Soil Bacterial Community Composition Research Articles

Urbanization Imprint on Soil Bacterial Communities in Forests and Grasslands

Urbanization alters land uses and creates heterogeneous environmental conditions in cities and their surroundings, which may directly or indirectly impact soil microorganisms. However, how urbanization affects soil bacterial diversity and community composition, particularly in different land use types, remains largely unknown. In this study, we collected 36 soil samples (18 forest and 18 grass soils) along a rural-suburban-urban gradient in Chang-Zhu-Tan agglomeration. The bacterial diversity and community composition were investigated using 16S rRNA gene sequencing that targeted the V3-V4 region. Our results showed that urbanization induced shifts in bacterial diversity and community composition in both forestlands and grasslands. Specifically, soil bacterial diversity was higher in urban areas than in their suburban and rural counterparts in forests and grasslands, particularly in forests, where significant increases were detected. Urbanization changed the most dominated soil bacterial community from Acidobacteria to Proteobacteria in forestland. Significant decrease and increase were observed in the relative abundance of Acidobacteria (e.g., Acidobacteriales, Acidobacteriia_Subgroup2 and Solibacterales) and Proteobacteria (e.g., Betaproteobacteriales, Myxococcales and Sphingomonadales), respectively, in the forests with increasing urbanization intensity. In contrast, Proteobacteria always dominated the soil bacterial community along the rural-suburban-urban gradient in grassland, and significant decrease and increase in Nitrospirae and Latescibacteria were induced by urbanization, respectively. In addition to urbanization and total nitrogen, total organic carbon and ratio of carbon and nitrogen were the main factors that related with the bacterial community in forest soils, whereas soil water content was the main factor related with soil bacterial community in the grasslands. Together, our results indicate that the urbanization results in shifts in bacterial community composition and diversity, but the extent varied between forest and grassland, which may due to different human management intensity.

Forest Gaps Modulate the Composition and Co-Occurrence Network of Soil Bacterial Community in Larix principis-rupprechtii Mayr Plantation

Forest gaps create a favorable microenvironment for the growth of the soil microbial community. This study aimed to explore the effects of gap-related microenvironmental heterogeneity on soil bacterial communities in Larix principis-rupprechtii Mayr forest gaps. Therefore, the redundancy analysis (RDA) and structure equations modeling (SEM) of affecting elements were further used to test the significance of forest gaps’ effect on soil bacterial community composition and co-occurrence structure complexity. The formation of forest gaps increased canopy opening (CO) and significantly increased soil moisture content (SW), soil temperature (ST) and the accumulation of acid phosphatase (PHO) and sucrase (INV) in the soil, and the G250 (forest gap size: >250 m2) was most conductive to the accumulation of light and soil total nutrient. G50, G70, and G100 (forest gap size: 50–70 m2, 70–100 m2, 100–125 m2) were most favorable for the natural regeneration of the L. principis-rupprechtii Mayr plantation. The light properties under the forest gaps were the most significant factor that influenced the soil bacterial community composition, followed by the size of the forest gap, with standard path coefficients (Std. PCs) of 0.45 and −0.37, respectively. The canopy opening (CO), relative light intensity (RLA) and leaf area index (LAI) were considered to be the most important environmental factors affecting bacterial community composition (Std. PCs: 0.97, 0.99, and −0.93, respectively). The natural regeneration density under the forest gap was the most significant factor influencing the complexity of the soil bacterial community co-occurrence network, followed by soil nutrients (Std. PCs: 0.87 and −0.76, respectively).

Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient

Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3−-N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.

Effect of Biochar on Soil Physiochemical Properties and Bacterial Diversity in Dry Direct-Seeded Rice Paddy Fields

