Bacterial Community Composition Research Articles

Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization.

Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.

Farm dairy effluent application

Dairy intensification produces a large amount of farm dairy effluents (FDE). The final disposal of FDE is generally to the soil as fertilizer. While this use of FDE as fertilizer has numerous benefits, such as reducing the application of synthetic fertilizers or improving soil quality, there are concerns about the environmental and health risks associated with microbial pathogens from animal waste, the spread of antibiotic resistance genes, nutrient losses and greenhouse gases (GHG) emissions. Furthermore, how this agricultural practice impacts the composition and functionality of soil microbial communities has not yet been elucidated. This thesis aimed to evaluate the impact of FDE applications on soil GHG emissions, the composition, activity and diversity of its microbial community, and health risks. The FDE were collected raw and from a two-stage stabilization lagoon. The N application rate normalized to 200 kg N ha−1 was divided into four seasonal applications compared to urea fertilization or a no-aggregate control. Soil samples were taken after each application for microbial and physicochemical characterization and GHG fluxes were measured up to twenty days after each application. The pasture was harvested according to typical grazing management. Repeated application of both types of FDE increased the soil nutrient status and enhanced microbial activity. Higher fescue pasture production and macronutrient content with FDE than the control positioned FDE application to soil as an alternative disposal. However, N2O emissions increased after applying both FDE’s, most notably with raw FDE. Soil microbial community composition was not significantly influenced by FDE applications, but functional diversity shifted with raw FDE. Lagoon storage effectively reduced organic C and total N along with pathogenic indicator bacteria and changed the bacterial community composition except in winter. Beta-lactam resistance genes were detected in both FDEs, but not in the soil after repeated applications.

Composition and Diversity of Gut Bacterial Community in Different Life Stages of Osmia excavata Alfken (Hymenoptera: Megachilidae).

Osmia excavata is an excellent pollinator in nature and plays a vital role in the conservation of agro-ecosystems and food security. Given the important role of the gut bacterial community in host health and regulation of host growth and development, using 16S rRNA gene sequencing data, the present study explored the composition of the gut bacterial community and its diversity at different life stages (eggs, young larvae, old larvae, young pupae, old pupae, and 1-day-old adults in cocoons) of the solitary bee Osmia excavata. The results showed that the core phyla in the gut of O. excavata at different life stages were Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota, and the core genera were Sodalis, Tyzzerella, and Ralstonia. The highest intestinal bacterial diversity was found in the Egg period, and the lowest bacterial alpha diversity was found in the 1-day-old Adult period; the bacterial diversity of O. excavata showed a process of decreasing, as it was growing from the Egg period to the 1-day-old Adult period. Our study found that O. excavata undergoes a significant change in the structure of the gut flora when it grows from the young pupae to old pupae stage, a period of growth that coincides with the process of cocooning and isolation from the external environment after food depletion. This suggests that food and environmental factors are key contributors to the structure of the bacterial community in the gut of solitary bees.

Refractory wastewater shapes bacterial assembly and key taxa during long-term acclimatization

Bacterial assembly and key taxa during long-term acclimatization in refractory wastewater treatment systems is of paramount importance for optimizing system performance and improving management strategies. Therefore, this study employed high-throughput sequencing, coupled with machine learning models and statistical analysis approaches, to comprehensively elucidate key features of bacterial communities and assembly processes in pesticide wastewater treatment systems. A nine-month monitoring showed substantial variation in diversity and composition of bacterial community between two interconnected biological treatment units (designated as BA and PA). Dynamics of bacterial communities in both units were similar. Moreover, water quality played crucial roles in regulating the bacterial community structure of activated sludge, which were primarily driven by deterministic patterns. Homogeneous selection contributed to 62.85 % and 64.43 % of the variations in BA and PA samples, respectively. Additionally, network analysis revealed significant modularity in bacterial compositions in both groups. Linear regression analysis identified major bacterial modules associated with metabolism and degradation functions. Notably, Module 2 in PA samples has significant positive correlations with functions related to metabolism of nucleotide, amino acid, and xenobiotics, as well as benzoate degradation. Furthermore, key taxa in ecological modules identified by Random Forest model, such as Pseudomonas, Sphingobium, and PHOS-HE28, were dominant populations with metabolism and degradation functions. Particularly, Sphingobium, appeared to be a potential multifunctional degrading bacterium, related to amino acid and xenobiotics metabolism, as well as fatty acid, valine, leucine, isoleucine, fluorobenzoate, and aminobenzoate degradation. These findings are important for developing operating strategies to maintain stable system performance during refractory wastewater treatment.

