Soil Bacterial Community Research Articles

Deciphering soil environmental regulation on reassembly of the soil bacterial community during wetland restoration

Soil bacteria are vital to regulate biogeochemical processes in wetlands, however, little is known about the patterns and mechanisms of soil bacterial re-organization during wetland restoration. Here, we used a space-for-time substitution approach and examined the ecological processes that drive soil bacterial assembly from cultivated to restored to natural wetlands. Results showed a decrease of soil bacterial α diversity and increase of bacterial community similarity and bacterial interaction (cooperation vs. competition) with years of restoration, which was dominantly influenced by deterministic processes. Identified bacterial keystone taxa (e.g. Variibacter, Acidibacter) with nutrient metabolism capacity exerted strong positive effect on bacterial interaction. Furthermore, changes of soil water condition and nutrient status showed dominantly direct positive effects on soil bacterial reassembly, while falling soil pH significantly promoted bacterial reassembly by increasing keystone taxa and bacterial interaction during wetland restoration. Overall, findings highlighted the crucial role of environmental filtering and its pathway in influencing keystone bacterial taxa that promotes the reassembly of bacterial community during wetland restoration. Our work thus provides a new crucial and timely insight for improving the management of soil bacterial community assembly within the plethora of current and future wetland restoration projects.

Characterizing the soil microbial community associated with the fungal pathogen Coccidioides immitis.

Coccidioidomycosis is a fungal disease affecting humans and other mammals, caused by environmental pathogens of the genus Coccidioides . Understanding the ecological factors that shape the distribution of Coccidioides in soils is important for minimizing the risk of human exposure, though this remains challenging due to the pathogen's highly variable spatial distribution. Here, we examined associations between the soil microbial community and Coccidioides immitis presence within the Carrizo Plain National Monument-a minimally disturbed grassland ecosystem, and the site of a longitudinal study examining the effects of rodents and their burrows on C. immitis presence in soils. Using internal transcribed spacer 2 (ITS2) and 16S sequencing to characterize the soil fungal and bacterial communities, we found over 30 fungal species, including several other members of the Onygenales order, that co-occurred with Coccidioides more frequently than expected by chance. Coccidioides -positive samples were significantly higher in microbial diversity than negative samples, an association partly driven by higher Coccidioides presence within rodent burrows compared to surface soils. Soil source ( i.e., rodent burrow versus surface soil) explained the largest amount of variation in bacterial and fungal community diversity and composition, with soils collected from rodent burrows having higher microbial diversity than those collected from adjacent surface soils. While prior evidence is mixed regarding associations between Coccidioides and microbial diversity, our study suggests that favorable microhabitats such as rodent burrows can lead to a positive association between soil diversity and Coccidioides presence, particularly in otherwise resource-limited natural environments.

Differential spatial responses and assembly mechanisms of soil microbial communities across region-scale Taiga ecosystems

Different soil microbial communities play distinct key roles in regulating forest ecosystem processes and functions. However, the differences in spatial variability and assembly mechanisms of various taiga forest soil microbial taxa remain poorly understood. Here, we assessed the spatial patterns of bacterial and fungal communities, their assembly processes, and the influencing factors in taiga forest ecosystems in Xinjiang, China. A significant distance decay pattern was observed in the similarity of bacterial and fungal communities, with bacterial communities exhibiting a more pronounced pattern than fungal communities. Stochastic and deterministic processes governed together to drive soil bacterial community assembly, whereas stochastic processes dominated fungal community assembly. The coexistence networks revealed that the interactions of bacterial and fungal networks in the four regions are primarily based on interspecies symbiosis, with fungal coexistence networks demonstrating greater stability than bacterial networks. Additionally, the study identified a positive relationship between the modularity of bacterial networks and dispersal limitation. Analysis of environmental factors revealed that soil pH primarily affects the characteristics and assembly mechanisms of bacterial communities, while vegetation conditions primarily affect fungal diversity and composition, with other unconsidered environmental variables influencing the fungal community assembly process. This study emphasized the distinct ways in which bacteria and fungi respond to environmental factors and interspecies interactions. Our results suggested that distinct restoration measures should be implemented for bacteria and fungi in future conservation efforts for forest soil microorganisms.

Cover cropping attenuates population growth of Macrophomina phaseolina by limiting weed biomass, despite asymptomatic colonization of cover crops.