The effects of biochar application on dry direct-seeded rice paddies remains unclear. Therefore, we applied biochar to dry direct-seeded rice paddy fields over 3 consecutive years to assess its effects on soil physicochemical properties and bacterial diversity (conventional fertilization [CK]; biochar + conventional fertilization [BC]). BC increased the content of 0.25–5 mm soil water-stable aggregate particles, but decreased that of <0.25 mm soil water-stable aggregates. At different soil depths, BC significantly reduced sand content and increased silt content. Compared to CK, BC significantly increased the available phosphorus and potassium content of the 0–10 and 10–20 cm soil layers. There were no significant differences in pH, organic matter, total nitrogen, total phosphorus, or total potassium content between the treatments at different soil depths. Compared to CK, BC significantly increased soil neutral phosphatase and catalase activities. Furthermore, BC significantly increased bacterial richness, but had no significant effect on bacterial diversity. According to Qualcomm sequencing analysis, BC increased the relative abundance of Verrucomicrobia, Chloroflexi, Bacteroidetes, Nitrospirae, Verrucomicrobiae, Blastocatellia_Subgroup_4, and Anaerolineae in soil compared to CK. The soil bacterial genera in BC had stronger interrelationships than those in CK. According to redundancy analysis, organic matter was the main environmental factor influencing bacterial community structure. Overall, biochar could promote soil nutrient conversion in dry direct-seeded rice paddies, improve soil effective nutrient content, change the composition of soil bacterial communities, and increase soil bacterial richness. Applying biochar in dry direct-seeded rice cultivation could help realize low-carbon agriculture.

Controlling factors for soil bacterial and fungal diversity and composition vary with vegetation types in alpine grasslands

Soil microbes have vital functions in terrestrial ecosystems, but the concurrent effects of soil microclimates, edaphic attributes, and plant properties on soil microbial diversity and community composition are rarely evaluated for different vegetation types. Here, we investigated the individual and interactive effects of these controlling factors on soil bacterial and fungal diversity and community composition in alpine meadow and alpine steppe on the Tibetan Plateau. We found that soil microbial diversity and community composition were mainly controlled by edaphic properties, followed by soil microclimates, plant coverage, and root biomass. Also, the dominant regulating effects of the abiotic and biotic factors varied largely with vegetation type. Specifically, soil pH was the main determinant for soil microbes in the alpine meadow, while soil total organic carbon (TOC) played a more important role than other factors for soil microbes in the alpine steppe. The structural equation modeling showed soil moisture (SM) had significant and direct effects on bacterial diversity and community composition in the alpine meadow, and that SM had indirect effects on bacterial diversity in the alpine steppe by positively affecting TOC. Bacterial community composition was mainly influenced by soil pH and TOC, while plant coverage and root biomass were relatively more determinants of fungal community composition. Our findings reveal the key factors controlling microbial diversity and composition in alpine grasslands, which provide insights into the response and adaptation of soil microorganisms to environmental changes and has implications for grassland functioning and management.

Effects of land-use intensity, grazing and fire disturbances on soil bacterial and fungal communities in subtropical wetlands

Bacteria and fungi are primary components in wetland soil microbial communities and provide essential ecosystem functions and services. Understanding responses of bacterial and fungal communities to multiple drivers of environmental change and their interactions is crucial for wetland conservation and management, particularly for those embedded in agricultural landscapes. Yet little is known about effect of agricultural land use and wetland management on soil microbial communities in subtropical seasonal wetlands. Here, we used a long-term whole-ecosystem wetland experiment to examine individual and interactive effects of upland land-use intensification, livestock grazing, and prescribed fire on soil bacteria and fungi. We asked: (1) How do land-use intensification, grazing and fire disturbances interact to alter taxonomic composition and functional potential of wetland soil bacterial and fungal communities? (2) To what extent would these management and disturbance effects on wetland microbial communities manifest through alterations in soil properties? Our results showed that both microbial taxonomic and functional composition are responsive to agricultural land use and wetland management. Upland land-use intensification was the strongest driver (as compared to fire and grazing) in shaping bacterial and fungal community composition. Specifically, land-use intensification increased functional richness of both bacteria and fungi, whereas grazing and fire only interactively affected bacterial functional richness. In addition, responses of bacterial and fungal species diversity to wetland management varied, where grazing and fire reduced fungal species diversity in wetlands embedded in low-intensity managed pastures, but none of these management practices altered bacterial species diversity. Further, we found that pH and secondary nutrients (i.e., Ca and Mg) availability were the most important soil properties that explain how agricultural land use and wetland management drive the composition of bacterial and fungal communities. Our findings suggest that integration of lime application into intensified land uses to neutralize soil pH could facilitate maintenance of microbial diversity and associated functions. Our results highlight the need to comprehensively assess management impacts on soil microorganisms, rather than using a single or few indicators, due to inconsistent responses of bacterial and fungal communities, as well as their varied taxonomic and functional responses.

