Microbial Community Structure Research Articles

Effects of experimental nutrient enrichment and eutrophication on microbial community structure and function in “marine lakes”

Biogeochemical cycling of nitrogen (N) and carbon (C) are regulated by microbial communities that can respond to altered N and C availability, yet the form, consistency, and magnitude of these responses remain poorly constrained. We enriched and eutrophied distinct microbial communities in “marine lakes” through experimental additions of N (5 μM NH4Cl), C (100 μM sucrose), and combined N+C (same forms and concentrations), examining microbial community responses via 16S rRNA sequencing in conjunction with functional responses represented by net community production (NCP) and community respiration (CR) measurements. Individual N or C additions drove significant shifts in microbial community structure only sporadically, and rarely with a corresponding difference in NCP or CR rates. In contrast, the combined addition of N+C elicited strong coincident responses in microbial community structure and function: NCP and CR rates shifted sharply toward heterotrophy and were correlated with multiple microbial networks (r2 = 0.309–0.599, P < 0.001) that included globally distributed marine bacteria. Across multiple experiments, the consistent response of one network, comprised primarily of gammaproteobacterial heterotrophs (particularly Vibrio and Alteromonas), led initially dissimilar communities to converge toward similar composition. However, the distinct response patterns of other more diverse networks were superimposed on top of this network, indicating that inorganic N and organic C enrichment have multilayered effects on microbial communities. Collectively our results demonstrate that elevated N and C alter microbial community structure and function, selecting for multiple microbial networks that compete for, and rapidly cycle, N and C.

The Study of Nitrogen and Phosphorus Removal Efficiency in Urbanized River Systems Using Artificial Wetland Systems with Different Substrates

This study evaluated the effectiveness of five commercial substrates (zeolite, volcanic rock, gravel, magic rack, and ceramic pellets) in removing nitrogen (N) and phosphorus (P) from urban river systems using constructed wetlands. By employing X-ray CT and NGS technologies, we analyzed the physical structure of the substrates and the microbial communities they harbor. The results indicated that volcanic rock and ceramic pellets, due to their high porosity and specific surface area, performed exceptionally well in nitrogen and phosphorus removal. Specifically, the microbial systems with these two substrates achieved ammonia nitrogen removal rates of 89.86% and 88.45%, total nitrogen removal rates of 78.78% and 74.97%, and total phosphorus removal rates of 92.67% and 80.82%, respectively, within a 7-day period. Furthermore, the microbial communities on volcanic rock and ceramic pellets were more diverse, which correlated with their high pollutant removal efficiency. The study further elucidated the synergistic role of substrate characteristics and microbial community structure and function in nitrogen and phosphorus removal, enhancing the understanding of the purification mechanisms in constructed wetlands. These findings provide a scientific basis for the ecological restoration of urban rivers and are significant for improving the quality of urban water environments.

Dispersal shapes compositional and functional diversity in aquatic microbial communities

ABSTRACT Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually “refined” into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence. IMPORTANCE We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.

Effects of grassland degradation on soil ecological stoichiometry and soil microbial community on the South of the Greater Khingan Mountains

