Decreased soil multifunctionality is associated with altered microbial network properties under precipitation reduction in a semiarid grassland

Microbial taxonomic diversity and functional genes mirror soil ecosystem multifunctionality in nonferrous metal mining areas

The pollution of metal ions triggers great risks of damaging biodiversity and biodiversity-driven ecosystem multifunctioning, whether microbial functional gene can mirror ecosystem multifunctionality in nonferrous metal mining areas remains largely unknown. Macrogenome sequencing and statistical tools are used to decipher linkage between functional genes and ecosystem multifunctioning. Soil samples were collected from subdams in a copper tailings area at various stages of restoration. The results indicated that the diversity and composition of soil bacterial communities were more sensitive than those of the fungal and archaeal communities during the restoration process. The mean method revealed that nutrient, heavy metal, and soil carbon, nitrogen, and phosphorus multifunctionality decreased with increasing bacterial community richness, whereas highly significant positive correlations were detected between the species richness of the bacterial, fungal, and archaeal communities and the multifunctionality of the carbon, nitrogen, and phosphorus functional genes and of functional genes for metal resistance in the microbial communities. SEM revealed that soil SWC and pH were ecological factors that directly influenced abiotic factor-related EMF; microbial diversity was a major biotic factor influencing the functional gene multifunctionality of the microbiota; and different abiotic and biotic factors associated with EMF had differential effects on whole ecosystem multifunctionality. These findings will help clarify the contributions of soil microbial diversity and functional genes to multifunctionality in degraded ecosystems.

Water-saving irrigation suppresses on soil-crop pathogenicity: Insight on the co-host of virulence factors and antibiotic resistance genes

Water-saving irrigation is increasingly being prioritized in agricultural production activities to conserve water resources and increase crop productivity. Yet, how water-saving irrigation affects soil-crop pathogenic, primarily involving in the prevalence of virulence factors (VFs) and antibiotic resistance genes (ARGs), remains unclear. Here we investigated the variations in the abundance of VFs and ARGs in the soil-crop system under different irrigation intensities, and explored the underlying mechanisms on suppressing the dissemination of ARGs and VFs. The results showed that irrigation intensities (50 %, 75 % and 100 % irrigation water, hereafter IW50, IW75 and IW100) did not significantly affect soil VFs and ARGs abundance, but was closely associated with their occurrences in roots and leaves. Water-saving irrigation (IW 50 and IW75) clearly reduced the proliferation of VFs and ARGs in crops, especially TEP, PhoP, basS, and evgS genes decreased by more than 80 % compared to recommended irrigation usage (IW100). And, the co-hosts largely contributed to the reduction of VFs and ARGs abundance. The network analysis demonstrated that the increase in negative interactions between co-hosts and non-cohosts after water-saving irrigation resulted in the decrease of co-hosts colonization. Further, the decline in H2O-O2, carbon and nitrogen metabolic functional genes indicated that water-saving irrigation can inhibit the microbial ability to utilize those resources, thus decreasing VFs and ARGs proliferation. Finally, we determined that IW75 was most beneficial for VFs and ARGs reduction and tomato production. The outcome deepened the understanding of suppression on the spread of VFs and ARGs by water-saving irrigation, thereby providing valuable guidance for sustainable water-efficient agricultural practices.

AHL-mediated quorum sensing drives microbial community succession and metabolic pathway in algal-bacterial biofilm system

Microalgae, ammonia-oxidizing bacteria (AOB), and anaerobic ammonium-oxidizing bacteria (AnAOB) have been proven to form an integrated algal-bacterial biofilm system with over 93 % of total nitrogen removal. Compared to conventional nitrification-denitrification process, this system operated without additional organic carbon or aeration. In order to understand the interaction mechanisms between bacteria and algae, this study investigated microbial community succession, the changes in metabolic pathways and the potential role of acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) during the formation of the algae/partial nitrification/anammox biofilm system. Within this algal-bacterial symbiotic biofilm, the dominant genera identified were Candidatus_Brocadia (AnAOB), Nitrosomonas (AOB), and Geitlerinema (microalgae), with relative abundances of 13.86 %, 6.37 %, and 2.88 %, respectively. Compared with the first two stages, the abundance of genes related to nitrogen metabolism pathways (anaerobic ammonium oxidation, denitrification, and ammonia assimilation) increased, indicating enhanced nitrogen transformation capacity in the algal-bacterial symbiotic stage. Co-occurrence network analysis also revealed enhanced microbial interactions, with increased negative correlations (from 36.07 % to 39.38 %), high average standard betweenness centrality (from 0.193 to 0.304), and reduced community vulnerability (from 0.037 to 0.028), contributing to biofilm stability and resilience. The variations in AHLs provided direct evidence for more frequent interspecies communication, facilitating the ecological reconfiguration in the biofilm. Overall, the close synergistic relationship between microalgae and bacteria supports stable biofilm development and high nitrogen removal efficiency.

Temperature and wind speed help fermentation-sourced microbiota reconstruct the airborne microbiota in the Chinese baijiu fermentation region

Microorganisms are vital components of airborne particles and are closely linked to human health and industrial processes. As industrialization advances, factories are exacerbating their impact on environmental microbial communities, an area where our understanding remains limited. In this study, we investigated air microorganisms surrounding Chinese baijiu fermentation facilities, aiming to explore the dispersal mechanisms of fermentation-sourced microbiota and their potential impacts on local airborne microbial communities. The results revealed a significant overlap between microbial communities from fermentation processes and the surrounding air, with 14 genera commonly found in both habitats, suggesting widespread and substantial dispersal of factory microorganisms. Due to this dispersal, fermentation-sourced Saccharopolyspora and Streptomyces have become central nodes in the airborne microbial network. Environmental factors played a pivotal role in the microbiota dispersal process. Higher temperatures may facilitate microbial proliferation and increase the dispersal of fermentation microorganisms (r = 0.30, P < 0.01), while higher wind speeds may lead to a dilution effect and limit the uniform dispersal of microorganisms (r = -0.22, P < 0.05). Furthermore, air-resident microorganisms restricted the proliferation of fermentation microorganisms (r = -0.60, P < 0.001). These results confirm the modifying effect of fermentation facilities on environmental microbial communities and establish a theoretical foundation for optimizing factory site selection.

