Bacterial Co-occurrence Network Research Articles

The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics.

Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We demonstrated that plant growth characteristics were strongly related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce IAA and siderophores) exhibited greater relative abundance in high- and medium performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, Azohydromonas. Conversely, the network within low performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.

The effects of straw return on soil bacterial diversity and functional profiles: A meta-analysis

Returning straw directly to agricultural fields increases soil carbon sequestration and influences soil microbial activities. However, the precise impacts of straw return on soil bacterial diversity, composition, and function profiles remain unclear, necessitating a comprehensive synthesis and standardized analysis. In this study, we conducted a meta-analysis of 729 original bacterial sequencing samples from fields with and without straw return to elucidate how soil bacteria respond to different experimental conditions after straw return (e.g., straw and fertilizer management practices and return duration). Our analysis revealed that overall straw return slightly increased the Chao 1 index while the Shannon index remained unaffected. However, we found strong responses depending on the experimental conditions of straw return. Particularly, bacterial community diversity increased significantly, particularly under high nitrogen, low straw addition, or continuous straw return. Furthermore, straw return altered bacterial community composition, elvating the abundance of Proteobacteria and Bacteroidetes, while decreasing Chloroflexi, Firmicutes, and Nitrospirae. Straw return also increased modularity in bacterial co-occurrence networks. Functional annotation analysis highlighted that straw return substantially enriched microbes involved in chemoheterotrophy, nitrogen fixation, and functional groups related to straw decomposition (chitinolysis, cellulolysis, xylanolysis), while inhibiting microbes associated with nitrification and nitrate reduction. Surprisingly, straw return did not impact the relative abundance of plant pathogens. Overall, our findings offer an in-depth understanding the effects of straw return on soil bacterial communities, including increased diversity, modified structure, and enhanced functional profiles related to straw decomposition.

Comparison of the Effects of LDPE and PBAT Film Residues on Soil Microbial Ecology.

The plastic film is extensively applied with limited recycling, leading to the long-run residue accumulation in soil, which offers a distinctive habitat for microorganisms, and creates a plastisphere. In this study, traditional low-density polyethylene (LDPE) plastic film and biodegradable polybutylene adipate terephthalate (PBAT) plastic film materials were selected to test their effects on soil microbial ecology. Based on high-throughput sequencing, compared to the soil environment, the alpha-diversity of bacterial communities in plastisphere was lower, and the abundance of Actinobacteria increased. Plastic film residues, as bacterial habitats, exhibited greater heterogeneity and harbor unique bacterial communities. The communities were distinguished between plastisphere and soil environment by means of a random-forest (RF) machine-learning model. Prominent distinctions emerged among bacterial functions between soil environment and plastisphere, especially regarding organics degradation. The neutral model and null model indicated that the constitution of bacterial communities was dominated by random processes except in LDPE plastisphere. The bacterial co-occurrence network of the plastisphere exhibited higher complexity and modularity. This study contributes to our comprehending of characteristics of plastisphere bacterial communities in soil environment and the associated ecological risks of plastic film residues accumulation.

Spatial distribution and assembly processes of bacterial communities in riverine and coastal ecosystems of a rapidly urbanizing megacity in China

Rapid urbanization has precipitated significant anthropogenic pollution (nutrients and pathogens) in urban rivers and their receiving systems, which consequentially disrupted the compositions and assembly of bacterial community within these ecosystems. However, there remains scarce information regarding the composition and assembly of both planktonic and benthic bacterial communities as well as pathogen distribution in such environments. In this study, full-length 16S rRNA gene sequencing was conducted to investigate the bacterial community composition, interactions, and assembly processes as well as the distribution of potential pathogens along a riverine-coastal continuum in Shenzhen megacity, China. The results indicated that both riverine and coastal bacterial communities were predominantly composed of Gammaproteobacteria (24.8 ± 12.6 %), Alphaproteobacteria (16.1 ± 9.8 %), and Bacteroidota (14.3 ± 8.6 %), while sedimentary bacterial communities exhibited significantly higher diversity compared to their planktonic counterparts. Bacterial community patterns exhibited significant divergences across different habitats, and a significant distance-decay relationship of bacterial community similarity was particularly observed within the urban river ecosystem. Moreover, the urban river ecosystem displayed a more complex bacterial co-occurrence network than the coastal ecosystem, and a low ratio of negative:positive cohesion suggested the inherent instability of these networks. Homogeneous selection and dispersal limitation emerged as the predominant influences on planktonic and sedimentary bacterial communities, respectively. Pathogenic genera such as Vibrio, Bacteroides, and Acinetobacter, known for their roles in foodborne diseases or wound infection, were also identified. Collectively, these findings provided critical insights into bacterial community dynamics and their implications for ecosystem management and pathogen risk control in riverine and coastal environments impacted by rapid urbanization.