Effects of the Application of Nutrients on Soil Bacterial Community Composition and Diversity in a Larix olgensis Plantation, Northeast China

Bacteria are among the most critical components in soil. The application of nutrients as an important management measure to maintain soil fertility can affect the structure of soil bacterial communities. The objective of this study was to explore the influence of the application of nutrients on the soil bacterial community composition and diversity in a Larix olgensis Henry plantation after thinning using Illumina high-throughput sequencing technology. In July 2015, a middle-aged (27 years old) Larix olgensis forest, afforested in the spring of 1988 (thinning was conducted in the winter of 2012), in MengJiagang National Forest Farm, Jiamusi City, China, was assessed. Four fertilizer treatments were applied, each replicated three times: nitrogen (N, 250 kg/ha); nitrogen + phosphorus (NP, nitrogen 250 kg/ha + phosphorus 50 kg/ha); nitrogen + phosphorus + potassium (NPK, nitrogen 250 kg/ha + phosphorus 50 kg/ha + potassium 30 kg/ha); and a control (CK, no fertilizer). In mid-August 2018, soil samples of a 0–10 cm soil layer were collected; the diversity and composition of soil bacteria under different the application of nutrients conditions were determined by Illumina high-throughput sequencing technology on the MiSeq platform. Our results found that: (1) compared with the CK treatment, long-term the application of nutrients significantly reduced the soil pH and soil total potassium content (p < 0.05); and (2) the continued application of nutrients increased the Chao1 richness index of the soil bacteria in the Larix olgensis plantation (p < 0.05); (3) soil organic carbon and soil total nitrogen were key drivers of the soil bacterial community structure. Therefore, the different long-term the application of nutrients regimes did not affect the stability of the soil ecosystem in the Larix olgensis plantation.

Effects of Tillage and Winter Cover Management in a Maize Soybean Rotation on Soil Bacterial and Fungal Community Composition

The abundance and distribution of soil microbial populations, i.e., microbial diversity is widely promoted as a key tenant of sustainable agricultural practices and/or soil health. A common approach to describing microbial diversity is phylogenetic analysis with high-throughput sequencing of microbial DNA. However, owing to the tremendous amounts of data generated, a continuing effort is required to better assess the effects of agricultural management systems on soil microbial diversity. Here, we report on the combined effects of management systems on bacterial and fungal diversity in a loessal agricultural soil located in north-central Mississippi, USA. Amplicon sequencing was performed using 16S rRNA-gene and ITS2 from soil samples collected from a three-year study with combinations of maize-soybean crop rotation, tillage practices, and winter vegetative covers. Differences were found in microbial fungal β-diversity among the management systems, with distinct clustering patterns for no-tillage combined with either winter weeds or bare-fallow. Management systems showed a significant influence on soil pH and bulk density, which were positively correlated with fungal community composition. Developments in the description and interpretation of soil microbial diversity will contribute to a more accurate understanding of its role in the various functions and processes important to agricultural soil management.

Deciphering soil amendments and actinomycetes for remediation of cadmium (Cd) contaminated farmland

Soil heavy metal pollution is one of the most serious environmental problems in China, especially cadmium (Cd), which has the most extensive contaminated soil coverage. Therefore, more economical and efficient remediation methods and measures are needed to control soil Cd contamination. In this study, different amendments (biochar (B), organic fertilizer (F), lime (L)) and actinomycetes (A) inoculants were applied to Cd contaminated farmland to explore their effects on wheat growth. Compared with Control, all treatments except A treatment were able to significantly increase the underground parts dry mass of wheat, with the highest increase of 57.19 %. The results showed that the B treatment significantly increased the plant height of wheat by 3.45 %. All treatments increased wheat SOD activity and chlorophyll content and reduced the MDA, which contributes to wheat stress resistance under Cd contamination. F, L and AF treatments can significantly reduce the Cd content in wheat above- and underground parts by up to 56.39 %. Soil amendments can modify the physical and chemical properties of the soil, which in turn affects the absorption of Cd by wheat. Moreover, the addition of soil amendments significantly affects the composition and structure of the rhizospheric soil bacterial community at the wheat jointing stage. The application of organic fertilizer increases the richness and diversity of the bacterial community, while lime makes it significantly decreases it. T-test and microbiome co-occurrence networks show that actinomycetes could not only effectively colonize in local soil, but also effectively enhance the complexity and stability of the rhizosphere microbial community. Considering the practical impact of different treatments on wheat, soil microorganisms, economic benefits and restoration of soil Cd contamination, the application of organic fertilizer and actinomycetes in Cd contaminated soil is a more ideal remediation strategy. This conclusion can be further verified by studying larger repair regions and longer consecutive repair cycles to gain insight into the repair mechanism.

