Bulk Soil Bacterial Communities Research Articles

Effects of short-term nitrogen and phosphorus addition on soil bacterial community of different halophytes.

The bulk soil bacterial community was more affected by nutrient addition. Nitrogen (N) and phosphorus (P) have different effects on bacterial community. Soil organic matter is a key factor influencing the response of bacterial community to nutrient addition. N and P influence on bacterial community changes with plants.

Effects of environmentally relevant concentrations of oxytetracycline and sulfadiazine on the bacterial communities, antibiotic resistance genes, and functional genes are different between maize rhizosphere and bulk soil.

Antibiotic contamination in soil has become a major concern worldwide. At present, it is not clear how two co-existed antibiotics with environmentally relevant concentrations would affect soil bacterial community structure, the abundances of antibiotic resistance genes (ARGs) and functional genes, and whether the effects of antibiotics would differ between rhizosphere and bulk soil. We conducted a greenhouse pot experiment to grow maize in a loess soil treated with oxytetracycline (OTC) or sulfadiazine (SDZ) or both at an environmentally relevant concentration (1 mg kg-1) to investigate the effects of OTC and SDZ on the rhizosphere and bulk soil bacterial communities, abundances of ARGs and carbon (C)-, nitrogen (N)-, and phosphorus (P)-cycling functional genes, and on plant growth and plant N and P nutrition. The results show that the effects of environmentally relevant concentrations of OTC and SDZ on bacterial communities and abundances of ARGs and functional genes differ between maize rhizosphere and bulk soil. The effects of two antibiotics resulted in a higher absolute abundances of accA, tet(34), tnpA-04, and sul2 in the rhizosphere soil than in the bulk soil and different bacterial community compositions and biomarkers in the rhizosphere soil and the bulk soil. However, OTC had a stronger inhibitory effect on the abundances of a few functional genes in the bulk soil than SDZ did, and their combination had no synergistic effect on plant growth, ARGs, and functional genes. The role of co-existed OTC and SDZ decreased shoot height and increased root N concentration. The results demonstrate that environmentally relevant concentrations of antibiotics shift soil microbial community structure, increase the abundances of ARGs, and reduce the abundances of functional genes. Furthermore, soil contamination with antibiotics can diminish agricultural production via phytotoxic effects on crops, and combined effects of antibiotics on plant growth and nutrient uptake should be considered.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Bacterial communities in the potato tuberosphere share similarities with bulk soil and rhizosphere communities, yet possess distinct features

To date, a paucity of studies have examined bacterial communities in tuberospheres. However, the function of these bacterial communities in healthy potato plants is still largely unknown. Here, we aimed to describe the structure and composition of tuberosphere bacteriomes and its capability to make organosulfur plant available using the rhizosphere and bulk soil bacterial community characteristics as a reference. Rhizosphere, tuberosphere and bulk soil was collected from two field grown potato varieties. Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Bacterial organosulfur mobilization indicators were evaluated with cultivation dependent and independent methods and were correlated (Spearman) with the relative abundance of bacterial families. The structure of tuberosphere bacterial communities either overlapped with the bulk soil or had similarities with the rhizosphere. Relative abundance of specific bacterial families were distinct between bulk soil, tuberosphere and rhizosphere. Tuberospheres had a tendency for higher arylsulfonate utilization compared to bulk soil. The families Sphingomonadaceae, Sphingobacteriaceae and Rhizobiaceae which presented a decline in their relative abundances from the rhizosphere to tuberosphere and bulk soil had positive correlations with organosulfur mobilizing indicators. Potato variety and soil characteristics played a role in structuring the tuberosphere bacterial communities. Tuberospheres represent an environment in-between bulk soil and rhizosphere indicative from the intermediate relative abundances of specific bacterial families. A moderately higher bacterial organosulfur mobilization activity in tuberospheres suggests that this microbial function may serve specific biological roles for potato tubers.