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.

Core microbes regulate plant-soil resilience by maintaining network resilience during long-term restoration of alpine grasslands

The alpine grasslands of the Qinghai-Tibetan Plateau (QTP), the world's highest plateau, have been severely degraded. To address this degradation, human-involved restoration efforts, including grassland cultivation, have been implemented. However, the impact of these practices on soil microbial community stability and its relationship with plant-soil system resilience has not been explored. In this study, we evaluate the effects of grassland restoration on microbial communities. We show that bacteria demonstrate higher composition resistance and resilience during the restoration process, when compared to fungi. The changes we observe in microbial community interactions support the stress gradient hypothesis. Our results emphasize the synergistic role of network resilience and the restoration of the plant-soil system. Importantly, we find that core microbial species significantly influence the resilience of the plant-soil system by sustaining the co-occurrence networks. These insights underscore the critical roles of microbial communities in grassland restoration and suggest new strategies for boosting grassland resilience by safeguarding core microbes.

Extreme Rainfall Amplified the Stimulatory Effects of Soil Carbon Availability on N2O Emissions

Ongoing climate change is predicted to increase the frequency and intensity of extreme rainfall, which will dramatically alter soil nitrous oxide (N2O) emissions, especially changes in soil organic carbon (SOC) due to anthropogenic management. However, our ability to predict this effect is limited owing to a dearth of research. Therefore, we selected two croplands in Northeast China with the same quantity but contrasting availability of SOC to explore the in situ dynamics of N2O fluxes and N-cycling microbes through 2-year field experiment and N2O production pathways by laboratory 15N-tracing experiment. In a normal rainfall year, the croplands with high (HCA) and low (LCA) SOC availability emitted 0.66 and 0.25 kg N2O-N ha-1 without N-fertilization and 2.03 and 1.51 kg N2O-N ha-1 with N-fertilization, respectively. In a record-breaking wet year, multiple heavy rainfall events caused water supersaturation in the low-lying HCA cropland over 2 months. Consequently, the background N2O emissions increased by 508% compared with the normal rainfall year, and the N-induced N2O emission factor increased from 0.77% to 2.24%. Soil dissolved organic carbon (DOC) was identified as the primary driver of larger N2O fluxes from HCA cropland which facilitated denitrification by fueling nirS- and nirK-denitrifiers metabolism. Furthermore, a greater N substrate supply via a faster mineralization-nitrification coupling process promoted the contribution of autotrophic nitrification to N2O in HCA cropland. The N2O pulses from HCA soils during the waterlogging period were derived from stimulated denitrification, which dominated N2O production (> 90%). Simultaneously, C availability enhanced and nitrate was produced via archaeal nitrification, leading to an increased nirS/nosZII ratio that fostered N2O production through incomplete denitrification. Overall, our findings highlight the importance of avoiding the amendment of exogenous organic materials with high C lability, particularly under climate extremes, to eliminate the potential positive feedback of SOC management on climate change by inducing N2O emissions.

Organic amendments enhance rhizosphere carbon stabilization in macroaggregates of saline-sodic soils by regulating keystone microbial clusters

Photosynthetic carbon plays a pivotal role in soil organic carbon (SOC) sequestration in agricultural soils. However, how organic amendments regulate photosynthetic carbon accumulation through multitrophic microbes at the aggregate scale, especially the core microbiota, remains unclear. Here, we conducted a13CO2-labeled rhizo-box experiment on a saline-sodic soil with five treatments: no fertilizer (Ctrl), chemical fertilizer, pig manure (PM), milk vetch straw (MV), and vermicompost. The 13C-SOC in the MV and PM treatments was 2.4 and 1.4 times greater than that in the Ctrl, respectively. Compared with the Ctrl, organic amendments significantly increased 13C-macroaggregate-associated OC (13C-Macro-OC) by 122.4-615.8 % and 13C-mineral-associated OC (13C-MAOC) by 123.6-564.5 % in macroaggregates (> 0.25 mm). The 13C-Macro-OC was significantly positively correlated with biodiversity, the relative abundances of bacteria (mainly Acidobacteriota and Firmicutes) and fungi (mainly Ascomycota and Mucoromycota) in the keystone microbial cluster, network complexity, and the proportion of negative cross-trophic associations. Structural equation modeling revealed that the root trait-induced core microbiota, following organic amendments, affected photosynthetic carbon accumulation via 13C-MAOC in macroaggregates. In summary, our findings highlight the positive effects of milk vetch straw on SOC accumulation and provide a theoretical basis for the targeted regulation of SOC accumulation in saline-sodic soils through organic amendments.

Phytostabilization potential and microbial response to the reclamation of native Cynodon dactylon in spoil heaps from a multiple-metal mining site in Southwest China

Phytocapping offers a sustainable approach for managing exposed tailings by mitigating pollutant spread and enhancing phytoremediation. This study investigates the potential of Bermudagrass (Cynodon dactylon) as a pioneering plant for rehabilitating tailings from an open-pit lead-zinc mine in Southwest China. Our findings demonstrate that Bermudagrass significantly improved soil quality and multifunctionality compared to adjacent bare tailings. Soil improvements included increases in organic matter (107%), total and available nitrogen (50% and 110%, respectively), available phosphorus (170%), and soil enzyme activities, including β-glucosidase (170%), sucrase (1729%), alkaline phosphatase (3722%), and acid phosphatase (168%). The reclamation process also promoted microbial community succession, altering community composition, improving microbial diversity, and enhancing bacterial biomass from (0.89 ± 0.54) × 1015 to (9.06 ± 3.25) × 1015 copies/g in rhizosphere soils. Greenhouse experiments further confirmed Bermudagrass's resilience to cadmium (Cd), with both mining and non-mining ecotypes thriving in tailing soils and Cd2+ hydroponic solutions (up to 44.5 μM) without evident phytotoxicity. Bermudagrass roots exhibited exceptional Cd accumulation (bioconcentration factor: 181-1006) while minimizing Cd translocation to shoots (translocation factor: <0.13). Inoculation with Funneliformis mosseae, a restored root-mutually symbiotic fungus, further mitigated Cd-induced phytotoxicity and enhanced plant growth. These findings highlight Bermudagrass as a promising pioneer species for phytostabilization in severely contaminated mining environments, with its rhizosphere microbiome playing a critical role in facilitating ecosystem restoration. Sustainable plant establishment in mine waste rock requires concurrent development of belowground fertility and healthy rhizospheric soil. Ultimately, successful revegetation depends on integrated above and belowground development to achieve long-term ecological restoration.