Advancements in the Use of Bacteriophages to Combat the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae.

Over the last several decades, kiwifruit production has been severely damaged by the bacterial plant pathogen Pseudomonas syringae pv. actinidiae (Psa), resulting in severe economic losses worldwide. Currently, copper bactericides and antibiotics are the main tools used to control this bacterial disease. However, their use is becoming increasingly ineffective due to the emergence of antibiotic resistance. In addition, environmental issues and the changes in the composition of soil bacterial communities are also concerning when using these substances. Although biocontrol methods have shown promising antibacterial effects on Psa infection under in vitro conditions, the efficiency of antagonistic bacteria and fungi when deployed under field conditions remains unclear. Therefore, it is crucial to develop a phage-based biocontrol strategy for this bacterial pathogen. Due to the specificity of the target bacteria and for the benefit of the environment, bacteriophages (phages) have been widely regarded as promising biological agents to control plant, animal, and human bacterial diseases. An increasing number of studies focus on the use of phages for the control of plant diseases, including the kiwifruit bacterial canker. In this review, we first introduce the characteristics of the Psa-induced kiwifruit canker, followed by a description of the diversity and virulence of Psa strains. The main focus of the review is the description of recent advances in the isolation of Psa phages and their characterization, including morphology, host range, lytic activity, genome characterization, and lysis mechanism, but we also describe the biocontrol strategies together with potential challenges introduced by abiotic factors, such as high temperature, extreme pH, and UV irradiation in kiwifruit orchards. The information presented in this review highlights the potential role of phages in controlling Psa infection to ensure plant protection.

Composition and diversity of soil bacterial communities under identical vegetation along an elevational gradient in Changbai Mountains, China.

Soil bacteria play important roles in biogeochemical cycling and biodiversity in mountain ecosystems. Past studies have investigated the bacterial community composition and diversity in elevation gradations covered by different vegetation types, but for a better assessment of elevation effects, here we studied bacterial communities in soil under identical vegetation cover. High-throughput amplicon sequencing of the V3-V4 region of bacterial 16S rDNA was used to investigate the diversity and composition bacterial communities in soil from 700 to 1,000 m above sea level collected on the north slope of Changbai Mountains, Northeast China. Obviously differences (p < 0.05) in soil physicochemical parameters (i.e., total nitrogen, nitrate and ammonium nitrogen, soil moisture content, available potassium, microbial biomass carbon and nitrogen) were observed at different elevations. Soil bacterial abundance indices (Richness, Chao1, ACE) differed significantly along the elevation gradient, whereas the Shannon index remained unchanged. Principal Coordinates Analysis indicated separated soil bacterial communities of the different elevations. The dominant phyla in all soil samples were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Bacteroidetes, which in combination reached 80%-85%. Soil pH to some extend related to soil bacterial community along altitude gradations. The relative abundance of a multiple phyla was negatively affected by the soil nutrients, such as ammonium and nitrate nitrogen, available potassium, soil moisture content, available phosphorus, microbial biomass nitrogen and soil organic C. The strongest effects were seen for Proteobacteria. The pH either positively or negatively correlated with specific genera. The soil bacterial function differed significantly among four elevations. The chemoheterotrophy, aerobic chemoheterotrophy and nitrification were the most dominant functions of soil bacteria among four elevations. Overall, the changes in soil physicochemical properties with elevation are important in shaping the bacterial diversity, composition and function in soil with the same above-ground vegetation of Changbai Mountains.

Forest succession improves the complexity of soil microbial interaction and ecological stochasticity of community assembly: Evidence from Phoebe bournei-dominated forests in subtropical regions.

