This study explored the effects of forest fires on soil microbial activity in forest soils classified by rock origin (igneous, metamorphic, and sedimentary) and stratified by subsoil depth (topsoil, subsoil). Microbial activity, indicated by average well color development (AWCD) and Shannon diversity indices, was higher in undamaged topsoils compared to fire-damaged ones. In contrast, fire-damaged subsoils, particularly in metamorphic and sedimentary soils, exhibited increased microbial activity over time due to organic matter decomposition. A significant increase in substrate utilization was observed in undamaged soils across all rock types (*p < 0.05, **p < 0.01) in topsoil, with sedimentary rock exhibiting the highest microbial diversity based on Shannon indices. The dehydrogenase activity followed a similar pattern, with reduced activity in fire-damaged topsoil but higher activity in damaged metamorphic and sedimentary subsoils. Principal component analysis (PCA) linked microbial indicators (AWCD, Shannon index) to mineral compositions like orthoclase and hornblende, highlighting the role of soil chemistry in shaping microbial responses to fire. These insights advance the understanding of fire-induced changes in soil microbial functions across diverse geological contexts.

AimsPecan (Carya cathayensis Sarg.) is an important forest trees in China, the application of chemical pesticides for disease control has caused severe damage to the soil, including reduced fertility and disruption of microbial communities. Although Trichoderma treatment has been shown to promote plant growth and improve soil quality, its effects on the growth promotion of pecan and the impact on soil microbial communities and physicochemical properties remained unclear.MethodsIn this study, we investigated the impact of T. asperellum TCS007 spore suspension and its fermented crude extract on the growth and development of pecan seedlings. We also explored the effects of TCS007 treatment on the nutrients, enzyme activities, and microbial diversity in the rhizosphere soil of pecan seedlings during their three main growth stages.ResultsTreatment with TCS007 spore suspension or crude extract promoted the growth of pecan seedlings, with significantly higher levels of leaf hormones and defense enzyme activity compared to the control (CK). Moreover, the content of soil organic matter and ammonium nitrogen, as well as the activity of soil enzymes such as catalase and urease, were all significantly higher than CK after treatment, and the soil pH shifted from slightly acidic to slightly alkaline. The results indicated that TCS007 treatment significantly increased the richness of beneficial fungi and bacteria in the soil.ConclusionThe results demonstrated that TCS007 treatment significantly promoted the growth of pecan plants, increased enzyme activity and nutrient content in the soil, and improved the soil micro-ecological environment.

A sustainable use of croplands should utilize beneficial services provided by their resident soil microbiome. To identify potentially adverse environmental effects on soil microbiomes in the future, a better understanding of their natural variability is fundamental. Here, we characterized the abundance and diversity of soil microbial communities over 2 years at two-week intervals on three neighboring fields at an operational farm in Northern Germany. Field soils differed in texture (clay, loam) and tillage (soil conservation vs. conventional). PCRamplicon analyses of soil DNA revealed distinct temporal variations of bacteria, archaea, fungi, and protists (Cercozoa and Endomyxa). Annual differences and seasonal effects on all microbial groups were detected. In addition to soil pH, prokaryotic communities varied with total soil C and N, but fungi with temperature and precipitation. The C/N ratio had contrasting effects on prokaryotic phyla and protistan classes, but all fungal phyla responded positively. Irrespective of the sampling date, prokaryotic and fungal but not protistan community compositions from the three soils were distinct. Compositional turnover rates were higher for fungi and protists than for prokaryotes and, for all, lower in clay. Conventional tillage had the strongest effect on protist diversity. In co-occurrence networks, most nodes were provided by prokaryotes, but highly connected nodes by predatory protists in the first, and by saprotrophic fungi in the second year. The temporal variation established here can provide insights of what is natural and thus below the limits of concern in detecting adverse effects on the soil microbiome.

