Function Of Soil Bacterial Communities Research Articles

Effects of soil conditioners on vineyard saline soil physicochemical properties and bacterial community in arid areas

AbstractSoil salinization adversely affects soil quality and ecosystem. Many researches have tried to ameliorate saline soils by soil conditioners. However, little is known about the differences in the responses of soil bacterial communities to natural and artificial conditioners applied to saline soils. Therefore, in this study, the effects of natural humic acid (IK), synthetic polymer (IP), and composite material (IF) (mixture of IK and IP (1:1)) on bacterial community structure and functional genes in saline soil were evaluated to clarify their differences. The results showed that the application of the three soil conditioners significantly reduced soil pH and Na+ content but increased soil alkaline phosphatase, urease, invertase and catalase activities, bacterial diversity, and nutrients, compared to the control (no conditioner). IK application increased bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, and KD4‐96) and metabolic functions (e.g., Two‐component system and Biosynthesis of amino acids) by increasing soil nitrogen and maintaining K+ and Na+ balance. IP application increased soil alkaline phosphatase and urease activities as well as bacterial relative abundance (e.g., Subgroup_6, RB41, MND1, Gemmatimonadaceae, and KD4‐96) and metabolic functions (e.g., Quorum sensing and carbon metabolism) by increasing soil organic carbon/nitrogen content. IF application increased the bacterial relative abundance of Subgroup_6, RB41, and MND1 by increasing soil available nitrogen and regulated their metabolic pathways (e.g., ABC transporters and microbial metabolism). On the whole, IK, IP, and IF could regulate the structure and function of soil bacterial community in saline soils. This study clarifies difference in the effects of different soil conditioners on the amelioration of saline soils from the perspective of soil microbiology, and provides a reference for the amelioration of saline soils in arid areas.

Micronutrients modulate the structure and function of soil bacterial communities

Soil micronutrients are increasingly recognized as critical regulators of biogeochemical cycling and terrestrial ecosystem processes. Despite substantial efforts establishing how belowground microbial communities respond to macronutrients such as N and P, responses to micronutrients remain poorly understood. This is of particular interest in tropical soils, where micronutrients are heterogeneously distributed and often deficient. Using nearly 300 soil samples that span broad gradients in soil micronutrients, we aimed to determine how differences in micronutrients (Ca, Mg, S) and secondary macronutrients (Mn, Fe, Zn) shape soil bacterial communities and their metabolic capabilities. Along with key soil parameters including pH and climatic predictors, we found that Ca, Mg, and Mn were important in shaping the composition and function of soil microbiomes. We also identified lineages that were consistently responsive to specific micronutrients, with those taxa found in low micronutrient conditions often associated with oligotrophic life history strategies. We detected a subset of metabolic attributes related to nutrient cycling that were strongly associated with specific micronutrients. Notably, Mn was important in predicting the abundance of gene systems related to P metabolism including control of Pho regulon and alkylphosphonate utilization, suggesting that it may be important mediators of these responses. Taken together, our results begin to establish a broader understanding of the extent to which belowground systems are shaped by micronutrients and the strategies that soil microbes employ in variable micronutrient environments.

Peanut-based intercropping systems altered soil bacterial communities, potential functions, and crop yield.

Intercropping is an efficient land use and sustainable agricultural practice widely adopted worldwide. However, how intercropping influences the structure and function of soil bacterial communities is not fully understood. Here, the effects of five cropping systems (sole sorghum, sole millet, sole peanut, sorghum/peanut intercropping, and millet/peanut intercropping) on soil bacterial community structure and function were investigated using Illumina MiSeq sequencing. The results showed that integrating peanut into intercropping systems increased soil available nitrogen (AN) and total nitrogen (TN) content. The alpha diversity index, including Shannon and Chao1 indices, did not differ between the five cropping systems. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) illustrated a distinct separation in soil microbial communities among five cropping systems. Bacterial phyla, including Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, were dominant across all cropping systems. Sorghum/peanut intercropping enhanced the relative abundance of phyla Actinobacteriota and Chloroflexi compared to the corresponding monocultures. Millet/peanut intercropping increased the relative abundance of Proteobacteria, Acidobacteriota, and Nitrospirota. The redundancy analysis (RDA) indicated that bacterial community structures were primarily shaped by soil organic carbon (SOC). The land equivalent ratio (LER) values for the two intercropping systems were all greater than one. Partial least squares path modeling analysis (PLS-PM) showed that soil bacterial community had a direct effect on yield and indirectly affected yield by altering soil properties. Our findings demonstrated that different intercropping systems formed different bacterial community structures despite sharing the same climate, reflecting changes in soil ecosystems caused by interspecific interactions. These results will provide a theoretical basis for understanding the microbial communities of peanut-based intercropping and guide agricultural practice.