Grassland which covers 40% of terrestrial land is an important ecosystem having a multitude of functions, which has suffered various degrees of degradation with the interaction between global climate change and unreasonable human utilization (e.g., grazing and reclamation). Improved understanding of soil and microbial community diversity during meadow steppe degradation is crucial for predicting degradation mechanisms and restoration strategies. Here, we used Illumina sequencing technology to investigate the patterns of soil microbial community structure and the driving factors of its change across different degradation degrees of meadow steppe [i.e., non-degraded grasslands (NDG), lightly degraded grasslands (LDG), moderately degraded grasslands (MDG), and severely degraded grasslands (SDG)] south of the Greater Khingan Mountains. Our results showed a significant variation in soil properties, enzyme activity, and soil metal elements across the degraded meadows. Soil available phosphorus (AP), urease (UE), and cellulase (CL) in soils increased with the intensity of grassland degradation. Grassland degradation significantly decreased soil bacterial and fungal richness. In addition, grassland degradation significantly increased the relative abundance of Firmicutes (from 1.65% to 5.38%) and Myxococcota (from 2.13% to 3.13%). Degradation considerably increased the relative abundance of Ascomycota (from 66.54% to 75.05%), but decreased Basidiomycota (from 18.33% to 9.92%). The relative abundance of nitrogen fixation and cellulolysis decreased significantly due to grassland degradation. For fungal functional guilds, the relative abundance of pathotrophs increased while saprotrophs decreased significantly with increasing severity of degradation. Total nitrogen (TP), AP, available potassium (AK), manganese (Mn), lead (Pb), UE, sucrase (SC), and alcalase protease (ALPT) were the main drivers of soil bacterial community composition, while TP, AP, AK, Pb, UE, and SC were the main drivers of soil fungal community composition in the degraded grassland. Our findings demonstrated that severe grassland degradation has an enormous effect on soil microbial communities and soil physicochemical dynamics. These findings improve our theoretical understanding of the interactions between soil microbial populations and soil environmental variables in degraded grassland.

Slow-Release Nitrogen Fertilizer Promotes the Bacterial Diversity to Drive Soil Multifunctionality

The application of slow-release nitrogen fertilizer not only economizes labor input, but also decreases the frequency of use of mechanical intakes, with significant implications in advancing modern intensive agricultural production. Whether slow-release nitrogen fertilizer application can influence the association between microbial diversity and soil multifunctionality remains controversial. This study analyzed the spatial variances of soil environmental factors, soil multifunctionality, and their correlations with bacterial and fungal communities under five nitrogen application rates. The key factors influencing the dominant microbial species and community structures at different spatial locations were determined by the slow-release nitrogen fertilizer application rate, and the driving factors and dominant species of soil multifunctionality were identified. In contrast to the control group, moderate slow-release nitrogen fertilizer application enhanced soil multifunctionality and ameliorated the resilience of microbial diversity loss at diverse spatial locations resulting from irrational nitrogen fertilizer application. The resilience of the fungal community to disturbances caused by fertilization was lower than that of the bacterial community. Bacterial diversity exhibited a significant correlation with soil multifunctionality, and the soil multifunctionality intensity under 240 kg ha−1 treatment increased by 159.01% compared to the CK. The main dominant bacterial communities and the dominant fungal community Ascomycota affected soil multifunctionality through slow-release nitrogen fertilizer application. Structural equation modeling and random forest analysis demonstrated that bacterial community diversity, particularly in bulk soil and the rhizosphere, community composition, and soil nitrogen form are the primary driving factors of soil multifunctionality. Results indicated that the microbial niche alterations induced by slow-release nitrogen fertilizer application positively affect soil multifunctionality.

Effects of dietary Brassica rapa L. polysaccharide on growth performance, immune and antioxidant functions and intestinal flora of yellow-feathered quail.