Forest succession is a central ecological topic, due to the importance of the associated dynamic processes for terrestrial ecosystems. However, very little is currently known about the community assembly and interaction of soil microbial communities along forest successional trajectories, particularly regarding the microbial community dynamics in contrasting seasons. To bridge these knowledge gaps, we studied soil bacterial and fungal community compositions, assemblages, and co-occurrence networks in a well-established successional gradient of Phoebe bournei-dominated forest, spanning about 65 years of forest development in a subtropical region. Illumina MiSeq sequencing of 16S and ITS genes was employed for the assessment of soil bacterial and fungal community composition and diversity, respectively. The relative abundance and α-diversity of soil bacteria and fungi showed a differential trend over forest succession. The dominant fungal phyla (Basidiomycota and Ascomycota) changed more frequently than the dominant bacterial phyla (Proteobacteria, Acidobacteriota, and Actinobacteriota), indicating that soil fungi have a more sensitive relationship with forest succession compared with bacteria. The soil microbial community variation induced by forest succession was significantly affected by soil total phosphorus, dissolved organic carbon content and pH. Compared to deterministic processes, stochastic processes mainly dominated the community assembly of soil microbial communities. Meanwhile, the relative importance of stochasticity in soil fungal communities increased in the later stages. In Particular, dispersal limitation and drift accounted for a large proportion of bacterial and fungal community assembly, respectively. In addition, the co-occurrence networks of soil microbial communities became more complex as succession proceeds. Soil bacteria and fungi exhibited more competition and cooperation along the forest successional gradient. Collectively, our findings suggest that forest succession improves the complexity of soil microbial interactions and the ecological stochasticity of community assembly in Phoebe bournei-dominated forests, providing key insights into the relationship between microbial communities and forest succession.

The effect of salinity on soil chemical characteristics, enzyme activity and bacterial community composition in rice rhizospheres in Northeastern Thailand

Saline soil is one of the major problems limiting rice productivity in the Northeastern area of Thailand. Thus, the aims of this study were to determine soil physicochemical analysis and soil enzyme activities, and bacterial communities in the rhizosphere of ‘RD 6’ rice grown in salt-affected rice fields. The Ban Thum sample showed the highest electrical conductivity (EC; greater than 6 dS m−1) and total Na, while the EC in other fields were at non- or slightly saline levels. The principal component analysis revealed that soil chemical characteristics and soil enzymes activities explained 73.4% of total variation. Soil enzyme activities including dehydrogenase and fluorescein diacetate (FDA) hydrolysis, and soil characteristics including organic matter (OM) and organic carbon (OC) were significantly negatively correlated to EC. This indicated that these soil properties were adversely impacted by salts. Interestingly, activities of all hydrolytic enzymes were not affected by soil salinity. Bacteria that were able to colonize the rhizosphere soils were Achromobacter cholinophagum, Rhizobium tarimense, and unculturable bacteria. In this regard, study on the relationship of soil chemical characteristics and soil enzyme activities together with bacterial communities provided promising data for assessing rice field soil quality in the future.

Plant types shape soil microbial composition, diversity, function, and co‐occurrence patterns in cultivated land of a karst area

AbstractPlants can alter microbial communities through root exudates, and change the characteristics of the soil. However, the relationship between soil microbial communities and environmental factors is not well understood. Here, we studied bacterial and fungal communities and their relationships with environmental factors. We integrated data of environmental factors, microbial composition, diversity, functional prediction, and co‐occurrence network from uncultivated, maize, cabbage, and cocozelle soils in a karst area of Southwest China. Soil bacterial and fungal community composition differed with plant types. Maize soil had more taxa and greater alpha diversity of bacteria and fungi than other soils. In maize soil, the relative abundance of Actinobacteria and Ascomycota was significantly lower than that in uncultivated soil, while its contents of soil organic matter (OM), alkali‐hydrolyzable nitrogen, and total nitrogen (TN) showed the opposite trend. These indicators were not significantly different between cabbage and cocozelle soils. The results of the Mantel test and the RDA analysis indicated that TN and OM were important drivers of bacterial and fungal communities. Functional prediction and network analysis showed that maize soil had a high nitrogen fixation capacity and a complex and stable network. To summarize, maize soil not had a low relative abundance of Ascomycota and high content of TN and OM, nitrogen fixation ability, and a rich microbial community. Therefore, cultivating maize is suitable for improving soil microbial community. These findings might help in formulating a reasonable cultivation management program to prevent land degradation in the karst areas.