Reduced soil ecosystem multifunctionality is associated with altered complexity of the bacterial-fungal interkingdom network under salinization pressure

Salinization processes profoundly impact soil quality and health, altering physical structure, chemical composition, and biological activity, particularly concerning soil microbial populations. Microbial communities play a pivotal role in maintaining soil ecosystem multifunctionality (EMF). Understanding the response of microbial communities to salinity stress is crucial for sustainable soil management and enhancing ecosystem resilience in arid and semi-arid regions. This study assessed microbial diversity, composition, and the properties of bacterial-fungal interkingdom networks, and explored their relationship with EMF in saline soil ecosystems in Ningxia. The findings revealed that soil salinization was more pronounced in Hongsipu (HSP) and Xidatan (XDT) compared to Huinong (HN). Bacterial diversity indices, including shannon and chao1, were more sensitive to soil type and salinity level than their fungal counterparts. High salinity levels significantly reduced bacterial diversity indices, even across different saline soil types. The structure and composition of bacterial and fungal communities were influenced by the type and degree of soil salinization. Despite these variations, the dominant bacterial phylum Proteobacteria (11.75%-24.88%) and fungal Ascomycota (47.93%-80.11%) remained consistent across salinized soil types and salinity levels. Salinity stress, however, substantially reduced network complexity and stability while promoting cooperative interactions between bacterial and fungal species. Correlation analyses indicated significant positive relationships between EMF and microbial community diversity, as well as network complexity and stability. When integrating the relationships between soil salinity, microbial diversity, network characteristics, and EMF, the positive, strong, and significant effect of network complexity on EMF persisted. These findings underscore the critical role of bacterial-fungal interkingdom network complexity as a key determinant influencing EMF in salinized soils. This study highlights the necessity of addressing microbial network properties to mitigate the adverse effects of salinity on soil ecosystems and maintain multifunctionality under salinization stress.

Temporal dynamics of soil microbial symbioses in the root zone of wolfberry: deciphering the effects of biotic and abiotic factors on bacterial and fungal ecological networks

Long-term monoculture of Lycium barbarum significantly affects its productivity and soil health. Soil microbiota, which mediate the sustainable development of soil ecosystems, are influenced by the age of wolfberry plants. However, the comprehensive effects of long-term cultivation of L. barbarum on the soil microbial community are not yet fully understood. Here, we assessed the effects of stand age on the diversity, composition, assembly, and symbiotic networks of bacterial and fungal communities in the root zone soil of L. barbarum using high-throughput sequencing technology. The results showed that stand age significantly affected the α-diversity of bacterial and fungal communities, as evidenced by the tendency of their Shannon and Chao1 indices to increase and then decrease. At the same time, the structure of soil bacterial and fungal communities was significantly influenced by tree age. However, Proteobacteria (28.77%-32.81%) was always the most dominant bacterial phylum, and Ascomycetes (49.72%-55.82%) was always the most dominant fungal phylum. A number of genus-level biomarkers were also identified in soils associated with roots of trees of varying ages. Additionally, stochastic processes dominated the assembly of soil bacterial communities, whereas the balance between stochastic and deterministic processes in the assembly of fungal communities fluctuated with stand age. The complexity and stability of bacterial and fungal community networks were notably affected by tree age, particularly in networks from 10- and 15-year-old trees. The partial least squares path modeling (PLS-PM) analysis emphasized that stand age can indirectly regulate the diversity and network complexity of both bacterial and fungal communities by influencing soil physicochemical properties. Furthermore, the bacterial community, but not the fungal community, exhibited direct and strong regulation of network complexity. The study offers valuable data for improving the soil quality and fruit yield of L. barbarum under long-term continuous cropping, which has implications for the sustainable development of the L. barbarum industry.

Enhanced rock weathering boosts ecosystem multifunctionality via improving microbial networks complexity in a tropical forest plantation

Afforestation is expected to contribute to mitigate global change by promoting carbon stocks and multiple ecosystem services. However, the success of plantations may be limited by the availability of soil nutrients. This is especially critical for plantations in tropical ecosystems which are known to be nutrient poor ecosystems. Enhanced rock weathering (ERW) represents a promising strategy for improving soil health and carbon sequestration in such ecosystems. We added wollastonite skarn, a calcium silicate rock, to soils in a rubber plantation in Yunnan, China, as part of an ERW strategy aimed at promoting soil functioning and biodiversity. Statistical significance was determined using a linear mixed-effects model, with p-values indicating the level of significance. The addition of wollastonite skarn significantly enhanced key ecosystem functions related to carbon, nitrogen, phosphorous, silicon, biodiversity, and pathogen control. However, it did not significantly affect soil enzyme activity. Some of these responses to the addition of wollastonite skarn may be associated with an increase in soil pH. Microbial network complexity played a critical role in explaining the changes in ecosystem multifunctionality in response to ERW, through both direct and indirect pathways. SYNTHESIS AND APPLICATIONS: Our findings suggest that ERW is a viable strategy for improving soil health and ecosystem resilience in tropical plantations, which are limited in nutrients. Thus, ERW has implications for carbon management and climate change mitigation.

