Bacterial Co-occurrence Network Research Articles

Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.

Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.

Diversity, composition, and assembly processes of bacterial communities within per- and polyfluoroalkyl substances (PFAS)-contained urban lake sediments

Per- and polyfluoroalkyl substances (PFAS) are widespread, highly persistent, and bio-accumulative compounds that are increasingly found in the sediments of aquatic systems. Given this accumulation and concerns regarding the environmental impacts of PFAS, their influence on sedimentary bacterial communities remains inadequately studied. Here, we investigated the concentrations of 17 PFAS in sediments from six urban lakes in Nanjing, China, and assessed their effects on the diversity, composition, potential interactions, and assembly mechanisms of sedimentary bacterial communities. Sediment concentrations of PFAS ranged from 4.70 to 5.28 ng·g−1 dry weight. The high concentrations of the short-chain perfluorobutanesulfonic acid (PFBS) suggested its substitution for the long-chain perfluorooctanesulfonic acid (PFOS). As alternatives to long-chain PFAS, short-chain PFAS had similar effects on bacterial communities. The short-chain perfluoropentanoic acid (PFPeA) and the long-chain perfluorotridecanoic acid (PFTrDA) were the most important PFAS related to the ecological patterns of the co-occurrence network and may alter the composition of the sedimentary bacterial communities in the urban lakes. The Anaerolineaceae family represented as keystone bacteria within the PFAS-affected bacterial co-occurrence network. Deterministic processes (65.9 %), particularly homogeneous selection (63.2 %), were the dominant process driving bacterial community assembly. PFAS promoted the phylogenetic clustering and influenced the community dispersal capabilities to shape bacterial community assembly. This study provides a comprehensive analysis of PFAS distribution in sediments across six urban lakes in Nanjing and provides novel insights into the effects of PFAS on sedimentary bacterial communities. Further research is required to elucidate the mechanisms underlying the impacts of PFAS on microbial communities and to evaluate their broader ecological consequences.

Plant litter crust enhances nitrogen accumulation by regulating microbial diversity and urease activity in semi-arid sandy soils

Plant litter plays a crucial role in regulating soil nitrogen (N) cycling in dryland ecosystems. However, the mechanisms by which plant litter crust drives microbial community composition to influence N levels in sandy soils remain unclear. In this study, we examined the effects of litter crust on sandy soil microhabitat characteristics (temperature, moisture, and porosity), microbial diversity and composition, urease activity, and soil N variables (total-N, nitrate-N, and ammonium-N) across different stages of litter crust development (including early-, mid-, and post-term) in a field setting. We found that litter crust promotes bacterial and fungal alpha diversity in sandy soils, leading to a shift in bacterial community composition from oligotrophs (i.e., Actinobacteria) to copiotrophs (i.e., Proteobacteria and Bacteroidetes), and a shift in fungal community composition dominance from Ascomycota to Basidiomycota. Litter crust enhances the complexity and stability of bacterial and fungal co-occurrence networks in sandy soils, especially in early- and mid-term stages of crust development. Additionally, litter crust increases nitrification (aerobic ammonia oxidation) and decreases denitrification (nitrate reduction) in these soils. Notably, the increase in soil moisture and urease activity, along with the decrease in soil temperature due to litter crust, effectively promotes N accumulation in sandy soils. Our results demonstrate that N levels during the litter crust period are mainly influenced by a combination of bacterial beta diversity and fungal alpha diversity at the 0–5 cm depth, and bacterial alpha diversity along with soil properties (i.e., soil variables and urease activity) at the 5–10 cm depth. Overall, our results reveal that litter crust contributes to N accumulation in sandy soils by regulating bacterial and fungal community composition and diversity, as well as by buffering soil temperature and soil moisture, and enhancing urease activity. These findings provide new insights into the critical role of soil microbes in maintaining N functions during litter crust development in semi-arid sandy ecosystems.