Soil Solarization Efficiently Reduces Fungal Soilborne Pathogen Populations, Promotes Lettuce Plant Growth, and Affects the Soil Bacterial Community.

Lettuce is the most cultivated leafy vegetable in Greece; however, due to the adopted intensive cropping system, its cultivation is susceptible to many soilborne pathogens that cause significant yield and quality losses. In the current study, the impact of various soil disinfestation methods such as solarization, chemical disinfestation, and application of a biofungicide were evaluated in a commercial field that has been repeatedly used for lettuce cultivation. The populations of soilborne pathogens Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Fusarium equiseti were measured via qPCR before and after the implementation of the specific disinfestation methods. Although all the tested methods significantly reduced the population of the four soilborne pathogens, soil solarization was the most effective one. In addition, solarization reduced the number of lettuce plants affected by the pathogens R. solani and F. equiseti, and at the same time, significantly influenced the growth of lettuce plants. Amplicon sequence analysis of 16S rRNA-encoding genes used to study the soil bacterial community structure showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in soil samples. In general, solarization had positive effects on Firmicutes and negative effects on Proteobacteria and Actinobacteria; soil fumigation with dazomet increased the relative abundance of Firmicutes and Proteobacteria and reduced the corresponding values of Actinobacteria; and biofungicide had no significant effects on the three predominant bacterial phyla. The bacterial community composition and structure varied after the application of the soil disinfestation treatments since they imposed changes in the α- and β-diversity levels. The results of this study are expected to contribute towards implementing the most effective control method against the most common soilborne pathogens in intensively cultivated fields, such as those cultivated with leafy vegetables.

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds

BackgroundAnimal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies (Pica pica) and great spotted cuckoos (Clamator glandarius) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin.ResultsWe demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies.ConclusionsOur findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite—host system.

Global analysis of soil bacterial genera and diversity in response to pH

Soil pH stands as a decisive factor in shaping bacterial diversity and community composition, yet predicting the pH preferences and traits of individual bacterial taxa is still incomplete. We surveyed 942 samples from seven biomes worldwide to unravel the responses of individual bacterial genus to soil pH. Our findings indicate that soil pH surpasses the influences of spatial and climatic factors (biomes) in affecting bacterial composition and diversity. We observed that a comparable proportion of genera had low pH optima (21%), high pH optima (18%), and neutral pH optima (18%). However, apart from genera with optima groups, only a small percentage of genera were low pH tolerant (0.8%) compared to those that were high pH tolerant (21%). This suggests that a greater number of non-extremophiles genera can tolerate alkaline conditions compared to acidic conditions. Bacterial richness forms unimodal relationship with soil pH, consistently increasing from acidic levels to neutral across all biomes. However, the decline in richness when pH rises beyond neutral was less pronounced. This can be attributed to the higher number of alkaline-tolerant genera compared to acidic-tolerant genera. As expected, genera with acidic optima are more prevalent in humid climates, such as tropical forests, arctic tundra, and boreal forests, whereas genera with alkaline optima are generally dominant in arid grasslands and drylands. Collectively, our results indicate that the probability of existence of at least 75% of genera in specific soil pH conditions can be predicted, irrespective of biome. The identification of the actual niche spaces occupied by individual soil bacterial genera forms the foundation for developing comprehensive hypotheses regarding the response of soil communities to changing soil conditions worldwide.

Distinct Bacterial Community Composition in Rice Paddy Soil of Ebonyi State, Nigeria: Elucidation of Community Structure and Soil Physicochemical Properties

Distinct Bacterial Community Composition in Rice Paddy Soil of Ebonyi State, Nigeria: Elucidation of Community Structure and Soil Physicochemical Properties

Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests.

Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.