Paddy-upland rotation combined with manure application: An optimal strategy for enhancing soil multifunctionality

Promoting soil multifunctionality is pivotal for maintaining agricultural productivity and sustainable agriculture, especially with the increasing global population and food demand. The effectiveness of different agricultural practices in enhancing soil multifunctionality and how the combination can maximize soil multifunctionality remains unknown. This study aimed to investigate the different impacts of rotation (paddy-upland rotation and dryland rotation) combined with fertilization (chemical fertilizer and manure) on soil multifunctionality, microbial community structure, and microbial networks. A two-year field experiment was conducted at the Fengqiu National Agro-Ecosystem Observation and Research Station in Henan Province, China, comparing the differences between rice-wheat rotation (paddy-upland rotation) and maize-wheat rotation (dryland rotation) combined with chemical fertilizer and pig manure. This finding revealed that paddy-upland rotation combined with manure application had the optimal effect in enhancing soil multifunctionality with a 216.25 % enhancement while contributing to a yield increase of 222.71 %. Notably, paddy-upland rotation and fertilization significantly promoted the soil bacterial network complexity and robustness, and these network properties were crucial factors in predicting soil multifunctionality. This study provides a new insight for developing a comprehensive strategy combining paddy-upland rotation with manure application in the future, which can help us to better improve soil health and agricultural sustainability.

Stable Soil Biota Network Enhances Soil Multifunctionality in Agroecosystems

Unraveling how agricultural management practices affect soil biota network complexity and stability and how these changes relate to soil processes and functions is critical for the development of sustainable agriculture. However, our understanding of these knowledge still remains unclear. Here, we explored the effects of soil management intensity on soil biota network complexity, stability, and soil multifunctionality, as well as the relationships among these factors. Four typical land use types representing a gradient of disturbance intensity were selected in calcareous and red soils in southwest China. The four land use types with increasing disturbance intensity included pasture, sugarcane farmland, rice paddy fields, and maize cropland. The network cohesion, the network topological features (e.g., average degree, average clustering coefficient, average path length, network diameter, graph density, and modularity), and the average variation degree were used to evaluate the strength of interactions between species, soil biota network complexity, and the network stability, respectively. The results showed that intensive soil management increased species competition and soil biota network complexity but decreased soil biota network stability. Soil microfauna (e.g., nematode, protozoa, and arthropoda) stabilized the entire soil biota network through top-down control. Soil biota network stability rather than soil biota network complexity or soil biodiversity predicted the dynamics of soil multifunctionality. Specifically, stable soil communities, in both the entire soil biota network and selected soil organism groups (e.g., archaea, bacteria, fungi, arthropoda, nematode, protozoa, viridiplantae, and viruses), support high soil multifunctionality. In particular, soil microfauna stability had more contributions to soil multifunctionality than the stability of soil microbial communities. This result was further supported by network analysis, which showed that modules 1 and 4 had greater numbers of soil microfauna species and explained more variation of soil multifunctionality. Our study highlights that soil biota network stability should be considered a key factor in improving agricultural sustainability and crop productivity in the context of increasing global agricultural intensification.

Windfarm construction alters soil multinutrient cycling by destabilizing microfauna community in a mountain ecosystem

In recent decades, investors attracted to wind power's promise of zero-emission electricity have fueled the proliferation of large windfarms across the world. However, the effects of windfarm construction with different land use subtypes (i.e., wind turbine, waste slag, and construction production and living areas) on soil microfauna community stability and subsequent consequences for ecosystem functioning remains poorly understood. Here, we evaluated how these three land use types affect soil microfauna community stability relative to natural vegetation types (forest, shrubland, and grassland) in a mountain area. We found that all three windfarm land use subtypes reduced soil multinutrient cycling and microfauna community stability compared with natural ecosystems. However, among these natural ecosystems, reductions of soil multinutrient cycling were 66.36% and 79.10% lower in grassland than in forest and shrubland, respectively. Reductions of soil nematode community stability were 62.15% and 77.22% lower in grassland than in forest and shrubland; as well as soil protist community stability were 74.01% and 56.74%, respectively. Interspecific interactions and environmental filtering jointly drove variation in soil microfauna community stability. Soil microfauna community stability was significantly and positively linked to soil multinutrient cycling, which has the potential to initiate cascading ecological consequences. Our finding implies that grasslands may be more suitable than shrublands or forests for windfarm development based on the responses of soil microfauna communities.

Seasonal responses of microbial communities to water quality variations and interaction of eutrophication risk in Gehu Lake

Gehu Lake, as a key upstream reservoir of Taihu Lake, China, plays a crucial role in improving the water quality, and eutrophication control of the Taihu Lake Basin. Although the microbial communities are significantly important in maintaining the ecological health of lake, the microbial response to water quality, especially for eutrophication has been rarely reported in Gehu Lake. In this study, the water quality parameters and the corresponding effects on the structure and function of microbial communities were determined seasonally. It was found that the poorest water quality in summer (Water Quality Index = 116.52) with severe eutrophication (Trophic Level Index >70), was primarily driven by agricultural non-point sources (33.4%) and seasonal pollution (23.8%). The chemical oxygen demand (COD) was the most important indicator of water quality that affected the concentration of Chlorophyll-a (Chla) according to Pearson correlation analysis (p < 0.001), random forest modeling (p < 0.01), and structural equation modeling (path coefficient = 0.926). Redundancy analysis revealed that total nitrogen, total phosphorus, Chla, and COD significantly influenced the microbial community (p < 0.05). Microbial co-occurrence networks demonstrated significantly seasonal variations, and winter exhibited a more complex structure under lower temperature and limited nutrients compared to the other seasons. In addition, the Chla-sensitive microbial species that involved in nitrogen and phosphorus metabolism were identified as the biological indicators of eutrophication in response to the changes of seasonal water quality. These findings have taken insights into the interactions between water quality and microbial communities, and might provide the basis for improvement of the ecological and environmental management of Gehu Lake, as well as the control of eutrophication in Taihu Lake.

