Search Results (86)

Soil salinization threatens agricultural sustainability and food security, especially in arid and semi-arid regions, yet how salinity gradients reshape multi-trophic networks and their associations with functional genes remain unclear. We investigated soil bacteria, fungi, protists, nematodes, and the carbon-fixation gene cbbL along a natural salinity gradient (electrical conductivity: 1.2–12.4 mS cm⁻¹) in Karamay, Xinjiang. Salinity acted as a key environmental filter, significantly differentiating biotic communities into low- and high-salinity groups. Compared with bacteria and fungi, protists and nematodes exhibit higher sensitivity to salinity shifts from non-saline to slightly saline soils, with their Shannon diversity decreasing by 74.2% and 50.4%, respectively (p < 0.05). High salinity significantly reduced the connectivity, modularity, and robustness of soil multi-trophic co-occurrence networks, resulting in 36.8% fewer edges, 24.2% lower modularity, and diminished network robustness compared to low-salinity conditions. Crucially, salinity was associated with functional decoupling, defined as a shift in the dominant drivers of microbial carbon sequestration potential. At low salinity, biotic factors explained 94.2% of cbbL variation, whereas at high salinity abiotic factors governed 86.1%, as shown by GBM (Gradient Boosting Machine) analyses. Our findings indicate that protists and nematodes can act as early warning indicators for soil salinization, and biotic network complexity represents a core metric for assessing saline soil ecosystem stability. This study reveals salinization-induced biota–function decoupling patterns and provides insights for saline soil health assessment and biotic restoration. Full article

Spent mushroom substrate (SMS) return is a vital strategy for agricultural waste recycling and soil fertility improvement, yet its ecological impacts of duration remain poorly understood. This study employed metagenomic sequencing to explore soil fertility, microbial dynamics, and nitrogen cycling across different SMS return durations (0, 1, and 3 years) within rice–mushroom crop rotation systems. Soil nutrients (organic matter, total nitrogen, total phosphorus) initially decreased and then increased throughout the rice growth cycle. The one-year return (y1) induced early nutrient depletion, whereas the three-year return (y3) significantly enhanced late-stage nutrient accumulation. With increasing duration, bacterial and archaeal assembly shifted from stochastic toward deterministic processes, while fungal diversity and stochasticity decreased continuously. Co-occurrence network analysis demonstrated that SMS return increased network complexity and intercommunity competition. This transition was accompanied by a functional shift in keystone taxa from those responsive to exogenous organic matter in y1 to those mediating nitrogen fixation, anammox, and sulfur metabolism in y3. Nitrogen cycling in y1 increased potential N₂O emission risks through nirS upregulation and nosZ downregulation, whereas y3 mitigated inorganic nitrogen loss by upregulating gene abundances of ammonia assimilation, nitrification, and DNRA genes. Notably, the structure of nitrogen-cycling genes fluctuated in y1 but was resilient to y0 levels in y3. These findings demonstrated that while initial SMS return triggered ecological fluctuations and environmental risks, continuous return (y3) achieved functional stability by reshaping microbial niches. This study highlights the importance of SMS return duration in balancing soil fertility enhancement with environmental risk mitigation in sustainable paddy ecosystems. Full article

Soybean is a globally important legume crop which fulfills most of its nitrogen (N) requirement through Biological Nitrogen Fixation (BNF) in symbiosis with Bradyrhizobium species, thereby reducing dependence on synthetic fertilizers and supporting more sustainable production systems. This review synthesizes current knowledge on the mechanism, capacity, and regulation of BNF in soybean, including nodule formation, nitrogenase activity and response to soil and environmental conditions. The evidence shows that BNF can provide a substantial share of the crop’s N uptake, although high-yielding systems frequently experience the “N gap”, which is a difference between a higher crop demand and a lower N supplied from BNF and existing soil reserves. This can be partially managed with strategies like inoculation, co-inoculation, re-inoculation or judicial application of N. This review further highlights the advances in microbial inoculant technologies, plant growth-promoting rhizobacteria (PGPR), soybean breeding and genetic engineering aimed at improving BNF stability, efficiency and capacity across different soil environments. Overall, the maximization of soybean BNF has strong potential to reduce synthetic fertilizer use, improve yield and seed quality, and enhance the economic and environmental sustainability of soybean-based systems. Full article