Bacterial assembly and succession patterns in conventional and advanced drinking water systems: From source to tap

Bacteria are pivotal to drinking water treatment and public health. However, the mechanisms of bacterial assembly and their impact on species coexistence remain largely unexplored. This study explored the assembly and succession of bacterial communities in two full-scale drinking water systems over one year. We observed a decline in bacterial biomass, diversity, and co-occurrence network complexity along the treatment processes, except for the biological activated carbon filtration stage. The conventional plant showed higher bacterial diversity than the advanced plant, despite similar bacterial concentrations and better removal efficiency. The biological activated carbon filter exhibited high phylogenetic diversity, indicating enhanced bacterial metabolic functionality for organic matter removal. Chlorination inactivated most bacteria but favored some chlorination-resistant and potentially pathogenic species, such as Burkholderia, Bosea, Brevundimonas, and Acinetobacter. Moreover, the spatiotemporal dynamics of the bacterial continuum were primarily driven by stochastic processes, explaining more than 78% of the relative importance. The advanced plant’s bacterial community was less influenced by dispersal limitation and more by homogeneous selection. The stochastic process regulated bacterial diversity and influenced the complexity of the species co-occurrence network. These findings deepen our understanding of microbial ecological mechanisms and species interactions, offering insights for enhancing hygienic safety in drinking water systems.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient.

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress.

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities.

Different rice production patterns exert varying comprehensive impacts on the agricultural environment. Integrated rice-fish farming, an advanced and rapidly developing agricultural production pattern, aims to improve resource utilization efficiency and enhance food productivity. To unravel the responses and internal interactions of the agricultural ecological environment to integrated rice-fish farming, we assessed and compared environmental factor, rice growth performance, and soil microbiome in both integrated rice-yellow catfish farming (IRYF) and rice monoculture (RM) systems. Our results revealed significant increases in the total nitrogen and ammonia concentrations in the paddy water and soil induced by the IRYF. Rice growth performance in the IRYF group surpassed that in the RM group. IRYF obviously impacted almost all dominant bacterial phyla, genera, and functional groups (top ten most abundant), enhancing the ability of bacteria to degrade and utilize organic matter. Additionally, IRYF led to noticeable reductions in the Shannon, Simpson, Chao 1, and Pielou_J indices. IRYF strengthened the interconnections between various taxonomic units in bacterial co-occurrence network, resulting in increased complexity, stability, and disturbance resistance in the soil bacterial community. IRYF notably facilitated the transition from a community assembly dominated by stochastic processes to one dominated by deterministic processes for the soil bacterial community. The deterministic process driving this transition was variable selection. All the environmental factors, except for soil nitrate, demonstrated relatively high contributions to alterations in soil bacterial communities, with environmental variables significantly positively correlated with the soil bacterial community in the IRYF group. Alterations in functionality, composition, and diversity of the soil bacterial community were clearly associated with most environmental variables and rice growth performance indices. Our research contributed to understanding the comprehensive impacts of integrated rice-fish farming on agricultural ecosystems and provide theoretical support for achieving the sustainable agricultural production and optimizing the rice production patterns.

Improved bacterial composition and co-occurrence patterns of rhizosphere increased nutrient uptake and grain yield through cultivars mixtures in maize

Crop diversification contributes to agricultural productivity and resources efficient utilization. However, whether cultivar mixtures in maize affects soil bacterial community, nutrient uptake, plant growth and yield remains unknown. A two-year lysimetric experiment was conducted using two maize cultivars (LY16 and JS501) with different root system architectures planted in monoculture or in mixture under normal fertilization (NF), reduced fertilization (RF) or no addition of fertilizer (CK) and was assessed at the silking stages. Cultivar mixtures and monoculture of LY16 had higher shoot biomass, nutrient uptake and total root length at silking stage, and grain yield than monoculture of JS501 under NF and RF conditions. Under NF and RF conditions, cultivar mixtures and monoculture of LY16 led to an increase in bacterial diversity, significant changes in community structure, and a high abundance of Bacteroidia and biomarkers of Chitinophagaceae and Saprospiraceae (Bacteroidia). Cultivar mixtures showed specific responses from modules of the rhizosphere bacterial community co-occurrence network, and the relative abundance of keystone taxa of cultivar mixtures was higher than that of monoculture of JS501. The keystone taxa had a broad and significant positive correlation with plant nutrient accumulation and grain yield. Cultivar mixtures showed similar assembly processes of Bacteroidia with monoculture of LY16, and the increased abundance of Chitinophagaceae may lead to a healthy rhizosphere bacterial community. Overall, our findings indicate that cultivar mixtures significantly affects the assembly and composition of the rhizosphere bacterial community, and thus benefits plant nutrient acquisition and plant growth. These findings could deepen our understanding of the facilitating effect of rhizosphere functional microbial community (e.g. plant nutrition uptake or immunity)of cultivar mixtures.

