Response Of Soil Microbial Communities Research Articles

Short-Term Response of Soil Microbial Community and Soil Biochemical Properties to Soybean Intercropping in a Cassava-Based Cropping System

A cassava-based cropping system study assessed the short-term response of soil chemical and biochemical properties and soil microbial communities to soybean intercropping. Two soybean varieties (‘Select Manchuria’ and ‘Tiwala 12’) were tested as intercrops. The treatments did not affect the soil’s chemical (pH, OM, N, P, K) and biochemical (basal respiration and dehydrogenase and urease enzyme activities) properties after one cropping period. Amplicon sequencing analysis found that intercropping promoted the abundance of bacterial orders Actinomycetales, Solibacterales, Sphingomonadales, and Rhodospirillales. These groups play active roles in organic matter decomposition and can potentially improve the soil quality in an area by enhancing the soil’s organic matter content. In terms of community analysis, principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed separation between mono and intercropping systems, while ANOSIM and PEMANOVA did not detect any significance between varieties and cropping systems for both bacterial and fungal data. These results suggest that, in the short term, introduction of soybean in a cassava-based cropping system affects selected microbial groups, but the overall influence in the microbial community is not distinctly detected.

Response of Soil Microbial Community Structure and Diversity to Mixed Proportions and Mixed Tree Species in Bamboo–Broad-Leaved Mixed Forests

Bamboo and broad-leaved mixed forests have been widely recognized for their advantages in maintaining ecological balance, improving soil fertility, and enhancing biodiversity. To understand the effects of mixed broad-leaved tree species and mixing ratios on soil microbial communities in bamboo and broad-leaved mixed forests, we quantified the structure and diversity responses of soil microbial communities to tree species and mixing ratios using high-throughput sequencing of the 16 S rRNA gene. Three bamboo and broad-leaved tree mixed forests were studied, including bamboo–Castanopsis chinensis Hance mixed forest (CCB), bamboo–Alniphyllum fortune (Hemsl.) Makino mixed forest (AFB), and bamboo–Choerospondias axillaris (Roxb.) B. L. Burtt & A. W. Hill mixed forest (CAB). We assessed the impact of tree species and mixing ratios on soil microbial communities by measuring soil properties and the diversity and composition of soil microbes. The results indicate that soil properties and the diversity and composition of microbial communities are highly dependent on broad-leaved tree species in mixed forests. The mixing ratios had a more pronounced effect on microbial diversity than on richness. In CAB, diversity peaked at mixing ratios of 10%–20% and 20%–40%. The presence of broad-leaved trees significantly altered the relationships among soil bacteria, with CAB showing the highest stability, likely due to the increased diversity and quantity of litter from Choerospondias axillaris. Our results show that the choice of broad-leaved tree species and their mixing ratios significantly influence soil microbial diversity and composition in bamboo–broad-leaf mixed forests. An optimal mixing ratio in CAB can maximize bacterial diversity and stability, providing insights for forest management and promoting ecosystem health and sustainability.

Metatranscriptomes of California grassland soil microbial communities in response to rewetting.

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought-providing a time series of short-term transcriptional response during rewetting.

Responses of soil and rhizosphere microbial communities to Cd-hyperaccumulating willows and Cd contamination