Macrophomina phaseolina is a fungus that causes charcoal rot in strawberry and a wide variety of crop species. Little is known about its potential to asymptomatically colonize crop plants or grow saprophytically on their tissues, both of which would create a potential for alternate, asymptomatic hosts to lead to increases in inoculum. To test the impact of cover cropping on M. phaseolina abundance, we conducted randomized-block field experiments in soils infested by M. phaseolina. None of the fifteen cover crop varieties showed symptoms of charcoal rot. All Fabaceae and Brassicaceae varieties were asymptomatically colonized at varying rates, but among Poaceae, M. phaseolina was recovered from only one individual oat plant. Soil samples collected at the time of planting, tillage, and 8 weeks post-tillage showed that cover cropping attenuated the growth of M. phaseolina relative to fallow plots harboring the weedy legume Medicago polymorpha. This weed species was abundantly colonized by this pathogen in both living root samples and plant residue collected 8 weeks after tillage. Cover cropping also influenced the diversity and composition of bulk soil bacterial and fungal communities, but these effects were not associated with M. phaseolina population density. Although M. phaseolina was not detected in living wheat tissues, it was recovered from wheat residue, suggesting that it may be facultatively saprophytic. These results suggest that cover cropping does not pose a risk for increasing disease caused by M. phaseolina and could be beneficial as conducive weed species, such as M. polymorpha, are suppressed.

The microbiome of continuous wheat rotations: minor shifts in bacterial and archaeal communities but a source for functionally active plant-beneficial bacteria

Continuous wheat cropping often leads to yield decline, with suspected causes including increased pathogen susceptibility, decreased root growth, or low nutrient use efficiency, though the exact causes remain unknown. Here, we investigated soil and root-associated bacterial and archaeal communities in wheat under rotation versus continuous cultivation, monitored fungal pathogen presence, and used beneficial bacteria to mitigate Gaeumannomyces tritici (Ggt) symptoms in greenhouse experiments. Sampling was conducted at two field sites with different soil textures over two years and at two plant developmental stages, capturing site-specific and seasonal fluctuations. By cultivation, 767 bacterial isolates were screened for plant-beneficial traits. Amplicon sequencing revealed minor effects on community structure due to wheat rotational position but pronounced effects related to site, year, and microhabitat. Rhizoplane isolates with plant-beneficial traits were mainly Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Stenotrophomonas, and Variovorax. Continuous wheat rotations showed the highest proportion of bacteria with fungal antagonistic potential, indicating plant roots’ recruitment of beneficial bacteria. Introducing Ggt in the greenhouse experiment altered the bacterial and archaeal community, confirming field study results and demonstrating that applying beneficial bacteria early in the season at the seedling stage can control Ggt and improve plant growth. This study highlights the dynamic nature of wheat's below-ground bacterial and archaeal community, influenced by soil type, season, and microhabitat, with wheat rotation playing a minor role. In addition, it confirms the potential of selected Bacillus and Pseudomonas isolates, whether used individually or in consortia, for microbe-assisted mitigation of yield decline in intensive wheat production.

Effects of transgenic modification on the bacterial communities in different niches of maize under glyphosate toxicity

Transgenic glyphosate-resistant maize has emerged as a way to expand the use of glyphosate for weed control. Studying the microbiome in the tissues and rhizosphere soil of transgenic plants is vital for understanding the glyphosate-resistant mechanism and optimizing the transgenic design of crops. In our study, the expression of a mutant cp4epsps gene in transgenic maize, which confers tolerance to glyphosate, was performed using the maize variety Xianyu 335 as the genetically modified acceptor line. This transgenic modification did not affect the initial bacterial community in the leaf, stem, or root of maize, but promoted a differential bacterial community in the rhizosphere soil. Under glyphosate application, the abundance of beneficial bacteria involved in N fixation and P solubilization in plant tissues and the rhizosphere soil of glyphosate-resistance maize were higher than those in the glyphosate-sensitive maize. In contrast, the abundance of pathogens had the opposite trend, suggesting that the enhanced health of transgenic maize prevented microbiome deterioration under glyphosate. The re-inoculation of bacterial strains isolated from glyphosate-resistance maize into the leaf and rhizosphere soil of glyphosate-sensitive maize resulted in an enhanced photosynthetic capacity in response to glyphosate, demonstrating the vital role of specific bacteria for glyphosate resistance. Our study provides important evidence of how transgenic maize tolerance to herbicides affects the bacterial communities across the maize niches under glyphosate toxicity.

