Soil Microbes Research Articles

A comprehensive review on phytoremediation of fly ash and red mud: exploring environmental impacts and biotechnological innovations.

Fly ash (FA) and red mud (RM) are industrial byproducts generated by thermal power plants and the aluminum industry, respectively. The huge generation of FA and RM is a significant global issue, and finding a safe and sustainable disposal method remains a challenge. These dumps contain harmful trace elements that have a significant impact on the environment and human health. It contributes to air, water, and soil pollution, disrupting the delicate balance of the ecosystems. It also introduces toxins into the food chain through biomagnification. Utilizing a vegetation cover can assist in addressing environmental health concerns associated with FA and RM dumps. Nevertheless, the presence of alkaline pH, toxic metals, the absence of soil microbes, and the pozzolanic properties of both FA and RM pose challenges to plant growth. Taking a comprehensive approach to the ecological restoration of these dumps through phytoremediation is crucial. This review examines the role of various factors in the ecological restoration of FA and RM dumps, specifically the use of naturally occurring plants. However, the issue of slow plant growth due to a lack of nutrients and microbial activities is being resolved through various advances, such as amendments in conjunction with organic matter, microbial inoculants, and the use of genetically modified plants. Research has demonstrated the benefits of using amendments to stimulate vegetation growth on FA and RM dumps. In this review, we explore various approaches to restoring FA and RM dumps and transforming them into productive sites that enhance the ecosystem services.

Overexpressing Carbonic Anhydrase Transgenic Rice Plants Maintain the Regular Soil Functions and Microbial Activities of Soil

Background: Genetically modified (GM) crops are focused on establishing desirable traits to support the food demand of increasing populations. The effect of transgenic plants on soil diversity has been highlighted by a lot of researchers. Some of them showed the negative effect of transgenic crop on soil microbes and the food chain. So there is an urgent need to develop transgenic plants with no harmful effects on environmental health. Methods: We have examined the effects salt tolerant carbonic anhydrase overexpressing transgenic rice plants on the physiology of rhizospheric microbes and their enzymatic activities. In the present study, we have used pot experiments in the greenhouse of Centurion University of Technology and management, Bhubaneswar, Odisha, India. Result: No significant variation in the soil properties viz., pH, Eh, organic C, P, K, N, Ca, Mg, S, Na and Fe+2 were observed. The population of bacteria, fungi and nematodes were remained same in the soil. The enzymatic activities like soil dehydrogenase, nitrate reductase, urease and alkaline phosphatase were not significantly affected. Further, plant growth promotion (PGP) functions such as HCN, siderophore, salicylic acid, GA, IAA, zeatin, were, not influenced considerably. The present study ecologically pertinent of salt tolerant CA transgenic rice to usual functions of the rhizospheric organisms.

Microbial mechanisms for CO2 and CH4 emissions in Robinia pseudoacacia forests along a North–South transect in the Loess Plateau

Forest soil microbes play a crucial role in regulating atmospheric-soil carbon fluxes. Environmental heterogeneity across forest types and regions may lead to differences in soil CO2 and CH4 emissions. However, the microbial mechanisms underlying these emission variations are currently unclear. In this study, we measured CO2 and CH4 emissions of Robinia pseudoacacia forests along a north–south transect in the Loess Plateau. Using metagenomic sequencing, we investigated the structural and functional profiles of soil carbon cycling microbial communities. Results indicated that the forest CO2 emissions of Robinia pseudoacacia was significantly higher in the north region than in the south region, while the CH4 emission was oppositely. This is mainly attributed to changes in gene abundance driven by soil pH and moisture in participating carbon degradation and methane oxidation processes across different forest regions. The gene differences in carbon fixation processes between regions primarily stem from the Calvin cycle, where the abundance of rbcL, rbcS, and prkB genes dominates microbial carbon fixation in forest soils. Random forest models revealed key genes involved in predicting forest soil CO2 emissions, including SGA1 and amyA for starch decomposition, TYR for lignin decomposition, chitinase for chitin decomposition, and pectinesterase for pectin decomposition. Microbial functional characterization revealed that interregional differences in CH4 emissions during methane metabolism may originate from methane oxidation processes, and the associated gene abundances (glyA, ppc, and pmoB) were key genes for predicting CH4 emissions from forest soils. Our results provide new insights into the microbial mechanisms of CO2 and CH4 emissions from forest soils, which will be crucial for accurate prediction of the forest soil carbon cycle in the future.