This study aimed to explore the impact of Brassica rapa L. polysaccharides (BRP) on the growth, immune response, antioxidant capacity, and cecal microbiota in yellow-feathered quails. A total of 250 one-day-old yellow-feathered quails, evenly divided by sex, were randomly assigned to five groups, with each group comprising ten replicates of five quails each. The control group (CON) received a basic diet, while the antibiotic control group (CTC) was fed a basic diet supplemented with chlortetracycline (0.05g/kg). BRP was administered at concentrations of 0.25g/kg (Low dose BRP, LBRP), 0.5g/kg (Medium dose BRP, MBRP), and 1g/kg (High dose BRP, HBRP). The duration of the experiment was 42 days. The results indicated that, compared to the CON group, the final body weight of quails in the MBRP group significantly increased (P < 0.05), and there was a significant difference in body weight between the LBRP group and the CTC group (P < 0.05). At 21 days of age, the average weights of the thymus and bursa of Fabricius in the MBRP group were significantly greater than those in the CON group (P < 0.05), with no significant difference observed when compared to the CTC group (P > 0.05); at 42 days of age, the average weight of the thymus in the MBRP group was significantly greater than that in the CON group (P < 0.05), with no significant difference observed compared to the CTC group (P > 0.05). At 21 days of age, the levels of IgA and IgG in the MBRP group were significantly elevated compared to the CON group (P < 0.05), with no significant difference noted compared to the CTC group (P > 0.05). Additionally, the MBRP group showed significant increases in CAT, T-SOD, and GSH-Px levels (P < 0.05) compared to the CON group; the levels of IL-1β and TNF-α were significantly reduced (P < 0.05), and the level of IL-10 was significantly elevated (P < 0.05) compared to the CON group. Furthermore, 16S rRNA sequencing revealed that BRP supplementation increased the populations of beneficial cecal bacteria such as Lactococcus, Weissella, Parabacteroides, and norank_f_Ruminococcaceae, and decreased the population of the harmful bacterium Campylobacter, indicating that BRP modulates the microbial community structure in the cecum of yellow-feathered quails. In summary, BRP enhanced the growth performance, serum immunoglobulin levels, antioxidant functions, and improved the intestinal microbiota in yellow-feathered quails.

Soil Microbial and Metabolomic Shifts Induced by Phosphate-Solubilizing Bacterial Inoculation in Torreya grandis Seedlings

Phosphorus is crucial for plant growth and development, but excess fertilizer not absorbed by plants often binds with metal ions like iron and manganese, forming insoluble compounds that contribute to soil environmental pollution. This study investigates the impact of Burkholderia sp., a phosphate-solubilizing bacterium utilized as a biofertilizer, on the fertility of T. grandis soil, alongside the associated shifts in soil metabolites and their relationship with microbial communities after inoculation. The soil microbial community structures and metabolite profiles were analyzed via amplicon sequencing and high-resolution untargeted metabolomics. The inoculation of phosphate-solubilizing bacteria led to a significant (p &lt; 0.05) enhancement in total phosphorus, potassium, and nitrogen concentrations in the soil, with a marked increase in available phosphorus in bulk soil (p &lt; 0.05). Moreover, the microbial community structure exhibited significant shifts, particularly in the abundance of bacterial phyla such as Acidobacteria, Chloroflexi, Proteobacteria, and the fungal phylum Ascomycota. Metabolomic analysis revealed distinct metabolites, including fatty acids, hormones, amino acids, and drug-related compounds. Key microbial taxa such as Chloroflexi, Proteobacteria, Acidobacteria, Verrucomicrobia, Mucoromycota, and Ascomycota indirectly contributed to soil phosphorus metabolism by influencing these differential metabolites. In conclusion, the application of phosphate-solubilizing bacteria offers an innovative approach to improving soil quality in T. grandis, promoting phosphorus utilization efficiency, and enhancing soil ecosystem health by optimizing microbial communities and metabolite compositions.

Insights into the Acute Stress of Glutaraldehyde Disinfectant on Short-Term Wet Anaerobic Digestion System of Pig Manure: Dose Response, Performance Variation, and Microbial Community Structure