Wet-dry or freeze-thaw alternation can regulate the impacts of farmland plastic pollution on soil bacterial communities and functions

The persistence of farmland plastic pollution has raised significant concerns regarding its potential long-term impacts on soil health in the context of global climate change. However, there are still gaps in the understanding of the impacts of plastic residues on soil microbial communities and functions in agricultural environments under unstable and extreme climatic conditions. In this study, the effects of plastic residues (two types and three shapes) on farmland soil bacterial communities and functions across varying environmental conditions were investigated through microscopic experiments. The results revealed that plastic residues subjected to wet-dry or freeze-thaw alternations exhibited greater degradation compared to those under natural conditions. The effects of plastic residue types and shapes on soil bacterial diversity and function were regulated by environmental factors. The plastic residues significantly reduced the stability of the bacterial network under natural condition (P < 0.05), whereas the opposite phenomenon was observed under wet-dry or freeze-thaw alternating conditions. Compared to under natural condition, lower numbers of bacterial functional pathways exhibiting significant differences due to plastic residues were observed under wet-dry or freeze-thaw alternating conditions. Significant associations were observed between soil bacterial communities and functions and various soil physicochemical properties under natural conditions (P < 0.05), and most of these associations were attenuated in the wet-dry or freeze-thaw alternations. This study demonstrated the potential impacts of plastic pollution on farmland soil microbiomes, which could be modulated by both residue characteristics and climatic conditions. Specifically, extreme environments could mitigate plastic-pollution-driven influences on soil microbiomes.

The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.

Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 -, SO4 2-, SO3) were found at Old Wallow, with conductivity and Cl- levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 2-, pH, and SO3, and for bacteria with moisture, Na2O, and Cl-. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.

Carbendazim adsorption on polyethylene microplastics and the toxicity mechanisms on cotton plants, soil enzyme activity and rhizosphere bacterial community under combined stress conditions

Polyethylene (PE) and carbendazim are common pollutants in soil, and their individual toxicities have been widely studied. However, there are few reports on PE as a carrier for carbendazim and their combined toxicity to plants and soil. Therefore, in this study, we focused on the adsorption effects of different PE particle sizes (25 μm, 150 μm) at different concentrations (1 %, 5 %, m/m) on carbendazim (2.0 mg·kg−1, 5.0 mg·kg−1) and the combined toxicity to cotton and soil microbiota. The results showed that the carbendazim adsorption by PE followed secondary kinetics and was consistent with the Freundlich model. Due to adsorption, the half-life of carbendazim in soil was extended (from 6.31 d to 14.20 d), and the capacity of carbendazim to control cotton Verticillium wilt was weakened. Combined stress exacerbated the inhibitory effects on cotton biomass, chlorophyll content, soil enzyme activity compared to the individual carbendazim or PE treatments. The high-throughput sequencing analysis indicated that combined stress (5.0 mg·kg−1 carbendazim, 5 % 25 μm PE) significantly reduced the richness and diversity, changed the structural composition of rhizosphere soil bacterial community, and greatly increased the abundance of bacteria with potential degrading functions, such as Marmoricola. Functional and network analysis showed that combined stress altered the soil microbial function and abundance, as well as the network structure and key bacterial groups, decreased the number of positively correlated connections. This study provides a theoretical basis for evaluating the effects of combined PE and carbendazim stress on crops and soils.

Oat/Soybean Intercropping Reshape the Soil Bacterial Community for Enhanced Nutrient Cycling

ABSTRACTIntercropping, particularly within legume‐based systems, has been shown to enhance yields and optimize resource use efficiency. Yet, the potential contribution of intercropping on soil microbial communities and functions to soil nutrients cycling are not fully understood. We conducted the same field experiments at Youyu (Site1) and Zhangbei (Site2) in Northern China to evaluate the impact of oat/soybean intercropping on the rhizosphere soil bacterial community structure, composition, and co‐occurrence networks. Our results indicated that intercropping significantly modified the bacterial community structure for both oat and soybean at Site1, with changes observed only in the oat community at Site2. Specifically, intercropping led to a substantial increase in the relative abundance of Bacteroidetes and Patescibacteria in the oat rhizosphere by 48.3% and 65.4% (Site1), respectively. Conversely, in the soybean rhizosphere at Site1, there was a notable decrease in the abundance of Patescibacteria and Nitrospirae by 32.4% and 40.0%, respectively. The soil bacterial functional groups demonstrated robust positive correlations with key soil parameters such as available nitrogen (Nmin), available phosphorus (Avail‐P), and the activities of nitrogen‐ and phosphorus‐acquiring enzymes in the rhizosphere. In conclusion, intercropping is an effective agricultural practice for enhancing nitrogen and phosphorus cycling by reshaping the soil bacterial community, offering a distinct advantage over monoculture practices. This insight underscores the potential of intercropping to foster sustainable soil nutrient management, highlighting the importance of integrating such practices into modern agricultural strategies to ensure long‐term productivity and environmental sustainability.