Characteristics of organic amendments induce diverse microbial metabolisms for exogenous C turnover in Mollisols

The response of microbial community to organic amendments is closely related to the amendment-derived carbon (C) turnover, which in turn influences the enhancement of soil organic C, including the quantity and quality. The objective of this study was to quantify the decomposition and retention of exogenous C derived from amendments, and to identify the microbial regulatory mechanisms of exogenous C turnover in response to the characteristics of organic amendments. The 13C-labelled glucose, straw and biochar, characterizing organic amendments with high, medium and low labilities, respectively, were used to conduct a 90-day incubation experiment, in conjunction with stable isotope probing technology and amino sugar molecular biomarkers. It was found that the cumulative mineralization of amendment-derived C increased with increasing the corresponding lability of organic amendment, and the decompositions of the added glucose, straw and biochar, expressed as a percentage of the initially added C, were 53.6 %, 37.0 %, and 0.6 %, respectively. Among all treatments, the addition of straw significantly enhanced the total dissolved organic C (DOC) concentration and its ratio to total organic C by increasing the input of exogenous DOC and reducing the decomposition of native soil DOC. The exogenous C use efficiency by microorganisms was significantly enhanced with decreasing the amendment lability, and showed a positive correlation with the total amendment-derived C. However, the microbial growth efficiency was the highest when straw was added, and was closely related to the concentration of amendment-derived DOC. Different functional groups of soil microbes exhibited distinct capacities to metabolize various organic amendments. Generally, the incorporation of amendment-derived C into microbial biomass was significantly affected by fungi and gram-positive (G+) bacteria, while the relative contributions of microbial communities incorporating amendment-derived C into necromass were decreased in the order of gram-negative (G−) bacteria > fungi > actinomycetes > G+ bacteria. From the perspective of microbial metabolism, the larger incorporations of exogenous C into microbial biomass and necromass were observed in the soil with mediumly labile amendment, which contributed to enhance the quantity and quality of organic C in soil. These results would be informative to optimize the organic amendment strategy for integrated soil fertility management.

Altitudinal Influences on Soil Microbial Diversity and Community Assembly in Topsoil and Subsoil Layers: Insights from the Jinsha River Basin, Southwest China

Altitudinal Influences on Soil Microbial Diversity and Community Assembly in Topsoil and Subsoil Layers: Insights from the Jinsha River Basin, Southwest China

Bioprospecting for sustainable and eco-friendly bioproducts: A case study of multi-enzyme production by soil microbes

Microbial multi-enzyme production is a promising research area involving microbes that can simultaneously synthesize numerous enzymes for the degradation of substrates with environmental sustainability and other industrial applications as the focus. During this study, we isolated, screened, and identified some multi-enzyme-producing microbes from three soil sites in Ibadan: Apete Dumpsite (ADS); Botanical Garden University of Ibadan- (BGUI); and Eleyele Cassava Processing Field- (ECPF). Precisely 500 g of soil were collected per point at different depths (0–10, 10–20, and 20–30 cm) and further analyzed. The microbial load and type and enzyme assays were determined. The highest average microbial count (6.9 × 108 CFU/g) was recorded in the ECPF soil sample at 0–10 cm depth, while the lowest microbial count of 3.3 × 105 CFU/g at 20–30 cm soil depth in BGUI. Multi-enzyme-producing microbes were identified phenotypically and molecularly. This study revealed an inverse relationship between microbial community composition and soil depth. Bacterial and fungal genera had higher species richness, biodiversity, and evenness than yeast from all sampled points. With significant amylolytic, proteolytic, lipolytic, cellulolytic, and pectinolytic activities, 22 of the 193 isolates were identified as multienzyme producers. The blasted 16S rRNA and ITS rRNA amplicon sequences compared with sequences in the NCBI gene bank identified Bacillus, Roseomonas, Aeromonas, Phanerochaete, Aspergillus, Fusarium, Trametes, and Rigidoporus species. Results from this study show that topsoils (0–10 cm), rich with organic matter, are good reservoirs of multienzyme-producing microorganisms- applicable for environmental sustainability and in other important industries for waste management, food processing, and biomaterial production.