Microbiota dynamics and source tracing during the growing, aging, and decomposing processes of Eucommia ulmoides leaves

Eucommia ulmoides, an important tree, faces serious threat to its growth from environmental stress, particularly climate change. Using plant microbes to enhance host adaptation to respond climate change challenges has been recognized as a viable and sustainable strategy. However, it is still unclear how the perennial tree microbiota varies across phenological stages and the links between respective changes in aboveground and belowground niches. Here, we sequenced 27 root and 27 leaf samples of E. ulmoides using 16S rRNA and ITS amplicon sequencing techniques. These samples were obtained from the three main phenological stages of leaves, including leaf growing, aging and decomposing stages. Results showed that the diversity, composition, and function of the leaf microbiota of E. ulmoides showed more obvious changes at three phenological time points compared to roots. Regarding alpha diversity, the root microbiota showed no difference across three sampling stages, while the leaf microbiota varied with sampling stages. Regarding beta diversity, the root microbiota clustered from different sampling stages, while the leaf microbiota exhibited distinct separation. Regarding composition and function, the dominant taxa and main functions of the root microbiota were the same in three sampling stages, while the leaf microbiota in the decomposing stage was obviously different from the remaining two stages. Additionally, taxa overlap and source-sink relationship existed between E. ulmoides microbiota. Specifically, the degree of overlap among root microbiota was higher than that of leaf microbiota in three sampling stages. The bidirectional source-sink relationship that existed between the root and leaf niches varied with sampling stage. During the leaf growing and aging stages, the proportion of microbial members migrating from roots to leaves was higher than the proportion of members migrating from leaves to roots. During the leaf decomposing stage, the migration characteristics of the fungal community between the root and leaf niches maintained the same as in the remaining two stages, but the proportion of bacterial members migrating from leaves to roots was significantly higher than that of members migrating from roots to leaves. Our findings provide crucial foundational information for utilizing E. ulmoides microbiota to benefit their host under climate change challenges.

Water periods impact the structure and metabolic potential of the nitrogen-cycling microbial communities in rivers of arid and semi-arid regions

This study examined the influence of water periods on river nitrogen cycling by analysing nitrogen functional genes and bacterial communities in the Qingshui River, an upstream tributary of the Yellow River in China. Nitrate nitrogen predominated as inorganic nitrogen during the low-flow seasons, whereas salinity was highest during the high-flow seasons. Overall, the functional gene abundance increased with decreasing water volume, and nitrogen concentrations were determined by various specific gene groups. The relative abundance of bacteria carrying these genes varied significantly across water periods. The abundance of Pseudomona, Hydrogenophaga (carrying narGHI and nirB genes), and Flavobacterium (carrying nirK, norBC, and nosZ genes) significantly increased during the low-flow seasons. Nitrogen transformation bacteria exhibited both symbiotic and mutualistic relationships. Microbial network nodes and sizes decreased with decreasing water volume, whereas modularity increased. Additionally, the water period affected the functional microbial community structure by influencing specific environmental factors. Among them, SO42- primarily determined the denitrification, dissimilatory nitrate reduction to ammonium, and assimilatory nitrate reduction to ammonium communities, whereas NO2--N and Mg2+ were the main driving factors for the nitrogen-fixing and nitrifying communities, respectively. These findings have substantial implications for better understanding the reduction in river nitrogen loads in arid and semi-arid regions during different water periods.

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.

Reclamation of abandoned cropland switches fungal community assembly from deterministic to stochastic processes

Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of abandoned agricultural land reclamation on the soil microbe is still poorly understood, especially for the microbial community assembly mechanisms. Here, we investigated the influence of reclamation on the relative importance of stochastic and deterministic processes in shaping microbial community assembly. After reclaiming abandoned cropland for corn and soybean cultivation, the fungal community assembly was shifted to stochastic processes, while bacterial communities remained predominantly influenced by stochastic processes. Our study revealed that reclamation did not significantly affect bacterial diversity, community niche breadth, and community similarity. In contrast, fungal communities exhibited lower alpha diversity, narrower niche breadths, greater niche overlap and higher community similarity in corn and soybean cultivation treatment in response to reclamation. Moreover, soil pH and soil available phosphorus were the most important environmental factors influencing fungal richness, niche breadths, community assembly processes, and community similarity. Together, the reclamation of abandoned cropland promoted the transformation of the fungal community assembly from deterministic process to a stochastic process, leading to decreased fungal diversity and broader ecological niche width, ultimately resulting in greater similarity among fungal communities. This finding provides insight into the varied responses of microbial diversity and ecological process to abandoned cropland reclamation, offering valuable guidance for the conservation and sustainable management of abandoned cropland in future land-use practices.

Resource recovery from legacy waste dumpsites in India: A path towards sustainable waste management

Legacy waste dumpsites have been a significant environmental concern in India for many years. These dumpsites are characterized by the uncontrolled disposal of Municipal Solid Waste (MSW) and have led to various types of pollution and disease outbreaks. As India faces the challenges of rapid urbanization and increased waste generation and with over 3000 legacy waste dumpsites in the country, the need to address these legacy waste dumpsites has become paramount. As we continue to struggle extensively for waste management as well as space, landfill mining has been recognized as a promising way of recovering resources in our country by employing various technological and engineering advancements to extract valuable materials and energy from legacy waste streams. Unlike existing waste management approaches, this review explores the application of a novel Recovery Potential Index (RPI) for legacy waste dumpsites in India, which evaluates the feasibility of waste treatment facilities based on waste compositions and recovered material quantities. Depending on the RPI, recovered fine fractions can be sold as city compost or used as fill material, while recyclable, combustible, and inert fractions could be directed towards appropriate recycling or landfill uses. Unscientific and uncontrolled landfill mining practices could lead to unanticipated impacts on the nearby environment in the form of heavy contamination, thereby presenting this practice as a challenge in addition to the immense opportunities it provides.

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.

