Erosion and deposition divergently affect the structure of soil bacterial communities and functionality

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

Impact of farmland mulching practices on the soil bacterial community structure in the semiarid area of the loess plateau in China

Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.

Increasing nitrogen (N) addition induces soil nutrient imbalances and is recognized as a major regulator of soil microbial communities. However, how soil bacterial abundance, diversity, and community composition respond to exogenous N addition in nutrient-poor and generally N-limited regions remains understudied. In this study, we investigated the effects of short-term exogenous N additions on soil bacterial communities using quantitative polymerase chain reaction (PCR) and Illumina Miseq sequencing in an in situ N addition field experiment. The results showed that a low nitrogen addition increased the observed species (Sobs) of the bacterial community, and with the increased nitrogen addition, the Sobs of bacteria gradually decreased, especially the unique OTUs. The relative abundance of Proteobacteria, Actinobacteria, and Gemmatimonadetes increased with increasing nitrogen addition, whereas the relative abundance of Chloroflexi and Firmicutes decreased. Soil properties play an important role in bacterial community structure at phylum or genus levels. Short-term nitrogen addition increased the proportion of nodes from Actinobacteria and Proteobacteria in the co-occurrence network and enhanced the stability of the microbial network. Actinobacteria may play an important role in constructing the network. Our study aims to explore the effects of nitrogen addition on the diversity, composition, and structure of soil bacterial communities in nutrient-poor areas caused by ecological disturbances.

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.

Heavy metal pollution poses a serious hazard to the soil bacterial community. In this study, the 16 s rRNA high-throughput sequencing technology was used to analyze bacterial diversity and structure of dry field soil at different levels of heavy metal pollution. Further, the relationships between soil parameters and bacterial community were analyzed. Based on the study findings, we classified the levels of heavy metal pollution in soil samples from the study area could be divided into four grades: high risk (HR), considerable risk (CR), moderate risk (MR) and low risk (LR). In this study, heavy metal concentrations and pH showed significant effect on bacterial community structure. The distribution of bacterial community richness and diversity was MR > LR > CR > HR. Bacterial communities such as Acidobacteria, Chloroflexi and Gemmatimonadetes were highly resistant to the lower pH (pH < 6.5) and the high levels of heavy metal pollution compared with other bacterial community, which were abundant in HR samples. However, Proteobacteria, Actinobacteria, Bacteroidetes and Latescibacteria were more abundant in alkaline soils (pH > 7.5). Further, available Cd, Pb and Zn concentrations were lower in alkaline soils than acidic soils, which reduced the impact of heavy metals on bacterial community diversity and structure.

Effect of early dry season induced by the Three Gorges Dam on the soil microbial biomass and bacterial community structure in the Dongting Lake wetland

Afforestation plays a pivotal role in ecosystem restoration, exemplified by the Saihanba Mechanized Forest Farm, the world's largest planted forest; however, the assembly mechanisms and interactions of soil microbial communities in such forests remain inadequately understood. This study aimed to elucidate the impact of different afforestation tree species, namely Larix gmelinii var. principis-rupprechtii, Picea asperata, and Pinus sylvestris var. mongolica, on soil bacterial diversity and community structure in comparison to grassland. Sixty soil samples were collected at a 20 cm depth, and high-throughput sequencing was employed to identify bacterial communities and assess their interactions with environmental factors. A total of 6528 operational taxonomic units (OTUs) were identified, with Solirubrobacter, Conexibacter, Bacillus, Massilia, Gaiella, Acidibacter, and Vicinamibacter being the dominant genera. Afforestation significantly impacted soil bacterial alpha diversity, with notable influence from key soil chemical properties, including available phosphorus (AP), cation exchange capacity (CEC), and the carbon-to-nitrogen ratio of soil organic matter (SOM-C/N). The Mantel test highlighted pH, the Normalized Difference Vegetation Index (NDVI), and spatial variable (dbMEM) as primary environmental factors influencing dominant bacterial genera. The bacterial community structure demonstrated deterministic homogeneous selection, wherein SOM-C/N emerged as a significant factor influencing the dissimilarity of soil bacterial communities. Furthermore, plantation soils exhibited a more complex network structure than grassland soil, highlighting the crucial role of bacterial communities in vegetation changes and providing valuable insights into their response to environmental factors during the reforestation process.

Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa

Simple SummaryTropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

Understanding how different land-use types shape soil bacterial communities and functions is critical for promoting sustainable land management and ecological restoration in fragile karst regions. This study evaluated the effects of different land-use types (pitaya [HF], maize [MF], sugarcane [SF], and paddy [PF] fields, forestland [FL], and grassland [AF]) on soil bacterial diversity, community composition, functional potentials, and co-occurrence networks in karst regions. The results showed that HF, MF, and PF exhibited the highest bacterial diversity (Shannon index), whereas SF had the lowest possibly because of continuous cropping and fertilization. Variance partitioning analysis revealed that soil bacterial community composition and functional potential were largely explained by the combined effects of land-use type and soil properties (34.8% for composition and 59.7% for functional potential), suggesting that land-use effects on bacterial communities are mainly mediated through changes in soil physicochemical properties. Hierarchical partitioning analysis further identified that soil texture, particularly silt and sand, and pH were the primary factors shaping bacterial community composition, whereas pH was the dominant driver of functional potential. Functional analysis indicated that HF enhanced nitrogen cycling processes, such as nitrification, aerobic nitrite oxidation, and aerobic ammonia oxidation; SF promoted carbon-related functions, including chemoheterotrophy, aerobic chemoheterotrophy, and cellulolysis; and PF favored iron and sulfur respiration. Co-occurrence network analysis demonstrated that HF had the most complex microbial interactions, likely attributable to no-tillage practices and favorable soil conditions, whereas PF showed the lowest network connectivity. Core bacterial groups such as Acidobacteria, Proteobacteria, Chloroflexi, and Actinobacteria, dominated in abundance but also functioned as keystone taxa, suggesting their critical roles in driving nutrient cycling and maintaining ecological stability. These findings suggest that no-till pitaya cultivation may help improve soil microbial diversity, functional potential, and ecological stability in fragile karst ecosystems, indicating its potential as a sustainable agricultural land-use practice. However, long-term monitoring and adaptive management are necessary to ensure sustained soil health.

Impact of sulfadiazine and chlorotetracycline on soil bacterial community structure and respiratory activity

High-throughput sequencing of 16S RNA genes of soil bacterial communities from a naturally occurring CO2 gas vent

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production.