Differential impact of Paenibacillus infection on the microbiota of Varroa destructor and Apis mellifera

The Western honey bee (Apis mellifera) is a vital agricultural pollinator whose populations are threatened by the parasitic mite Varroa destructor and associated pathogens. While the impact of Paenibacillus species on honey bees, particularly Paenibacillus larvae causing American foulbrood, is documented, their effect on the microbiota of Varroa mites remains unclear. This study aimed to investigate the influence of Paenibacillus sp. on the bacterial communities of Varroa mites and adult honey bees. We hypothesized that Paenibacillus sp. would significantly alter the microbiota of Varroa mites but have minimal effect on that of adult honey bees. Utilizing 16S rRNA sequencing data from a previous study, we reanalyzed samples categorized into four groups based on Paenibacillus sp. infection load: highly infected and lowly infected honey bees (A. mellifera) and mites (V. destructor). Infection status was determined by Paenibacillus sp. read counts, with more than three reads indicating high infection. Microbial diversity was assessed using alpha and beta diversity metrics. Co-occurrence networks were constructed to visualize bacterial community assemblies, and network robustness was evaluated through node addition and removal tests. Keystone taxa were identified based on eigenvector centrality and relative abundance. Highly infected Varroa mites exhibited a significant reduction in alpha diversity and a markedly different bacterial community composition compared to lowly infected mites (p < 0.05). Their bacterial co-occurrence networks showed decreased connectivity and robustness, indicating a disruptive effect of Paenibacillus sp. In contrast, adult honey bees displayed no significant differences in alpha diversity or network structure between highly and lowly infected groups (p > 0.05), suggesting a resilient microbiota. Keystone taxa analysis revealed fewer central species in highly infected Varroa mites, potentially impacting network stability. High Paenibacillus sp. infection is associated with significant alterations in the microbiota of Varroa mites, disrupting bacterial communities and potentially affecting mite physiology. The microbiota of adult honey bees appears more robust against Paenibacillus sp. influence. These findings enhance our understanding of the complex interactions within the "honey bee–mite–microorganism" system and may inform future strategies for managing Varroa mite infestations and associated pathogens.

Effects of Microbial Organic Fertilizer, Microbial Inoculant, and Quicklime on Soil Microbial Community Composition in Pepper (Capsicum annuum L.) Continuous Cropping System

The additions of microbial organic fertilizer (MOF), a microbial inoculant (MI), and quicklime (Q) are considered to be sustainable practices to restore land that has been damaged by continuous cropping of pepper (Capsicum annuum L.). However, the combined effects of these three additives on pepper yield, soil chemical properties, and soil microbial communities were unclear. The experimental design consists of 13 treatment groups: the untreated soil (control); soil amended solely with three treatments for each of MOF (1875–5625 kg ha−1), MI (150–450 mL plant−1), and Q (1500–4500 kg ha−1); and soil amended with combinations of MOF, MI, and Q at three comparable concentrations. A significant increase in pepper fruit diameter, length, yield, and soil available nitrogen, phosphorus, and potassium contents occurs upon exclusive and combined applications of MOF, MI, and Q. Pepper yield was greatest (29.89% more than control values) in the combined treatment with concentrations of 1875 kg ha−1 MOF, 150 mL plant−1 MI, and 1500 kg ha−1 Q. The application of Q increased soil pH and reduced soil–fungal richness. The application of MOF, MI, and Q increased the relative abundance of bacterial genera and the complexity of bacterial and fungal co-occurrence networks compared with control levels. The combined application of MOF, MI, and Q resulted in the greatest microbial network complexity. A Mantel test revealed the key role of soil available nitrogen content and bacterial diversity in the regulation of pepper growth and yield. We conclude that the combined application of MOF, MI, and Q improves soil nutrient availability and modifies soil microbial community composition, significantly promoting plant growth and pepper yield during continuous cultivation.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

The contribution of seasonal variations and Zostera marina presence to the bacterial community assembly of seagrass bed sediments