Fertilization treatments affect soil CO2 emission through regulating soil bacterial community composition in the semiarid Loess Plateau

A growing body of literature have emphasized the effects of fertilization regimes on soil respiration and microbial community in the semiarid region, however, fertilization treatment effects on the soil CO2 emission, soil bacterial community, and their relationships from long-term experiments is lacking. In the present study, we investigated the effects of long-term fertilization regimes on soil bacterial community and thereafter on soil CO2 emission. A 9-year field experiment was conducted with five treatments, including no fertilizer (NA) and four fertilization treatments (inorganic fertilizer (CF), inorganic plus organic fertilizer (SC), organic fertilizer (SM), and maize straw (MS)) with equal N input as N 200 kg hm–2. The results indicated that CO2 emission was significantly increased under fertilization treatments compared to NA treatment. The bacterial abundance was higher under MS treatment than under NA treatment, while the Chao1 richness showed opposite trend. MS treatment significantly change soil bacterial community composition compared to NA treatment, the phyla (Alphaproteobacteria and Gammaproteobacteria) and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae) were higher, while the Acidobacteriota was lower under MS treatment than under NA treatment. CO2 emission was positively correlated with the abundance of Alphaproteobacteria, Gammaproteobacteria, and keystone taxa, negatively correlated with these of Acidobacteriota. Random forest modeling and structural equation modeling determined soil organic carbon, total nitrogen, and the composition and network module III of the bacterial community are the main factors contribute to CO2 emission. In conclusion, our results suggest that the increased CO2 emission was affected by the varied of soil bacterial community composition derived from fertilization treatments, which was related to Alphaproteobacteria, Gammaproteobacteria, Acidobacteriota, and potential keystone taxa (Nitrosomonadaceae and Beijerinckiaceae), and highlight that the ecological importance of the bacterial community in mediating carbon cycling in the semiarid Loess Plateau.

Effects of Invasive Plant Diversity on Soil Microbial Communities

Native plant communities can be invaded by different numbers of alien plant species or by the same number of alien plant species with different levels of evenness. However, little is known about how alien invasive plant species richness and evenness affect soil microbial communities. We constructed native herbaceous plant communities invaded by exotic plants with different richness (1, 2, 4 and 8 species) and evenness (high and low) and analyzed soil physico-chemical properties and the diversity and composition of soil fungal and bacterial communities by high-throughput Illumina sequencing. Overall, the species richness and evenness of invasive plants had no significant effect on bacterial and fungal alpha diversity (OTUs, Shannon, Simpson, Chao1 and ACE) or the soil physico-chemical properties. However, invasive species richness had a significant impact on the relative abundance of the most dominant fungi, Ascomycota and Bipolaris, and the dominant bacteria, Actinobacteriota, which increased with increasing invasive species richness. The relative abundance of the dominant microbial groups was significantly correlated with the relative abundance of some specific invasive plants in the community. This study sheds new light on the effects of plant co-invasion on soil microbial communities, which may help us understand the underlying mechanisms of multiple alien plant invasion processes from the perspective of soil microorganisms.

A 40 % paddy surface soil organic carbon increase after 5-year no-tillage is linked with shifts in soil bacterial composition and functions

Soil organic carbon (SOC) is related to soil fertility, crop yield, and climate change mitigation. Paddy soil is a significant carbon (C) sink, but its C sequestration potential has not been realized as the various driving factors are still not fully understood. We performed a 5-year paddy field experiment in southern China to estimate tillage effects on SOC accumulation and its relation with soil bacteria. The C input from rice residue, SOC content, CO2 flux, soil bacterial community composition, and predicted functions were analyzed. No-tillage (NT) increased (p < 0.05) rice residue C inputs (by 12.6 %–15.9 %), SOC (by 40 % at the surface soil layer compared with conventional tillage, CT), and CO2 fluxes compared with reduced tillage (RT) and CT. Also, NT significantly altered the soil bacterial community. The random forest model showed that the predicted bacterial functions of “Degradation/Utilization/Assimilation Other”, “C1 Compound Assimilation”, and “Amin and Polyamine Degradation” were the most important functions associated with SOC accumulation. Analysis of metabolic pathway differences indicated that NT significantly decreased the BENZCOA-PWY (anaerobic aromatic compound degradation) and the AST-PWY (L-arginine degradation II). Therefore, the rapid paddy SOC increase is associated with both residue C input (from higher rice yields) and the degradation functions regulated by soil bacteria.