Temporal shifts in the phytoplankton network in a large eutrophic shallow freshwater lake subjected to major environmental changes due to human interventions

Phytoplankton communities are crucial components of aquatic ecosystems, and since they are highly interactive, they always form complex networks. Yet, our understanding of how interactive phytoplankton networks vary through time under changing environmental conditions is limited. Using a 29-year (339 months) long-term dataset on Lake Taihu, China, we constructed a temporal network comprising monthly sub-networks using "extended Local Similarity Analysis" and assessed how eutrophication, climate change, and restoration efforts influenced the temporal dynamics of network complexity and stability. The network architecture of phytoplankton showed strong dynamic changes with varying environments. Our results revealed cascading effects of eutrophication and climate change on phytoplankton network stability via changes in network complexity. The network stability of phytoplankton increased with average degree, modularity, and nestedness and decreased with connectance. Eutrophication (increasing nitrogen) stabilized the phytoplankton network, mainly by increasing its average degree, while climate change, i.e., warming and decreasing wind speed enhanced its stability by increasing the cohesion of phytoplankton communities directly and by decreasing the connectance of network indirectly. A remarkable shift and a major decrease in the temporal dynamics of phytoplankton network complexity (average degree, nestedness) and stability (robustness, persistence) were detected after 2007 when numerous eutrophication mitigation efforts (not all successful) were implemented, leading to simplified phytoplankton networks and reduced stability. Our findings provide new insights into the organization of phytoplankton networks under eutrophication (or re-oligotrophication) and climate change in subtropical shallow lakes.

Response of bacterial ecological and functional properties to anthropogenic interventions during maturation of mine sand soil

Soil formation is a complex process that starts from the biological development. The ecological principles and biological function in soil are of great importance, whereas their response to anthropogenic intervention has been poorly understood. In this study, a 150-day microcosmic experiment was conducted with the addition of sludge and/or fermented wood chips (FWC) to promote the soil maturation. The results showed that, compared to the control (natural development without anthropogenic intervention), sludge, FWC, and their combination increased the availability of carbon, nitrogen, and potassium, and promoted the soil aggregation. They also enhanced the cellulase activity, microbial biomass carbon (MBC) and bacterial diversity, indicating that anthropogenic interventions promoted the maturation of sand soil. Molecular ecology network and functional analyses indicated that soil maturation was accomplished with the enhancement of ecosystem functionality and stability. Specifically, sludge promoted a transition in bacterial community function from denitrification to nitrification, facilitated the degradation of easily degradable organic matter, and enhanced the autotrophic nutritional mode. FWC facilitated the transition of bacterial function from denitrification to ammonification, promoted the degradation of recalcitrant organic matter, and simultaneously enhanced both autotrophic and heterotrophic nutritional modes. Although both sludge and FWC promoted the soil functionality, they showed distinct mechanistic actions, with sludge enhancing the physical structure, and FWC altering chemical composition. It is also worth emphasizing that sludge and FWC exhibited a synergistic effect in promoting biological development and ecosystem stability, thereby providing an effective avenue for soil maturation.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Elevational distribution patterns and drivers factors of fungal community diversity at different soil depths in the Abies georgei var. smithii forests on Sygera Mountains, southeastern Tibet, China

Introduction

Soil fungal communities play a crucial role in maintaining the ecological functions of alpine forest soil ecosystems. However, it is currently unclear how the distribution patterns of fungal communities in different soil layers of alpine forests will change along the elevational gradients.

Material and methods

Therefore, Illumina MiSeq sequencing technology was employed to investigate fungal communities in three soil layers (0-10, 10-20, and 20-30 cm) along an elevational gradient (3500 m to 4300 m) at Sygera Mountains, located in Bayi District, Nyingchi City, Tibet.

Results and discussion

The results indicated that: 1) Soil depth had a greater impact on fungal diversity than elevation, demonstrating a significant reduction in fungal diversity with increased soil depth but showing no significant difference with elevation changes in all soil layers. Within the 0-10 cm soil layer, both Basidiomycota and Ascomycota co-dominate the microbial community. However, as the soil depth increases to 10-20 and 20-30 cm soil layers, the Basidiomycota predominantly dominates. 2) Deterministic processes were dominant in the assembly mechanism of the 0-10 cm fungal community and remained unchanged with increasing elevation. By contrast, the assembly mechanisms of the 10-20 and 20-30 cm fungal communities shifted from deterministic to stochastic processes as elevation increased. 3) The network complexity of the 0-10 cm fungal community gradually increased with elevation, while that of the 10-20 and 20-30 cm fungal communities exhibited a decreasing trend. Compared to the 0-10 cm soil layer, more changes in the relative abundance of fungal biomarkers occurred in the 10-20 and 20-30 cm soil layers, indicating that the fungal communities at these depths are more sensitive to climate changes. Among the key factors driving these alterations, soil temperature and moisture soil water content stood out as pivotal in shaping the assembly mechanisms and network complexity of fungal communities. This study contributes to the understanding of soil fungal community patterns and drivers along elevational gradients in alpine ecosystems and provides important scientific evidence for predicting the functional responses of soil microbial ecosystems in alpine forests.

Plant diversity is more important than soil microbial diversity in explaining soil multifunctionality in Qinghai-Tibetan plateau wetlands

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes

Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.

The effect of AMF combined with biochar on plant growth and soil quality under saline-alkali stress: Insights from microbial community analysis

Arbuscular mycorrhizal fungi (AMF) and biochar application individually can enhance plant tolerance to saline-alkali stress and promote plant growth efficiency. However, little is known about the potential synergistic effects of their combination on improving plant growth and soil quality under saline-alkali stress. This experiment adopted the potted method to explore the effects of four treatments on switchgrass growth and soil quality: biochar (BC), Rhizophagus irregularis (Ri), biochar + Ri (BR) and a control without biochar or Ri (CK). Compared to the CK treatment, the switchgrass biomass increased by 92.4 %, 148.6 %, and 177.3 % in the BC, Ri, and BR treatment groups, respectively. Similarly, the rhizosphere soil quality index increased by 29.33 %, 22.7 %, and 49.1 % in the respective treatment groups. The BR treatment significantly altered the rhizosphere soil microbial composition and diversity. Notably, compared to the other treatments, the archaeal α-diversity in the BR group showed a significant decrease. BR treatment significantly increased the relative abundance of bacteria, fungi and archaea at the genus level (e.g., Bacillus, Trichome and candidatus_methanopenens). Network analysis showed that the complexity and closeness of interactions between different microbial taxa were stronger in the BC, Ri and BR treatments than in the CK treatment, with BR being the more prominent. In summary, biochar combined with Ri has a better effect on promoting the growth of switchgrass under saline-alkali stress, improving the quality of saline-alkali soil, and increasing soil microbial diversity. This study provides a new approach for the efficient development and utilization of saline-alkali land.