Drought induces substitution of bacteria within taxonomic groups in the rhizosphere of native maize from arid and tropical regions

In Mexico, maize landraces are usually cultivated in milpa polyculture agroecosystems, which are maintained with ancestral practices, i.e. with very low external inputs such as chemicals and without irrigation systems. Several studies have characterized soil and maize-root microbiota from different milpas, however, robust experimental approaches are necessary to understand the relationship between a healthy microbial community structure and the health of milpa plants. We tested the hypothesis that different maize varieties not only differ in the microorganisms enriched in their rhizospheric environment, but also in the responses of these communities to drought. By suspending irrigation, we induced drought experimentally in three varieties of maize: one landrace from an arid milpa, one from a tropical milpa, and a commercial hybrid. The treatment elicited stress symptoms and growth declines in all three maize varieties. Nevertheless, the maize landrace from arid milpa displayed a better performance in biomass accumulation. The drought treatment did not significantly affect bulk soil bacterial communities; in contrast, all three varieties had shifts in their rhizospheric microbiomes, indicating that these responses were related to the presence of plant roots. The varieties differed in their changes of root-associated microbiota in response to drought, with only Paenarthrobacter genus increasing in all three. Responses mainly consisted of increases in the abundance of certain groups (e.g. Verrucomicrobiota) and substitution of strains within groups (e.g. Group 6 Acidobacteriota, family Streptomycetacea, and many others). The landrace from an arid region had the most bacteria substituted under drought, suggesting that a more stringent selection of microorganisms in roots could be part of the response of this landrace to drought. We propose that drought-tolerant maize landraces from arid milpas could be the source of bacterial strains or communities that aid drought-sensitive varieties in coping with reduced water availability expected due to climate change.

Changes in bacterial community structure and root metabolites in Themeda japonica habitat under slight and strong karst rocky desertification

Microorganisms can quickly respond to vegetation succession, and plants also regulate the structure of microbial community through root exudates or by affecting soil nutrients. Themeda japonica is a dominant plant species in karst rocky desertification (KRD) regions, but it is currently unclear the role of soil bacterial communities, interact with T. japonica during the KRD process. The purpose of this study is to explore the variation of soil metal element content, soil enzyme activity, soil bacterial communities and soil environment factor/root metabolites of T. japonica, and the relationship between soil bacterial communities and root metabolites in different degrees of KRD. Our results showed that the significant changes was found in soil metal element content and soil enzyme activity from slight KRD to strong KRD. Metabolic analysis demonstrated that the strong KRD environment increased the organic acid content of T. japonica roots, decreased the amino acids and sugars content. The specific metabolic pathways of Citrate cycle (TCA cycle), carbon fixation in photosynthetic organisms, glyoxylate and dicarboxylate metabolism and pyruvate metabolism were altered to help T. japonica adapt to the harsh environment. In addition, there was significant difference in beta diversity among bulk soil, rhizosphere and root endophytic bacterial community. With the aggravation of KRD, the abundance of Proteobacteria was decreased, while the abundance of Actinobacteria was increased. KRD also enhanced positive interactions between bacterial communities, and made the inter species associations of endophytic bacteria more sensitive. Mantel analysis showed that potassium (K), magnesium (Mg), cadmium (Cd) lead (Pb) and invertase (Inv), alkaline phosphatase (Alp), catalase (Cat), and aconitic acid, alanine, fructose, glucose, L-malic acid, palmitic acid, saccharic acid and serine significantly influence bacterial communities in bulk soil and rhizosphere. These results implied that root metabolites and soil characteristics might jointly affect the bacterial community in KRD area during the process of T. japonica in adapting to different rocky desertification.

A microecological research reveals seasonal variation in rhizosphere-endophytic bacteria and growth and development of Codonopsis pilosula root

