Search Results (228)

Wetland degradation in soda saline–alkali ecosystems can profoundly alter belowground microbial communities, yet its effects on bacterial phylogenetic distribution and predicted ecological characteristics remain insufficiently understood. This study investigated soil physicochemical properties, enzyme activities, and bacterial communities across a wetland degradation gradient in the Halahai Provincial Nature Reserve, China, including reed wetland (RW), meadow steppe (MS), and degraded Suaeda saline patches (DS). Soil analyses were integrated with 16S rRNA gene amplicon sequencing, phylogenetic reconstruction, and FAPROTAX and BugBase prediction. DS showed significantly higher pH and electrical conductivity, but lower soil water content, organic carbon, nutrient availability, and urease activity than RW and MS. Alpha diversity analysis indicated that DS had lower bacterial richness and diversity, but higher dominance, whereas RW and MS did not differ significantly. Beta-diversity analysis revealed clear habitat-dependent separation, with DS harboring the most distinct community structure. Taxonomic and phylogenetic analyses indicated enrichment of Gemmatimonadota and the RCP2-54 lineage in DS, whereas RW and MS were more strongly associated with Pseudomonadota, Acidobacteriota, and related groups. Predicted functional and phenotypic analyses further suggested a shift toward stress-related and degradation-associated traits in DS. These findings demonstrate that wetland degradation reshaped the taxonomic composition, phylogenetic distribution, and predicted ecological characteristics of soil bacterial communities in this fragile ecosystem. Full article

Intensive monoculture exacerbates soil compaction and sodification in the West Liao River Plain. This study evaluated legacy effects of diversified 3-year rotations on sodic soil health (ESP > 15%, ECe < 4 dS m⁻¹) during two subsequent maize seasons. Rotations incorporating salt-tolerant forages and deep-rooted crops (sugar beet–Echinochloa–sorghum and Echinochloa–tall fescue–silage corn) significantly reduced bulk density (8.6–13.1%) and exchangeable sodium percentage (up to 14.1 percentage points) relative to continuous monoculture. Treatments with maximum desalination (22.6% reduction) enhanced fungal α-diversity by 98.0%, while forage-dominated systems enriched Acidobacteriota by 35.2%, shifting bacterial communities toward oligotrophic dominance. Structural equation modeling confirmed that rotation effects on enzyme activity were mediated through reduced bulk density and ESP. These systems provide effective biological models for sustainable maize cultivation in sodic soils via synergistic physical-chemical-biological amelioration. Full article

Under-forest cultivation of morels is increasingly constrained by soil ecological deterioration, which has become a major obstacle to its sustainable development. This study characterized hyphosphere soil microbiomes of Morchella sextelata M. Kuo under pine canopy at four distances from the fruiting body: 0 cm (R), 20 cm (R₂₀), 40 cm (R₄₀), and uncultivated control (CK). Bacterial and fungal community composition and diversity were analyzed using Illumina NovaSeq high-throughput sequencing. Results showed that the dominant bacterial phyla were Proteobacteria and Acidobacteriota, with RB41, Sphingomonas, and Dongia as the dominant genera. Relative to CK, the abundances of Acidobacteriota and RB41 in R increased by 4.45% and 6.16%, respectively, whereas R₂₀ was enriched in Proteobacteria (+7.77%), Sphingomonas (+0.95%), Dongia, and Bradyrhizobium. For fungi, Ascomycota and Basidiomycota were the dominant phyla, with the principal genera being Sebacina, Microbotryales_gen_Incertae_sedis, and Oidiodendron. Compared with CK, morel cultivation decreased the abundances of Ascomycota and Oidiodendron, with the greatest reductions in R₂₀ (by 8.73% and 3.67%, respectively), while increasing the abundances of Basidiomycota, Sebacina, and Microbotryales_gen_Incertae_sedis, again most markedly in R₂₀, by 17.56%, 14.82%, and 5.74%, respectively. Morel cultivation significantly reduced microbial diversity and evenness (Shannon, Simpson, and Pielou), with the lowest diversity and highest dominance in Zone R. Partial least squares structural equation modeling (PLS-SEM) revealed that soil chemical properties and enzyme activities negatively drove dominant bacterial genera but positively drove dominant fungal genera. Overall, under-forest cultivation of M. sextelata significantly reduced hyphosphere microbial diversity and reshaped microbial community structure in a distance-dependent manner: Zone R was dominated by Acidobacteriota; Zone R₂₀ was enriched with nitrogen-cycling beneficial bacteria (Dongia, Sphingomonas, and Bradyrhizobium) and beneficial fungi (Sebacina and Microbotryales_gen_Incertae_sedis); Zone R₄₀ exhibited relatively optimal fungal diversity. Full article

Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology. Full article

Purpose: Black soils in Northeast China are declining in fertility under intensive fertilization, motivating strategies that integrate crop residue return with microbial inoculation. We conducted a field experiment to test whether maize straw return combined with compound microbial inoculants improves soil properties, bacterial communities, and soybean performance. Methods: A field experiment compared four treatments: fertilization alone (F), fertilization + inoculants (CF), fertilization and straw (SF), and fertilization and straw with inoculants (CSF). Soil physicochemical properties, enzyme activities, 16S rDNA-based bacterial communities, and soybean agronomic yield were measured across growth stages. Results: CSF produced the highest soybean performance, and increased yield by 3.91–5.46% compared with F. CSF increased soil pH, moisture, and nutrient availability (notably available P and K) and enhanced sucrase, urease, catalase, and acid phosphatase activities compared with other treatments. Bacterial communities were dominated by Acidobacteriota and Proteobacteria. CSF increased bacterial abundance and shifted community composition, and pH and available P were key factors associated with community variation. Conclusions: Co-applying maize straw and compound microbial inoculants enhances soybean yield while improving soil biochemical functioning and reshaping bacterial communities in black soil. Full article

Background: Root-knot nematodes (RKNs) are destructive parasites affecting both agricultural and natural plants. Fagopyrum tataricum, a phenolic-rich edible and medicinal plant, has antidiabetic, anti-inflammatory, and anticancer properties, yet the impact of RKN infection on its rhizosphere microbiome remains unclear. Methods: We employed full-length 16S rRNA gene sequencing (FL16S) to profile bacterial communities in the rhizosphere of healthy and RKN-infected F. tataricum plants. Results: FL16S classified 78.41% of operational taxonomic units (OTUs) at the genus level and 69.18% at the species level. Healthy plants showed higher richness, diversity, and evenness, while principal co-ordinate analysis (PCoA) and PERMANOVA indicated significant RKN-associated shifts in community composition. Dominant phyla included Bacteroidota, Proteobacteria, Patescibacteria, Verrucomicrobiota, Actinobacteriota, Acidobacteriota, and Chloroflexi, with Abditibacteriota enriched in healthy and Acidobacteriota in diseased rhizospheres. At the OTU level, 66 differentially abundant taxa were identified, including nine hub OTUs in healthy plants, suggesting keystone roles in network stability. Network analyses revealed reduced diversity, interactions, and altered intra- and inter-phylum dynamics under RKN infection. Conclusions: These findings provide insight into rhizosphere microbial responses to RKN parasitism in F. tataricum and identify potential microbial biomarkers and biocontrol targets, supporting microbiome-based management strategies. Full article

Alpine treeline and shrubline ecotones are climatically sensitive transition zones where vegetation shifts strongly influence belowground microbial processes. Soil bacteria and fungi, as core component of the soil microbiome, play vital roles in nutrient cycling and plant–soil interactions within these fragile ecosystems. However, the structure and diversity of soil microbial communities across the treeline–shrubline transition remain poorly understood. Here, we investigated soil bacterial and fungal communities across treeline and shrubline ecotones in two mountain on the eastern Tibetan Plateau. We further examined how soil physicochemical properties shaped microbial community assembly. Our results demonstrated that the community composition of both bacteria and fungi differed significantly between the treeline and shrubline ecotones, while the Shannon index showed no significant variation. At the phylum level, Proteobacteria, Actinobacteriota, and Acidobacteriota dominated bacterial communities, while Ascomycota and Basidiomycota were the predominant fungal phyla. Both the network complexity of soil bacterial and fungal communities changed significantly across ecotones. Specifically, bacterial network complexity increased significantly toward the shrubline, whereas fungal network complexity declined. Bacterial community compositions were co-regulated by both environmental and vegetation factors, while fungal community compositions were only regulated by soil pH. Redundancy analysis revealed that soil organic carbon, pH, and moisture were the primary drivers of bacterial community (38.17%), whereas vegetation cover, soil organic carbon, and moisture explained the largest proportion of fungal community (44.79%). Our findings reveal the distribution patterns and underlying shift mechanisms of microbial communities between the treeline and shrubline ecotone. These insights are crucial for mountain biodiversity conservation and for improving predictions of forest responses to climate change. Full article