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics.

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.

Ensilage using Leuconostoc lactis and Weissella confusa reduces microbial risk and enhances hygienic quality of whole-crop corn

This study combined applied PICRUSt2 and BugBase tools to evaluate the effects of these two strains on the fermentation characteristics, microbial community, potential microbial risk and hygienic quality of whole-crop corn (WCC) silage. Fresh WCC harvested at the dough stage was ensiled with distilled water (CON), Leuconostoc lactis (LS) and Weissella confusa (WA) for 2, 4, 8, 15 and 30 days. After ensiling, all WCC silages presented desirable fermentation with high lactic acid and Lactobacillus proportions, low pH and ammonia nitrogen levels and absent butyric acid. Ensiling decreased the complexity of bacterial co-occurrence networks, and the Lc. lactis and W. confusa inoculation further decreased the complexity. The inoculation of W. confusa suppressed the most pathogenic pathways and related modules associated with zoonosis. In bacterial phenotype predicted analysis, although CON had lower proportions of ‘Potentially pathogenic’ than fresh material, this undesirable phenotype declined to negligible levels via LS and WA inoculation. Even for well-fermented WCC silages, the risk of pathogens remained after 30 days of ensiling. Therefore, WA could be developed as a promising fast start-up inoculant for reducing pathogenic contamination and improving hygienic quality of silage.Graphical

Core Soil Microorganisms and Abiotic Properties as Key Mechanisms of Complementary Nanoscale Zerovalent Iron and Nitrification Inhibitors in Decreasing Paclobutrazol Residues and Nitrous Oxide Emissions.

Agrochemical residues and nitrous oxide (N2O) emissions have caused considerable threats to agricultural soil ecology. Nanoscale zerovalent iron (nZVI) and nitrification inhibitors might be complementary to each other to diminish soil agrochemical residues and N2O emissions and enhance soil bacterial community diversities. Compared to the control, the nZVI application declined soil paclobutrazol residues by 5.9% but also decreased the bacterial community co-occurrence network node. Combined nZVI and Dicyandiamide applications significantly decreased soil N2O emission rates and paclobutrazol residues but promoted Shannon diversity of the bacterial community. The increased soil pH, ammonium nitrogen, and Actinobacteriota could promote soil paclobutrazol dissipation. The nZVI generated double-edged sword effects of positively decreasing paclobutrazol residues and N2O emissions but negatively influencing soil multifunctionalities. The nZVI and Dicyandiamide could be complementary to each other in diminishing soil agrochemical residues and N2O emission rates but promoting soil bacterial community diversities simultaneously.

Temporal dynamics of rhizosphere bacterial community in the Robinia pseudoacacia–Mesorhizobium loti symbiotic system for remediation of cadmium-contaminated soils

Rhizobia can be used to enhance the phytoremediation of cadmium-contaminated soils by legumes, and a symbiotic nitrogen-fixing system has been shown to reshape the structure of rhizosphere microbiota in a mining area. However, little is known about the temporal dynamics and possible roles of rhizosphere microbiota in rhizobia-enhanced phytoremediation. A rhizobox experiment was conducted using Robinia pseudoacacia alone or inoculated with Mesorhizobium loti HZ76 under greenhouse conditions. Rhizosphere bacterial communities were characterized over a 90-day period at three levels of cadmium (determined by the distance from the mining area; uncontaminated: 0.08 mg kg−1, contaminated: 0.39 and 1.72 mg kg−1). Rhizobial inoculation considerably improved the phytoremediation efficiency, such as increasing plant biomass and cadmium accumulation by approximately two times at 90 days after planting. The bacterial community structure shifted remarkably with increasing duration of remediation. Bacterial diversity exhibited a decreasing trend in the first 60 days and then recovered at 90 days. Despite having no discernible impact on the bacterial community structure in the rhizosphere, rhizobial inoculation enabled the enrichment of potentially beneficial taxa (e.g., Microvirga, Mesorhizobium, Diaphorobacter, Steroidobacter, Brevundimonas) with resistance to heavy metals and involvement in nutrient cycling. The bacterial co-occurrence networks of low and high cadmium-contaminated soils showed the highest average degree and clustering coefficient at 60 and 30 days, respectively. Some bacterial taxa involved in nitrogen fixation (e.g., Rhizobacter, Mesorhizobium), denitrification (e.g., Niastella, Nitrospira), and carbon turnover (e.g., Solirubrobacter, Brevundimonas) were found to be potential keystone taxa. The collective findings clarify possible mechanisms by which rhizosphere bacteria participate in phytoremediation of cadmium-contaminated mining soils using the R. pseudoacacia–M. loti symbiotic system.

