned above could be revered after the removing of mulching. Structural equation modeling showed two main pathways that mulching leads to magnesium and calcium deficiency in Lei-bamboo, one is directly by lowering soil magnesium and calcium content, the other one is indirectly by improving RMC network interactions, a sign of weakened mutualism between RMC and plant roots that hampering the uptake of nutrients. This research highlights the quick magnesium and calcium deficiency caused by mulching in Lei-bamboo forest and the contribution of RMC in amplify the effects of soil magnesium and calcium deficiency, which offers valuable information on balancing fertilization pattern for future sustainable Lei-bamboo cultivation.

Topography- and depth-dependent rhizosphere microbial community characteristics drive ecosystem multifunctionality in Juglans mandshurica forest

Rhizosphere microbial community characteristics and ecosystem multifunctionality (EMF), both affected by topographic factors, are closely correlated. However, more targeted exploration is yet required to fully understand the variations of rhizosphere microbial communities along topographic gradients in different soil layers, as well as whether and how they regulate EMF under specific site conditions. Here, we conducted relevant research on Juglans mandshurica forests at six elevation gradients and two slope positions ranging from 310 to 750 m in Tianjin Baxian Mountain. Results demonstrated that rhizosphere soil physicochemical properties and enzyme activities of both layers (0-20 cm and 20-40 cm) varied significantly with elevation, while only at top layer did slope position have significant impacts on most indicators. Bacterial richness and diversity were higher in the top layer at slope bottom and middle-high elevation, the difference in fungi was not as noticeable. Both topographic factors and soil depth significantly impacted microbial community structure, with Candidatus_Udaeobacter of bacteria, Mortierella, Sebacina, and Hygrocybe of fungi mainly contributing to the dissimilarity between communities. EMF rose with increasing elevation, bacteria were more critical drivers of this process than fungi, and topographic factors could affect EMF by altering bacterial diversity and dominant taxa abundance. For evaluating EMF, the aggregate structure of sub layer and the carbon cycle-related indicators of top layer were of higher importance. Our results revealed the depth-dependent characteristics of the rhizosphere microbial community along topographic gradients in studied stands, as well as the pivotal regulatory role of bacteria on EMF, while also highlighting depth as an important variable for analyzing soil properties and EMF. This work helps us better understand the response of individuals and communities of J. mandshurica to changing environmental conditions, further providing a scientific reference for the management and protection of secondary forests locally and in North China.

Fungal community characteristics of the last remaining habitat of three paphiopedilum species in China

Paphiopedilum armeniacum, Paphiopedilum wenshanense and Paphiopedilum emersonii are critically endangered wild orchids. Their populations are under severe threat, with a dramatic decline in the number of their natural distribution sites. Ex situ conservation and artificial breeding are the keys to maintaining the population to ensure the success of ex situ conservation and field return in the future. The habitat characteristics and soil nutrient information of the last remaining wild distribution sites of the three species were studied. ITS high-throughput sequencing was used to reveal the composition and structure of the soil fungal community, analyze its diversity and functional characteristics, and reveal its relationship with soil nutrients. The three species preferred to grow on low-lying, ventilated and shaded declivities with good water drainage. There were significant differences in soil alkali-hydrolyzed nitrogen and available phosphorus among the three species. There were 336 fungal species detected in the samples. On average, there were different dominant groups in the soil fungal communities of the three species. The functional groups of soil fungi within their habitats were dominated by saprophytic fungi and ectomycorrhizae, with significant differences in diversity and structure. The co-occurrence network of habitat soil fungi was mainly positive. Soil pH significantly affected soil fungal diversity within their habitats of the three paphiopedilum species. The study confirmed that the dominant groups of soil fungi were significantly correlated with soil nutrients. The three species exhibit comparable habitat inclinations, yet they display substantial variations in the composition, structure, and diversity of soil fungi. The fungal functional group is characterized by a rich presence of saprophytic fungi, a proliferation of ectomycorrhizae, and a modest occurrence of orchid mycorrhizae. The symbiotic interactions among the soil fungi associated with these three species are well-coordinated, enhancing their resilience against challenging environmental conditions. There is a significant correlation between soil environmental factors and the composition of soil fungal communities, with pH emerging as a pivotal factor regulating fungal diversity. Our research into the habitat traits and soil fungal ecosystems of the three wild Paphiopedilum species has established a cornerstone for prospective ex situ conservation measures and the eventual reestablishment of these species in their native landscapes.