Mapping, Distribution, Function, and High-Throughput Methodological Strategies for Soil Microbial Communities in the Agroecosystem in the Last Decades

The intricate interplay between SMCs and agroecosystems has garnered substantial attention in recent decades due to its profound implications for agricultural productivity, ecosystem sustainability, and environmental health. Understanding the distribution of SMCs is complemented by investigations into their functional roles within agroecosystems. Soil microbes play pivotal roles in nutrient cycling, organic matter decomposition, disease suppression, and plant‒microbe interactions, profoundly influencing soil fertility, crop productivity, and ecosystem resilience. Elucidating the functional diversity and metabolic potential of SMCs is crucial for designing sustainable agricultural practices that harness the beneficial functions of soil microbes while minimizing detrimental impacts on ecosystem services. Various molecular techniques, such as next-generation sequencing and high-throughput sequencing, have facilitated the elucidation of microbial community structures and dynamics at different spatial scales. These efforts have revealed the influence of factors such as soil type, land management practices, climate, and land use change on microbial community composition and diversity. Advances in high-throughput methodological strategies have revolutionized our ability to characterize SMCs comprehensively and efficiently. These include amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics, which provide insights into microbial taxonomic composition, functional potential, gene expression, and protein profiles. The integration of multiomics approaches allows for a more holistic understanding of the complex interactions within SMCs and their responses to environmental perturbations. In conclusion, this review highlights the significant progress made in mapping, understanding the distribution, elucidating the functions, and employing high-throughput methodological strategies to study SMCs in agroecosystems.

Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment

The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5–35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86–181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25–35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.

Bacterial and fungal keystone taxa play different roles in maintaining community resistance and driving soil organic carbon dynamics in response to Solidago Canadensis invasion

The invasion of alien plants has significant implications for vegetation structure and diversity, which could lead to changes in the carbon (C) input from vegetation and change the transformation and decomposition processes of C, thereby altering the dynamics of soil organic carbon (SOC) within ecosystems. Whether alien plant invasion increases the SOC stock and changes SOC fractions consistently within regional scales, and the underlying mechanisms driving these SOC dynamics remain poorly understood. This study investigated SOC dynamics by comparing the plots that suffered invasion and non-invasion of Solidago Canadensis across five ecological function areas in Anhui Province, China, considering climate, edaphic factors, vegetation, and soil microbes. The results demonstrated that the impact of S. Canadensis invasion on SOC storage was not consistent at each site in the 0–20 cm soil layer, as indicated by the range of SOC content (5.94–12.45 g kg−1) observed at non-invaded plots. Stable SOC exhibited similar response patterns with SOC to plant invasion, whereas labile SOC did not. In addition, bacterial and fungal communities were shifted in structure at each site by plant invasion. Bacterial communities exhibited greater resistance to S. Canadensis invasion than did fungal communities, as evidenced by three aspects of the resistance indices—community resistance, phylogenetic conservation, and network complexity. The mechanisms driving SOC dynamics under S. Canadensis invasion were explored using structural equation models. This revealed that fungal keystone taxa responsible for community resistance controlled stable SOC fractions. In contrast, bacterial keystone taxa had the opposite effect on labile and stable SOC. Climatic and edaphic factors were also involved in the labile and stable SOC dynamics. Overall, this study provides novel insights into the dynamics of SOC under S. Canadensis invasion on a regional scale.

Reduced ligninase‐cellulase ratio enhances soil carbon sequestration following afforestation of agricultural land