Autotrophic carbon-fixing microbes can assimilate atmospheric carbon dioxide into biomass via the Calvin–Benson–Bassham (CBB) cycle (their primary carbon fixation pathway), thereby reinforcing soil carbon sequestration in the plantation ecosystem; however, the succession of RubisCO-harboring microbial communities across stand ages remains poorly understood. Here, we investigated the community succession of microbes carrying the gene encoding RubisCO, a key enzyme in the CBB cycle, across a stand-age chronosequence in a Picea asperata plantation ecosystem. Our results revealed a progressive decrease in microbial α-diversity and a significant restructuring of community composition with increasing stand age, characterized by an enrichment of Proteobacteria and a concomitant depletion of Actinobacteria. While the Shannon–Wiener index was most strongly correlated with soil total nitrogen content, redundancy analysis identified soil pH as the predominant environmental driver of community turnover, a relationship that was found to be threshold-dependent, with substantial community shifts occurring in response to pH variations of 0.5 to 1.0 units. These findings suggest that sustaining the diversity of RubisCO-harboring microbes in older stands—a process potentially enhanced by soil nitrogen management—provides a viable strategy for augmenting the carbon sequestration capacity of managed forests through targeted microbiome regulation. Full article

Microplastics (MPs) are emerging pollutants that affect soil–microbe interactions in paddy ecosystems. Periphytic biofilms (PBs) are complex microbial consortia that ubiquitously distribute at the soil–water interface of paddy ecosystems, playing essential roles in nutrient cycling and pollutant migration. However, whether MPs affect the community composition of PBs remains largely unknown. This microcosm study investigated the effects of three types of MPs (polyacrylonitrile, PAN; polyethylene, PE; and polyethylene terephthalate, PET) on the community characteristics of PBs via high-throughput sequencing (16S/18S rRNA) technology. Results showed that the addition of all MPs significantly increased the biomass and chlorophyll-a content of PBs, with PAN inducing the maximum increase (by 331.9% and 128.6%). However, all MPs had no significant effect on the PB α-diversity of bacterial and eukaryotic communities (p > 0.05). As for PB composition, PAN and PET increased the relative abundance of Cyanobacteria, Proteobacteria and Holozoa, PE increased that of Cyanobacteria, Bacteroidota and Blastocladiomycota, and all MPs decreased the relative abundance of Chloroflexi, Actinobacteriota and Basidiomycota. Furthermore, PET decreased the predicted functional potential of natural polymer degradation (cellulolysis, ligninolysis, xylanolysis, ureolysis), nitrogen fixation and nitrate ammonification, while PE increased predicted potential for plastic degradation, nitrate reduction and denitrification. Co-occurrence network analysis suggested that the PE network showed higher connectivity and lower modularity, while the PAN network showed higher modularity. This study advances our understanding of soil MPs–microbe interactions under high-concentration conditions. It also suggests that PB community characteristics may serve as potential bioindicators for soil MP pollution. Full article

Promoting the agricultural recycling of biogas slurry (BS) is crucial for sustainable development, yet its long-term ecological impacts remain unclear. Through a multi-year field trial in a sugarcane system, this study examined the effects of BS application (0, 3, and 6 years) on the soil properties, bacterial communities, and functional genes for C, N, P, and S cycling. The results revealed distinct two-phase patterns of changes in soil properties, microbial communities, and functional genes. Short-term (3-year) application induced a “disturbance” phase, characterized by significant acidification (pH decreased by 17.91%), a surge in nitrate-N (increased by 757.27%), and a transient decline in bacterial richness. Long-term (6-year) application drove a “functional restructuring” phase, reversing acidification and significantly increasing soil organic matter (29.05%) and total nitrogen (TN) (20.81%). Bacterial richness recovered, and community composition distinctively restructured. Functional gene analysis revealed shifts in gene abundance that transitioned from high abundance in the short term to a new balance favoring processes like N fixation. Co-occurrence network analysis indicated that this functional shift was associated with core microbial modules (e.g., Firmicutes) and changes in soil pH and SOM. This study suggests that, although short-term application causes significant adjustments, sustained and appropriate BS application can ultimately enhance soil fertility and promote a functionally reorganized state by reshaping microbial interaction networks. It presents a microbial ecological basis for the safe and sustainable use of BS in circular agriculture. Full article