Eucalyptus and Native Broadleaf Mixed Cultures Boost Soil Multifunctionality by Regulating Soil Fertility and Fungal Community Dynamics

The growing recognition of mixed Eucalyptus and native broadleaf plantations as a means of offsetting the detrimental impacts of pure Eucalyptus plantations on soil fertility and the wider ecological environment is accompanied by a clear and undeniable positive impact on forest ecosystem functions. Nevertheless, the question of how mixed Eucalyptus and native broadleaf plantations enhance soil multifunctionality (SMF) and the mechanisms driving soil fungal communities remains unanswered. In this study, three types of mixed Eucalyptus and native broadleaf plantations were selected and compared with neighboring evergreen broadleaf forests and pure Eucalyptus plantations. SMF was quantified using 20 parameters related to soil nutrient cycling. Partial least squares path modeling (PLS-PM) was employed to identify the key drivers regulating SMF. The findings of this study indicate that mixed Eucalyptus and native broadleaf plantations significantly enhance SMF. Mixed Eucalyptus and native broadleaf plantations led to improvements in soil properties (7.60-52.22%), enzyme activities (10.13-275.51%), and fungal community diversity (1.54-29.5%) to varying degrees compared with pure Eucalyptus plantations. Additionally, the mixed plantations exhibit enhanced connectivity and complexity in fungal co-occurrence networks. The PLS-PM results reveal that soil properties, fungal diversity, and co-occurrence network complexity directly and positively drive changes in SMF. Furthermore, soil properties exert an indirect influence on SMF through their impact on fungal diversity, species composition, and network complexity. The findings of this study highlight the significant role of mixed Eucalyptus and native broadleaf plantations in enhancing SMF through improved soil properties, fungal diversity, and co-occurrence network complexity. This indicates that incorporating native broadleaf species into Eucalyptus plantations can effectively mitigate the negative impacts of monoculture plantations on soil health and ecosystem functionality. In conclusion, our study contributes to the understanding of how mixed plantations influence SMF, offering new insights into the optimization of forest management and ecological restoration strategies in artificial forest ecosystems.

High-elevation-induced decrease in soil pH weakens ecosystem multifunctionality by influencing soil microbiomes

Plant environmental stress response has become a global research hotspot, yet there is a lack of clear understanding regarding the mechanisms that maintain microbial diversity and their ecosystem services under environmental stress. In our research, we examined the effects of moderate elevation on the rhizosphere soil characteristics, microbial community composition, and ecosystem multifunctionality (EMF) within agricultural systems. Our findings revealed a notable negative correlation between EMF and elevation, indicating a decline in multifunctionality at higher elevations. Additionally, our analysis across bacterial and protistan communities showed a general decrease in microbial richness with increasing elevation. Using random forest models, pH was identified as the key environmental stressor influencing microbial communities. Furthermore, we found that microbial community diversity is negatively correlated with stability by mediating complexity. Interestingly, while pH was found to affect the complexity within bacterial networks, it did not significantly impact the ecosystem stability along the elevation gradients. Using a Binary-State Speciation and Extinction (BiSSE) model to explore the evolutionary dynamics, we found that Generalists had higher speciation rates and lower extinction rates compared to specialists, resulting in a skewed distribution towards higher net diversification for generalists under increasing environmental stress. Moreover, structural equation modeling (SEM) analysis highlighted a negative correlation between environmental stress and community diversity, but showed a positive correlation between environmental stress and degree of cooperation & competition. These interactions under environmental stress indirectly increased community stability and decreased multifunctionality. Our comprehensive study offers valuable insights into the intricate relationship among environmental factors, microbial communities, and ecosystem functions, especially in the context of varying elevation gradients. These findings contribute significantly to our understanding of how environmental stressors affect microbial diversity and ecosystem services, providing a foundation for future ecological research and management strategies in similar contexts.

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal-Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems.

Biodiversity drives ecosystem multifunctionality in sandy grasslands?