AbstractIntroductionAfforestation of agricultural land is one of the most essential approaches to mitigate climate change by enhancing the sequestration of atmospheric carbon (C) into the soil. C‐degrading extracellular enzymes produced by soil microbes regulated the decomposition and fate of sequestrated soil organic carbon (SOC), with potential divergent variations following afforestation across different ecosystem scales. However, the feedbacks of different C‐degrading enzymes and their relationships with SOC following afforestation of agricultural land remain unclear.Materials and MethodsWe investigated the changes in enzyme activity and their relationships with SOC in soil aggregates across two typical climatic vegetation restoration regions in China, and explored the mechanisms through which changes in enzyme activity contribute to SOC sequestration following afforestation of agricultural land.ResultsAfforestation of agricultural land generally decreased ligninase activity and increased cellulase activity across various aggregate fractions, compared to the adjacent croplands in both subtropic (Danjiangkou Reservoir, DJK) and temperate (Maoershan, MES) region. Additionally, the ratio of ligninase to cellulase (L:C) was lower in afforested lands than in the croplands, with L:C as the major factor explaining the variations of SOC sequestration following afforestation. Specifically, ligninase and L:C were negatively correlated with SOC, whereas cellulase showed positive correlations with SOC. Further analyses suggested that microbial biomass C and nitrogen (MBC and MBN) and the ratio of SOC and total nitrogen (SOC:TN) were important factors influencing L:C and subsequently regulating SOC. These results suggest that shifts in microbial enzyme production from ligninase to cellulase following afforestation, reduced the decomposition of recalcitrant C, thus contributing to SOC sequestration.ConclusionOur work underscores the critical role of reduced L:C in enhancing SOC sequestration following the restoration of croplands to afforested lands. These findings advance the understanding of the influence of microbial community physiological adaptations on C sequestration across different land use types.

Reconciling Top‐Down and Bottom‐Up Estimates of Ecosystem Respiration in a Mature Eucalypt Forest

AbstractEcosystem respiration (Reco) arises from interacting autotrophic and heterotrophic processes constrained by distinct drivers. Here, we evaluated up‐scaling of observed components of Reco in a mature eucalypt forest in southeast Australia and assessed whether a land surface model adequately represented all the fluxes and their seasonal temperature responses. We measured respiration from soil (Rsoil), heterotrophic soil microbes (Rh), roots (Rroot), and stems (Rstem) in 2018–2019. Reco and its components were simulated using the CABLE–POP (Community Atmosphere‐Biosphere Land Exchange–Population Orders Physiology) land surface model, constrained by eddy covariance and chamber measurements and enabled with a newly implemented Dual Arrhenius and Michaelis‐Menten (DAMM) module for soil organic matter decomposition. Eddy‐covariance based Reco (Reco.eddy, 1,439 g C m−2 y−1) was slightly higher than the sum of the respiration components (Reco.sum, 1,295 g C m−2 y−1) and simulated Reco (1,297 g C m−2 y−1). The largest mean contribution to Reco was from Rsoil (64%) across seasons. The measured contributions of Rh (49%), Rroot (15%), and Rstem (22%) to Reco.sum were very close to model outputs of 46%, 11%, and 22%, respectively. The modeled Rh was highly correlated with measured Rh (R2 = 0.66, RMSE = 0.61), empirically validating the DAMM module. The apparent temperature sensitivities (Q10) of Reco were 2.22 for Reco.sum, 2.15 for Reco.eddy, and 1.57 for CABLE‐POP. This research demonstrated that bottom‐up respiration component measurements can be successfully scaled to eddy covariance‐based Reco and help to better constrain the magnitude of individual respiration components as well as their temperature sensitivities in land surface models.

Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

AbstractMicrobes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession.

Effects of Metribuzin on Soil Microbiome and Weed Management Under Varying Planting Practices and Potato Seed Dormancy