Saline–alkali soils suffer from severe deficiencies in available phosphorus, and externally added phosphorus is readily immobilized by metal ions in the soil. Therefore, activating inorganic phosphorus in the soil represents a significant challenge. In this study, 35 salt–alkali-tolerant bacteria were isolated from rhizosphere soils (pH 9.20–9.68). Three phosphate-solubilizing strains (HA2, HPA5, and KA1) capable of growing under severe saline–alkali stress conditions (pH 10, 5% NaCl) and possessing multiple plant growth-promoting traits (nitrogen fixation, potassium solubilization, siderophore production, and IAA secretion) were screened and co-cultured to form the microbial consortium HHK. It was hypothesized that this consortium might exhibit synergistic effects, resulting in significantly higher phosphorus solubilization capacity compared to individual strains. The results showed that under saline–alkali stress, the phosphate solubilization capacity of HHK (484.59 ± 15.79 mg/L) was significantly higher than that of any single strain (285.59 ± 12.60 mg/L). Non-targeted metabolomics and enzyme assays indicated that HHK solubilizes P via organic acids (e.g., citric, L-malic acid) and synergistically modulates core metabolic pathways, including ABC transport, TCA cycle, and glycolysis, alleviating oxidative damage and maintaining cellular homeostasis. Short-term soil incubation confirmed that HHK significantly increased available phosphorus (53.67%) and soil fertility, indicating its potential as a biofertilizer. Full article

Over the past few decades, legume-based intercropping has emerged as a strategic agronomic practice to enhance the sustainability and resilience of agro-ecosystems, thanks to its ability to perform biological nitrogen fixation and store soil organic carbon. The present study, given the growing recognition of agroecological practices, aims to analyze through a global bibliometric analysis the research conducted between 1986 and 2025 on legume–non-legume intercropping, with particular emphasis on its ecological and agronomic benefits. The investigation, carried out according to the PRISMA protocol on the Scopus database, selected 167 original English-language articles, excluding reviews, conference proceedings, modeling studies, and meta-analyses. China and India are identified as the most productive countries. Co-occurrence and bibliographic coupling analyses highlight thematic clusters centered on soil fertility, microbial communities, productivity, and the mitigation of environmental impact. Furthermore, management practices such as integrated rotations, cover crops, and agroforestry systems amplify the benefits in terms of carbon accumulation and resilience to adverse climate conditions. The distribution of publications by journal highlights the centrality of journals such as Agriculture, Ecosystems & Environment and Plant and Soil. Overall, the data confirm the crucial role of intercropping as a pillar of the agroecological transition, underscoring the need for policies and research programs capable of amplifying its global adoption. The findings of this study may guide future interdisciplinary research and evidence-based policy decisions aimed at optimizing the design of resilient intercropping systems, tailored to address the challenges posed by climate change and the growing demands of global food security. Full article

Natural gas represents a pivotal transitional clean energy resource, and biogenic coalbed methane (CBM) is ubiquitously distributed in coal reservoirs worldwide. In the context of carbon neutrality targets and the growing demand for large-scale commercial CBM exploitation, innovative technological solutions are urgently required. CBM bioengineering aims to substantially enhance CBM production by stimulating biomethane generation, promoting gas desorption, and improving reservoir permeability, while simultaneously enabling effective CO₂ sequestration. The potential for biomethane generation is largely governed by the intrinsic physicochemical characteristics of coal, including aromatic structures, maceral composition, and pore–fracture architecture. In addition, hydrogeological conditions—such as geothermal gradients, pH variability, and redox potential—play critical roles in regulating microbial functional gene expression and metabolic enzyme synthesis. Core pretreatment strategies in coalbed gas bioengineering can be broadly classified into approaches that enhance coal bioconversion potential and those that optimize functional microbial consortia. Electric fields and conductive materials can influence microbial community structure by enriching electroactive microorganisms and facilitating interspecies electron transfer. In addition to engineered conductive interventions, reservoir environmental conditions also play an important role in shaping methanogenic community structure. Experimental observations under reservoir-relevant CO₂ pressure and temperature conditions indicate that deep coalbed environments are associated with shifts in methanogenic community composition, including an increased relative abundance of hydrogenotrophic methanogens. These observations suggest that physicochemical conditions in deep coal seams may favor hydrogen-dependent CO₂ reduction pathways, thereby supporting hydrogenotrophic methanogenesis and contributing to biomethane generation. The integration of supercritical CO₂ with microbially acclimated stimulation fluids as an innovative reservoir fracturing strategy offers multiple advantages, including effective reservoir stimulation, permanent carbon sequestration, and sustainable biomethane generation. Future research should focus on modulating coal matrix bioavailability, optimizing microbial consortia, enhancing interspecies metabolic synergies, and advancing carbon fixation bioprocesses to facilitate the large-scale implementation of coalbed gas bioengineering systems. This review synthesizes recent advances in microbially mediated CBM enhancement and CO₂ sequestration, with a particular focus on field-scale evidence and the key challenges that must be addressed for large-scale implementation. Full article