Codonopsis pilosula is a medicinal and edible plant. Its chemical composition and pharmacological effects have been extensively studied. However, temporal, especially seasonal variabilities of bacterial composition driving nutrient cycling are poorly understood in rhizosphere and endosphere of C. pilosula. This study aimed to investigate the relationships and distinctions among soil physicochemical characteristics, microbial diversity, and functions of C. pilosula under different seasonal conditions in Longxi, China, and how these factors influenced C. pilosula growth. Physicochemical characteristics, enzymatic activities, growth state and metabolite analysis of C. pilosula in the soil were conducted using multispectral techniques. High-throughput sequencing methods were employed to analyze the alpha- and beta-diversity of rhizospheric and endophytic bacterial communities. Seasonal changes (P < 0.05) significantly influenced physiological indicators, bacterial diversity, community structure, and ecological niche breadth of C. pilosula, which were affected by environmental variables and soil enzymes. The neutral community model indicated that stochasticity played a substantial role in bacterial community development in rhizosphere soil. Furthermore, the microbial diversity was influenced by the soil's electrical conductivity, urease, and catalase activities, as well as phosphorus and potassium concentrations. Seasonal fluctuations significantly impacted the growth, development, metabolite content, and stress resistance indicators, such as antioxidant enzymes, in C. pilosula. By analyzing the temporal characteristics between plant and soil indicators, this study provides insights into regulating environmental factors during C. pilosula growth to enhance its yield and quality.Main conclusion Both rhizosphere soil physicochemical factors and bacterial diversity indices showed strong correlations. Phylogenetic and taxonomic differences existed between rhizosphere and bulk soil bacterial communities of Codonopsis pilosula in different seasons.

The core microbiota as a predictor of soil functional traits promotes soil nutrient cycling and wheat production in dryland farming

Abstract Host plants and the microbiota living in the rhizosphere are interdependent, mutually reinforced and mutually beneficial but the assembly, functions and microbial interactions of the host‐associated microbiota are still unclear. Herein, winter wheat was selected as a test plant to explore the assembly process of total bacteria from bulk soil (BS) and rhizosphere soil (RS), and phoD‐harbouring bacteria in RS at a long‐term (14 years) trial site. We also identified core microbes that are potentially relevant to soil carbon (C), nitrogen (N) and phosphorus (P) cycling genes and soil biogeochemical properties, and investigated the relationships between soil variables, functional genes and wheat productivity. The results showed that the microhabitat of the plant, rather than P fertilizer input, was the main factor affecting the microbial diversity, composition and co‐occurrence networks. The BS bacterial community was driven by deterministic processes but the RS and phoD bacterial communities were dominated by stochastic processes. The influence of deterministic processes decreased with increasing soil nutrient content. A core microbial community consisted of 10 OTUs in different microhabitats and was significantly related to soil functional genes and properties. In the rhizosphere soil, significant correlations were found between soil variables, soil functional bacteria and genes, and crop productivity. Synthesis and applications. This study provides empirical evidence that the assembly process of the microbial community is governed by environmental factors in various soil environments and provides new perspectives on the sustainable improvement of crop productivity. Read the free Plain Language Summary for this article on the Journal blog.

Changes in rice rhizosphere and bulk soil bacterial communities in the Doñana wetlands at different growth stages

The Doñana wetlands comprise an emblematic Mediterranean landscape protected as a UNESCO World Heritage Site. Some parts of these wetlands have been transformed into intensive rice cultivation areas, which are currently the most productive rice-growing areas in Europe. We examined the bacterial communities in these domesticated soils as they are key for plant health and productivity and have a strong influence on biochemical cycles. To identify the bacteria, we used metabarcoding analysis coupled with metabolic predictions and co-occurrence networks. This analysis was performed in the bulk and rhizosphere soils during different stages in the growing season. These soil compartments had a greater effect on the bacterial communities than the plant phenological stages. The diversity and richness of the bacterial population inhabiting the rhizosphere was much lower than that in the bulk soil, comprising taxa that were significantly more represented in this soil compartment, such as bacteria from the genus Hydrogenophaga, three genera from the order Rhizobiales, and unclassified genera from the families Desulfocapsaceae and Actinobacteria. Rhizosphere co-occurrence networks revealed a high number of negative connections, indicating unstable bacterial communities that may be highly influenced by biotic and abiotic factors. Rhizosphere networks mostly rely on two taxa belonging to the phyla Proteobacteria and Cyanobacteria, which are the predicted network hubs in this soil compartment. The bulk soil conserved high bacterial diversity and richness that was stable throughout the growth period of rice. Anaerobic bacteria from genera Marmoricola, the uncultured Gemmatimonadota bacteria SDR1034 terrestrial group, Anaerolinea, and the sulphur oxidizer, Thiobacillus were highly represented. This analysis provides valuable information for understanding bacterial diversity in the rhizosphere of rice cultivated in this region, which is critical for enhancing plant growth and productivity.