Prediction of Soil Bacterial Community Structure and Function in Minqin Desert-oasis Ecotone Artificial Haloxylon ammodendron Forest

Exploring the effects of artificial Haloxylon ammodendron forest planting on the structure and function of a desert soil bacterial community provides data reference for soil micro-ecological restoration and land quality improvement in desert oasis transition zones. Illumina high-throughput sequencing technology and PICRUSt2 functional prediction analysis were used to identify and analyze the structure and function of soil bacterial communities, and the Mantel correlation test and RDA analysis were used to explain the physicochemical factors affecting the structure and function of soil bacterial communities. The results showed that:① the soil bacterial OTU number, Chao1 index, and Shannon index were significantly higher in the H. ammodendron forest than in the mobile dune soil, and the PCoA analysis and Adonis test showed significant differences in the soil bacterial community structure between H. ammodendron and mobile dune soil (P=0.001). ② A total of 34 phyla, 89 classes, 174 orders, 262 families, and 432 genera of bacteria were detected in all samples, and the phyla Proteobacteria, Actinobacteria, Cyanobacteria, and Chloroflexi accounted for 76.05% of the relative abundance of soil bacteria, which belonged to the dominant soil bacteria, among which the relative abundance of Actinobacteria in H. ammodendron forest soil was extremely significantly higher than that in mobile dune soil (P < 0.01). ③PICRUSt2 function prediction revealed that the soil bacterial community of H. ammodendron forest included six categories of primary functions and 28 categories of secondary functions, among which the metabolism of carbohydrates, metabolism of amino acids, and metabolism of cofactors and vitamins were all greater than 10% in relative abundance and were the main metabolic functions of H. ammodendron forest soil bacteria. ④ The planting of H. ammodendron forest significantly improved the nutrient content of soil organic matter and other nutrients. Soil pH, organic matter, total nitrogen, and fast-acting phosphorus were the main physicochemical factors affecting the bacterial community, with soil organic matter significantly affecting the soil bacterial community structure (P < 0.05) and metabolic function (P < 0.05). In conclusion, the artificial H. ammodendron forest helped to increase desert soil microbial diversity, increase the relative abundance of soil bacterial metabolic function genes, and improve the desert soil microenvironment.

Effects of Vegetation Types and Seasonal Dynamics on the Diversity and Function of Soil Bacterial Communities in the Upper Reaches of the Heihe River