BackgroundThe pollution of soil by heavy metals, particularly Cd, is constitutes a critical international environmental concern. Willow species are renowned for their efficacy in the phytoremediation of heavy metals owing to their high Cd absorption rate and rapid growth. However, the mechanisms underlying microbial regulation for high- and low-accumulating willow species remain poorly understood. Therefore, we investigated the responses of soil and rhizosphere microbial communities to high- and low-Cd-accumulating willows and Cd contamination. We analyzed soil properties were analyzed in bulk soil (SM) and rhizosphere soil (RM) planted with high-accumulating (H) and low-accumulating (L) willow species.ResultsRhizosphere soil for different willow species had more NH4+ than that of bulk soil, and RM-H soil had more than RM-L had. The available phosphorus content was greater in hyper-accumulated species than it was in lower-accumulated species, especially in RM-H. Genome sequencing of bacterial and fungal communities showed that RM-L exhibited the highest bacterial diversity, whereas RM-H displayed the greatest richness than the other groups. SM-L exhibited the highest diversity and richness of fungal communities. Ralstonia emerged as the predominant bacterium in RM-H, whereas Basidiomycota and Cercozoa were the most enriched fungi in SM-H. Annotation of the N and C metabolism pathways revealed differential patterns: expression levels of NRT2, NarB, nirA, nirD, nrfA, and nosZ were highest in RM-H, demonstrating the effects of NO3-and N on the high accumulation of Cd in RM-H. The annotated genes associated with C metabolism indicated a preference for the tricarboxylic pathway in RM-H, whereas the hydroxypropionate-hydroxybutyrate cycle was implicated in C sequestration in SM-L.ConclusionsThese contribute to elucidation of the mechanism underlying high Cd accumulation in willows, particularly in respect of the roles of microbes and N and C utilization. This will provide valuable insights for repairing polluted soil using N and employing organic acids to improve heavy metal remediation efficiency.

Dynamics of microbial community and functional genes during bioremediation of PAHs-contaminated soil by two biostimulants

Biostimulation is a favored approach in bioremediation strategies for polycyclic aromatic hydrocarbons (PAHs). However, the addition of some biostimulants can instead be counterproductive to the soil. In this study, rhamnolipid and leaf litter were added as aids to PAHs biodegradation in soil. Quantitative Real-time PCR (qPCR) and 16 S ribosomal RNA (16 S rRNA) techniques were used to investigate the structural-functional response of soil microbial communities and changes in PAHs functional genes during 82 days of the degradation process. The study reveals that rhamnolipid and leaf litter increase the degradation rate of Benzo(a)pyrene by 20.49% and 11.64%, respectively, while having little effect on the degradation rate of phenanthrene. During the degradation process, each biostimulant increases the number of different bacterial genera capable of degrading PAHs, which influences both the structure and function of the microbial community and alters microbial diversity. Additionally, functional gene abundance was enhanced during degradation and showed an inverse relationship with residual PAHs concentration in the soil. These results indicate that different biostimulants have varying effects on microorganisms. This study enhances the understanding of useing of two biostimulants to degrade soil PAHs.

Soil microbial community responses to long-term experimental warming in an alpine Dryas octopetala heath in Norway

Over the last century, high-altitude and high-latitude regions have experienced global warming at rates higher than the worldwide average. Climate change influences complex soil-microbe-plant-atmosphere interactions, leading to changes in plant-associated soil microbial diversity and functioning and alterations in nutrient cycling, carbon fluxes, and storage. This study analyzed how two decades of global warming simulated by open-top chambers (OTCs) affected soil bacterial and fungal communities in an alpine dwarf-shrub heath dominated by Dryas octopetala in Norway. We collected soil samples from 10 OTCs and 10 control plots and compared their physicochemical properties, microbial biomass, extracellular enzyme activities, and bacterial and fungal community diversity and composition. Warming did not significantly affect the bacterial community despite the tendency to reduce alpha diversity and increase the degree of specialisation. In contrast, two decades of warming significantly affected fungal community composition, which was dominated by ectomycorrhizal Basidiomycota. While there was no significant effect on the total fungal community diversity, a significant shift in saprotrophic Ascomycota taxa was observed between the warmed and control plots. Their positive correlations with oxidative enzymes and fungal biomass suggest that long-term warming might lead to an increase in fungal biomass and the activity of oxidative enzymes, promoting the decomposition of more recalcitrant biopolymers. This may result in an increase in CO2 flux into the atmosphere and a decrease in ecosystem C storage.