Rhizosphere and bulk soil bacterial community succession is influenced more by changes in soil properties than in rhizosphere metabolites across a maize growing season

The rhizosphere microbiome composition shifts across plant developmental stages. In addition, the bulk soil microbiome also changes during the growing season. However, the factors governing the rhizosphere and bulk soil microbiome succession across plant development are still not well identified. In this study we analyzed the changes in rhizosphere and bulk soil bacterial community structure through 16S rRNA amplicon sequencing across three maize growth stages (vegetative leaf 5 [V5], vegetative leaf 10 [V10] and reproductive stage 2 [R2]), as well as their correlations with temporal shifts in soil physicochemical properties and in root metabolites quantified in rhizosphere soils by LC/GC–MS. Twelve maize genotypes were used in a replicated field experiment for a comprehensive study. Results indicated significant correlations between the rhizosphere and bulk soil bacterial community succession with the temporal changes in rhizosphere metabolites and soil physicochemical properties. The changes in soil properties (mainly soil N and moisture) across stages explained more of the variation in the rhizosphere and bulk soil bacterial communities than the rhizosphere metabolites. However, shifts in rhizosphere metabolites (mainly sugars and gibberellins) across stages also strongly affected the rhizosphere bacterial community succession, but this effect was weaker on the bulk soil bacterial community. In addition to the changes in microbiome composition and diversity, we also detected changes in soil microbial respiration between plant developmental stages, with greater microbial activity at the V10 stage. In sum, our study showed that changes in soil properties have a great influence on both rhizosphere and bulk soil bacterial community succession across a growing season. The changes in plant root metabolites across the cropping season also affected the succession of the belowground bacterial communities, but the impact was much larger on the rhizosphere than on the bulk soil microbiome. Understanding the ecological processes shaping the belowground microbiomes through time is pivotal to develop future strategies for the most appropriate crop management across the whole growing season.

Effects of short‐term nitrogen addition on rhizosphere and bulk soil bacterial community structure of three halophytes in the Yellow River Delta

AbstractThe total amount and rate of atmospheric nitrogen (N) deposition are constantly increasing, which substantially influences the soil microbial community structure and function. However, it is still unclear whether the responses of different plant rhizosphere soil bacterial community to short‐term N addition was consistent. Based on 16s rRNA sequencing, we investigated the responses of rhizosphere and bulk soil bacterial community of halophytes (salt‐absorbing, salt‐rejecting, and salt‐secreting plant) to short‐term N addition in the Yellow River Delta. The bacterial community α‐diversity of Suaeda salsa (salt‐absorbing plant) was significantly higher in rhizosphere soil than in bulk soil, while no significant difference between Phragmites communis (salt‐rejecting plant) rhizosphere and bulk soil bacterial community α‐diversity was found. The differences were mainly ascribed to the higher N uptake capacity of P. communis, which resulted in no difference in N content between rhizosphere and bulk soil. The short‐term N addition significantly increased the α‐diversity of bacterial community in the rhizosphere soil of Aeluropus sinensis (salt‐secreting plant), but there was no effect on the α‐diversity of bacterial community in the rhizosphere soil of P. communis. Nitrogen addition enhances the salt uptake capacity of A. sinensis and alleviates the salt stress of bacterial growth. The relative abundance of Bacteroidetes for S. salsa and A. sinensis was significantly higher in rhizosphere soil than in bulk soil, and the relative abundance of Actinobacteria for P. communis and S. salsa was higher and lower in rhizosphere soil than in bulk soil, respectively. Salt‐absorbing of S. salsa leads to elevated rhizosphere soil salinity. Higher salinity and abundant carbon promote the Bacteroidetes and inhibit the Actinobacteria. Short‐term N addition caused an increase in the relative abundance of Gemmatimonadetes in halophyte rhizosphere soil and a decrease in the relative abundance of Firmicutes in S. salsa and A. sinensis bulk soil, which may be due to the different response of C:N of root secretions to N addition in halophytes. The relative abundance of rhizosphere soil denitrifying bacteria was higher in S. salsa and A. sinensis than in P. communis, while the reverse was observed for N‐fixing bacteria. The relative abundance of denitrifying bacteria decreased in P. communis and increased in S. salsa and A. sinensis. The low N soil environment of P. communis promotes the activity of N‐fixing bacteria, and the abundant N content of S. salsa and A. sinensis soil promotes the denitrification process. The research clarified that the response of soil bacterial community to short‐term N addition Treatment differed due to the influence of plant species and that N additions had smaller effects on the bacterial community than plant species.