China has significant mineral resources, but prolonged extraction has caused considerable environmental degradation. Interactions among rhizosphere, phyllosphere, and soil microorganisms, along with host plants, are essential for supporting plant growth and increasing stress tolerance. This study employed high-throughput sequencing to assess microbial diversity and community structure related to four common tree species in the mountainous areas of Shanxi Province, with samples collected from three regions over two seasons and three locations. The dominant fungal and bacterial phyla identified were Ascomycota, Basidiomycota, Mortierellomycota, Pseudomonadota, Actinobacteriota, Gemmatimonadota, Acidobacteria, Myxococcota, and Firmicutes. Alpha-diversity analysis revealed that Taiyue Mountain exhibited the highest fungal diversity among the plots, while Liushenyu displayed the highest bacterial diversity. Alpha-diversity was greater in spring than in summer across the seasons. Significant differences in Alpha-diversity were observed among different tree species, with Betula platyphylla showing the lowest diversity. In comparison to phyllosphere microorganisms, rhizosphere and soil microorganisms exhibited higher diversity, richness, and evenness. Beta-diversity analysis indicated significant differences in fungal and bacterial community composition between spring and summer samples, as well as among samples from leaves, roots, and soil. The assessment of soil physicochemical properties and redundancy analysis demonstrated that soil moisture content and organic matter were key factors influencing the composition of fungal and bacterial communities. These findings provide valuable insights into the structural changes in plant microbial communities in mining areas and the restoration of damaged ecosystems.

Acid sulfate soils impact surrounding ecosystems with pronounced environmental damage via leaching of strong acidity along with the concurrent mobilization of toxic metals present in the soils and, in consequence, they are often described as the nastiest soils on Earth. Within Sweden, acid sulfate soils are distributed mainly under the maximum Holocene marine limit that stretches the length of the country, some 2000 km north to south. Despite only minor geographical differences in the geochemical composition of the Swedish acid sulfate soils, their field oxidation zone microbial community compositions differ along a north-south regional divide. This study compared the 16S rRNA gene amplicon-based microbial community compositions of field oxidation zones (field tested pH 6.5) collected from the same field sites throughout Sweden that had acidified (final pH = 20 degrees C) greater than what was experienced by the field oxidation zone samples when sampled (similar to 2 degrees C-9 degrees C). These data suggested that in the absence of significant geochemical differences, temperature was the predominant driver of microbial community composition in Swedish acid sulfate soil materials.

The objective of this study was to evaluate the applicability of soil pH and chlorophyll content as predictive indicators of damage in paddy fields affected by HCl spills, based on causal relationships. Five doses of HCl (e.g., 1, 50, 100, 200, and 500-fold of PNEC) were added to the paddy mesocosm during the rice heading stage. In the 7th week after the acid addition, rice grain quality (e.g., 1000-grain weight and filled grain ratio), soil microbial diversity (e.g., Operational Taxonomic Units (OTUs) and Shannon index), and soluble nutrients (e.g., NH4+, NO3-, SiO2, P2O5, and basic cations) were measured. Causal relationships among variables were analyzed using the Partial Least Square Path Model (PLS-PM). At the dose of 500xPNEC, all rice plants lodged when pH < 4. At 100xPNEC and 200xPNEC, the number of immature grains increased, resulting in a reduction in grain quality of over 18%. At 200xPNEC, the microbial OTUs and the Shannon index decreased by 30%. Notably, the proportion of Planctomycetes, the dominant phylum in the control soil, decreased. The reduction of Planctomycetes led to excessive NH4+ accumulation in the soil, which leads to an undesirable increase of chlorophyll content thereby deteriorating grain quality. The causal relationship suggests that information of soil pH and leaf chlorophyll can aid us in predicting damage for grain quality and microbial diversity.