Responses of soil nutrients and microbial communities to the application of spent mushroom substrates

Responses of soil nutrients and microbial communities to the application of spent mushroom substrates

Role of endogenous soil microorganisms in controlling antimicrobial resistance after the exposure to treated wastewater

The reuse of treated wastewater (TWW) for irrigation appears to be a relevant solution to the challenges of growing water demand and scarcity. However, TWW contains not only micro-pollutants including pharmaceutical residues but also antibiotic resistant bacteria. The reuse of TWW could contribute to the dissemination of antimicrobial resistance in the environment. The purpose of this study was to assess if exogenous bacteria from irrigation waters (TWW or tap water-TP) affect endogenous soil microbial communities (from 2 soils with distinct irrigation history) and key antibiotic resistance gene sul1 and mobile genetic elements intl1 and IS613. Experiments were conducted in microcosms, irrigated in one-shot, and monitored for three months. Results showed that TP or TWW exposure induced a dynamic response of soil microbial communities but with no significant increase of resistance and mobile gene abundances. However, no significant differences were observed between the two water types in the current experimental design. Despite this, the 16S rDNA analysis of the two soils irrigated for two years either with tap water or TWW resulted in soil microbial community differentiation and the identification of biomarkers from Xanthomonadaceae and Planctomycetes families for soils irrigated with TWW. Low-diversity soils were more sensitive to the addition of TWW. Indeed, TWW exposure stimulated the growth of bacterial genera known to be pathogenic, correlating with a sharp increase in the copy number of selected resistance genes (up to 3 logs). These low-diversity soils could thus enable the establishment of exogenous bacteria from TWW which was not observed with native soils. In particular, the emergence of Planctomyces, previously suggested as a biomarker of soil irrigated by TWW, was here demonstrated. Finally, this study showed that water input frequency, initial soil microbial diversity and soil history drive changes within soil endogenous communities and the antibiotic resistance gene pool.

Soil Fertility and Bacterial Community Composition in Response to the Composting of Biochar-Amended Chicken Manure

Amidst the burgeoning expanse of the poultry sector, the escalation of chicken manure production has ensued, potentially exacerbating ecological contamination. However, the application of chicken manure is bound to transmute the habitat of edaphic microorganisms, precipitating an alteration in the soil’s microbial consortium. The composting of biochar-amended chicken manure and wood chips (biochar composting products, BCPs) was used to improve Chinese cabbage (Brassica campestris L.) production and regulate soil properties and bacterial community structure. On the 40th day of Chinese cabbage growth, soil and Chinese cabbage were collected for laboratory analysis. The effects of different proportions of BCPs (0, 1%, 3%, 5% and 7% biochar) on soil fertility, enzyme activity, the microbial community and the growth of Chinese cabbage were studied under facility conditions. The results showed that the growth performance and quality of Chinese cabbage were significantly increased with increasing BCP ratios. Soil fertility indicators including pH, AN, AP, AK and SOM were significantly increased, except for the pH value in the 1% BCP group. The activities of phosphatase, catalase and urease were increased for all groups of BCP treatment. The soil microbial community response was significantly different, and the application of 5% and 7% BCPs reduced the abundance, diversity and evenness of soil bacteria. Chinese cabbage growth performance was positively correlated with an increase in BCP supplemental levels in the range of 3–5%. Also, the abundance, diversity and uniformity of the soil microbial community were improved in the 3% BCP treatment group. Therefore, the dominant bacterial phyla were Bacteroidetes, Actinobacteriota, Gemmatimonadota, Myxococcota, Bdellovibrionota and Firmicutes, especially the Bradyrhizobium of Proteobacteria. BCP treatment reduced the degradation of soil organic matter. In addition, it also improved the relative abundance of sequences associated with improving soil fertility. Collectively, these findings offer insights for the re-evaluation of application management strategies for BCP organic fertilizers.