Effects of nitrogen and phosphorus imbalance input on rhizosphere and bulk soil bacterial community of Suaeda salsa in the Yellow River Delta

IntroductionThe effects of nitrogen (N) and phosphorus (P) addition on soil microbial diversity have been widely studied, however, the response of bacterial community to N and P imbalance input remains unclear.MethodsUsing a high-throughput Illumina Miseq sequencing platform, N and P imbalance addition experiment was conducted to characterize the rhizosphere and bulk soil bacterial community of Suaeda salsa (S. salsa) in the Yellow River Delta.ResultsThe results showed that the rhizosphere soil bacterial community α-diversity was significantly higher than bulk soil. The rhizosphere soil Bacteroidetes and Actinobacteria were higher and lower than bulk soil, respectively. N and P imbalance input had small effects on the composition and α -bacterial diversity of the rhizosphere soil, while significantly increasing the bulk soil bacterial diversity and remarkably changing the community composition. Differences in the response of rhizosphere and bulk soil bacterial community to N and P imbalance input were caused by soil organic matter (SOM) content. The N and P imbalance input increased the relative abundance of bulk soil Eutrophic bacteria and decreased the relative abundance of the predicted oligotrophic bacteria (Acidobacteria,Chorolflexi). Rhizosphere and bulk soil bacterial community α-diversity was significantly correlated with SOM, salt, total carbon (TC) and total N (TN) content, with SOM and salt having the greatest effect on bulk soil bacterial community composition.DiscussionThere may be a threshold N-P input ratio between 15:1 and 45:1. This threshold is the optimal ratio for increasing the diversity of bacterial community.

Brassica seed meal fumigation restores beneficial bacterial communities by enriching taxa with high resistance and resilience

PurposeBrassica seed meals (BSMs) are widely used as biofumigants to control various soil-borne plant diseases. However, the mechanism of bacterial community reconstruction following fumigation with BSMs remains poorly understood.MethodsIn the present study, to decipher the mechanism of bacterial community reconstruction in fumigated soil and to understand the effect of bacterial communities in fumigated soil on rhizosphere recruitment and subsequent disease control, we investigated the bulk soil and rhizosphere bacterial communities using field experiments in soils treated with various fumigants (Brassica campestris seed meal, Brassica juncea seed meal, and the chemical fumigant dazomet) in two greenhouses subsequently used to grow tomato and cantaloupe, respectively.ResultsThis study revealed that bulk soil bacterial community composition changed significantly after fumigation extinction and recovery. Firmicutes and Proteobacteria, showing high resistance and resilience in the extinction and recovery processes, respectively, represented the key microorganisms for community reconstruction and rhizosphere recruitment. Moreover, nutrients supplied by BSMs, especially available phosphorus (AP), in fumigated soils determined the post-restoration changes in bacterial community composition. Additionally, BSMs showed greater potential than chemical fumigant dazomet in rebuilding beneficial bacterial communities and controlling potential soil pathogens by enriching gram-positive phyla Firmicutes and Actinobacteria and their respective affiliated genera Bacillus and Streptomyces.ConclusionThese results provide a fundamental ecological understanding of the response of soil-inhabiting microbes to fumigation and the reconstruction of soil beneficial bacterial communities after BSM fumigation. Thus, this study improves the understanding of the effects of biofumigants on soil-borne plant disease control in agriculture.

Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin.

Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.