Large-scale mining activities generate significant amounts of waste that accumulates in the environment. These wastes, known as mine tailings, contain high levels of heavy metals, posing risks to human health and causing severe damage to ecosystems. In this study, we determined the heavy metal content of mine tailings in the Sierra de Huautla Biosphere Reserve (REBIOSH), Mexico, and investigated their effect on microbial composition. One of the sites historically contaminated with metals was sampled in three different locations, labeled S1, S2, and S3. A fourth site free of heavy metals (S4) was also used as a control. Our results showed high levels of As, Pb, Cd, and Ag, potentially dangerous metals that exceed thresholds set by international regulatory agencies. Metal contamination indices indicated moderate to extreme enrichment for As, Cd, and Pb, posing potential ecological risks. A metagenomic study of mine tailings showed a core specie-specific microbiome covered by Sinimarinibacterium flocculans, Jiangella anatolica, Thiobacillus denitrificans, Fontimonas thermophile, Sphingomonas koreensis. These may be associated with the processing of heavy metals. A comparative study using the ALDEx2 revealed that less represented species like Variovorax paradoxus, Usitatibacter rugosus, Usitatibacter palustris, Sphingosinicella microcystinivorans, Sphingobium yanoikuyae, and Stella humosa may serve as microbial markers in metal-contaminated environments. In addition, we detected rare or low-abundance species belonging to the phylum Armatimonadota, Candidatus Melainobacteriota, Candidatus Saccharimonadota, Chlamydiota, Deinococcota, Elusimicrobiota, Bacillota, Rhodothermota and Verrucomicrobiota, which could play an important role in ecosystems contaminated with heavy metals. Also, we found site-specific taxonomic representatives such as Nitrososphaera gargensis and Nitrospira nitrificans dominating the S3 ecosystem; Ensifer aridi (S2 and S1), N. nitrificans (S2), while Reyranella soli dominate the S1 soil. These organisms could be crucial for nitrogen access in oligotrophic environments and underscore the adaptability of microbial life to extreme conditions. This is the first comprehensive study of the microbial composition in this important ecological site of the Mexican geography and can provide future guidance for the management and biological treatment of mining wastes.

The effectiveness of almond shell-derived biochar (ASB) in immobilizing soil heavy metals (HMs) and its impact on soil microbial activity and diversity have not been sufficiently studied. Hence, a pot study was carried out to investigate the effectiveness of ASB addition at 2, 4, and 6 % (w/w) w /w) on soil biochemical characteristics and the bioavailability of Cd, Cu, Pb, and Zn to tomato ( Solanum lycopersicum L.) plants, as compared to the control (contaminated soil without ASB addition). The addition of ASB promoted plant growth (up to two-fold) and restored the damage to the ultrastructure of chloroplast organelles. In addition, ASB mitigated the adverse effects of HMs toxicity by decreasing oxidative damage, regulating the antioxidant system, improving soil physicochemical properties, and enhancing enzymatic activities. At the phylum level, ASB addition enhanced the relative abundance of Actinobacteriota, , Acidobacteriota, , and Firmicutes while decreasing the relative abundance of Proteobacteria and Bacteroidota. . Furthermore, ASB application increased the relative abundance of several fungal taxa ( Ascomycota and Mortierellomycota) ) while reducing the relative abundance of Basidiomycota in the soil. The ASB-induced improvement in soil properties, microbial community, and diversity led to a significant decrease in the DTPA-extractable HMs down to 41.0 %, 51.0 %, 52.0 %, and 35.0 % for Cd, Cu, Pb, and Zn, respectively, as compared to the control. The highest doses of ASB (ASB6) significantly reduced the metals content by 26.0 % for Cd, 78.0 % for Cu, 38.0 % for Pb, and 20.0 % for Zn in the roots, and 72.0 % for Cd, 67.0 % for Cu, 46.0 % for Pb, and 35.0 % for Zn in the shoots, as compared to the control. The structural equation model predicts that soil pH and organic matter are driving factors in reducing the availability and uptake of HMs. ASB could be used as a sustainable trial for remediation of HMs polluted soils and reducing metal content in edible plants.