The outbreak of epidemics such as African swine fever has intensified the use of disinfectants in pig farms, resulting in an increasing residual concentration of disinfectants in environmental media; however, the high-frequency excessive use of disinfectants that damage pig farm manure anaerobic fermentation systems and their mechanisms has not attracted enough attention. Especially, the complex effects of residual disinfectants on anaerobic fermentation systems for pig manure remain poorly understood, thus impeding the application of disinfectants in practical anaerobic fermentation systems. Herein, we explored the effects of glutaraldehyde disinfectant on methane production, effluent physicochemical indices, and microbial communities in a fully automated methanogenic potential test system (AMPTSII). The results show that adding glutaraldehyde led to remarkable alterations in methane production, chemical oxygen demand (COD), volatile solids (VS), and polysaccharide and phosphorus concentrations. During the anaerobic process, the production of methane displayed a notable decrease of 5.0–98% in all glutaraldehyde treatments, and the trend was especially apparent for treatments containing high levels of glutaraldehyde. Comparisons of the effluent quality showed that in the presence of 0.002–0.04% glutaraldehyde, the COD and total phosphorus (TP) increased by 12–310% and 15–27%, respectively. Moreover, the addition of 0.01–0.08% glutaraldehyde decreased the ammonium (NH4+-N) concentration and VS degradation rate by 7.7–15% and 4.9–26.2%. Furthermore, microbiological analysis showed that the glutaraldehyde treatments had adverse effects on the microbial community. Notably, certain functional bacteria were restrained, as highlighted by the decreases in relative abundance and microbial diversity by 1.3–17% and 0.06–21%, respectively. This study provides a theoretical basis for the rational use of disinfectants in anaerobic fermentation systems.

Biotic and abiotic factors affecting soil microbial carbon use efficiency

Soil microbial carbon use efficiency (CUE) refers to the efficiency of microorganisms in converting absorbed carbon into their own biomass carbon. Soil microbial CUE is a key parameter to understanding the soil carbon cycle. Biotic and abiotic factors are widely considered to be important factors influencing CUE. However, the related underlying mechanisms remain unclear. This review elaborates on the concept of soil microbial CUE and the various approaches used for its measurement. We reviewed the effects of various abiotic factors, such as temperature, soil moisture, pH, nutrient addition, and substrate type, and biotic factors, such as microbial community structure and diversity, on CUE. Finally, we discussed the focus areas that future studies need to further explore. We hope this review can provide a comprehensive understanding of the factors impacting soil microbial CUE, which is a fundamental step to improving soil carbon storage capacity.

Effect of exogenous thermophilic biocontrol agent inoculum on the high temperature chicken manure composting

IntroductionAerobic composting is an effective method for utilizing chicken manure. However, its low carbon to nitrogen (C/N) ratio leads to slow heating and short high-temperature phases, which reduce composting efficiency and product quality.MethodsTo address this issue, splinted mushroom cultivation residues were added to adjust the C/N ratio, and exogenous thermophilic composting strains were introduced to increase composting temperature. This study analyzed the relationship between physicochemical metabolites and microbial community structure during high-temperature chicken manure composting.Results and discussionBased on metagenomic and physicochemical analyses, results showed that the exogenous microbial agents extended the thermophilic phase by three-times, reduced the heating phase duration by 75%, and increased nitrogen, phosphorus, potassium, and soluble organic carbon contents by 3.61, 21.63, 7.21, and 39.03%, respectively. Genes associated with amino acid metabolism were significantly enriched during the heating phase, while genes involved in the tricarboxylic acid cycle were more active in the thermophilic phase. During the thermophilic phase, bacterial diversity and richness decreased compared to the heating and cooling phases. Functional microbes such as Bacillus, Caldicoprobacter, and Virgibacillus showed a positive correlation with the key differential metabolites. While Actinomadura, Saccharomonospora, Paenibacillus, and Aneurinibacillus displayed an opposite correlation. Further experiments demonstrated that the increased temperature during the thermophilic phase triggered the upregulation of oleic acid metabolism and piperidine metabolism pathways in functional microorganisms, leading to the production of heat stabilizers and protective agents like oleic acid, gallic acid, and 2-piperidone. This phenomenon helped maintain microbial viability during the thermophilic phase and improved composting efficiency.

Close correlation between sugarcane ratoon decline and rhizosphere ecological factors.