Biological soil crusts (BSCs) are critical ecological components in arid lands. Their formation and stability hinge on the assembly and interactive networks of cyanobacteria-led bacterial communities. Yet, how different functional cyanobacteria shape the underlying microbial structure and assembly rules is poorly understood. Here, we cultivated artificial algal crusts using two representative cyanobacteria: the nitrogen-fixing Leptolyngbya sp. and the non-nitrogen-fixing Microcoleus vaginatus (M. vaginatus CM01). A total of six treatments were established based on the presence or absence of spraying with in situ BSCs leachate: a control group without inoculation of algae or bacteria (soil, S); a treatment group sprayed only with bacterial suspension (soil + bacteria, SB); a treatment group sprayed only with M. vaginatus CM01 (soil + M. vaginatus CM01, SM); a treatment group co-inoculated with both BSCs leachate and M. vaginatus CM01 (soil + M. vaginatus CM01 + bacteria, SMB); a treatment group inoculated only with Leptolyngbya sp. CT01 (soil + Leptolyngbya sp. CT01, SL); and a treatment group co-inoculated with Leptolyngbya sp. CT01 and biocrust leachate (soil + Leptolyngbya sp. CT01 + bacteria, SLB). By integrating 16S rRNA gene sequencing, neutral community modeling (NCM), and structural equation modeling (SEM), we dissected differences in Cyano-BSCs development, bacterial community composition, co-occurrence networks, and assembly mechanisms. Inoculation with M. vaginatus CM01 (SM, SMB) superiorly promoted Cyano-BSCs development: the SM group achieved the highest coverage (23.33%), while the SMB group showed marked increases in organic matter (OM, 4.10 g·kg⁻¹) and chlorophyll a (Chla, 13.40 μg·g⁻¹), alongside a >5-fold rise in bacterial, cyanobacterial, and nitrogen-fixation gene abundances versus controls. The mechanism centers on extracellular polymeric substances (EPS) secreted by M. vaginatus, which homogenized the microenvironment, suppressed stochastic bacterial dispersal (NCM, SM: R² = 0.698), and enhanced deterministic selection. This process forged a highly cooperative network (89.74% positive links, average degree 34.71) that directionally enriched Cyanobacteria (relative abundance 40.40%). The Shannon index of Cyano-BSCs from the group (SMB) reached 7.72 ± 0.09, reflecting high microbial community diversity. SEM confirmed M. vaginatus directly regulated bacterial assembly (path coefficient = 0.59, p < 0.05) and indirectly improved the soil environment (path coefficient = 0.64, p < 0.05), establishing a “cyanobacteria-community-environment” feedback loop. Conversely, the Leptolyngbya sp. groups (SL, SLB), despite enriching nitrogen-fixing bacteria and fungi, exhibited low carbon fixation efficiency (notably 1.26 g·kg⁻¹ OM in SL) and lack of EPS; communities remained stochastic (NCM, SL: R² = 0.751) with no effective regulatory pathway—a pattern mirrored in S and SB groups. Our findings demonstrate that M. vaginatus acts as a core engineer of biological soil Cyano-BSCs formation via an “EPS-mediated habitat filtering—functional group enrichment—cooperative network assembly” cascade, enforcing deterministic community construction. Leptolyngbya sp., with limited niche-constructing ability, fails to exert comparable control. This work provides a targeted framework for the artificial restoration of Cyano-BSCs in arid zones. Full article