Dual roles of microbes in mediating soil carbon dynamics in response to warming

Understanding the alterations in soil microbial communities in response to climate warming and their controls over soil carbon (C) processes is crucial for projecting permafrost C-climate feedback. However, previous studies have mainly focused on microorganism-mediated soil C release, and little is known about whether and how climate warming affects microbial anabolism and the subsequent C input in permafrost regions. Here, based on a more than half-decade of in situ warming experiment, we show that compared with ambient control, warming significantly reduces microbial C use efficiency and enhances microbial network complexity, which promotes soil heterotrophic respiration. Meanwhile, microbial necromass markedly accumulates under warming likely due to preferential microbial decomposition of plant-derived C, further leading to the increase in mineral-associated organic C. Altogether, these results demonstrate dual roles of microbes in affecting soil C release and stabilization, implying that permafrost C-climate feedback would weaken over time with dampened response of microbial respiration and increased proportion of stable C pool.

Anthropogenic restoration exhibits more complex and stable microbial co-occurrence patterns than natural restoration in rubber plantations

Forest restoration is an effective method for restoring degraded soil ecosystems (e.g., converting primary tropical forests into rubber monoculture plantations; RM). The effects of forest restoration on microbial community diversity and composition have been extensively studied. However, how rubber plantation-based forest restoration reshapes soil microbial communities, networks, and inner assembly mechanisms remains unclear. Here, we explored the effects of jungle rubber mixed (JRM; secondary succession and natural restoration of RM) plantation and introduction of rainforest species (AR; anthropogenic restoration established by mimicking the understory and overstory tree species of native rainforests) to RM stands on soil physico-chemical properties and microbial communities. We found that converting tropical rainforest (RF) to RM decreased soil fertility and simplified microbial composition and co-occurrence patterns, whereas the conversion of RM to JRM and AR exhibited opposite results. These changes were significantly correlated with pH, soil moisture content (SMC), and soil nutrients, suggesting that vegetation restoration can provide a favorable soil microenvironment that promotes the development of soil microorganisms. The complexity and stability of the bacterial-fungal cross-kingdom, bacterial, and fungal networks increased with JRM and AR. Bacterial community assembly was primarily governed by stochastic (78.79 %) and deterministic (59.09 %) processes in JRM and AR, respectively, whereas stochastic processes (limited dispersion) predominantly shaped fungal assembly across all forest stands. AR has more significant benefits than JRM, such as a relatively slower and natural vegetation succession with more nutritive soil conditions, microbial diversity, and complex and stable microbial networks. These results highlight the importance of sustainable forest management to restore soil biodiversity and ecosystem functions after extensive soil degradation and suggest that anthropogenic restoration can more effectively improve soil quality and microbial communities than natural restoration in degraded rubber plantations.

Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava (Manihot esculenta Crantz)

Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.

Effects of vegetation degradation on soil microbial communities and ecosystem multifunctionality in a karst region, southwest China

Vegetation degradation caused by intense human disturbances poses a significant challenge to the preservation and improvement of ecosystem functions and services in the karst region of southwest China. Soil microorganisms are major regulators of ecosystem multifunctionality (EMF). Currently, there is a dearth of knowledge regarding the effects of vegetation degradation on soil microbial communities and their corresponding multiple ecosystem functions in karst regions. In this study, we selected the vegetation degradation sequences of second natural forest (NF), agroforestry (AS) and cropland (CL) to investigate the diversity of bacterial, fungal and protistan communities, and their hierarchical co-occurrence network, and EMF to explore the relationships between them. Compared to the NF, the carbon cycling index, nitrogen cycling index, soil water regulation power, and the EMF were significantly decreased by 8.2%-50.6%, 48.7%-86.8%, 19.8%-24.5%, and 31.4%-69.5% in the AS and CL, respectively. The development of EMF can be explained by the fungal, protistan and microbial hierarchical β-diversity, as well as the complexity (e.g. degree) of microbial hierarchical interactions during the process of vegetation degradation. Notably, correlations between the abundances of sensitive amplicon sequence variants (sASVs) for different karst vegetation types and EMF varied in distinct network modules, being positive in module 1 and negative in module 2. Moreover, the relative abundance of keystone taxa in fungal and protistan communities provided greater contributions to EMF than the bacterial communities. Additionally, random forest modeling showed that carbon and nitrogen sources, and soil water content, and trace elements (e.g. exchangeable magnesium, iron, manganese, and zinc) were identified as key driving factors of the EMF. Collectively, our findings demonstrate that vegetation degradation obviously alters soil microbial diversities and hierarchical interactions, emphasizing their key role in maintaining ecosystem functions and health in karst regions.

Microbial difference and its influencing factors in ice-covered lakes on the three poles

Most lakes in the world are permanently or seasonally covered with ice. However, little is known about the distribution of microbes and their influencing factors in ice-covered lakes worldwide. Here we analyzed the microbial community composition in the waters of 14 ice-covered lakes in the Hoh Xil region of northern Qing-Tibetan Plateau (QTP), and conducted a meta-analysis by integrating published microbial community data of ice-covered lakes in the tripolar regions (the Arctic, Antarctica and QTP). The results showed that there were significant differences in microbial diversity, community composition and distribution patterns in the ice-covered tripolar lakes. Microbial diversity and richness were lower in the ice-covered QTP lakes (including the studied lakes in the Hoh Xil region) than those in the Arctic and Antarctica. In the ice-covered lakes of Hoh Xil, prokaryotes are mainly involved in S-metabolic processes, making them more adaptable to extreme environmental conditions. In contrast, prokaryotes in the ice-covered lakes of the Arctic and Antarctica were predominantly involved in carbon/nitrogen metabolic processes. Deterministic (salinity and nutrients) and stochastic processes (dispersal limitation, homogenizing dispersal and drift) jointly determine the geographical distribution patterns of microorganisms in ice-covered lakes, with stochastic processes dominating. These results expand the understanding of microbial diversity, distribution patterns, and metabolic processes in polar ice-covered lakes.

Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability

Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.

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.

Impact of artificial mixing and oxygenation on bacteria in a water transfer reservoir: Community succession and the role in water quality improvement

Artificial mixing and oxygenation induced by water-lifting aerations (WLAs) have the potential to improve water quality in reservoirs. However, there is a limited understanding of the bacterial community composition, assembly, and mechanisms behind water quality improvement under the influence of WLAs, especially in a water transfer reservoir. Here, the dynamics and relationship between water quality, bacterial diversity, and composition during the pre-operation, in-operation, and post-operation stages of WLAs were analyzed using high-throughput sequencing technology to explore the effects of artificially regulated bacteria on water quality improvement. WLAs operation led to the elimination of water stratification, significant bottom oxygenation, and reduction in nutrient concentrations. In addition, the operation of WLAs significantly changed the bacterial community composition, with an increase in richness, negligible difference in diversity, and a significant increase in the abundance of species with pollutant degradation functions, resulting in a shift from stochastic to deterministic processes of the bacterial community assembly. As a result, enhancement of the dominant bacteria responsible for organic matter degradation and denitrification and suppression of the emergence of algae-related bacteria were observed during the WLAs operation, and the ecosystem stability improved. Multiple analyses indicated a direct correlation between artificial mixing and oxygenation; changes in the bacterial community; and the reduction of nitrogen, phosphorus, and permanganate index in the water column. This study provides novel insights into in situ water quality enhancement and a valuable reference for understanding bacterial change patterns under artificially intervened conditions in water transfer reservoirs.

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 patterns and drivers of leaf functional traits of Robinia pseudoacacia and Pinus tabulaeformis plantations along a precipitation gradient in the Loess plateau, China

Changes in precipitation patterns in arid and semi-arid regions can reshape plant functional traits and significantly affect ecosystem functions. However, the synchronous responses of leaf economical, anatomical, photosynthetic, and biochemical traits to precipitation changes and their driving factors have rarely been investigated, which hinders our understanding of plants' ecological adaptation strategies to drought tolerance in arid areas. Therefore, the leaf traits of two typical plantations (Robinia pseudoacacia, RP and Pinus tabulaeformis, PT) along the precipitation gradient in the Loess Plateau, including economical, anatomical, photosynthetic, and biochemical traits, were investigated in this study. The results show that the leaf photosynthetic traits of RP and PT increase along the precipitation gradient, whereas leaf biochemical traits decrease. The anatomical traits of PT decrease with increasing precipitation, whereas no significant variation was observed for RP. Random Forest analysis show that LNC, LDMC, Chl, and PRO are leaf traits that significantly vary with the precipitation gradient in both plantations. Correlation analysis reveals that the traits coordination of RP is better than that of PT. The LMG model was used to determine driving factors. The results suggest that MAP explains the variation of PT leaf traits better (30.38%-36.78%), whereas SCH and SPH contribute more to the variation of RP leaf traits (20.88%-41.76%). In addition, the piecewise Structural Equation Model shows that the climate and soil physical and chemical properties directly affect the selected leaf functional traits of RP, whereas only the soil chemical properties directly affect the selected leaf functional traits of PT. The results of this study contribute to the understanding of the ecological adaptation of plants to environmental gradients and highlight that correlations among leaf traits should be considered when predicting plant adaptation strategies under future global change scenarios.

Drought Sensitivity of Spring Wheat Cultivars Shapes Rhizosphere Microbial Community Patterns in Response to Drought

Drought is the most important natural disaster affecting crop growth and development. Crop rhizosphere microorganisms can affect crop growth and development, enhance the effective utilization of nutrients, and resist adversity and hazards. In this paper, six spring wheat varieties were used as research material in the dry farming area of the western foot of the Greater Khingan Mountains, and two kinds of water control treatments were carried out: dry shed rain prevention (DT) and regulated water replenishment (CK). Phenotypic traits, including physiological and biochemical indices, drought resistance gene expression, soil enzyme activity, soil nutrient content, and the responses of potential functional bacteria and fungi under drought stress, were systematically analyzed. The results showed that compared with the control (CK), the leaf wilting, drooping, and yellowing of six spring wheat varieties were enhanced under drought (DT) treatment. The plant height, fresh weight (FW), dry weight (DW), net photosynthetic rate (Pn) and stomatal conductance (Gs), soil total nitrogen (TN), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), microbial biomass phosphorus (MBP), organic carbon (SOC), and soil alkaline phosphatase (S-ALP) contents were significantly decreased, among which, FW, Gs and MBC decreased by more than 7.84%, 17.43% and 11.31%, respectively. By contrast, the soil total phosphorus (TP), total potassium (TK), and soil catalase (S-CAT) contents were significantly increased (p < 0.05). TaWdreb2 and TaBADHb genes were highly expressed in T.D40, T.L36, and T.L33 and were expressed at low levels in T.N2, T.B12, and T.F5. Among them, the relative expression of the TaWdreb2 gene in T.L36 was significantly increased by 2.683 times compared with CK. Soil TN and TP are the most sensitive to drought stress and can be used as the characteristic values of drought stress. Based on this, a drought-tolerant variety (T.L36) and a drought-sensitive variety (T.B12) were selected to further analyze the changes in rhizosphere microorganisms. Drought treatment and cultivar differences significantly affected the composition of the rhizosphere microbial community. Drought caused a decrease in the complexity of the rhizosphere microbial network, and the structure of bacteria was more complex than that of fungi. The Shannon index and network modular number of bacteria in these varieties (T.L36) increased, with rich small-world network properties. Actinobacteria, Chloroflexi, Firmicutes, Basidiomycota, and Ascomycota were the dominant bacteria under drought treatment. The beneficial bacteria Bacillus, Penicillium, and Blastococcus were enriched in the rhizosphere of T.L36. Brevibacillus and Glycomyce were enriched in the rhizosphere of T.B12. In general, drought can inhibit the growth and development of spring wheat, and spring wheat can resist drought hazards by regulating the expression of drought-related genes, regulating physiological metabolites, and enriching beneficial microorganisms.