Potential utilization of vitamin C industrial effluents in agriculture: Soil fertility and bacterial community composition

The potential of industrial effluents from vitamin C (VC) production was assessed for agricultural applications by monitoring plant growth, soil properties, and microbial community structure. The results demonstrated that two types of effluents—residue after evaporation (RAE) and concentrated bacterial solution after ultrafiltration (CBS)—had positive effects on the yield and VC content of pak choi. The highest yield and VC content were achieved with a combined RAE-CBS treatment (55.82 % and 265.01 % increase, respectively). The soil fertility was also enhanced by the application of RAE and CBS. Nitrate nitrogen and organic carbon contents in the soil were positively correlated with the RAE addition, while ammonium nitrogen and available phosphorus were positively correlated with the CBS addition. The diversity of bulk and rhizosphere soil bacterial communities increased significantly after the addition of RAE-CBS. The abundance of Sphingomonas and Rhizobium significantly increased after the RAE-CBS treatment, which affected aromatic compound hydrolysis and nitrogen fixation positively. Changes in plant growth and soil fertility were closely related to the upregulation of functional gene expression related to C, N, and P cycling. RAE and CBS application exerted various positive synergistic effects on plant growth, soil fertility, and bacterial community structure. Consequently, the study results confirmed the potential of RAE and CBS application in agriculture. This study provides an innovative solution for utilizing VC industrial wastewater in agriculture in a resourceful and economically beneficial manner while alleviating the corresponding environmental burden.

Grass-legume mixtures enhance forage production via the bacterial community

Forage monoculture and grass (Gramineae)-legume mixtures are the two most commonly used planting patterns for establishing farming grasslands, but the effects of these planting patterns on the rhizosphere bacterial community and forage production are still unclear. In this study, we carried out a field experiment on the Tibetan Plateau, and observed that grass-legume mixtures significantly increased forage production over monocultures (P < 0.05). We investigated the effects of these two planting patterns on rhizosphere and bulk soil bacterial communities, and found that the grass-legume mixtures altered the community structure and composition of the grass rhizosphere bacterial community, while the bacterial community of bulk soils remained unchanged. Source tracker analysis demonstrated that 50.77% and 34.72% of the changes in mixture rhizosphere of two gramineous grasses were derived from the legume, illustrating that the legume greatly influenced the grass rhizosphere in grass-legume planting. The molecular ecological network analysis demonstrated that network vulnerability and robustness of the mixtures were significantly higher than that of monoculture, indicating that the grass-legume mixtures provided a favorable condition for microbial interactions. Besides, by using structural equation modeling, it was found that the stability and complexity of the bacterial community network had significant positive correlations with forage production, while the soil physicochemical properties had no significant direct correlations, suggesting the rhizosphere bacterial community played a critical role in enhancing plant growth in grass-legume mixtures. This study provides a new insight into the mechanism behind the enhancement of forage production in the grass-legume mixture planting pattern.

Possible effects of temperature on bacterial communities in the rhizosphere of rice under different climatic regions.

Global warming is an indisputable fact. However, the effect of warming on the rhizosphere bacterial community of crops is not well understood. Therefore, we carried out pot experiments with three rice (Oryza sativa L.) varieties in black soil across three climatic regions of northeast China to simulate temperature change, and analyzed the response of the rhizosphere bacterial community to different temperatures. Results showed that climate had stronger effects on rhizosphere bacterial communities than rice variety. The rhizosphere bacterial diversity differed significantly among the three climatic regions and positively correlated with the mean daily average temperature (MAveT), mean daily maximum temperature (MMaxT), and mean daily minimum temperature (MMinT), and negatively correlated with the daily temperature range (DTR). Principal co-ordinate analysis revealed that bulk soil bacterial communities maintained a high similarity across the three climatic regions, while rhizosphere bacterial communities notably varied. This change was significantly correlated with MAveT, MMaxT, MMinT, and DTR. Compared with bulk soil, Proteobacteria and Bacteroidetes were enriched in the rhizosphere, while Actinobacteria was depleted. Moreover, these changes were strengthened by increasing the temperature and decreasing DTR. Additionally, correlation analysis revealed that changes in rhizosphere bacterial communities were closely related to the formation of rice yields. Our study revealed that the increasing temperature indirectly reshapes the rhizosphere bacterial community that may promote rice production in areas with lower temperatures.

Pea-Wheat Rotation Affects Soil Microbiota Diversity, Community Structure, and Soilborne Pathogens.