The stability and effectiveness of the anaerobic digestion (AD) system are significantly influenced by temperature. While majority research has focused on the composition of the microbial community in the AD process, the relationships between functional gene profile deduced from gene expression at different temperatures have received less attention. The current study investigates the AD process of potato peel waste and explores the association between biogas production and microbial gene expression at 15, 25, and 35 degrees C through metatranscriptomic analysis. The production of total biogas decreased with temperature at 15 degrees C (19.94 mL/g VS), however, it increased at 35 degrees C (269.50 mL/g VS). The relative abundance of Petrimonas, Clostridium, Aminobacterium, Methanobacterium, Methanothrix, and Methanosarcina were most dominant in the AD system at different temperatures. At the functional pathways level 3, alpha-diversity indices, including Evenness (Y = 5.85x + 8.85; R-2 = 0.56), Simpson (Y = 2.20x + 2.09; R-2 = 0.33), and Shannon index (Y = 1.11x + 4.64; R-2 = 0.59), revealed a linear and negative correlation with biogas production. Based on KEGG level 3, several dominant functional pathways associated with Oxidative phosphorylation (ko00190) (25.09, 24.25, 24.04%), methane metabolism (ko00680) (30.58, 32.13, and 32.89%), and Carbon fixation pathways in prokaryotes (ko00720) (27.07, 26.47, and 26.29%), were identified at 15 degrees C, 25 degrees C and 35 degrees C. The regulation of biogas production by temperature possibly occurs through enhancement of central function pathways while decreasing the diversity of functional pathways. Therefore, the methanogenesis and associated processes received the majority of cellular resources and activities, thereby improving the effectiveness of substrate conversion to biogas. The findings of this study illustrated the crucial role of central function pathways in the effective functioning of these systems.

This study investigated the change in the microbiome of tomato rhizosphere soils after the invasion of Ralstonia solanacearum and analyzed the correlation between microbes and soil physicochemical properties. Diversity analyses of the bacteria in healthy and diseased rhizosphere soil samples (HRS and DRS) revealed that HRS had a higher species diversity and were compositionally different from DRS (P <= 0.05). Substantial differences in the relative abundance of Actinobacteria (37.52% vs 28.96%, P <= 0.05) and Proteobacteria (29.20% vs 35.59%, P <= 0.05) were identified in HRS and DRS, respectively. Taxonomic composition analysis showed ten differentially abundant genera, and seven of them (Gaiella, Roseisolibacter, Solirubrobacter, Kribbella, Acidibacter, Actinomarinicola, and Marmoricola) are more abundant in HRS. Soil pH and enzyme activities were negatively correlated with the abundance of R. solanacearum. The contents of total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkaline nitrogen (alkaline N), available phosphorus (AP), available potassium (AK), NO3-N(NN), NH4(+)-N (AN), and organic matter (OM) were all significantly increased in DRS. The composition and richness of protozoa in the samples show significant differences. Cephalobus, Acrobeles, Heteromita, norank_Tylenchida, and Rotylenchulus were enriched in DRS. Microbial interaction networks revealed that the HRS networks were more complex than the DRS networks. Overall, the results of this study demonstrate that healthy soil has a more complex microbial community structure and higher enzyme activity, and the invasion of R. solanacearum damages the soil microbial system. IMPORTANCE How does the invasion of Ralstonia solanacearum affect tomato rhizosphere bacteria and protozoa? Which microbial changes can affect the growth of R. solanacearum? To date, most research studies focus on bacteria, with little research on protozoa, and even less on the synergistic effects between protozoa and bacteria. Here, we analyzed the correlation between tomato rhizosphere bacterial and protozoan communities and soil physicochemical properties during the invasion of R. solanacearum. We found that the diversity and abundance of rhizosphere microorganisms in healthy rhizosphere soil samples (HRS) were significantly higher than those in diseased rhizosphere soil samples (DRS), and there were significant changes in soil pH and enzyme activity. Overall, in this study, the analysis of microbial changes during the invasion of R. solanacearum provides a theoretical basis for the prevention and control of bacterial wilt.