Rhizosphere ecological factors that affect sugarcane ratoons are crucial components in the feedback mechanisms between the sugarcane plant and soil environment. However, systematic investigations on these dynamics are lacking. Therefore, this study investigated the relationship between sugarcane ratoon decline and rhizosphere ecological factors. In first-year sugarcane ratoons, ecological factors such as soil available potassium content, soil nitrogen fixation, and soil peroxidase activity were significantly positively correlated with sugarcane growth (P < 0.05) compared to that of third-year sugarcane ratoons. Significant intergroup disparities in the rhizosphere soil microbial community structure were observed based on different ratoon ages (P < 0.01), while highly significant intergroup differences in endophytic microbial community structure were observed based on a Jaccard distance analysis (P < 0.01). Generalised additive model analysis revealed a significant positive correlation (P < 0.05) between sugarcane growth properties and the alpha diversity of rhizosphere soil bacteria and endophytic bacteria but a predominantly negative correlation (P > 0.05) between the alpha diversity of endophytic fungi and key sugarcane growth indicators. The deterioration of mainly non-microbial ecological factors in rhizosphere soil (P < 0.05) with increasing ratoon age may represent a significant factor contributing to sugarcane ratoon decline. The fungal community significantly impacted soil enzyme activity, while the microbial community indirectly influenced sugarcane yield through its effect on soil enzyme activity. Therefore, endophytic fungi, particularly Ascomycota species, may play a crucial role in sugarcane diseases.

Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.

The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.

Exploring plant-microbe interactions in adapting to abiotic stress under climate change: a review

Climatic change and extreme weather events have become a major threat to global agricultural productivity. Plants coexist with microorganisms, which play a significant role in influencing their growth and functional traits. The rhizosphere serves as an ecological niche encompassing plant roots and is a chemically complex environment that supports the growth and development of diverse plant-interactive microbes. Although plant-microbe interactions have been extensively investigated however, limited exploration have been made how abiotic stresses affect the structure and assembly of microbial communities in the rhizosphere. This review highlights climate change influence on plant growth, functional traits, and microbial communities. It explores plant mechanisms for mitigating abiotic stress, such as removing reactive oxygen species (ROS), regulating antioxidant activity and indole-3-acetic acid (IAA) production, and controlling growth-inhibitory ethylene levels through colonization by bacteria producing ACC deaminase. Additionally, we elaborated the systematic communicatory network steered by hormonal crosstalk and root exudation, which can modulate and initiate the dialogues between plants and surrounding microbes. This network ultimately promotes the chemotactic movement of microbes towards the rhizosphere, facilitating their early colonization. Finally, we reviewed the recent advancements for understanding how plant-microbe interactions foster resilience under climate stress.

Enhanced activity of mixed-culture electroactive biofilms and sulfamethoxazole removal efficiency by adding N-acyl-homoserine lactones in bio-electrochemical system

ABSTRACT The addition of exogenous quorum sensing signaling molecules significantly enhanced the degradation efficiency of antibiotics, such as chloramphenicol in bio-electrochemical systems (BESs). However, the effects and mechanisms by which AHLs addition in BES facilitated the removal of sulfamethoxazole (SMX) remained inadequately explored. This study systematically compared the electrochemical performance and SMX removal efficiency in BES under two conditions: with and without the addition of N-acyl-homoserine lactones (AHLs) signaling molecules. In comparison to the control group, the AHL-treated group exhibited an increase in maximum output voltage from 340 to 489.67 mV, alongside a notable enhancement in SMX removal efficiency over 120 h ranging from 14.65% to 15.76%. Analyses of the live and dead cells and extracellular polymeric substances (EPS) composition revealed that following AHLs addition, both the ratio of live to dead cells and protein content within EPS increased by 12.66% and 74.37%, respectively. Furthermore, microbial community structure analysis indicated that after AHLs supplementation, there was a marked increase in the abundance of electroactive microorganisms as well as antibiotic-degrading and nitrogen-removing bacteria. Notably, Klebsiella – characterised by its electroactivity along with antibiotic degradation and nitrogen removal capabilities – exhibited a relative abundance reaching 56.84% in AHL, reflecting an increase of 28.31% compared to Blank; additionally, electroactive bacteria Dysgonomonas showed a relative abundance rise of 2.49%. Collectively, these findings suggested that enhancements in SMX removal efficiency upon AHLs addition were primarily driven by improvements in electrochemical performance coupled with alterations in microbial community structure.