BackgroundMicroorganisms play pivotal roles in seagrass ecosystems by facilitating material and elemental cycling as well as energy flux. However, our understanding of how seasonal factors and seagrass presence influence the assembly of bacterial communities in seagrass bed sediments is limited. Employing high-throughput sequencing techniques, this study investigates and characterizes bacterial communities in the rhizosphere of eelgrass (Zostera marina) and the bulk sediments across different seasons. The research elucidates information on the significance of seasonal variations and seagrass presence in impacting the microbial communities associated with Zostera marina.ResultsThe results indicate that seasonal variations have a more significant impact on the bacterial community in seagrass bed sediments than the presence of seagrass. We observed that the assembly of bacterial communities in bulk sediments primarily occurs through stochastic processes. However, the presence of seagrass leading to a transition from stochastic to deterministic processes in bacterial community assembly. This shift further impacts the complexity and stability of the bacterial co-occurrence network. Through LEfSe analysis, different candidate biomarkers were identified in the bacterial communities of rhizosphere sediments in different seasons, indicating that seagrass may possess adaptive capabilities to the environment during different stages of growth and development.ConclusionsSeasonal variations play a significant role in shaping these communities, while seagrass presence influences the assembly processes and stability of the bacterial community. These insights will provide valuable information for the ecological conservation of seagrass beds.

Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure

Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.

Enhanced Soybean Growth and the Associated Ion Balance, Nutrient Accumulation, and Rhizosphere Bacterial Community When Intercropped with Suaeda salsa in Saline Soils

Halophyte-based desalinization is emerging as a promising technology for saline agriculture. However, few studies have integrated halophytes into intercropping systems. This study investigated Suaeda salsa and soybean intercropping and the associated mechanisms, including changes in salt, nutrients, and bacterial communities at three salt treatments (control, 3‰, and 5‰). The results showed that regardless of salt treatment, soybean biomass and P content significantly increased in intercropping compared with monocropping, by an average of 32% and 51%, respectively (p &lt; 0.05), indicating interspecific facilitation. Under 5‰ salt, soybean mortality decreased from 37% in monocropping to 10% in intercropping, and shoot Na decreased by over 60% in intercropping; the rhizosphere Na+, Cl−, and NO3−–N decreased in intercropping by over 75% compared with monocropping, and the response ratios correlated negatively with S. salsa biomass (p &lt; 0.01). The soybean rhizosphere bacterial community in intercropping was enriched with the genera Sphingomonas, Salinimicrobium, Lysobacter, Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium, and Ramlibacter, and the bacterial co-occurrence network exhibited increases in the number of nodes and edges, average degree, and average clustering coefficient. Considering the combined effects, the soybean biomass of intercropping correlated positively with bacterial co-occurrence network parameters, including average degree and number of edges, independent of tissue salt and nutrient content, and that of monocropping correlated negatively with tissue salt content. These results demonstrate that S. salsa intercropping could alleviate salt stress in soybean by creating a low-salt environment and improving its nutrient accumulation and rhizosphere bacterial community, and emphasize the importance of microbial communities in influencing soybean growth.

The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment.

This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.

The herbicidal activity of pre-emergence herbicide cinmethylin and its potential risks on soil ecology: pH, enzyme activities and bacterial community

BackgroundThe herbicide cinmethylin, which was originally registered for use in rice fields, has the potential to control grass weeds in wheat fields before the emergence of wheat. However, its herbicidal activity against various troublesome grass weeds that infest wheat fields in China and its relationships with soil pH, soil enzymes and soil bacteria are not well known. Here, the effects of applying cinmethylin on the soil surface were tested on six grass weeds, and its impacts on soil characteristics, including the soil pH, soil enzymes and bacterial community, were evaluated.ResultsAlopecurus aequalis, A. japonicus and A. myosuroides were highly sensitive to cinmethylin, with GR50 values of 78.77, 61.49 and 119.67 g a.i. ha− 1, respectively. The half-lives of cinmethylin at 1-, 10- and 100-fold the recommended rates were estimated at 26.46 − 52.33 d. Cinmethylin significantly increased the soil pH but decreased the activities of soil sucrase and urease. At 10- and 100-fold the recommended rate of cinmethylin, the bacterial abundance and diversity significantly decreased at 30 and 60 days after cinmethylin treatment. Cinmethylin at 100-fold the recommended rates largely promoted bacterial co-occurrence network complexity. Cinmethylin at high concentrations temporarily inhibited the abundance of the Nitrospira genus, as indicated by the copy numbers of the ammonia-oxidising archaea (AOA) amoA and ammonia-oxidising bacteria (AOB) amoA genes. Further analysis revealed that soil pH was negatively related to soil urease, and a significantly positive correlation was detected between soil urease and soil nitrification.ConclusionCollectively, the application of cinmethylin at the recommended field dose had nearly no effect on the soil ecosystem, but its potential risks at high concentrations deserve further attention.