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly

BackgroundMicrobial communities are of tremendous importance for ecosystem functioning and yet we know little about the ecological processes driving the assembly of these communities in the environment. Here, we used an unprecedented experimental approach based on the manipulation of physical distance between neighboring cells during soil colonization to determine the role of bacterial interactions in soil community assembly. We hypothesized that experimentally manipulating the physical distance between bacterial cells will modify the interaction strengths leading to differences in microbial community composition, with increasing distance between neighbors favoring poor competitors.ResultsWe found significant differences in both bacterial community diversity, composition and co-occurrence networks after soil colonization that were related to physical distancing. We show that reducing distances between cells resulted in a loss of bacterial diversity, with at least 41% of the dominant OTUs being significantly affected by physical distancing. Our results suggest that physical distancing may differentially modulate competitiveness between neighboring species depending on the taxa present in the community. The mixing of communities that assembled at high and low cell densities did not reveal any “home field advantage” during coalescence. This confirms that the observed differences in competitiveness were due to biotic rather than abiotic filtering.ConclusionsOur study demonstrates that the competitiveness of bacteria strongly depends on cell density and community membership, therefore highlighting the fundamental role of microbial interactions in the assembly of soil communities.

Comparison of Intestinal Bacteria of Procambarus clarkii Farmed in Various Rice Paddy Regions.

The aim of this study was to assess the regional differences of Procambarus clarkii through analyzing gut microbiota in specimens from different areas in China. The P. clarkii were collected from ten integrated rice-crayfish farming systems locating across ten major producing areas as follows: Feixi (FX), Suqian (SQ), Yangzhou (YZ), Xuyi (XY), Qianjiang (QJ), Jianli (JL), Honghu (HH), Yueyang (YY), Changsha (CS), and Nanxian (NX). The composition of gut microbiota was assessed by analyzing 16S rRNA sequences. The PCoA results indicated significant differences in microbial community composition among the ten areas (R = 0.999, p = 0.001). The intestinal microbial diversity in P. clarkii cultured in rice fields from YY and CS exceeded that of other regions, with NX displaying the least diversity. At the phylum level, Proteobacteria were most abundant in HH, while Firmicutes showed increased relative abundances in FX and SQ, contrasted by lower relative abundances of Bacteroidetes in these areas. At the genus level, Ralstonia, Amedibacillus, Bacteroides, Anaerorhabdus, and Dysgonomonas were the dominant bacteria. The bacterial co-occurrence networks analysis revealed that the community structures in locations FX, SQ, XY, HH, and NX were comparatively simplistic, whereas those in the YZ, QJ, JL, YY, and CS regions displayed as more complex. In summary, the diversity and relative abundance of intestinal bacteria exhibits regional variability. These findings can offer theoretical data for evaluating the quality of P. clarkii aquaculture.

Responses of soil bacterial and fungal community structure and functions to different plant species in a mixed forest plantation in a semi-arid region of China

Soil microbial communities play important roles in biogeochemical cycles and ecosystem functioning. However, how tree and grass species affect soil microbial structure and functions in semi-arid regions is poorly understood. In this study, we used sequencing of representative genes and bioinformatic analysis to compare the soil bacterial and fungal communities and their functional groups among legume and non-legume broad-leaved plantations, conifer plantations, artificial grassland, and adjacent farmland in a semi-arid area of Northern China. We found that soil bacterial diversity and abundance were significantly increased by legume plantations, especially Robinia pseudoacacia, compared to farmland. Soil bacterial communities were dominated by K-strategists in plantation soils and by r-strategists in farmland and grassland soils. Soil fungal communities showed contrasting patterns between Ascomycetes and Basidiomycota across treatments, and the highest abundance of nutrient indicator taxa Mortierellomycota was observed in plantation soils. Functional analysis revealed that afforestation altered the capacity of soil bacteria for organic compound mineralization and C and N cycling, and that different plant species enriched different types of ectomycorrhizal and saprophytic fungi. Moreover, we found that plantations and grasslands formed more connected but less complex and stable bacterial co-occurrence networks than farmland, and that conifer plantations increased the closeness of soil fungal networks compared to broad-leaved plantations. Our results suggest that tree and grass species play a key role in shaping the soil microbial community structure and functional groups, and provide valuable information for choosing suitable tree and grass species for ecosystem restoration and management in semi-arid regions.

Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome

BackgroundUndernutrition (UN) is a critical public health issue that threatens the lives of children under five in developing countries. While evidence indicates the crucial role of the gut microbiome (GM) in UN pathogenesis, the strain-level inspection and bacterial co-occurrence network investigation in the GM of UN children are lacking.ResultsThis study examines the strain compositions of the GM in 61 undernutrition patients (UN group) and 36 healthy children (HC group) and explores the topological features of GM co-occurrence networks using a complex network strategy. The strain-level annotation reveals that the differentially enriched species between the UN and HC groups are due to discriminated strain compositions. For example, Prevotella copri is mainly composed of P. copri ASM1680343v1 and P. copri ASM345920v1 in the HC group, but it is composed of P. copri ASM346549v1 and P. copri ASM347465v1 in the UN group. In addition, the UN-risk model constructed at the strain level demonstrates higher accuracy (AUC = 0.810) than that at the species level (AUC = 0.743). With complex network analysis, we further discovered that the UN group had a more complex GM co-occurrence network, with more hub bacteria and a higher clustering coefficient but lower information transfer efficiencies. Moreover, the results at the strain level suggested the inaccurate and even false conclusions obtained from species level analysis.ConclusionsOverall, this study highlights the importance of examining the GM at the strain level and investigating bacterial co-occurrence networks to advance our knowledge of UN pathogenesis.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42−), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42− levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus

Gut microbiota, or the collection of diverse microorganisms in a specific ecological niche, are known to significantly impact human health. Decreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand how the microbiome differs between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively. Microbiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. Two age- and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial community compositions were generated via DADA2. Metrics of microbial diversity and similarity between groups were computed. Biomarker analyses were performed to determine discriminating taxa. Bacterial co-occurrence networks were constructed to examine ecological patterns. A tight microbiota cluster was observed in the Dutch women, which overlapped with some of the SAS microbiota. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed, i.e., contained fewer inter-taxonomic correlational relationships. Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes, Odoribacter splanchnicus, and Lachnospira were enriched in the Dutch gut. Haemophilus, Bifidobacterium, and Anaerostipes hadrus discriminated the SAS gut. All but Lachnospira and certain strains of Haemophilus are known to produce SCFAs. The Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was not detected in the SAS. Among several potential gut microbial biomarkers, Haemophilus parainfluenzae likely best characterizes the ethnic minority group, which is more predisposed to T2DM. The higher prevalence of T2DM in the SAS may be associated with the gut dysbiosis observed.

Soil Microbial Biomass and Bacterial Diversity Enhanced through Fallow Cover Cropping in Rice–Fish Coculture

Traditional rice production is often reliant on the unsustainable practice of utilizing intensive inputs in monoculture cropping systems. Alternatives fallow cover cropping and rice–fish coculture (RFC) offer promising solutions. However, the potential of fallow cover cropping in RFC remains underexplored, and its impact on soil microbes is poorly understood. In this study, assessments of soil–plant–microbe interactions were conducted across three cover cropping systems: Chinese milk vetch (Astragalus sinicus L.) single cropping (CM), Rapeseed (Brassica napus L.) single cropping (RP), and a combination of Chinese milk vetch and rapeseed intercropping (CM_RP). These systems were evaluated with and without nitrogen (N) addition, encompassing both the RFC and rice monoculture (RMC) systems. The findings indicate a notable increase in soil microbial biomass nitrogen (MBN) with CM. Soil microbial biomass carbon (MBC), influenced more by N-fertilizer than crop species, decreased with N addition. In the RFC system, the soil bacterial co-occurrence network exhibited more connections, yet negative links increased. CM_RP displayed similarities to CM without N but shifted closer to RP with N addition. N addition in intercropping significantly increased the root–shoot ratio (R/S) of A. sinicus, associated with decreased aboveground biomass and total root length. Compared to RMC, RFC with N addition reduced the relative abundance of Anaerolineaceae in CM while increasing Bacillus and Pontibacter across cover cropping systems. Overall, with N addition, both RFC and RMC showed decreased soil bacterial diversity indices. Changes in soil bacterial diversity correlated significantly with soil MBC, MBN, and plant R/S. Continuous fallow cover cropping altered soil microbial biomass and affected cover crop biomass distribution, impacting bacterial composition in paddy soil. These results shed light on how bacterial communities respond to N addition and fallow cover cropping in RFC and RMC systems, offering insights for sustainable nutrient management in paddy systems.