Intensive cultivation based on monocultures has a significant impact on ecosystem function, and sustainable agriculture must rely on alternative methods, including crop rotation. On the Canadian prairies, the use of pulse crops is a common practice, but few studies have investigated the impact on soil microorganisms. Here, we studied the effect of pea, wheat, pea–wheat rotation, and fallow in bulk soil bacterial and fungal communities. We characterized soil microbiota by high-throughput sequencing of 16S and 18S rRNA genes for bacteria and eukaryotes. Different crop rotations and fallow significantly modified soil community composition, as well as bacterial and fungal diversity. Pea alone caused a strong reduction of bacterial and fungal richness and diversity compared to wheat, pea–wheat rotation, and fallow. Notably, pea–wheat rotation increased the abundance of Fusarium graminearum compared to other management practices. The bacterial community was less responsive to crop rotation identity compared to the fungal microbiota, and we found minor differences at the phylum level, with an increase in Actinobacteria in fallow and Firmicutes in wheat. In summary, our study demonstrated that rotations alter bulk soil microbial community diversity and composition in Canadian prairies. The frequent use of pea in rotation with wheat should be carefully evaluated, balancing their ecological effects on nitrogen mineralization, water conservation, and impact on beneficial, as well as pathotrophic, fungi.

Assessing synergistic effects of crop rotation pattern, tillage practice, and rhizosphere effect on soil bacterial community structure and assembly in China's Loess Plateau farmlands

Soil bacterial communities are important soil regulators in agroecosystems. However, few studies have investigated the influences of integrated agricultural management practices on farmland soil bacterial community diversity and assembly processes. In this study, we assessed the impact of crop species (maize and soybean), tillage practice (chisel plow tillage, CPT; zero tillage, ZT; plow tillage, PT), rhizosphere effect (rhizosphere and bulk soils), and their interactions on the soil bacterial communities in Loess Plateau farmlands. Conservation tillage significantly increased soil moisture (SM), clay and sand fractions, and carbon and nitrogen levels; whereas silt fraction and pH decreased. Rhizosphere effect significantly improved soil texture and decreased SM, pH, total nitrogen, and nitrate nitrogen. Soybean cultivation significantly increased SM, silt fraction, and pH; while clay fraction decreased. Additionally, the rhizosphere effect decreased the competition among rhizosphere bacterial communities (edges: rhizosphere = 926, bulk = 1095; density: rhizosphere = 0.157, bulk = 0.184) and increased the structural complexity of the community network (modularity: rhizosphere = 0.857, bulk = 0.556); moreover, conservation tillage and soybean cultivation increased community network complexity (modularity: CPT = 0.879, ZT = 0.742, PT = 0.495; maize = 0.525, soybean = 0.888). Although the phylogenetic clustering of rhizosphere bacterial communities caused by the rhizosphere effect was lower than that of bulk soil bacterial communities (2.13%), it had no significant influence on rhizosphere or bulk soil bacterial community assembly, and deterministic processes dominated the formation of soil bacterial community structure. In conclusion, clarifying the variations in soil bacterial communities under integrated agricultural management practices can help predict trends in soil bacterial community function which can, in turn, effectively guide biological management decision-making in farming operations. Our findings may provide additional insights into the underground processes in farmland and facilitate the development of conservation farming operations as sustainable agricultural practices.

Host ancestry and morphology differentially influence bacterial and fungal community structure of Rhododendron leaves, roots, and soil

Rhododendron are popular ornamental plants that are well-known for forming mycorrhizal associations with ericoid fungi, but little is known about how host traits influence their microbiome more broadly. This study investigated leaf, root, rhizosphere soil, and bulk soil bacterial and fungal community structure for 12 Rhododendron species, representing four taxonomic clades with different leaf habits. Samples were collected when ephemeral hair roots colonized by ericoid mycorrhizae were absent, and microbial community structure was compared to leaf and root morphology for the same plants. Root morphology and the fungal communities of roots and rhizosphere soil were primarily structured by host ancestry. Leaf bacterial and fungal communities were even more distinct across clades than for roots or rhizosphere, and microbial communities of leaves and bulk soil were similarly structured by clade-wise differences in leaf morphology, suggesting a role for Rhododendron leaf litter in belowground microbial community structure. This work sheds new light on host traits influencing microbial community structure of ericaceous plants, showing a strong influence of ancestry, but also that different host traits drive bacterial and fungal communities across different plant compartments, suggesting future work on factors that drive similarity among close relatives in the non-ericoid microbes associating with Rhododendron.