土地利用驱动的土壤性状变化影响微生物群落结构和功能

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

BackgroundGeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau.ResultsA total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes.ConclusionsHigh overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.

Logistics and time demands necessitate soil storage under laboratory conditions after sampling because soil properties cannot always be determined immediately. There have been a number of studies about the effects of storage on biophysical properties; however, there has been little reference to paddy soils, which experience the alternation of wetting and drying phases. Our aims were to determine the impacts of sample storage on microbial activity and community structure in paddy field soil. We pre-incubated paddy soil to reach two states: flooded (F) and drained (D). Samples were then stored at −20 and 4 °C or air-dried. After 30 days, one part of the stored soils was used to measure key soil indices and the other part of the soil was incubated for 7 days prior to reassessment. Total phospholipid fatty acid (PLFA) was used to characterize the microbial biomass. MicroResp™ and Illumina next-generation sequencing techniques were adopted to analyze the change of microbial community activity and structure, respectively. Results showed that the various storage treatments did not affect the total PLFA in drained and flooded soil except for the flooded soil stored at 4 °C. Basal respiration was unusually increased in the drained soil after storage but recovered after a 7-day re-incubation. In contrast, the impact on flooded soils was minimal. Further, the soil community-level physiological profile (CLPP) was affected by storage, but microbial community structure remained mostly unchanged. Sequencing also showed that α diversity of the flooded paddy soil was higher than that in the drained soil. The effect of storage on drained paddy soil using these indices was mainly consistent with previous studies on non-flooded cultivated soils, while the effect on flooded soil suggested a different mechanism from that in drained soil. Although the microbial function and community structure were different between drained and flooded paddy soils, the various storage approaches all altered the microbial functional structure to some extent but kept the microbial community structure largely intact.

Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor

In recent years, the frequency and intensity of anthropogenic wildfires have drastically increased, significantly altering terrestrial ecosystems worldwide. These fires not only devastate vegetative cover but also impact soil environments and microbial communities, affecting ecosystem structure and function. The extent to which fire severity, soil depth, and their interaction influence these effects remains unclear, particularly in Pinus tabulaeformis forests. This study investigated the impact of wildfire intensity and soil stratification on soil physicochemical properties and microbial diversity within P. tabulaeformis forests in North China. Soil samples were collected from different fire severity zones (Control, Light, Moderate, High) and depths (topsoil: 0-10 cm; subsoil: 10-20 cm). Analyses included measurements of soil pH, organic carbon (SOC), total nitrogen (TN), and other nutrients. Microbial diversity was assessed using 16S rRNA gene sequencing. Our findings revealed significant variations in soil pH, SOC, TN, and other nutrients with fire severity and soil depth, profoundly affecting microbial community composition and diversity. Soil pH emerged as a critical determinant, closely linked to microbial α-diversity and community structure. We found that fire severity significantly altered soil pH (p = 0.001), pointing to noteworthy changes in acidity linked to varying severity levels. Topsoil microbial communities primarily differentiated between burned and unburned conditions, whereas subsoil layers showed more pronounced effects of fire severity on microbial structures. Analysis of bacterial phyla across different fire severity levels and soil depths revealed significant shifts in microbial communities. Proteobacteria consistently dominated across all conditions, indicating strong resilience, while Acidobacteriota and Actinobacteriota showed increased abundances in high-severity and light/moderate-severity areas, respectively. Verrucomicrobiota were more prevalent in control samples and decreased significantly in fire-impacted soils. Chloroflexi and Bacteroidota displayed increased abundance in moderate and high-severity areas, respectively. Correlation analyses illustrated significant relationships between soil environmental factors and dominant bacterial phyla. Soil organic carbon (SOC) showed positive correlations with total nitrogen (TN) and alkaline hydrolysable nitrogen (AN). Soil pH exhibited a negative correlation with multiple soil environmental factors. Soil pH and available phosphorus (AP) significantly influenced the abundance of the phylum Myxococcota. Soil water content (WC) significantly affected the abundances of Acidobacteriota and Actinobacteriota. Additionally, ammonium nitrogen (NH4 +-N) and nitrate nitrogen (NO3 --N) jointly and significantly impacted the abundance of the phylum Chloroflexi. This study highlights the significant long-term effects of anthropogenic wildfires on soil microenvironment heterogeneity and bacterial community structure in P. tabulaeformis forests in North China, 6 years post-fire. Our findings demonstrate that fire severity significantly influences soil pH, which in turn affects soil nutrient dynamics and enhances microbial diversity. We observed notable shifts in the abundance of dominant bacterial phyla, emphasizing the critical role of soil pH and nutrient availability in shaping microbial communities. The results underscore the importance of soil stratification, as different soil layers showed varying responses to fire severity, highlighting the need for tailored management strategies. Future research should focus on long-term monitoring to further elucidate the temporal dynamics of soil microbial recovery and nutrient cycling following wildfires. Studies investigating the roles of specific microbial taxa in ecosystem resilience and their functional contributions under varying fire regimes will provide deeper insights. Additionally, exploring soil amendments and management practices aimed at optimizing pH and nutrient availability could enhance post-fire recovery processes, supporting sustainable ecosystem recovery and resilience.