Exploring the composition and function profiles of bacteria from wood- and soil-feeding termites for effective degradation of lignin-based aromatics

Lignocellulosic biomass (LCB) in the form of agricultural, forestry, and agro-industrial wastes is globally generated in large volumes every year. The chemical components of lignocellulosic biomass render them a substrate valuable for biofuel production. However, the rigid association of lignin, cellulose, and hemicellulose component of LCB forms a complex, hierarchical, and recalcitrant structure, which inhibits the solubilization of LCB resources for biofuel production. The learning from termites (wood-feeding and soil-feeding) and further application of their gut bacteria for lignin degradation and bioconversion remain unexplored or at its early stage. With reference to this scientific knowledge gap, this study seeks to highlight the culturable gut bacterial community in soil- and wood-feeding termites, namely Pericapritermes nitobei and Microcerotermes sp., respectively to design a future biorefinery and bioremediation technologies. In this study, a total of 40 and 67 bacterial isolates were indeed identified from Pericapritermes nitobei and Microcerotermes sp., respectively. The identified isolates from both termite species were actually classified into four different phyla: Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes, where the phylum Actinobacteria dominated gut bacteria isolates identified from P. nitobei at 47.5 % while Proteobacteria were dominant in wood-feeding termite, Microcerotermes sp. at 46.27 %. At the genus level, the bacterial isolates enriched from the gut of Microcerotermes sp. belonged to 17 different genera, among which the bacterial genus Streptomyces (28 %) was most prevalent, followed by Enterobacter (11 %). Meanwhile, 9 genera were recorded for gut bacterial isolates from P. nitobei and were dominated by Streptomyces (37.5 %), followed by Acinetobacter (25 %). In general, the gut bacterial symbionts from both termites showed a congruency at the phyla level but were more diverged at a lower classification, inferring that different termite species evolved a unique repertoire of gut bacteria. Moreover, 61 % and 55 % of the gut bacterial isolates from the wood- and soil-feeding termites demonstrated a significant and multifunctional role in the hydrolysis of three lignocellulolytic substrates, including carboxymethyl cellulose, beechwood xylan, and aniline blue dye, indicating their unique functions and assistance to the host for the degradation of lignocellulose or other xenobiotic compounds from soil.

Changes in soil microbial community and function across stand age of Cryptomeria japonica var. sinensis plantations in subtropical China

Microbial communities are important influencing factors in soil biogeochemical cycling. Differences in stand age can affect microbial communities and functions by altering soil biochemical characteristics. Studying the changes in soil microbial communities and functions at different ages of Cryptomeria japonica var. sinensis can provide a theoretical basis for the scientific management of plantations. Therefore, we collected soil samples from different soil depths from 7- (7a), 13- (13a), 24- (24a), 33- (33a), and 53-year (53a) C. japonica var. sinensis plantations, to assess the differences in soil biochemical characteristics, soil bacterial and fungal communities, soil enzyme activity, and soil respiration rate. Results showed that as the stand age increases, the ACE and Shannon indices of fungal communities showed an initial increase followed by a decrease, whereas the Chao 1 index showed an increasing trend. The ACE and Shannon indices of bacterial communities did not change with stand age, but the Chao1 index decreased with an increase in stand age. In addition, the fungal ACE and Chao1 indices and bacterial Shannon index were higher at the 0–15 cm depth than at the 15–30 cm depth. Soil microbial community composition varied with stand age and soil depth, including Proteobacteria and Unclassified_k_Fungi relative abundances, and their functional groups' (nitrogen cycling-related bacteria, saprophytic fungi, pathogens, and ectomycorrhizal fungi) relative abundances. In addition, stand age will indirectly affect soil microbial function by influencing soil biochemical characteristics and microbial communities at the 0–15 cm depth, whereas at the 15–30 cm depth, there is no direct or indirect impact on the above indicators. In summary, significant variations exist in soil microbial communities and their functions across stand ages, and these differences will further vary between soil depths. Our research contributes to a better understanding of the impact of different ages of afforestation on soil biogeochemical cycling, providing valuable microbial information for the sustainable management of C. japonica var. sinensis forests in the future.