The Addition of Glutamine Enhances the Quality of Huangjiu by Modifying the Assembly and Metabolic Activities of Microorganisms during the Fermentation Process.

In this study, the effects of adding glutamate (Glu), glutamine (Gln), aspartate (Asp), and asparagine (Asn) on the flavor formation of Huangjiu were investigated, and the effect of Gln concentration on the quality, microbial community structure, and flavor development of Huangjiu was further explored. Varied Gln concentrations influenced yeast growth, sugar utilization, microbial communities, and quality attributes. Additional Gln promoted yeast cell counts and sugar depletion. It increased the complexity of bacterial co-occurrence networks and reduced the impact of stochastic processes on assembly. Correlation analysis linked microorganisms to flavor compounds. Isolation experiments verified the role of Saccharomyces cerevisiae, Aspergillus chevalieri, Bacillus altitudinis, and Lactobacillus coryniformis in flavor production under Gln conditions. This research elucidated the microbiological mechanisms by which amino acid supplementation, especially Gln, enhances Huangjiu quality by modulating microbial metabolic functions and community dynamics during fermentation. This research is significant for guiding the production of Huangjiu and enhancing its quality.

Key microbial taxa play essential roles in maintaining soil muti-nutrient cycling following an extreme drought event in ecological buffer zones along the Yangtze River.

Climatic extremes, especially extreme droughts, are occurring more frequently and profoundly impacting biogeochemical processes. However, the relative importance of microbial communities on soil nutrient cycling and community maintenance under natural extreme drought events remains elusive. During a record-breaking drought in the Yangtze River Basin (YRB) in the summer of 2022, we collected ambient soils and drought-affected bare and vegetated soils in ecological buffer zones from two sites with similar soil and vegetation characteristics along the YRB, and examined the relative contribution of soil bacterial communities in supporting multi-nutrient cycling index (MNCI) involving carbon-, nitrate- and phosphorus-cycling and their associations with microbial network. Extreme drought decreased (p < 0.05) bacterial α-diversity but increased MNCI in vegetated soils at both sites, while both remained unchanged (p > 0.05) in bare soils, possibly as a result of vegetation releasing rhizodeposits under drought which selectively recruited bacterial communities. Bacterial community compositions were shifted (p < 0.05) only in vegetated soils, and they exerted more influence than α-diversity on soil MNCI. Notably, the Anaerolineae, identified as a biomarker enriched in vegetated soils, had close associations with enzyme activities and soil MNCI at both sites, suggesting their potential recruitment by vegetation to withstand drought. Furthermore, key ecological clusters (Module 1) in bacterial co-occurrence networks at both sites supported (p < 0.05) higher MNCI, despite no substantial variation in network structure due to drought. Specifically, the most important taxa within Module 1 for predicting soil MNCI revealed by random forest modeling analysis (R2=0.44 - 0.63, p < 0.001), such as B1-7BS, SBR1031 and Nocardioides, could be deeply involved in soil nitrogen-cycling, suggesting an essential role of specialized interactions of bacterial communities in maintaining soil multifunctionality. Overall, this study demonstrates that changes in biomarkers and functional taxa under extreme drought may better reflect the biological mechanisms involved in microbial communities impacting ecosystem function, which may aid in forecasting the ecological consequences of ongoing climate change in the ecological buffer zones along the YRB.

Plateau zokor disturbance enhances soil bacterial diversity and reduces network complexity

Rodent disturbances are considered as the key factors that affect grassland ecological restoration worldwide. Although the impact of rodent disturbances on plant diversity and ecosystem functions has been extensively studied, our understanding of how such activities shape soil bacterial community networks and their functional roles remains limited. In this study, we employed 16S rRNA sequencing to investigate soil bacterial communities between undisturbed alpine meadow and zokor mounds at different successional stages. Additionally, we analyzed the co-occurrence networks and potential functions within the alpine meadow ecosystem. The results revealed that (1) the disturbance by plateau zokors altered the soil bacterial community structure, increased bacterial diversity and reduced network complexity. Also, there were synergistic interactions among key species in the soil bacterial co-occurrence network; (2) soil organic carbon (SOC) and total nitrogen (TN) were identified as the key environmental variables that shape soil bacterial communities; (3) functional predictions based on FAPROTAX indicated that the disturbance by plateau zokors significantly affected the functional groups involved in carbon (C) and nitrogen (N) cycling. Overall, these findings significantly enhance our understanding of how small mammal activities influence the soil nutrient cycling and bacterial community in the Qinghai-Tibet Plateau (QTP) alpine meadow.

Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism.

Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.

Wheat domestication alters root metabolic functions to drive the assembly of endophytic bacteria.

The domestication process progressively differentiated wild relatives from modern cultivars, thus impacting plant-associated microorganisms. Endophytic bacterial communities play vital roles in plant growth, development, and health, which contribute to the crop's sustainable development. However, how plant domestication impacts endophytic bacterial communities and relevant root exudates in wheat remains unclear. First, we have observed that the domestication process increased the root endophytic microbial community diversity of wheat while decreasing functional diversity. Second, domestication decreased the endophytic bacterial co-occurrence network stability, and it did significantly alter the abundances of core microorganisms or potential probiotics. Third, untargeted LC-MS metabolomics revealed that domestication significantly altered the metabolite profiles, and the abundances of various root exudates released were significantly correlated with keystone taxa including the Chryseobacterium, Massilia, and Lechevalieria. Moreover, we found that root exudates, especially L-tyrosine promote the growth of plant-beneficial bacteria, such as Chryseobacterium. Additionally, with L-tyrosine and Chryseobacterium colonized in the roots, the growth of wild wheat's roots was significantly promoted, while no notable effect could be found in the domesticated cultivars. Overall, this study suggested that wild wheat as a key germplasm material, and its native endophytic microbes may serve as a resource for engineering crop microbiomes to improve the morphological and physiological traits of crops in widely distributed poor soils.

Association between plant microbiota and cadmium uptake under the influence of microplastics with different particle sizes

Plant microbiota are an important factor impacting plant cadmium (Cd) uptake. However, little is known about how plant microbiota affects the Cd uptake by plants under the influence of microplastics (MPs) with different particle sizes. In this study, bacterial structure and assembly in the rhizosphere and endosphere in pakchoi were analyzed by amplicon sequencing of 16S rRNA genes under the influence of different particle sizes of polystyrene microplastics (PS-MPs) combined with Cd treatments. Results showed that there were no significant differences observed in the shoot endophytes among different treatments. However, compared to Cd treatment, larger-sized PS-MPs (2 and 20 μm) significantly increased community diversity and altered the structural composition of rhizosphere bacteria and root endophytes, while smaller-sized PS-MPs (0.2 μm) did not. Under the treatment of larger-sized PS-MPs, the niche breadth of rhizosphere bacteria and root endophytes were significantly increased. And larger-sized PS-MPs also maintained stability and complexity of bacterial co-occurrence networks, while smaller-sized PS-MPs reduced them. Furthermore, compared to Cd treatment, the addition of larger particle size PS-MPs decreased the proportion of homogeneous section, while increased the proportion of drift in root endophytic bacterial community assembly. The role of larger-sized MPs in the community assembly of rhizosphere bacteria was opposite. Using random forest and structural equation models, the study found that larger-sized PS-MPs can promote the colonization of specific bacterial taxa, such as Brevundimonas, AKAU4049, SWB02, Ellin6055, Porphyrobacter, Sphingorhabdus, Rhodobacter, Erythrobacter, Devosia and some other bacteria belonging to Alphaproteobacteria, in the rhizosphere and root endosphere. The colonization of these taxa can may induce the formation of biofilms in the roots, immobilize heavy metals through oxidation processes, and promote plant growth, thereby reducing Cd uptake by pakchoi. The findings of this study provide important insights into the microbial mechanisms underlying the influence of MPs with different particle sizes on plant Cd uptake.