The process of interaction between the plant and soil microbial communities holds the key to understanding the biogeochemical cycle and preserving the stability of vegetation ecosystems. Owing to this significance, the primary goal of this research was to give a starting point and reference methods to restore local vegetation. The vegetation distribution in the mountainous area of the upper reaches of the Heihe River Basin had notable vertical zonality, which was characterized by five typical vegetation types, including cushion vegetation(CV), herbage meadow(HM), forest steppe(FS), mountainous steppe(MS), and desert grassland(DG). The organization and diversity of soil bacterial communities in various vegetation types were examined using high-throughput sequencing techniques in both the winter and summer seasons. Sampling sites were chosen in each of the five common vegetation types in turn. Additionally, based on the FAPROTAX database, the predicted functions of microbial communities were evaluated for different vegetation types and seasons. The redundancy analysis and structural equation model were also used to investigate the primary environmental elements and uncover the mechanisms affecting the soil bacterial populations. The findings revealed that:① the physical and chemical properties of soil differed significantly among vegetation types and seasons, and the property indices varied dissimilarly with depth. In particular, the soil water content(SWC) and nutrient content of total organic carbon(TOC) and total nitrogen(TN) were significantly higher in forest grassland(FS). ② The divergences of α-diversity indices among seasons(P<0.05) were greater than that of vegetation types(P>0.05). The Chao1 index measuring the abundance of the bacterial community was higher in winter. According to the Shannon index, the species of the bacterial community were dispersed in a "W" shape in the summer and a "hump" form in the winter with altitude. ③ The predominant phyla of the bacterial community, composed of Acidobacteria, Proteobacteria, and Actinobacteria, did not significantly differ from one another. However, the organization of the bacterial community presented a significant variation seasonally at the genus level. ④ The primary functions of the soil bacterial population, which largely consisted of chemoheterotrophy, nitrification, and aerobic ammonia oxidation, were not significantly different among vegetation types and seasons. ⑤ The key factors affecting soil bacterial communities at the genus level varied significantly among seasons, with soil temperature(ST), total organic carbon(TOC), and pH in winter and soil water content(SWC), carbon-nitrogen ratio(C/N), and pH in summer. ⑥ Synergized by interrelated environmental factors, soil physical and chemical features exerted a more direct impact on the diversity and functionality of bacterial communities compared with vegetation types, including significantly changing the abundance of Acidobacteria and Bacteroidetes, as well as the role of nitrification and ammonia oxidation. Hence, improving the carbon and nitrogen contents in soil nutrients would help to enhance the diversity and function of bacterial communities. The findings of this study provided a model for determining the mechanism of regional vegetation degradation and preserving the stability of alpine ecosystems in this area by revealing the seasonal distribution pattern of bacterial communities and the key biological processes beneath the typical vertical vegetation band in the upper reaches of the Heihe River.

Effects of Long-term Tillage on Soil Bacterial Community Structure and Physicochemical Properties of Dryland Wheat Fields in Northern China

To explore the effects of long-term tillage on bacterial community structure in different soil layers of dryland wheat fields and its relationship with soil physicochemical properties, a long-term field experiment was conducted from 2016 to 2021 in Wenxi Experimental Demonstration Base of Shanxi Agricultural University, Shanxi Province. We studied the effects of no-tillage (NT), subsoiling-tillage (ST), and deep plowing (DP) on soil physicochemical properties; α and β diversity of the bacterial community; and dominant and different species of phyla and genera in different soil layers. Additionally, PICRUSt2 was used to predict the metabolic function of soil bacterial community. The results revealed that subsoiling-tillage and deep plowing significantly increased the soil water content in the 20-40 cm soil layer and significantly decreased the soil organic carbon content in the 0-20 cm soil layer compared with that under no-tillage for five consecutive years. Compared with that under deep plowing, subsoiling-tillage significantly increased soil water content, soil organic carbon content, dissolved organic carbon content, and dissolved organic nitrogen content in the 0-20 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing increased the α diversity of the soil bacterial community in the 0-40 cm soil layer, and subsoiling-tillage was higher than deep plowing. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundances of Acidobacteria and Nitrospirae in the 0-20 cm soil layer and Acidobacteria, Chloroflexi, Gemmatimonadetes, Rokubacteria, GAL15, and Nitrospirae in the 20-40 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundance of Nitrospira in the 0-20 cm soil layer and Rubrobacter and Streptomyces in the 20-40 cm soil layer. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundance of Acidobacteria and Gemmatimonadetes in the 0-40 cm soil layer. Redundancy analysis demonstrated that the contents of soil organic carbon, dissolved organic carbon, and dissolved organic nitrogen in the 0-20 cm soil layer exerted positive effects on Actinobacteria and Blastococcus, and the soil water content in the 0-40 cm soil layer exerted positive effects on Acidobacteria, Chloroflexi, and Gemmatimonadetes under subsoiling-tillage. The results of PICRUSt2 prediction showed that subsoiling-tillage and deep plowing significantly increased the relative abundance of amino acid metabolism and the metabolism of cofactors and vitamins but decreased the relative abundance of lipid metabolism of bacterial communities in the 20-40 cm soil layer compared with that under no-tillage. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundances of amino acid metabolism in the 0-40 cm soil layer and other amino acid metabolism in the 0-20 cm soil layer. In conclusion, subsoiling-tillage or deep plowing could increase the soil water content, α diversity of the soil bacterial community, and their metabolic capacity in the dryland wheat fields during the summer fallow period. The relative abundance of Acidobacteria and Gemmatimonadetes and the ability of amino acid metabolism of the bacterial community were increased by subsoiling-tillage, and thus the contents of soil dissolved organic carbon and dissolved nitrogen can be increased.

Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile.

Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p>0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.

Effects of novel Cd mobilization bacteria and bone meal on the structure and function of soil bacterial communities and cadmium phytoremediation potential

Phytoremediation techniques for heavy metals in soils are inefficient due to phytotoxicity and low bioavailability of heavy metals in soils. Therefore, it is crucial to improve the bioavailability of cadmium (Cd) in soils and plant biomass. In this study, bacteria (L8) with high tolerance to heavy metals were isolated and screened from landfills. Bone meal (BM) was used as an organic amendment to form a synergistic enhancement system with L8 to improve the efficiency of phytoextraction of Cd from soil. A total of four treatments were set up: Control treatment (CK), L8 treatment (T1), 0.5% bone meal treatment (T2), and 0.5% bone meal + L8 treatment (T3). Compared with CK, ryegrass biomass and Cd accumulation in the T3 treatment group increased by 28.36% and 131.81%, respectively. Microbiome and metabolome analyses showed that the combination of bone meal and L8 significantly altered the inter-root microbial community and increased the levels of metabolites associated with the stress response. The combination of bone meal and L8 increased ryegrass biomass and plant detoxification. This was mainly attributed to an increase in the content of amino acids, esters, carbohydrates and sugars in the soil, as well as an increase in antioxidants and soil enzyme activity associated with stress tolerance.The results of this study provide novel insights into efficient remediation of heavy metals in soils, and present a simple and environmentally friendly method to facilitate the mobilization and phytoextraction of Cd from contaminated soils.

Nano-Nd2O3 reduced soil bacterial community function by altering the relative abundance of rare and sensitive taxa.

Nanoparticulate-Nd2O3 (nano-Nd2O3) has been excessively utilized in agriculture, industry, and medicine. Hence, nano-Nd2O3 can have environmental implications. However, the impact of nano-Nd2O3 on alpha diversity, composition, and function of soil bacterial communities has not been thoroughly evaluated. We amended soil to achieve different concentrations of nano-Nd2O3 (0, 10, 50, and 100mgkg-1 soil) and incubated the mesocosms for 60days. On days 7 and 60 of the experiment, we measured the effect of nano-Nd2O3 on alpha diversity and composition of soil bacterial community. Further, the effect of nano-Nd2O3 on the function of soil bacterial community was assessed based on changes in the activities of the six potential enzymes that mediate the cycling of nutrients in the soil. Nano-Nd2O3 did not alter the alpha diversity and composition of the soil bacterial community; however, it negatively affected community function in a dose-dependent manner. Specifically, the activities of β-1,4-glucosidase and β-1,4-n-acetylglucosaminidase that mediate soil carbon and nitrogen cycling, respectively, were significantly affected on days 7 and 60 of the exposure. The effect of nano-Nd2O3 on the soil enzymes correlated with changes in relative abundances of the rare and sensitive taxa, viz., Isosphaerales, Isosphaeraceae, Ktedonobacteraceae, and Streptomyces. Overall, we provide information for the safe implementation of technological applications that use nano-Nd2O3.