As a critical aquatic–terrestrial ecological transition zone, the lake littoral zone exhibits steep biogeochemical gradients and plays a vital role in regulating submerged microbial communities and their functions. This study aims to reveal how multi-scale environmental gradients influence microbial succession processes along desert lake littoral zones, as well as the distribution patterns of functional genes involved in carbon (C), nitrogen (N), and sulfur (S) cycling. The results demonstrated that microbial alpha-diversity in the vadose zone exhibited significant individual variability horizontally, while showing pronounced inter-group differences vertically. Horizontally, a distinct functional succession was observed from the shore to the water’s edge, with microbial potential shifting progressively from aerobic oxidative types toward anaerobic reductive types. Vertically, the root-intensive layer fostered more complex co-occurrence networks through enhanced interspecific interactions, suggesting higher functional resilience compared to other layers. Further analysis identified soil moisture as the primary environmental filter driving microbial composition, explaining 27.7% of the variation. Structural equation modeling (SEM) further elucidated that pH and Total Organic Carbon (TOC) were the key regulators of carbon fixation and sulfur oxidation genes, while Total Nitrogen (TN) dominated the distribution patterns of nitrogen cycling genes. These findings deepen the mechanistic understanding of microbial-mediated element cycling in desert lakeshore zones and provide a theoretical basis and data support for maintaining the functions of these fragile ecosystems. Full article

Identifying plant-growth-promoting rhizobacteria tolerant to saline–alkali conditions is critical for developing effective microbial agents and multi-strategy approaches to remediate saline–alkali soil. Two salt–alkali-tolerant bacterial strains—phosphorus-solubilizing Bacillus pumilus JL-C and cellulose-decomposing B. halotolerans XW-3—were isolated from saline–alkali soil, with both exhibiting multiple plant-growth-promoting properties, including nitrogen fixation and the generation of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase. Alfalfa pot experiments were conducted under four treatments: a control, the strain JL-C treatment, the strain XW-3 treatment, and a co-inoculation treatment (JL-C/XW-3), all mixed with corn straw and applied to the saline–alkali soil. The results demonstrated that the co-inoculation treatment yielded the most significant growth-promoting effects on alfalfa, showing enhanced antioxidant enzyme activities; increased contents of proline, soluble sugar, and protein; reduced malondialdehyde content; lowered pH and electrical conductivity; elevated activities of key enzymes; and increased levels of available nitrogen, phosphorus, potassium, and organic matter content in the soil. The pot experiments were confirmed by field experiments. The results of 16S rRNA high-throughput sequencing revealed changes in the bacterial community composition in the alfalfa rhizosphere, showing shifts in the relative abundance of several bacterial taxa often reported as plant-associated or potentially beneficial. This study establishes a combined remediation strategy for saline–alkali soil utilizing complex microbial agents and corn straw. Full article

To address the challenges of low land use efficiency, soil degradation, and high management costs in Ilex asprella cultivation, this study established an I. asprella–Grona styracifolia intercropping system and systematically evaluated its effects on soil nutrient cycling, microbial communities, and crop growth. Field experiments were conducted in Yunfu City, Guangdong Province, with monoculture (LCK for I. asprella, DCK for G. styracifolia) and three intercropping densities (HDT, LDT, MDT). Combining 16S rRNA sequencing and metagenomics, we analyzed the functional profile of the rhizosphere microbiome. The results showed that intercropping significantly increased the biomass of G. styracifolia, with the medium-density (MDT) treatment increasing plant length and fresh weight by 41.2% and 2.4 times, respectively, compared to monoculture. However, high-density intercropping suppressed the accumulation of medicinal compounds. In terms of soil properties, intercropping significantly enhanced soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and available nitrogen (AN) in the rhizosphere of both plants. Specifically, AN in the I. asprella rhizosphere increased by 18.9%. Soil urease and acid phosphatase activities were also elevated, while pH decreased. Microbial analysis revealed that intercropping reshaped the rhizosphere microbial community structure, significantly increased the Shannon diversity index of bacteria in the G. styracifolia rhizosphere, and enhanced the complexity of the microbial co-occurrence network. Metagenomic analysis further confirmed that intercropping enriched functional genes related to carbon fixation, nitrogen cycling (nitrogen fixation, assimilatory nitrate reduction), and organic phosphorus mineralization (the phoD gene), thereby driving the transformation and availability of soil nutrients. These findings demonstrate that the I. asprella–G. styracifolia intercropping system, particularly at medium density, effectively improves soil fertility and land use efficiency by regulating rhizosphere microbial functions, providing a theoretical basis for the sustainable ecological cultivation of I. asprella. Full article