AbstractWeed infestation in potato field has become a major concern to smallholder farmers and environment, requiring sustainable intervention. This study aimed to determine (i) whether metribuzin application rate (0, 0.5, 1 (standard), 1.5, and 2 kg ai ha−1) has effects on soil microbes and soil nutrients in the short term using potted soil and (ii) the influence of potato seed dormancy (short; Shangi variety and long; Unica variety) and planting technique (surface, ridge, or furrow planting) on the efficacy of weed management practice (metribuzin (480 g L−1) herbicide and hoeing) in the field. Bacterial colony counts were recorded upon isolation from the potted soil. Soil nutrients were also analysed before and after metribuzin treatment. Data on crop growth (height and stem count), weed abundance, yield, costs, and revenues were recorded from a field experiment. Morphologically distinct bacterial strains were tested for Gram reaction and response to carbon utilization using analytical profile index kits (API 50 CH and 20 NE). In total, nine distinct bacterial strains were isolated and all were Gram positive, with variation in response to carbon substrates. Concentration of 2.0 kg a.i ha−1 significantly (p ≤ 0.05) reduced bacterial count in the first day, followed by an increase in the subsequent incubation days, while 1.0 and 1.5 kg a.i ha−1 concentrations had the highest colony development index and species richness. Significant effects of metribuzin on soil pH, total N, and total organic C in the short term were revealed. Notably, weedy plots had the highest Shannon weed index. Weeds reduced stem count and height growth by 57% and 62% respectively. Plots with Shangi had 9.8% lower weed count than those with Unica and hence higher yield was recorded from the former. While surface planting had the lowest weed control efficacy, crop growth attributes, and yield, furrow and ridge planting were not significantly different. Weed abundance and crop growth attributes in metribuzin and hand-hoed plots did not differ significantly, yet hoeing resulted in 5.30 t ha−1 above that obtained from plots managed using metribuzin. Higher dry matter and tuber yield were observed from hoed plots with Shangi planted in furrow or ridge. Use of metribuzin resulted in higher net benefit ratio and marginal rate of return than hand hoeing. The results reveal that use of metribuzin early and later in the potato growing phase can minimize weed infestation, but the efficacy depends on planting method and seed dormancy.

ORGANIC FERTILIZER: NEED OF INDIA

Organic fertilizers are naturally available mineral sources that contain moderate amount of plant essential nutrients. They are capable of mitigating problems associated with synthetic fertilizers. They reduce the necessity of repeated application of synthetic fertilizers to maintain soil fertility. They gradually release nutrients into the soil solution and maintain nutrient balance for healthy growth of crop plants. They also act as an effective energy source of soil microbes which in turn improve soil structure and crop growth. Organic fertilizers are generally thought to be slow releasing fertilizers and they contain many trace elements. They are safer alternatives to chemical fertilizers. However, the improper use of organic fertilizers leads to overfertilization or nutrient deficiency in the soil. Hence, controlled release of organic fertilizers is an effective and advanced way to overcome these impacts and maintain sustainable agriculture yield.[a]

Differential Effects of Sulfur Fertilization on Soil Microbial Communities and Maize Yield Enhancement

Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This study investigates the impact of different S fertilizer types on maize yield and the structure and stability of soil microbial communities, with a particular focus on abundant and rare taxa. S fertilization led to significant increases maize yield on two typical soils (black soil and sandy soil) (5.3–24.3%) and altered soil properties, including reducing pH (0.04–0.20) and increasing the available sulfur (AS) content (3.8–8.0 mg kg−1), with ammonium sulfate having a more pronounced effect than elemental sulfur. Microbial analysis revealed distinct impacts on the diversity and community structure of both abundant and rare taxa. Elemental sulfur reduced the alpha diversity of abundant taxa more than ammonium sulfate, while NMDS indicated significant shifts in community structures, particularly among abundant taxa. Network analysis showed that S fertilization decreased the complexity of microbial interactions among rare taxa, with ammonium sulfate leading to simpler networks and elemental sulfur resulting in higher modularity. SEM highlighted that the diversity of rare taxa played a crucial role in influencing maize yield, alongside direct effects from soil properties such as AS and SAR (aryl sulfatase). Functional predictions demonstrated that amino acid metabolism and xenobiotic biodegradation and metabolism pathways were enriched in rare taxa, suggesting significant implications for soil health and crop productivity. This study provides new insights into the roles of abundant and rare bacterial taxa under S fertilization, emphasizing their importance in optimizing fertilization strategies for enhanced crop yield in specific soil types.

Exploring microbial dynamics, metabolic functions and microbes–metabolites correlation in a millennium paddy soil chronosequence using metabolome and microbiome