The Ningxia Yellow River Irrigation District in China has long been influenced by flood irrigation and intensive fertilizer input under its particular geological and climatic constraints, and this region is characterized by low soil organic matter, poor nutrient status, low permeability, high pH, and widespread salinization. This cross-sectional field study compared the soil physicochemical properties and microbial communities among saline–alkali soil (SAS), straw-returning farmland (SR), and traditionally managed farmland (FM). EC was higher in SAS (approximately 4.21 dS·m⁻¹) than in SR and FM (approximately 0.23 and 0.30 dS·m⁻¹, respectively), whereas TOC and C/N were higher in SR (approximately 1.00% and 10.58, respectively) than in FM (approximately 0.78% and 8.69) and SAS (approximately 0.43% and 8.81). Bacterial and fungal communities showed different distribution patterns among the three farmland types. Compared with fungi, bacterial community structure and richness varied more clearly across soils differing in salinity and organic matter status. Variations in microbial community composition were accompanied by differences in soil salinity and carbon- and nitrogen-related properties. Acidobacteriota was positively correlated with soil carbon and nitrogen variables and negatively correlated with pH and EC, while Ascomycota was positively correlated with total carbon (TC) and TOC. These results show that straw-returning farmland differed from saline–alkali soil and traditionally managed farmland in both soil properties and microbial community characteristics, highlighting potential soil–microbe associations in saline-affected agricultural systems. Full article

Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño–Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11–17% of β-diversity, exceeding the contribution of intra-annual seasonality (6–12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems. Full article

Atmospheric nitrogen (N) deposition is an important global change driver in forest ecosystems, yet its long-term effects on belowground microbial communities in cold-temperate coniferous forests remain insufficiently understood. In this study, endpoint shotgun metagenomic sequencing was used to evaluate bulk soil microbial communities after 12 years of experimental N addition in a Larix gmelinii-dominated forest in the Greater Khingan Mountains of northeastern China. Four treatments were included: control (0 kg N ha⁻¹ yr⁻¹), low N (25 kg N ha⁻¹ yr⁻¹), medium N (50 kg N ha⁻¹ yr⁻¹), and high N (75 kg N ha⁻¹ yr⁻¹). Microbial alpha diversity did not differ significantly among treatments, although moderate N addition showed a tendency to maintain relatively higher richness and diversity. In contrast, beta-diversity analysis indicated clear shifts in community composition along the N addition gradient. Pseudomonadota, Acidobacteriota, and Actinomycetota dominated the microbial communities, with Pseudomonadota tending to increase under N enrichment, whereas some oligotrophic groups showed reduced relative abundance. Functional annotation showed that metabolism-related genes remained dominant across treatments, and carbohydrate-active enzyme profiles suggested altered microbial potential for complex carbon decomposition under long-term N input. Nitrogen addition also modified the abundance patterns of some antibiotic resistance genes and mobile genetic elements, although overall resistome differentiation among treatments remained limited. These results provide endpoint metagenomic evidence that long-term N addition can reshape bulk soil microbial community composition and selected functional potentials in cold-temperate coniferous forest soils, even when overall alpha diversity remains relatively stable. Full article

Clarifying the responses of microbial communities in distinct microhabitats like roots, the soil, and litter layers to secondary succession is critical for predicting the effects of global climate change on ecosystem functions. We investigated the microbial activities, compositions, and networks in these microhabitats of Fagus lucida forests ranging from 40 to 200 years. The results showed that soil physicochemical properties decreased with forest succession, except for NH₄⁺-N and available phosphorus, which decreased at the early stage. All vector angles of extracellular enzyme stoichiometry that were greater than 45° indicated that phosphorus was the key limiting element for microorganisms. The microbial community shifted from r- to K-strategists with forest succession, displaying the replacement of most bacterial phyla by Proteobacteria and Acidobacteriota, and an increase in the Acidobacteriota: Proteobacteria ratio, especially in the soil and litter layers. Soil properties, particularly NH₄⁺-N and pH, significantly affected the bacterial diversity and structure. Moreover, the bacterial network complexity increased with succession, particularly in the litter layer, and the topological properties of bacterial networks showed a stronger influence on microbial activities compared with those of fungal networks. The richness of keystone taxa in the litter layer was higher than in the soil layer and roots. However, the fungal community dominated by symbiotrophs showed lower sensitivity to soil nutrient changes and greater resilience to forest succession, displaying stable diversity and decreased network complexity, particularly in the roots. Ectomycorrhizal fungi (e.g., Russula) dominated the fungal guilds, and their abundance increased with forest succession, accompanied by a decrease in pathogenic fungi. Plant roots with significantly higher phosphatase activities played a stronger role than soils in structuring the litter microbial community, as reflected by similar carbon- and nitrogen-acquiring enzyme activities, microbial compositions, a greater share of taxa, and closer community distance. Our results revealed the increasingly important role of plant roots with forest succession in structuring the microbial community and nutrient cycling in the soil and litter layers. Full article