Conversion to Greenhouse Cultivation from Continuous Corn Production Decreases Soil Bacterial Diversity and Alters Community Structure

Changes in crop types and long-term monoculture substantially impact soil microbial communities. Exploring these changes and their influencing factors is of great significance for addressing the challenges posed by continuous cropping. Soil surface layer samples from greenhouse tomatoes fields cultivated for 5 (Y5), 9 (Y9), 13 years (Y13), and a surrounding corn field (CK) as a control were analyzed. The Y13 sample showed a significant increase in the relative abundance of Pseudomonadota (43.1%) and a decrease in Actinobacteria (50.3%) compared to the CK sample. Soil bacterial alpha diversity generally declined from the CK to Y13 (0.1–22.2%) sample, with a small peak in Y9 for Chao1 and Observed_species. Significant differences in Chao1 and Observed_ species were observed between the CK and Y13 samples. Beta diversity analysis revealed a pronounced variation in soil bacterial community structure across planting years, with the divergence from the CK sample intensifying over time. In comparison to the Y5 vs. CK samples, Y9 and Y13 exhibited marked differences from the CK across the same and broader metabolic pathways, suggesting a potential convergence of microbial activities over time. The Y9 and Y13 samples showed significantly higher biosynthesis abundance (7.50% and 6.36%, respectively) than the CK. In terms of soil physicochemical indices, the carbon–nitrogen ratio was the primary factor influencing soil bacterial composition. In conclusion, we found that crop alteration and continued planting changed the soil’s bacterial composition and increasing planting years suppressed the soil’s bacterial diversity, leading to a stable bacterial ecology after nine years. Implementing appropriate measures during this critical period is vital for optimal soil utilization.

Soil bacterial communities are influenced by mulching methods and growth stages in dryland wheat fields

Soil bacterial communities are influenced by mulching methods and growth stages in dryland wheat fields

Potential functional profiling of soil microbial communities under long-term application of tannery sludge

This study investigated the impact of Cr contamination on the functional profiling of bacterial and archaeal communities in a tropical soil. The contaminated soil contained ∼300 mg kg⁻¹ of Cr due to the long-term application of tannery sludge. The FAPROTAX database was used to assess the potential functional profiling of bacterial and archaeal communities based on 16S rRNA gene phylogeny. The results showed a higher relative abundance of Actinobacteria, Proteobacteria, and Firmicutes. Additionally, an increased relative abundance of Bacillaceae and Paenibacillaceae was observed in Cr-contaminated soil. The functional profiling predicted eleven potential functions, with Cr contamination negatively affecting chemoheterotrophy, nitrification, ammonia oxidation, and nitrogen fixation. This study reveals that Cr contamination significantly impacts the functional profiling of soil bacterial and archaeal communities, emphasizing the importance of monitoring and mitigating Cr contamination to preserve soil function.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling.

In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied. This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities. Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth. In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers.

The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.

Methane-oxidizing bacterial community dynamics in sub-alpine forest soil.

Methane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities.

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

Impact of a Potent Strain of Plant Growth-Promoting Bacteria (PGPB), Bacillus subtilis S1 on Bacterial Community Composition, Enzymatic Activity, and Nitrogen Content in Cucumber Rhizosphere Soils.

Antagonistic bacterial strains from Bacillus spp. have been widely studied and utilized in the biocontrol of phytopathogens and the promotion of plant growth, but their impacts on the rhizosphere microecology when applied to crop plants are unclear. Herein, the effects of applying the antagonistic bacterium Bacillus subtilis S1 as a biofertilizer on the rhizosphere microecology of cucumbers were investigated. In a pot experiment on cucumber seedlings inoculated with S1, 3124 bacterial operational taxonomic units (OTUs) were obtained from the rhizosphere soils using high-throughput sequencing of 16S rRNA gene amplicons, and the most abundant phylum was Proteobacteria that accounted for 49.48% in the bacterial community. S1 treatment significantly reduced the abundances of soil bacterial taxa during a period of approximately 30days but did not affect bacterial diversity in the rhizosphere soils of cucumbers. The enzymatic activities of soil nitrite reductase (S-Nir) and dehydrogenase (S-DHA) were significantly increased after S1 fertilization. However, the activities of soil urease (S-UE), cellulase (S-CL), and sucrase (S-SC) were significantly reduced compared to the control group. Additionally, the ammonium- and nitrate-nitrogen contents of S1-treated soil samples were significantly lower than those of the control group. S1 fertilization reshaped the rhizosphere soil bacterial community of cucumber plants. The S-CL activity and nitrate-nitrogen content in rhizosphere soil affected by S1 inoculation play important roles in altering the abundance of rhizosphere soil microbiota.