BackgroundPaddy soil is a typical soil type affected by anthropogenic management and factors related to natural soil formation. The evolution from mudflats to typical paddy soils can significantly affect the soil microecology. Previous studies have reported the evolution of soil physicochemical properties, microbes, and related soil environmental factors in a millennium paddy soil chronosequence. However, the potential biological mechanisms of changes in metabolites and microbes–metabolites interaction are poorly understood. Therefore, a combination of high-throughput sequencing and environmental pseudotargeted metabolomics techniques was adopted to explore the effects of the millennium paddy soil chronosequence on microbial communities, metabolites, and their functions and interactions.ResultsThe soil ecology changed greatly in the first 60 years of the transition from mudflat to paddy planting. Among the microbial communities, the response of the bacteria to the chronosequence was more sensitive than that of fungi. Among them, the bacterial communities of Proteobacteria, Bacteroidetes, Acidobacteria, and Nitrospirae exhibited regular succession over the chronosequence, but the fungal communities did not show regular changes. Bacterial function prediction revealed that the beginning of the critical stage of the evolution from mudflat to paddy soil involved the organic matter cycle and energy flow. In contrast, fungi were characterized mainly by pathogenic and saprophytic functions. The results of the principal component analysis of the metabolites revealed a similar pattern of change as that of the microbes. Seventy-five characteristic metabolites exhibited three trends of change during the development of the paddy soil chronosequence. Twenty-five differentially active metabolic pathways, including glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and galactose metabolism, were enriched. In addition, correlation analysis revealed that long-chain fatty acids, short-chain fatty acids, phenolic acids, carbohydrates, and polyalcohols significantly regulate the microbial communities in paddy soil.ConclusionsCombining metabolome and microbiome has expanded the overall understanding of the development of paddy soil under anthropogenic management. During the development of a paddy soil chronosequence, the synergistic regulation of soil physicochemical properties and metabolites in the microbial community results in increased productivity. This study provides a new perspective on microbes and metabolites interaction.Graphical

Characteristics of Pinus hwangshanensis Rhizospheric Fungal Community along Huangshan Mountain's Elevation Gradients, China.

Elevation gradients strongly influence the diversity pattern of soil microorganisms. To date, many studies have elucidated the response of soil microbes to changes in elevation gradients. However, the effects of these gradients on the assembly mechanisms and network complexity of rhizospheric microbial communities remain underexplored. To bridge this knowledge gap, this study assessed the response of rhizospheric fungal communities of Pinus hwangshanensis along different elevation gradients in the Huangshan Mountain scenic area with regard to diversity, community composition, and assembly mechanisms using high-throughput amplicon sequencing. The results revealed significant differences in rhizospheric fungal community composition across three elevation gradients. The soil organic matter and pH were the most relevant factors influencing the changes in rhizospheric fungal community composition. The rhizospheric fungal diversity was significantly lower at both low and high elevations compared to the medium elevation. The rhizospheric fungal community assembly showed a more deterministic process at low and high elevations than at the medium elevation, indicating that stronger environmental filtering contributed to reduced fungal diversity at the extremes of the elevation gradient. In addition, rhizospheric pathogens, particularly Dermateaceae, acted as keystone taxa, diminishing the stability of co-occurrence networks at the medium elevation. This study contributes to a more comprehensive understanding of rhizospheric fungal community patterns and their ecological functions along elevation gradients in mountainous regions.

Influence of Varied Phosphorus Fertilizer Ratios on the Rhizosphere Soil Microbial Community in Idesia polycarpa Seedlings

Phosphorus (P) is crucial for tree growth and development, and it significantly influences the rhizosphere microbial community. However, the effects of phosphorus addition on the microbial communities in the rhizosphere soil of Idesia polycarpa remain understudied. In this study, two-year-old “Yuji” Idesia polycarpa seedlings were used to investigate the effects of phosphorus fertilization at four different levels of 0 g (control, CK), 0.92 g (low phosphorus, LP), 1.83 g (medium phosphorus, MP), and 2.75 g (high phosphorus, HP) per plant. The fertilizers were applied every 40 days over 120 days. MiSeq high-throughput sequencing of the 16S rRNA and ITS1 genes was employed to analyze the microbial community composition and diversity of bacteria and fungi in the rhizosphere soil under different phosphorus levels. The results showed that compared with CK treatment, the application of phosphorus fertilizer changed the physicochemical properties of the soil. The LP treatment significantly increased the soil pH, while the HP treatment group exhibited the highest soil-available phosphorus (AP) content. LP treatment significantly increased the number of microbial OTUs in the early and rapid growth stages and the richness and diversity of microbial communities. In addition, the bacterial community structure was significantly correlated with soil pH and AP, while the fungal community had no significant effect. The primary metabolic pathway function of bacteria in the rhizosphere soil of Idesia polycarpa seedlings is mainly metabolism, while fungi are mainly biosynthesis. Compared with CK treatment, 20 differential metabolic pathways were screened out in the bacterial community. Only two differential metabolic pathways were screened out in the fungal community by LP treatment at 120 days. In summary, applying low-level phosphate fertilizer is conducive to promoting the diversity of rhizosphere soil microorganisms. Therefore, potted planting of Idesia polycarpa seedlings is more suitable for applying low phosphorus levels.