Light grazing alleviates aeolian erosion–deposition effects on microbial communities in a semi-arid grassland

BackgroundSoil erosion affects the stability of terrestrial ecosystems and ecosystem services by directly or indirectly impacting the cycling of soil materials and energy and reducing the fertility of grassland soils. However, research on microbial adaptation to grazing and soil erosion is limited, particularly in relation to grassland ecosystem restoration. Here, we assess microbial communities subjected to simulated soil erosion and grazing in a semi-arid grassland of Inner Mongolia, China.ResultsNo significant change was observed in soil variables. However, the structure of the soil microbial community underwent significant changes as a result of soil erosion and soil erosion plus grazing, leading to a significant increase in the relative abundance of Cyanobacteria (116.80% vs 116.38%). Wind erosion and deposition contributed to an increase in the network complexity of soil bacterial and fungal communities. However, much of this effect was alleviated by grazing. Simultaneously, aeolian processes and grazing regulate soil microbial community assembly, leading to inconsistent patterns of change in bacterial and fungal communities. Under wind erosion and deposition, the relative contribution of deterministic processes (4.44% vs 31.11%) in bacterial communities increased, while the relative contribution of stochastic processes (2.23% vs 20%) in fungal communities reduced. Grazing resulted in a decrease in the relative contribution of deterministic processes (8.89%) in the bacterial community and an increase in the relative contribution of stochastic processes (8.89%) in the fungal community.ConclusionThis study presents a comprehensive investigation of the response of soil microbial communities to aeolian erosion–deposition and grazing in a semi-arid grassland. Our findings indicate that microbial communities in the semi-arid grassland show resistance to external disturbances and that light grazing mitigates the effects of aeolian erosion–deposition on microbial communities, which is essential for maintaining the stability and biodiversity of grassland ecosystems.

Changes in microbial composition explain the contrasting responses of glucose and lignin decomposition to soil acidification in an alpine grassland

Soil acidification often suppresses microbial growth and activities, resulting in a negative impact on soil organic carbon (C) decomposition. While the detrimental effects of acidification on soil and plant properties have been extensively studied, less attention has been paid on the shifts in soil microbial communities and their influences of the decomposition of organic C with different chemical complexities. Taking advantage of an acid addition experiment in a Tibetan alpine meadow, here we examined the response of soil microbial communities to soil acidification and microbial effect on the decomposition of organic C with different chemical complexities (i.e., glucose and lignin, representing labile and recalcitrant C respectively). We found that soil acidification had no impact on microbial respiration and microbial abundance even though it decreased bacterial diversity significantly. Soil acidification increased the relative abundance of some microbial taxa, like Alphaproteobacteria and Acidobacteriia in bacteria increased by 36 %, 284 %, and Eurotiomycetes, Sordariomycetes and Leotiomycetes in fungi increased by 145 %, 279 % and 12.7-fold, but decreased the relative abundance of Acidimicrobiia by 33 % in highest acid addition treatment. Changes in microbial communities (bacterial and fungal community composition, the diversity of bacterial community and the ratio of fungi to bacteria) are significantly related to the decomposition of glucose and lignin. More specifically, soil acidification decreased the decomposition of glucose but increased the decomposition of lignin, indicating a trade-off between the decomposition of labile and recalcitrant soil organic C under soil acidification. Overall, shifts in microbial communities under soil acidification might be accompanied by an increased ability to break down more recalcitrant C. This trade-off between the decomposition of labile and recalcitrant C may change soil C quality under future acid deposition scenarios.

Untargeted metabolomics to study changes in soil microbial community in response to tillage practices

Soil microbes are the main drivers of nutrient turnover in agro-ecosystems. The series of biochemical processes involved by these microorganisms are inseparable from the regulation of metabolites in the root-zone soils. Therefore, understanding the evolution of microbial communities driven by root-zone soil metabolites will help optimize agricultural management practices. Based on a field experiment, we explore the changes in soil properties, microbes, and metabolites under three tillage practices such as no-tillage with straw mulching (NTS), rotary tillage, and plough tillage with straw returning (RTS and PTS) based on untargeted metabolomics. We found that NTS helped to enhance nutrient contents and enzyme activities in the 0–20 cm soil layer. Specifically, compared with RTS and PTS, NTS increased grain yield by 6.4 % and 8.5 %, and SOC by 13.3 % and 5.7 %, respectively, but decreased pH by 2.8 % and 1.1 %. In addition, compared with NTS, RTS and PTS decreased the fungal richness by 16.5 % and 8.1 %, and decreased the fungal shannon index by 16.4 % and 9.2 %. However, tillage practices did not result in substantial differences in the alpha diversity of bacterial community. Both bacterial and fungal community composition were substantially affected by tillage practices and they were both significantly correlated with soil metabolites. In the symbiotic networks, NTS significantly increased the abundance of microorganisms with high connectivity, while RTS significantly increased the concentration of metabolites with high connectivity. Amino acids, as the main drivers, were significantly and positively associated with bacterial and fungal community composition, mainly enriched in the metabolic pathways of D − glutamine and D − glutamate metabolism and arginine and proline metabolism, and correlated with soil properties negatively and carbohydrates positively, directly or indirectly affecting soil microbial community composition. Our findings would provide new insight into metabolomics for the in-depth understanding of the metabolic mechanism for soil microbial community changes in dryland wheat fields under different tillage practices.