Lima bean (Phaseolus lunatus L.), an important legume in semiarid environments, often exhibits low yield, requiring strategies to enhance symbiotic nitrogen fixation and nutrient-use efficiency. This study evaluated the effects of single and combined inoculation with Bradyrhizobium elkanii (strain BR 2003) and Azospirillum brasilense (strain Ab-V5) on nitrogen metabolism, nutrient uptake, plant growth, and residual soil fertility in P. lunatus. Four varieties were subjected to four treatments: control (nitrogen fertilization), single inoculation with B. elkanii or A. brasilense, and co-inoculation. All inoculation strategies significantly increased root nodulation, nitrogen assimilation, and the accumulation of key macronutrients. Root nodulation increased from 1 to 12 nodules per plant in the control treatments to up to 277 nodules per plant under inoculation, while shoot nitrogen content increased by up to 91% in ‘Raio de Sol’ and 87% in ‘Cearense’. Increases in P and K were also observed, including a 48% increase in shoot P in ‘Manteiga’ and up to a 100% increase in shoot K in ‘Raio de Sol’, whereas root K increased by up to 90% under co-inoculation. The ‘Raio de Sol’ and ‘Manteiga’ varieties exhibited the most pronounced increases in growth and biomass. Additionally, inoculation improved post-cultivation soil indicators, including pH and available P and K in specific genotype-microbe combinations, and reduced electrical conductivity. These results demonstrate the strong contribution of microbial inoculation to nitrogen assimilation and nutrient acquisition, supporting its use as a promising alternative to conventional nitrogen fertilization in lima bean cultivation. Full article

Fertilization regimes impact the carbon cycle processes in paddy soils. However, the effects of shifting fertilization regimes on the structure of microbial communities and functional genes involved in soil carbon (C)-cycling remain unclear. A long-term field experiment was established with three paired fertilization shift treatments: chemical fertilizer (CF) and CF to normal-rate organic fertilizer (CF-NOM); normal-rate organic fertilizer (NOM) and NOM to CF (NOM-CF); high-rate organic fertilizer (HOM) and HOM to CF (HOM-CF). Metagenomic sequencing and bioinformatics analysis were employed to investigate the effects of fertilization shifts on soil C-cycling microbial community structure, functional genes, and environmental factors. The results showed that compared to CF treatment, CF-NOM significantly increased soil organic carbon (SOC), mineral-associated organic carbon (MAOC), particulate organic carbon (POC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), and the emissions of CO₂ and CH₄ (p < 0.05). The NOM-CF led to significant reductions in MAOC, MBC, DOC, and CO₂ and CH₄ emissions. The HOM-CF shift caused significant decreases in SOC, MAOC, POC, MBC, DOC, and CO₂ and CH₄ emissions. Fertilization shifts had no significant effect on the α-diversity of C-cycling microbial communities (p > 0.05), but β-diversity showed a significant restructuring of community composition. Network analysis indicated that fertilization shifts increased positive microbial correlations while reducing network modularity. C-cycling functional genes responded sensitively to fertilization disturbances, especially key genes in the carbon fixation pathway (cdhDE, cooS). Redundancy analysis indicated that soil bulk density (BD) and POC are key environmental factors regulating functional differences in carbon metabolism, which collectively influenced microbial community structure and functional gene abundance along with other factors. We concluded that the C-cycling process in paddy soil was greatly altered by shifts in fertilization regimes, influenced by microbial diversity, functional genes, and network structure linked to soil characteristics. Full article