Depth-dependent responses of soil bacterial communities to salinity in an arid region

Soil salinization adversely affects soil fertility and plant growth in arid region worldwide. However, as the drivers of nutrient cycling, the response of microbial communities to soil salinization is poorly understood. This study characterized bacterial communities in different soil layers along a natural salinity gradient in the Karayulgun River Basin, located northwest of the Taklimakan desert in China, using the 16S rRNA Miseq-sequencing technique. The results revealed a significant filtering effect of salinity on the bacterial community in the topsoil. Only the α-diversity (Shannon index) in the topsoil (0–10 cm) significantly decreased with increasing salinity levels, and community dissimilarity in the topsoil was enhanced with increasing salinity, while there was no significant relationship in the subsoil. BugBase predictions revealed that aerobic, facultatively anaerobic, gram-positive, and stress-tolerant bacterial phenotypes in the topsoil was negatively related to salinity. The average degree and number of modules of the bacterial co-occurrence network in the topsoil were lower under higher salinity levels, which contrasted with the trends in the subsoil, suggesting an unstable bacterial network in the topsoil caused by higher salinity. The average path length among bacterial species increased in both soil layers under high salinity conditions. Plant diversity and available nitrogen were the main drivers affecting community composition in the topsoil, while available potassium largely shaped community composition in the subsoil. This study provides solid evidence that bacterial communities adapt to salinity through the adjustment of microbial composition based on soil depth. This information will contribute to the sustainable management of drylands and improved predictions and responses to changes in ecosystems caused by climate change.

Changes in soil bacterial community diversity and its network stability under different grazing intensities in plateau rangelands

Grassland degradation is a significant ecological challenge, it changes the grassland environment, including the structure of soil microbial communities. Grazing is a critical factor in this process, yet the impact of different grazing intensities on soil bacterial communities, particularly in unique environments like the Qinghai-Tibet Plateau, remains poorly understood. This study utilized a full-length 16 S rRNA gene sequencing technology combined with environmental factors to assess the impacts of the Holba sheep grazing on soil bacterial community diversity in Zhongba County, Shigatse City, Qinghai-Tibet Plateau. The specific aim was to explore the changes in soil bacterial community diversity and stability under contrasting grazing intensities: prohibited grazing, light grazing, moderate grazing, and heavy grazing. The results showed that grazing activities significantly altered the diversity of bacterial communities, particularly under light and heavy grazing. The spatial dissimilarity in soil bacterial communities was mainly driven by species turnover (i.e., species replacement), which was more pronounced under heavy grazing. The number of keystone species increased with the grazing intensity of the bacterial co-occurrence network. Under heavy grazing, bacterial communities showed the highest number of keystone species and the community stability. Environmental factors such as exchangeable magnesium (EM), soil available kalium (SAK), and soil pH were the most important environmental variables impacting changes in bacterial community structure by influencing community α-diversity and stability. This study enhances our understanding of the response mechanisms of soil microbial communities to grazing intensities and other environmental stresses in grassland ecosystems. In addition, this study also provides important references and guidance for microbial diversity research in extreme environments. These findings are crucial for promoting the sustainable management and conservation of grassland ecosystems in climatically harsh areas such as the Qinghai-Tibet Plateau.

Reducing Application of Nitrogen Fertilizer Increases Soil Bacterial Diversity and Drives Co-Occurrence Networks.

Reducing nitrogen fertilizer application highlights its role in optimizing soil bacterial communities to achieve sustainable agriculture. However, the specific mechanisms of bacterial community change under these conditions are not yet clear. In this study, we employed long-term field experiments and high-throughput sequencing to analyze how varying levels of nitrogen application influence the soil bacterial community structure and co-occurrence networks. The results show that reducing the nitrogen inputs significantly enhances the diversity and evenness of the soil bacterial communities, possibly due to the diminished dominance of nitrogen-sensitive taxa, which in turn liberates the ecological niches for less competitive species. Furthermore, changes in the complexity and stability of the bacterial co-occurrence networks suggest increased community resilience and a shift toward more mutualistic interactions. These findings underline the potential of reduced nitrogen application to alleviate competitive pressures among bacterial species, thereby promoting a more diverse and stable microbial ecosystem, highlighting the role of competitive release in fostering microbial diversity. This research contributes to our understanding of how nitrogen management can influence soil health and offers insights into sustainable agricultural practices.