Plant communities and soil microbiomes play a crucial role in regulating ecosystem multifunctionality (EMF). However, whether and how aboveground plant diversity, belowground soil microbial diversity and interactions with environmental factors affect EMF in sandy grasslands under climate change conditions is unclear. Here, we selected 15 typical grassland communities from the Horqin sandy grassland along temperature and precipitation gradients, using the mean annual temperature (AMT), mean annual precipitation (AP), soil temperature (ST), soil water content (SW) and pH as abiotic factors, and plant diversity (PD) and soil microbial diversity (SD) as biodiversity indicators. The effects of biodiversity and abiotic factors on individual ecosystem functions and EMF were studied. We found that PD and its components, plant species richness (SR), species diversity (PR) and genetic diversity (GD), had significant effects on aboveground biomass (AGB) and major factors involved in ecosystem nitrogen cycling (plant leaf nitrogen content (PLN) and soil total nitrogen content (STN)) (P < 0.05). Soil fungal diversity (FR) has a greater impact on ecosystem function than soil bacteria (BR) and archaea (ABR) in sandy grasslands and mainly promotes the accumulation of soil microbial carbon and nitrogen (MBC, MBN) (P < 0.05), STC and STN (P < 0.01). PD and two types of SD (FR and ABR) significantly regulated EMF (P < 0.01). Among the abiotic factors, soil pH and SW regulated EMF (P < 0.05), and SW and ST directly drove EMF (P < 0.05). PD drove EMF significantly and indirectly (positively) through soil pH and ST (P < 0.001), while SD drove EMF weakly and indirectly (negatively) through AP and PD (P > 0.05). PD was a stronger driving force on EMF than SD. These results improve our understanding of the drivers of multifunctionality in sandy grassland ecosystems.

Granular bacterial inoculant alters the rhizosphere microbiome and soil aggregate fractionation to affect phosphorus fractions and maize growth

The constraint of phosphorus (P) fixation on crop production in alkaline calcareous soils can be alleviated by applying bioinoculants. However, the impact of bacterial inoculants on this process remains inadequately understood. Here, a field study was conducted to investigate the effect of a high-concentration, cost-effective, and slow-release granular bacterial inoculant (GBI) on maize (Zea mays L.) plant growth. Additionally, we explored the effects of GBI on rhizosphere soil aggregate physicochemical properties, rhizosphere soil P fraction, and microbial communities within aggregates. The outcomes showed a considerable improvement in plant growth and P uptake upon application of the GBI. The application of GBI significantly enhanced the AP, phoD gene abundance, alkaline phosphatase activity, inorganic P fractions, and organic P fractions in large macroaggregates. Furthermore, GBI impacted soil aggregate fractionation, leading to substantial alterations in the composition of fungal and bacterial communities. Notably, key microbial taxa involved in P-cycling, such as Saccharimonadales and Mortierella, exhibited enrichment in the rhizosphere soil of plants treated with GBI. Overall, our study provides valuable insight into the impact of GBI application on microbial distributions and P fractions within aggregates of alkaline calcareous soils, crucial for fostering healthy root development and optimal crop growth potential. Subsequent research endeavors should delve into exploring the effects of diverse GBIs and specific aggregate types on P fraction and community composition across various soil profiles.

Microbial network structure, not plant and microbial community diversity, regulates multifunctionality under increased precipitation in a cold steppe

It is known that the dynamics of multiple ecosystem functions (i. e., multifunctionality) are positively associated with microbial diversity and/or biodiversity. However, how the relationship between microbial species affects ecosystem multifunctionality remains unclear, especially in the case of changes in precipitation patterns. To explore the contribution of biodiversity and microbial co-occurrence networks to multifunctionality, we used rainfall shelters to simulate precipitation enhancement in a cold steppe in Northeast China over two consecutive growing seasons. We showed that an increased 50% precipitation profoundly reduced bacterial diversity and multidiversity, while inter-annual differences in precipitation did not shift microbial diversity, plant diversity, or multidiversity. Our analyses also revealed that increased annual precipitation significantly increased ecosystem, soil, nitrogen, and phosphorous cycle multifunctionality. Neither increased precipitation nor inter-annual differences in precipitation had a significant effect on carbon cycle multifunctionality, probably due to the relatively short period (2 years) of our experiment. The co-occurrence network of bacterial and fungal communities was the most dominant factor affecting multifunctionality, the numbers of negative interactions but not positive interactions were linked to multifunctionality. In particular, our results provided evidence that microbial network topological features are crucial for maintaining ecosystem functions in grassland ecosystems, which should be considered in related studies to accurately predict the responses of ecosystem multifunctionality to predicted changes in precipitation patterns.

Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off

Introduction

Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown.

Methods

In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs.

Results

The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs.

Discussion

Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.