Alfalfa Increases the Soil N Utilization Efficiency in Degraded Black Soil Farmland and Alleviates Nutrient Limitations in Soil Microbes

Alfalfa (Medicago sativa L.) can fix N naturally within soils, which makes alfalfa cultivation useful for enhancing soil fertility while minimizing environmental impacts from pesticides, fertilizers, and soil pollution. To assess the influence of alfalfa cropping on degraded black soil, we determined the nutrient stoichiometry of the soil and soil microbial biomass under four corn cultivation systems at the Harbin Corn Demonstration Base (Heilongjiang, China), which is located in Wujia (126°23′ E, 45°31′ N), Shuangcheng district, Harbin, Heilongjiang Province. The cultivation systems included continuous corn cultivation for more than 30 years (CK), 2 years of alfalfa–corn rotation (AC), three years of alfalfa cropping (TA), and four years of alfalfa cropping (FA). Overall, AC, TA, and FA treatment increased the soil pH, reduced the soil salinity, and increased the organic matter content of the 0–15 cm soil layer. TA and FA presented soil nutrient levels comparable to those of degraded cornfields that were fertilized annually. The TA and FA treatments increased the soil available N:P, soil N:P, and soil C:P ratios. Moreover, TA significantly increased the soil microbial biomass P (SMBP) in the 0–15 cm (surface) soil layer and reduced the soil microbial biomass C (SMBC):SMBP ratio. AC, TA, and FA increased the storage and mineralization rates of soil N and alleviated the microbial P limitations in degraded black soil farmland. Compared with FA, TA resulted in greater improvements in the quality of degraded black soil farmland. The ability of alfalfa to enhance soil fertility makes an important component of sustainable agricultural practices aimed at rehabilitating degraded soils.

Microbial community storm dynamics signal sources of "old" stream water.

Accurate characterization of the movement of water through catchments, particularly during precipitation event response, is critical for hydrological efforts such as contaminant transport modeling or prediction of extreme flows. Abiotic hydrogeochemical tracers are commonly used to track sources and ages of surface waters but provide limited details about transit pathways or the spatial dynamics of water storage and release. Alternatively, biotic material in streams is derived from thousands of taxa originating from a variety of environments within watersheds, including groundwater, sediment, and upslope terrestrial environments, and this material can be characterized with genetic sequencing and bioinformatics. We analyzed the stable water isotopes (δ18O and δ2H) and microbiome composition (16S rRNA gene amplicon sequencing) of the Marys River of western Oregon, USA during an early season storm to describe the processes, storage, and flowpaths that shape surface water hydrology. Stable water isotopes (δ18O and δ2H) typified an event response in which stream water is composed largely of 'old' water introduced to the catchment before the storm, a common though not well understood phenomenon. In contrast, microbial biodiversity spiked during the storm, consisting of early- and late-event communities clearly distinguishable from pre-event communities. We applied concentration-discharge (cQ) analysis to individual microbial taxa and found that most Alphaproteobacteria sequences were positively correlated (i.e., were mobilized) with discharge, whereas most sequences from phyla Gammaproteobacteria and Bacteroidota were negatively correlated with discharge (i.e., were diluted). Source predictions using the prokaryote habitat preference database ProkAtlas found that freshwater-associated microbes composed a smaller fraction of the microbial community during the stream rise and a larger fraction during the recession, while soil and biofilm-associated microbes increased during the storm and remained high during recession. This suggests that the "old" water discharged during the storm was likely stored and released from, or passed through, soil- and biofilm-rich environments, demonstrating that this approach adds new, biologically derived tracer information about the hydrologic pathways active during and after this event. Overall, this study demonstrates an approach for integrating information-rich DNA into water resource investigations, incorporating tools from both hydrology and microbiology to demonstrate that microbial DNA is useful not only as an indicator of biodiversity but also functions as an innovative hydrologic tracer.