Mixed or chloride salty ions dominate in saline soils, and exert wide-ranging adversely affect on soil biological processes and soil functions. The objectives of this study were to (1) explore the impacts of mixed (0, 3, 6, 10, 20 and 40 g Cl–/SO42– salt/kg dry soil) and chloride (0, 1.5, 3, 5, 8 and 15 g Cl– salt/kg dry soil) salts on soil enzyme activities, soil physiological functional (Biolog) profiles and microbial community structure by using soil enzymatic, Biolog-Eco microplates as well as denaturing gradient gel electrophoresis (DEEG) methods, and (2) determine the threshold concentration of soil electronic conductivity (EC1:5) on maintaining the functional and structural diversity of soil microbial community. The addition of either Cl– or mixed Cl–/SO42– salt obviously increased soil EC, but adversely affected soil biological activities including soil invertase activity, soil microbial biomass carbon (MBC) and substrate-induced respiration (SIR). Cl– salt showed a greater deleterious influence than mixed Cl–/SO42– salt on soil enzymes and MBC, e.g., the higher soil MBC consistently appeared with Cl–/SO42– instead of Cl– treated soil. Meanwhile, we found that SIR was more reliable than soil basal respiration (SBR) on explaining the changes of soil biological activity responsive to salt disturbance. In addition, microbial community structures of the soil bacteria, fungi, and Bacillus were obviously affected by both salt types and soil EC levels, and its diversity increased with increasing of mixed Cl–/SO42– salt rates, and then sharply declined down after it reached critical point. Moreover, the diversity of fungal community was more sensitive to the mixed salt addition than other groups. The response of soil physiological profiles (Biolog) followed a dose-response pattern with Cl– (R2=0.83) or mixed Cl–/SO42– (R2=0.89) salt. The critical threshold concentrations of salts for soil physiological function were 0.45 dS/m for Cl– and 1.26 dS/m for Cl–/SO42–, and those for soil microbial community structural diversity were 0.70 dS/m for Cl– and 1.75 dS/m for Cl–/SO42–.

Shifts in soil microbial community functional gene structure across a 61-year desert revegetation chronosequence

Effects of land-use conversion from paddy field to orchard farm on soil microbial genetic diversity and community structure

Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9–17% in predicting the structure of soil microbial communities with up to 69–78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.

The role of nitrogen in mediating algal-microbial interactions in a rocky intertidal ecosystem

An assessment of the soil microbial status after 17 years of tillage and mineral P fertilization management

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems

Microbial biomass and community structure play a significant role in soil carbon cycling. There is a large amount of organic carbon in the subsoil, but most studies on soil microbial community have focused on the surface soil. The changes and influencing mechanisms of microbial community in subsoil are unclear. We analyzed soil microbial biomass and community structure at different soil depths (0-20, 20-40, 40-60, 60-80, and 80-100 cm) in three typical forests in southwest China, Xishuangbanna tropical rain forest, Ailao Mountain subtropical broad-leaved forest, and Lijiang temperate coniferous forest, by using phospholipid fatty acid technology, to explore their variation characteristics and influencing factors in different forests and soil depths. The results showed that contents of soil organic carbon and total nitrogen decreased gradually, microbial biomass declined significantly. The ratio of Gram-positive bacteria to Gram-negative bacteria (G+:G-) reduced gradually, while the ratio of fungi to bacteria (F:B) increased with the increasing soil depth. Microbial community turned from G--dominated which adapted to eutrophic environment into G+-dominated which adapted to oligotrophic environment. The three forest types differed little in soil microbial biomass, but different significantly in microbial community structure. Ailao Mountain subtropical broad-leaved forest and Lijiang temperate coniferous forest had much higher F:B at 0-20 cm than Xishuangbanna tropical rain forest, while significantly higher G+:G- at 0-100 cm in Xishuangbanna tropical rain forest was observed. Results of the redundancy analysis showed that the contents of soil organic carbon and total nitrogen were the main factors determining microbial biomass, with combined explanation of 78.3%. Results of the stepwise regression analysis showed that C:N was the most important driving factor on F:B and G+:G-. The change in microbial community structure and the decrease in biomass along soil profile might strongly affect the dynamics of soil organic carbon in southwest China forests.

Variation of soil microbial community abundance and structure has great implications for soil fertility and nutrient cycling. A better understanding of soil microbial community dynamics under different land use types is undoubtedly needed in order to develop sustainable land use schemes. The current study aimed to assess how soil microbial community changed after replacement of maize–soybean crop by sugarcane, mulberry, or forage grass crop in a karst area of Southwest China. Mature forests were included for comparison. Phospholipid fatty acid (PLFA) method was used to characterize soil microbial community abundance and structure. The abundances of total PLFAs and PLFAs of bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi were significantly increased in the forage grass field but not in the sugarcane and mulberry fields relative to the maize–soybean field. Total PLFAs' abundance in the forage grass field was increased by 81% compared with that in the maize–soybean field but was about 52% lower than that in the forest. The microbial community structure was not distinguished as much as the microbial abundance among the five land use types. Soil organic carbon (SOC) was identified as the primary factor affecting both soil microbial abundance and structure. Soil microbial community abundance was positively correlated with SOC, but the ratios of fungal to bacterial PLFAs and Gram‐positive to Gram‐negative bacterial PLFAs were negatively correlated with SOC. Our findings suggest that the replacement of the maize–soybean rotation system by forage grass cultivation has the potential to improve soil fertility in the karst region, Southwest China.

Chemical fertilizer reduction with organic fertilizer effectively improve soil fertility and microbial community from newly cultivated land in the Loess Plateau of China