Simplifying network complexity of soil bacterial community exposed to short-term carbon dioxide and ozone enrichment in a paddy soil

Global atmospheric changes are characterized by increases in carbon dioxide (CO2) and ozone (O3) concentrations, with important consequences for the soil microbial community. However, the influences of CO2 and O3 enrichment on the biomass, diversity, composition, and functioning of the soil bacterial community remain unclear. We investigated the effects of short-term factorial combinations of CO2 (by 200 ppm) and O3 (by 40 ppb) enrichment on the dynamics of soil bacterial community in paddy soils with two rice varieties (Japonica, Nangeng 5055 (NG5055) vs. Wuyujing 3 (WYJ3)) in an open top chamber facility. When averaged both varieties, CO2 and O3 enrichment showed no individual or combined effect on the abundance or diversity of soil bacterial community. Similarly, CO2 enrichment did not exert any significant effect on the relative abundance of bacterial phyla. However, O3 enrichment significantly reduced the relative abundance of Myxococcota phylum by a mean of 37.5%, which negatively correlated to root N content. Compared to ambient conditions, soil bacterial community composition was separated by CO2 enrichment in NG5055, and by both CO2 and O3 enrichment in WYJ3, with root N content identified as the most influential factor. These results indicated that root N was the top direct predictor for the community composition of soil bacteria. The COG (cluster of orthologous groups) protein of cell motility was significantly reduced by 5.8% under CO2 enrichment, and the COG protein of cytoskeleton was significantly decreased by 14.7% under O3 enrichment. Furthermore, the co-occurrence network analysis indicated that both CO2 and O3 enrichment decreased the network complexity of the soil bacterial community. Overall, our results highlight that continuous CO2 and O3 enrichment would potentially damage the health of paddy soils through adverse impacts on the associations and functional composition of soil microbial communities.

Soil bacterial community mediates temporal stability of plant community productivity in degraded grasslands

Temporal stability of plant community productivity (‘plant community stability’ hereafter) in the face of environmental disturbance is essential for maintenance of ecosystem functioning. However, most existing studies that examined the biotic drivers of plant community stability concentrated on plant attributes, neglecting the potential stabilizing effects of soil microbes. Here, we conducted a 5-year field experiment to quantify plant community stability (i.e., the ratio of the temporal mean of community biomass to its standard deviation over this period) at four grassland sites with no, moderate, severe, and extreme degradation statuses in northern China. Soil bacterial communities were determined with 16S ribosomal RNA gene sequences. Our results demonstrated that high bacterial network complexity and relative abundance of oligotrophs were beneficial to improve plant community stability of moderately and severely degraded grasslands. The strong impacts of bacterial community composition on plant community stability indicated that particular taxa, especially oligotrophs and copiotrophs, determined stability. The positive relationship between bacterial network complexity and plant community stability supported the central ecological belief that complexity begets stability. Together, these findings provide a new insight into the importance of soil bacterial community composition and network complexity for buffering negative effects of grassland degradation on plant community stability.

Long-acting mechanisms of concentrated urea application — High urea concentrations are biological inhibitors

The concentrated application of urea (CAU; including band and hole placements) promotes cereal crop (e.g., rice and summer maize) yields and nitrogen (N) use efficiency by prolonging the retention of N fertilizer in the soil and reducing N loss. However, the long-acting mechanisms of CAU are not well understood. This study investigated the interactions between N transformation and soil microbes in the special micro-region around the fertilization point with the CAU, using a simulation experiment with two types of soil (silty loam and sandy loam). The soil samples were subjected to six N treatments: 1000, 3000, 5000, 10,000, 30,000 mg N kg−1, and dicyandiamide with 1000 mg N kg−1; no urea treatment was a control. Soil bacterial community compositions (examined using MiSeq sequencing), the abundance of ammonia-oxidizing microbes (quantified using real-time PCR), including ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and the soil chemical properties were assessed at 20 and 60 days after urea application. The high soil ammonium concentration caused by CAU affected the soil bacterial community by changing the soil chemical properties. Soil ammonium concentration and pH were the main factors affecting microbial communities and amoA gene abundance of AOA and AOB. The 10,000 and 30,000 mg N kg−1 dosages for the silty loam soil and 30,000 mg N kg−1 dosage for the sandy loam soil in this simulation experiment significantly (p < 0.05) reduced bacterial α-diversity, amoA gene abundance of AOA and AOB, and inhibited nitrification throughout the culture period. However, the inhibitory effects of high soil N application concentration on nitrification weakened as the culture time increased. Overall, CAU acted as a biological nitrification inhibitor by maintaining high soil ammonium concentration, which decreases activity of AOA and AOB amoaA genes for a long time (>60 days).