Ecological safety evaluation of chlorpyrifos on agricultural soil: Effects on soil microbes

The health of farmland soils is directly related to the proper application of pesticides. Chlorpyrifos is a widely used broad-spectrum organophosphorus insecticide, and its ecological security risk to farmland soils requires evaluation. A trial was conducted to study the effects of chlorpyrifos on soil microbes in a wheat–maize rotation field. A 45 % chlorpyrifos emulsion was sprayed at the recommended and dual doses, after which the chlorpyrifos residue, soil microbial content, bacterial community structure, functional microbial abundance, and enzyme activities were measured. The results showed that chlorpyrifos had a half-life of 8.94–9.88 and 2.17–2.18 days in soil for wheat and maize, respectively. Although the final chlorpyrifos residues in the crop grains were lower than the maximum residue limit recommended by the Chinese government, soil fungal abundance was significantly inhibited, and the structure and function of soil bacterial communities were disturbed. Furthermore, the quantities of nitrification-related genera (Acidobacteria GP4 and Acidobacteria GP6) and functional genes (AOB-amoA and AOA-amoA) decreased, whereas those of denitrification-related functional genes (nirS and nirK) and urease activity increased. Gemmatimonas and alkaline phosphatase involved in phosphorus cycling were activated, and the abundance of cbbLR and cbbLG genes involved in carbon fixation decreased. The integrated biomarker response index showed that nirK and β-glucosidase were the most sensitive indicators in wheat and maize stages. The present study provides toxicological data and theoretical guidance for the ecological safety evaluation and rational application of chlorpyrifos in soil.

Effects of Chinese Milk Vetch Returning Incorporated with Chemical Fertilizer Reduction on the Composition and Function of Soil Bacterial Communities in Paddy Fields

Chinese milk vetch (Astragalus sinicus L.) is an important organic nutrient resource in the southern Henan rice-growing area. Thus, the effects of Chinese milk vetch (MV) returning incorporated with reduced chemical fertilizer on the physicochemical properties and bacterial community characteristics in paddy soil were studied. These results can provide a certain theoretical basis for the improvement of soil fertility and reduction of chemical fertilizer in this area. A field experiment was conducted for 12 consecutive years, involving six fertilization treatments (blank control, CK; 100% chemical fertilizer, F100; 80% chemical fertilizer+22.5 t·hm-2 MV, MV1F80; 80% chemical fertilizer+45 t·hm-2 MV, MV2F80; 60% chemical fertilizer+22.5 t·hm-2 MV, MV1F60; and 60% chemical fertilizer+45 t·hm-2 MV, MV2F60). The high-throughput sequencing method was used to compare the effects of different fertilization treatments on soil bacterial community diversity, composition, and structural characteristics. The FAPROTAX function prediction method was used to analyze the abundance differences of functional groups between different fertilization treatments. Additionally, combined with soil physicochemical properties and bacterial community characteristics, we explored the key soil environmental factors that changed the structure and functional characteristics of the soil bacterial community. Compared with that under CK, the soil bulk density (BD) under the MV returning incorporated with reduced chemical fertilizer treatment was decreased, whereas soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and total potassium (TK) were increased by 12.7%-35.5%, 38.2%-65.7%, 66.7%-95.2%, and 20.3%-31.6%, respectively. Compared with that under the F100 treatment, the Sobs index and Shannon diversity index of the bacterial community under the MV returning incorporated with reduced chemical fertilizer were decreased, and the Sobs index and Shannon diversity index were significantly positively correlated with BD (P<0.05) but significantly negatively correlated with SOC and TN (P<0.05). Compared with that under the F100 treatment, the relative abundances of Firmicutes under the MV1F80 and MV2F60 treatments were significantly increased by 82.2% and 67.4% (P<0.05), but the relative abundances of Acidobacteria were significantly reduced by 32.6% and 40.5% (P<0.05), respectively. The relative abundance of Actinobacteria under the MV2F60 treatment was significantly increased by 30.0% (P<0.05) compared with that under the F100 treatment. According to RDA analysis, soil SOC, TN, and TK were the main soil environmental factors that significantly affected bacterial community (P<0.05). Compared with that under CK and the F100 treatment, the abundance of functional groups of chemoheterotrophy, nitrogen fixation, fermentation, and ureolysis under the MV returning incorporated with reduced chemical fertilizer treatment were improved, whereas the abundance of functional groups of animal parasites or symbionts, all human pathogens, and human pathogen pneumonia were reduced, particularly under MV1F80 and MV2F60. To summarize, the long-term MV returning to the field incorporated with reduced chemical fertilizer improved the soil physical and chemical properties, thus changing the structure and functional characteristics of the soil bacterial communities, contributing to the improvement in the soil fertility, stability, and health of micro-ecosystems in paddy fields, thus ensuring the green and sustainable development of regional agriculture.