The Diversity and Composition of Soil Microbial Communities Differ in Three Land Use Types of the Sanjiang Plain, Northeastern China.

In recent years, the Sanjiang Plain has experienced drastic human activities, which have dramatically changed its ecological environment. Soil microorganisms can sensitively respond to changes in soil quality as well as ecosystem function. In this study, we investigated the changes in soil microbial community diversity and composition of three typical land use types (forest, wetland and cropland) in the Sanjiang Plain using phospholipid fatty acid analysis (PLFA) technology, and 114 different PLFA compounds were identified. The results showed that the soil physicochemical properties changed significantly (p < 0.05) among the different land use types; the microbial diversity and abundance in cropland soil were lower than those of the other two land use types. Soil pH, soil water content, total organic carbon and available nitrogen were the main soil physico-chemical properties driving the composition of the soil microbial community. Our results indicate that the soil microbial community response to the three different habitats is complex, and provide ideas for the mechanism by which land use changes in the Sanjiang Plain affect the structure of soil microbial communities, as well as a theoretical basis for the future management and sustainable use of the Sanjiang plain, in the northeast of China.

Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process

Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.

Afforestation alters soil microbial community composition and reduces microbial network complexity in a karst region of Southwest China

AbstractSoil microbial community plays important roles in altering ecological processes and biogeochemical cycles in ecosystems. However, little is known about how afforestation influences the diversity, composition, and ecological network of soil microbial community in karst regions. In this study, soil samples were collected from one farmland (FL) and three afforestation lands including one bamboo forest (BA), one landscape tree planting forest (LAT), and one orange orchard (ORO) in a karst region of Southwest China. The bacterial and fungal communities were characterized using the high‐throughput sequencing approach, and soil properties including soil organic carbon, pH, soil water content, and soil total and available nutrient contents were measured under different land use treatments. Results showed that conversion from FL to BA and LAT significantly reduced the Shannon diversity of bacterial community. At the phylum level (top 10), genus level (top 30), and operational taxonomic units (OTUs) level, afforestation from FL resulted in significant changes in nine phyla, 24 genera, and 31.32% OTUs of bacterial community, and in three phyla, 13 genera, and 11.62% OTUs of fungal community. The number of nodes, number of negative edges, connectivity, average degree, and relative modularity of the microbial network under afforestation lands decreased by 9.33%–18.66%, 47.98%–72.75%, 0.45%–5.93%, 14.73%–22.29%, and 6.46%–23.50%, respectively, compared with FL. The soil organic carbon, total potassium and total phosphorus were identified as the key soil properties affecting the microbial community. Compared with LAT and ORO, the changes in bacterial and fungal communities under BA were more obvious because of the higher contents in soil organic carbon (13.48%) and total potassium (27.18%). In conclusion, afforestation significantly changed compositions and ecological network complexity of soil microbial community in karst regions, and conversion from FL to BA had stronger influences on the changes of soil microbial community than other afforestation lands in Southwest China. These findings provide the context necessary to evaluate the responses of soil microbial community to land use changes in karst regions.

A positive feedback to climate change: The effect of temperature on the respiration of key wood-decomposing fungi does not decline with time.