Contribution of pectin-degrading bacteria to the quality of cigar fermentation: an analysis based on microbial communities and physicochemical components

ObjectiveThis study aims to investigate the effects of pectin-degrading bacteria on the microbial community and physicochemical properties during the fermentation process of cigar tobacco, evaluating its potential in reducing green bitterness and enhancing aroma.MethodsBy isolating and screening pectin-degrading bacteria, high-throughput sequencing and physicochemical analysis were employed to compare the microbial flora and physicochemical component differences in different treatment groups of cigar tobacco. Furthermore, correlation analysis was performed to examine the relationships between these variables.ResultsThe results showed that the strains YX-2 and DM-3, isolated from the cigar tobacco variety “Yunxue No. 1,” exhibited strong pectin-degrading abilities. Phylogenetic analysis revealed that strain YX-2 is highly homologous to Bacillus flexus, while strain DM-3 is highly homologous to Bacillus siamensis. After fermentation, the addition of strains YX-2 and DM-3 significantly reduced the pectin content in the tobacco leaves, increased the total sugar and reducing sugar content, reduced green bitterness, and markedly enhanced the total aroma components. Notably, DM-3 exhibited outstanding performance in the production of Maillard reaction products. Microbial community analysis showed that the addition of pectin-degrading bacteria significantly increased the diversity of both bacteria and fungi, especially in the TDM3 group, where the relative abundance of Pseudomonas was notably elevated. Correlation analysis revealed that Pseudomonas had a significant positive correlation with both reducing sugar and total sugar, and a significant negative correlation with pectin, indicating its important role in sugar metabolism and pectin degradation. Additionally, fungal genera such as Cercospora were significantly negatively correlated with total sugar and total nitrogen, while Eurotium was closely associated with pectin degradation and reducing sugar accumulation.ConclusionThis study found that the addition of Pectin-degrading bacteria YX-2 and DM-3 significantly optimized the microbial community structure during the cigar tobacco fermentation process and improved the physicochemical properties of the tobacco leaves, with notable effects in reducing green bitterness and enhancing aroma.

Effects of cotton peanut rotation on crop yield soil nutrients and microbial diversity.

Using high-throughput sequencing technology, investigate the soil microbial diversity in the root zone after cotton-peanut rotation.Various planting patterns, including cotton continuous cropping (MC), peanut continuous cropping (HC), peanut-cotton-peanut rotation (HR), and fallow (X), were established to assess variations in crop yield, soil nutrients, and soil microbial diversity. Significant differences were observed in crop yield, soil nutrients, and soil microbial community structure among different planting patterns. The HR system significantly increased the output compared with the HC and MC systems. Additionally, HR exhibited significantly lower total nitrogen (N) and basic nitrogen (BN) contents than HC and MC, whereas MC showed lower total potassium (K) and available potassium (AK) contents. HR led to a decrease in soil bacterial diversity but an increase in fungal diversity, with Ascomycota and Mortierellomycota being dominant. Various bacteria (Chloroflexi, Bacteroidota, and Actinobacteriota) associated with organic matter degradation and nutrient cycling were found across different planting systems, enhancing material cycling efficiency. Furthermore, Planctomycetota bacteria related to crop nutrient synthesis and Glomeromycota bacteria aiding plant nutrient absorption were significantly higher in the MC system than in the HR or HC systems. Redundancy analysis indicated a significant negative correlation between crop rotation and soil fungal community, whereas Ascomycota exhibited a significant negative correlation with organic matter. Peanut-cotton rotation can mitigate soil nutrient loss, enhance beneficial microorganism diversity, suppress harmful bacterial populations, stabilize ecosystems, and boost crop yield.

Microbial diversity in the arid and semi-arid soils of Botswana.

To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.