Time-Dependent Effect of Graphene on the Microbial Activity of the Soil Under Single and Repeated Exposures

ABSTRACT Graphene (GR) has huge industrial and biomedical potential, and its adverse effect on soil microorganisms has been evaluated in ecotoxicological studies. These studies focused on single exposure to GR, but repeated exposures with low concentration are more likely to occur under actual exposure scenario. In this study, we compared the impact of single and repeated exposures of GR on structure, abundance and function of soil bacterial community based on soil enzyme activity and high-throughput sequencing. The results displayed that after 4 days of incubation the activities of urease and fluorescein diacetate esterase increased by approximately 12% and 4% upon repeated exposure to GR (biweekly 15 mg doses GR for the two-exposure experiment, 10 mg doses GR for the three-exposure experiment, resulting in the same final concentration of 300 mg/kg), respectively. Instead, the activities of urease and fluorescein diacetate esterase decreased by 13% and 6% upon single exposure (30 mg for the single-exposure experiment), respectively. As the incubation time increased to 60 days, these activities showed little difference. The alpha diversity of soil bacterial community under repeated exposures increased more than that under single exposure, demonstrating that a low concentration chronic exposure to GR increase the diversity within a specific bacterial community. The PCoA and sample level clustering tree showed single exposure to GR after 4 days alter the soil bacterial community to some extent. During the entire incubation process, no matter what kind of exposure scenarios to GR, the majority of bacterial phylotypes at the phylum level had no great change except for Proteobacteria and Actinobacteria according to the relative abundance of phylotypes. These results elucidated the repeated exposures to GR increased the metabolic activity and diversity of the soil microbial community as compared with single exposure. This study can provide a new perspective on the impact of carbon nanomaterials on soil microbial community.

Structural Diversity and Its Temporal Variation in the Soil Bacterial Community Under Plantations of Taxodium distichum in the Riparian Zone of the Three Gorges Reservoir Area

The riparian zone supports important ecological functions and acts as an ecotone connecting terrestrial and aquatic areas. Soil microbes under the revegetation of woody species are crucial to the biogeochemical cycle of nutrients. Here, soil samples were collected to examine the soil microbes during different emergence phases in 2019 (May:T1, July:T2, and September:T3) in the riparian zone of the Three Gorges Reservoir, China. The variations in the bacterial community were evaluated using high-throughput sequencing. The results showed that:during the emergence phases, soil properties such as pH value (pH), ammonium nitrogen (NH4+-N), and nitrate-nitrogen (NO3--N) and soil enzymes changed significantly(P<0.05), and soil bacterial α diversity also changed with time. Except for the Chao1 index, the richness of rhizosphere soil bacteria showed T1>T2>T3, whereas the α diversity of non-rhizosphere soil bacteria showed T3>T1>T2. The redundancy analysis (RDA) test implied that soil urease, NH4+-N, pH, and NO3--N were the key factors structuring the microbial community. Proteobacteria and Acidobacteria were the two dominant components among the 60 phyla that were detected in the soil. Based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) prediction, metabolism was the basic function of soil bacterial communities of Taxodium distichum; in the secondary functional layer, the metabolic pathways related to carbon, nitrogen, and phosphorus mainly included amino acid metabolism, carbohydrate metabolism, lipid compound metabolism, and energy metabolism, and the relative abundance of each metabolic function had a certain time difference in different periods. These findings could help us better understand how soil microbes change after restoring vegetation in the Three Gorges Reservoir area.