Heterotrophic soil microorganisms are responsible for ~50% of the carbon dioxide released by respiration from the terrestrial biosphere each year. The respiratory response of soil microbial communities to warming, and the control mechanisms, remains uncertain, yet is critical to understanding the future land carbon (C)-climate feedback. Individuals of nine species of fungi decomposing wood were exposed to 90 days of cooling to evaluate the medium-term effect of temperature on respiration. Overall, the effect of temperature on respiration increased in the medium term, with no evidence of compensation. However, the increasing effect of temperature on respiration was lost after correcting for changes in biomass. These results indicate that C loss through respiration of wood-decomposing fungi will increase beyond the direct effects of temperature on respiration, potentially promoting greater C losses from terrestrial ecosystems and a positive feedback to climate change.

Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests.

In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.

Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum.

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

The Changes in Soil Microbial Communities and Assembly Processes along Vegetation Succession in a Subtropical Forest

Soil microbes are the primary drivers of the material cycling of the forest ecosystem, and understanding how microbial structure and composition change across succession assists in clarifying the mechanisms behind succession dynamics. However, the response of soil microbial communities and assembly processes to succession is poorly understood in subtropical forests. Thus, through the “space instead of time” and high throughput sequencing method, the dynamics of the soil bacterial and fungal communities and assembly process along the succession were studied, where five succession stages, including Abandoned lands (AL), Deciduous broad-leaved forests (DB), Coniferous forests (CF), Coniferous broad-leaved mixed forests (CB), and Evergreen broad-leaved forests (EB), were selected in a subtropical forest on the western slope of Wuyi Mountain, southern China. The results demonstrated that succession significantly decreased soil bacterial α-diversity but had little effect on fungal α-diversity. The composition of soil bacterial and fungal communities shifted along with the succession stages. LEfSe analysis showed the transition from initial succession microbial communities dominated by Firmicutes, Bacteroidota, Ascomycota, and Chytridiomycota to terminal succession communities dominated by Actinobacteriota and Basidiomycota. Distance-based redundancy analysis (db-RDA) revealed that soil total organic carbon (TOC) was the main factor explaining variability in the structure of soil bacterial communities, and multiple soil environmental factors such as the TOC, soil total nitrogen (TN), C:N ratio, and pH co-regulated the structure of fungi. The null models illustrated that deterministic processes were dominant in the soil bacterial communities, while the stochastic processes contributed significantly to the soil fungal communities during succession. Collectively, our results suggest that different patterns are displayed by the soil bacterial and fungal communities during the succession. These findings enhance our comprehension of the processes that drive the formation and maintenance of soil microbial diversity throughout forest succession.

Dynamic Changes of Soil Microbial Communities During the Afforestation of Pinus Armandii in a Karst Region of Southwest China

Clarifying the response of soil microbial communities to vegetation restoration is essential to comprehend biogeochemical processes and ensure the long-term viability of forest development. To assess the variations in soil microbial communities throughout the growth of Pinus armandii plantations in the karst region, we utilized the “space instead of time” approach and selected four P. armandii stands with ages ranging from 10 to 47 years, along with a grassland control. The microbial community structure was determined by conducting Illumina sequencing of the 16 S rRNA gene and the ITS gene, respectively. The results demonstrated that afforestation with P. armandii significantly influenced soil microbial communities, as indicated by notable differences in bacterial and fungal composition and diversity between the plantations and the control. However, soil microbe diversity did not display significant variation across stand ages. Moreover, the bacterial community exhibited higher responsiveness to age gradients compared to the fungal community. Soil physicochemical factors play a critical role in elucidating microbial diversity and community composition variations during restoration processes. TN, AN, TP, AP, SOC, AK, and pH were the most significant influencing factors for the composition of bacterial community, while TC, SOC, pH, and TCa were the most significant influencing factors for the composition of fungal community. Our findings indicate substantial changes in soil bacterial and fungal communities across successive stages of development. Additionally, the changes in dominant bacteria and fungi characteristics across the age gradient were primarily attributed to variations in the prevailing soil conditions and chemical factors.