Karst Ecosystem: Moso Bamboo Intercropping Enhances Soil Fertility and Microbial Diversity in the Rhizosphere of Giant Lily (Cardiocrinum giganteum)

Intercropping affects soil microbial community structure significantly; however, the effects on understory medicinal plants in karst areas remain unclear. We investigated the effects of four intercropping systems (Moso bamboo, Chinese fir, bamboo-fir mixed forest, and forest gap) on the rhizosphere microbial communities of giant lily (Cardiocrinum giganteum), an economically important medicinal plant in China. We assessed the intercropping impact on rhizosphere microbial diversity, composition, and co-occurrence networks and identified key soil properties driving the changes. Bacterial and fungal diversity were assessed by 16S rRNA and ITS gene sequencing, respectively; soil physicochemical properties and enzyme activities were measured. Moso bamboo system had the highest fungal diversity, with relatively high bacterial diversity. It promoted a distinct microbial community structure with significant Actinobacteria and saprotrophic fungi enrichment. Soil organic carbon, total nitrogen, and available potassium were the most influential drivers of microbial community structure. Co-occurrence network analysis revealed that the microbial network in the Moso bamboo system was the most complex and highly interconnected, with a higher proportion of positive interactions and a greater number of keystone taxa. Thus, integrating Moso bamboo into intercropping systems can enhance soil fertility, microbial diversity, and ecological interactions in the giant lily rhizosphere in karst forests.

Subsurface microbial community structure shifts along the geological features of the Central American Volcanic Arc.

Subduction of the Cocos and Nazca oceanic plates beneath the Caribbean plate drives the upward movement of deep fluids enriched in carbon, nitrogen, sulfur, and iron along the Central American Volcanic Arc (CAVA). These compounds fuel diverse subsurface microbial communities that in turn alter the distribution, redox state, and isotopic composition of these compounds. Microbial community structure and functions vary according to deep fluid delivery across the arc, but less is known about how microbial communities differ along the axis of a convergent margin as geological features (e.g., extent of volcanism and subduction geometry) shift. Here, we investigate changes in bacterial 16S rRNA gene amplicons and geochemical analysis of deeply-sourced seeps along the southern CAVA, where subduction of the Cocos Ridge alters the geological setting. We find shifts in community composition along the convergent margin, with communities in similar geological settings clustering together independently of the proximity of sample sites. Microbial community composition correlates with geological variables such as host rock type, maturity of hydrothermal fluid and slab depth along different segments of the CAVA. This reveals tight coupling between deep Earth processes and subsurface microbial activity, controlling community distribution, structure and composition along a convergent margin.

Influence of combined application of tetracycline and streptomycin on microbial diversity and function in rice soil.

A microcosm experiment was performed to quantify the residues of antibiotics [tetracycline (TC), streptomycin (STR), and streptocycline (STC; a mixture of TC and STR)] in rice soil and to assess their impact on microbial community structure and function using Illumina-MiSeq metagenomic analysis. Antibiotics were applied at half the recommended dose (0.5RD), recommended dose (RD), and double the recommended dose (2RD). At RD, TC was degraded in soil within 9days of its application, whereas it took 21days for STR and STC to degrade below limit of quantification (LOQ) level. The residue data were fitted in decay models, and half-lives (DT50) were 46.5-53.3h and 177.6-198h for TC and STR, respectively. Soil enzyme activities (dehydrogenase, β-glucosidase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase) were negatively affected in the antibiotic-treated soil. Targeted metagenomic analysis showed that the major bacterial phyla such as Chloroflexi, Actinobacteria, Planctomycetes, Crenarchaeota, and Gemmatimonadetes were suppressed by antibiotic treatments as compared to control. Shannon, Simpson, ACE, and Chao1 diversity indices showed that bacterial diversity decreased with the application of antibiotics, and decrease in bacterial diversity was more prominent in case of STC as compared to TC and STR. Overall, the combination of antibiotics negatively affected the soil microbial community structure and function in comparison to their individual application.