Effects of the fungicide trifloxystrobin on the structure and function of soil bacterial community

Trifloxystrobin has been widely applied to prevent fungal diseases because of its high efficiency and desirable safety characteristics. In the present study, the effects of trifloxystrobin on soil microorganisms were integrally investigated. The results showed that trifloxystrobin inhibited urease activity, promoted dehydrogenase activity. Downregulated expressions of the nitrifying gene (amoA), denitrifying genes (nirK and nirS), and carbon fixation gene (cbbL) were also observed. Soil bacterial community structure analysis showed that trifloxystrobin changed the abundance of bacteria genera related to nitrogen and carbon cycle in soil. Through the comprehensive analysis of soil enzymes, functional gene abundance, and soil bacterial community structure, we concluded that trifloxystrobin inhibited both nitrification and denitrification of soil microorganisms, and also diminished the carbon-sequestration ability. Integrated biomarker response analysis showed that dehydrogenase and nifH were the most sensitive indicators of trifloxystrobin exposure. It provides new insights about trifloxystrobin environmental pollution and its influence on soil ecosystem.

Soil bacterial community characteristics and ecological function prediction of alfalfa and crop rotation systems in the Loess Plateau, Northwest China

In order to understand the effects of lucerne cropping rotation on the bacterial community of loess soil, a long-term field experiment was conducted in rain-fed agricultural area of Loess Plateau. The cropping systems included continuous lucerne (Medicago sativa, LC), lucerne removed and rotated with spring wheat (Triticum aestivum, LFW), lucerne removed and rotated with corn (Zea mays, LFC), lucerne removed and rotated with potato (Solanum tuberosum, LP), and lucerne removed and rotated with continuous millet (Panicum miliaceum, LM). Based on 16S rRNA high-throughput sequencing technology, we investigated soil bacterial community structure and diversity in different cropping systems, and predicted ecological function using PICRUSt method. The results showed that the dominant phyla of loess soil bacteria were Actinomycetes (20.3%-32.0%), Proteobacteria (19.2%-23.0%), Acidobacteria (12.4%-14.2%) and Chloroflexus (11.0%-12.7%). The dominant genus was Bacillus (1.9%) in lucerne-corn system and Pseudarthrobacter (2.5%) in other treatments. Rotation with annual crops decreased the relative abundance of Actinobacteria and increased that of Chloroflexi and Firmicutes. Redundancy analysis showed that the main soil factors driving soil bacterial community structure were nitrate, ammonium, and total nitrogen. PICRUSt function prediction results showed that metabolism (78.6%-79.1%) was the main function of soil bacterial communities in loess soil. Rotation with continued annual crops significantly decreased the abundance of soil bacterial carbohydrate metabolism functional genes, and significantly increased the abundance of functional genes for soil bacterial cofactors and vitamin metabolism, neurodegenerative diseases, and immune system. In conclusion, lucerne removed and rotated with continuous annual crops changed soil bacterial community structure and ecological functions. This study provided theoretical reference to explore succession characteristics of soil bacteria and to select succeeding crops for alfalfa in loess soil.

Aeration increases soil bacterial diversity and nutrient transformation under mulching-induced hypoxic conditions