Although coral bleaching–associated microbial changes have been widely studied, bacterial succession during bleaching, particularly in partly bleached corals, remains poorly understood. Here, we investigated bacterial community dynamics in healthy, partly bleached, and bleached Goniopora sp. collected from the Sanya Coral Reef Conservation District, South China Sea. A total of 599,003 valid sequences were obtained and clustered into 5094 operational taxonomic units (OTUs). These OTUs spanned 45 bacterial phyla and were identified by 16S rRNA gene sequencing, revealing a highly diverse bacterial community associated with Goniopora sp. Alpha diversity differed significantly among health statuses, with partly bleached Goniopora sp. (PBG) exhibiting the highest bacterial diversity (Shannon index: 6.25 ± 0.11), followed by bleached Goniopora sp. (BG) (5.49 ± 0.18) and healthy Goniopora sp. (HG) (3.04 ± 0.17). Beta diversity analyses showed clear separation of microbial community structures among HG, PBG, and BG. Successional analyses revealed a progressive decline in putatively beneficial bacterial taxa, including the phylum Pseudomonadota and the genus Cohaesibacter with increasing bleaching severity, whereas the relative abundance of opportunistic or stress-associated bacteria, such as Blastopirellula, Mycobacterium, and some unclassified taxa, increased. Notably, many bacterial taxa, including Acidobacteriota, Woeseia and Ruegeria, displayed non-linear abundance patterns, with pronounced shifts during the partly bleached stage. These findings highlight substantial microbial restructuring during coral bleaching and underscore the importance of the partly bleached status as a transitional phase in coral-associated bacterial succession. Full article

Soil- and plant-associated fungi and bacteria are an important part of many ecosystems as they can affect plant health, growth and stress tolerance. However, it remains poorly understood whether the microbiomes differ between conifer species growing in the same site conditions and between tree ecosystem compartments. The main aim of the study was to describe and compare the microbiomes of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) H. Karst.), growing in a boreal forest common garden experiment on adjacent forest plots, to analyse the tree species effect on the composition of the needle and surface soil organic-mineral horizon microbiomes. The needle and surface soil organic-mineral horizon bacterial and fungal microbiomes were simultaneously analysed by full-length 16S and ITS sequencing on a long-read sequencing platform; however, the bacterial analysis was restricted to soil samples. The highly abundant bacterial phyla in both pine and spruce soil were Actinomycetota, Pseudomonadota, Planctomycetota and Acidobacteriota. The dominant fungal phyla in pine and spruce surface organic-mineral soil was Basidiomycota, while the needles were dominated by Ascomycota. The results showed an effect of tree species on the soil bacterial and fungal microbiomes and needle fungal microbiomes based on alpha diversity, which was higher for Norway spruce compared to Scots pine. The results indicated that Norway spruce might be able to support higher microbial diversity, which could potentially be due to differences in needle longevity, root exudates, litter input and its degradation, between pine and spruce. Furthermore, the results indicated distinct microbiomes between the soil and needle compartments. Full article

To investigate the main drivers of rhizosphere soil microbial community structure and diversity in Camellia reticulata, this study collected rhizosphere soil samples from six regions at two soil depths (0–30 cm and 30–60 cm). Using high-throughput sequencing, we systematically analyzed the effects of soil environmental factors on microbial communities. The results showed that the dominant bacterial phyla were Proteobacteria, Acidobacteriota, Chloroflexi, Actinobacteriota, and Bacteroidota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Alpha diversity of both bacterial and fungal communities was higher in surface soils (0–30 cm) than in deeper layers (30–60 cm), although the differences were not statistically significant (p > 0.05). Soil pH, potassium content (K), and catalase activity (S-CAT) were identified as the main environmental factors significantly correlated with microbial community structure. Network analysis identified Acidobacteriota and Ascomycota as highly connected taxa within microbial networks, suggesting their potential importance in maintaining network structure. This study reveals the vertical differentiation characteristics of rhizosphere microbial communities in C. reticulata and their responses to environmental factors, providing a theoretical basis for cultivation management and rhizosphere microecological regulation. Full article

Straw returning is an effective means of improving soil structure and increasing soil organic matter content. However, few studies have been conducted on the effects of corn straw returning on the soil microorganism community in soybean crops. In this paper, taking conventional combined tillage (CT) as a control, the effects of no-tillage with straw mulching (NTS), no-tillage with stubble retention (NT), and deep plowing with straw incorporation (DT) on soil bacterial community under a corn–soybean rotation system were studied. The results showed that the contents of soil total nitrogen, total phosphorus, available phosphorus, the activities of soil urease and acid phosphatase, and soil bacterial richness and diversity in the NTS treatment were significantly higher than those in other treatments. Moreover, the NTS treatment increased the abundance of Acidobacteriota and MND1 (unclassified bacterial genus) in the soil. The number of unique OTUs in the NTS treatment was the greatest (26.67%), with that of the CT treatment being the smallest (7.22%). Redundancy analysis (RDA) revealed that soil total nitrogen, total phosphorus, and available phosphorus are the key driving changes in bacterial community. Consequently, NTS treatment was the optimal approach for both soil fertility improvement and bacterial community optimization. This approach combines straw mulching and no-tillage, which not only exerts the nutrient supply effect of straw but also reduces the impact of soil disturbance on microbial habitats. Full article