Soil oxygen (O2) deficiency induced by organic mulching is easy to overlook. Aeration has been shown to potentially alleviate soil hypoxia stress. However, the responses of soil bacterial communities to such mulching-induced hypoxic conditions and aeration remain elusive. Therefore, a three-year field experiment, consisting of mulching (T1), mulching with aeration (TA1, poor aeration; TA2, strong aeration), and no-mulching (CK) treatments, was conducted in bamboo (Phyllostachys praecox) plantations. According to our results, the strong aeration treatment (TA2) alleviated soil acidification, increased soil nutrient availability, and significantly increased soil O2 content by 18.44% (P < 0.05) when compared with T1. In addition, TA2 significantly increased soil β-glucosidase, invertase, urease, and acid phosphatase activities compared with CK and T1 (P < 0.05). The alpha diversity indices with TA2 treatment were the highest, indicating that aeration increased the species richness and diversity of bacteria. The changes in bacterial community composition associated with TA2 treatment (i.e., an increase in Firmicutes, Verrucomicrobia, and Faecalibacterium abundance and a decrease in Chloroflexi and Bradyrhizobium abundance) were mainly related to nutrient and O2 content. Mantel Test results suggested that soil O2 content and temperature were the key factors shaping bacterial community composition. Structural equation modeling revealed that soil O2 content had a positive and direct influence on bacterial community diversity. Functional annotation of prokaryotic taxa predicted that TA2 significantly increased the relative abundance of bacterial communities associated with nitrification, nitrogen fixation, and ureolysis. Our results demonstrated that optimal soil aeration conditions (17.60% of O2 content) could enhance the diversity and function of soil bacterial communities. Overall, the findings of this study could serve as a benchmark for alleviating soil hypoxia caused by organic mulches, which is important for increasing the functionality of nutrient cycling bacterial communities in the soil.

Consistent responses of soil bacterial communities to bioavailable silicon deficiency in croplands

Soil bacterial communities play a crucial role in the maintenance of agro-ecosystem functions. Silicon (Si) fertilization has important impacts on the structure and function of soil bacterial communities. However, bioavailable Si in agricultural soils is projected to become depleted because of continuous intensive farming practices. It is urgently needed to investigate how bacterial communities respond to the Si deficiency in agricultural soils. Here, we reveal that the contents of the dissolved and reactive fractions of Si in soils have seriously decreased at the field scale. The reactive Si levels in the topsoil in rice fields (77.83 ± 41.14 mg/kg) were lower than the reported critical limit of Si for plant growth (85 mg/kg) and therefore require special attention. We investigated the composition of soil bacterial communities in these Si-deficient soils. Most dominant bacterial phyla and their subtaxa were significantly correlated with the reactive Si content. Modules II, IV, VI, and VIII within a co-occurrence network were significantly correlated with the reactive Si content. Notably, bacterial groups related to nitrogen, carbon, sulfur, and iron cyclings significantly changed in the Si-deficient soils. Soil reactive Si showed strong direct and indirect relationships with the composition of soil bacterial communities in croplands. The findings of this study will be useful for raising awareness of the need to improve agricultural Si fertilization for agro-ecosystem health and sustainability.

Response of soil bacterial community structure and function under two salt-tolerant plants in a coastal saline soil area of eastern Hebei province of China

The plants Feicai (Sedum aizoon L.) and dandelion(Taraxacum mongolicum Hand.-Mazz.) have good salt tolerance, and can improve soil quality and the micro-ecological environment. Coastal saline-soil plots planted with S. aizoon and T. mongolicum and bare plots were used to explore their effects on the microbial community structure of coastal saline soil. The diversity and function of soil bacterial communities were analyzed using Illumina MiSeq high-throughput sequencing technology. The results showed that the α-diversity of soil bacterial communities were higher in planted than in bare plots, in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The soil bacterial communities also changed after planting S. aizoon and T. mongolicum. The LDA effect size analysis showed that there were 37 indicator species among the three plot types. Correlation analysis of environmental factors showed that EC, AP, and OM were the main factors influencing bacterial community composition in this coastal saline soil. The PICRUSt functional prediction showed that the numbers of metabolic functions of bacterial communities were in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The results provide a theoretical basis and plant species for developing salt-tolerant bacterial resources and phytoremediation of coastal saline soil.

High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River.

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

The use of green manures contributes to sustainable soil and nutrient management in agriculture; however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan, Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control (NF), milk vetch as green manure without chemical fertilizer (GM), winter fallow and chemical fertilizer (CF), and a combination of chemical fertilizer and milk vetch (GMCF). Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33% (F = 36.59, P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils; however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen (N), and sulfur (S) changed after several years of milk vetch utilization (linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.