Synergistic changes in bacterial community composition, function, and soil characteristics of tomato rhizosphere soil under long-term monoculture conditions

Tomato is widely cultivated all over the world, and long-term monoculture has resulted in decreased tomato yields and stunted plant growth. Soil bacterial communities have a profound effect on plant growth and health, and the effect of different planting years on rhizosphere soil microorganisms of tomato is not clear. In this study, metagenomic sequencing was used to analyze the rhizosphere soil microorganisms of tomatoes cultivated continuously for 3, 6 years (short-term continuous cropping), 9, and 12 years (long-term continuous cropping) (LZ3, LZ6, LZ9, LZ12). The results showed that the pH in LZ9 was significantly higher than that in the other treatments, the relative abundance of Planctomycetes and Candidatus Rokubacteria in LZ3 were higher than those in the other treatments, the relative abundance of Proteobacteria was significantly higher in LZ6 and LZ9 than that in the other treatments, and the relative abundance of Chloroflexi and Bacteroidetes in LZ12 were higher than those in the other treatments. At the genus level, the relative abundance of Nocardioides, Sphingomonas, Pseudolabrys were lower in LZ3 than that in other treatments, and the relative abundance of Gaiella was significantly higher in short-term continuous cropping than that in LZ9. The pH, hydrolyzable nitrogen (HN), and available potassium (AK) were the most important factors driving the changes in microbial communities. The relative abundance of amino acid metabolism, terpenoid and polyketide metabolism decreased significantly with years of continuous cropping, and that total nitrogen (TN), HN, and available phosphorus (AP) were significantly correlated with translation, amino acid metabolism, and cell growth and death. Continuous cropping leads to nutrient imbalance in tomato soils, which affects the structure and functional composition of soil microbial communities, providing insights into microbial community response to continuous tomato cropping, but further in-depth studies are needed.

Compositional change of bacterial communities in oil-polluted seawater amid varying degrees of nanoplankton bacterivory

Petroleum hydrocarbons are being released into the marine environment continuously. They will undergo weathering and may eventually be biodegraded by bacteria and other microbes. While nanoplankton (2–20 μm) are the major consumers of marine bacteria, their effect on the process of biodegradation of oil hydrocarbons is still debated. A 14-day microcosm experiment was conducted to investigate the effects of crude oil hydrocarbons on nanoplankton bacterivory and bacterial community in coastal waters. The coefficients of population growth (0.56–1.80 d−1 for all treatments considered) and grazing mortality (0.38–1.65 d−1 for all treatment considered) of bacteria estimated with the dilution method did not differ among the treatments of control (Ctrl), low dose chemically dispersed oil (LDOil, 2 μL L−1 of crude oil), and high dose chemically dispersed oil (HDOil, 8 μL L−1 of crude oil). Bacterial abundance ranged between 0.21–0.86 × 106 cells mL−1 on average for all treatments. The lack of drastic increases in the cell density of bacterial cells in the oil-loaded treatments was observed throughout the experiment period. Sequencing analysis of the 16S rRNA gene revealed the progressive changes in the community compositions of bacteria in all treatments. The relatively high abundance of oil-degrading bacteria, including Cycloclasticus and Alcanivorax on Days 3–14 of the experiment reflected the presence of biodegradation of oil in the LDOil and HDOil treatments. Throughout the 14 days, the community composition of bacteria in the LDOil and HDOil treatments became more similar and they both differed from that in the Ctrl treatment. This study concluded that, in oil-polluted seawater, the changes in the bacterial community composition were mainly resulting from the addition of chemically dispersed crude oil.

Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum

BackgroundPenicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed.ResultsThe results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting.ConclusionsIn conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum.

Differences in Early Root Endophytic Bacterial Communities between Japanese Sake Rice Cultivars and Table Rice Cultivars

Sake, which is produced mainly from japonica rice (Oryza sativa subsp. japonica), is one of the most important alcohol products in Japan. In this study, we aimed to investigate a hypothesis that the early root endophytic bacterial communities in Japanese sake rice cultivars would be distinct from those in table rice cultivars, comparing four sake rice cultivars and two table rice cultivars. Rice roots in the vegetative stage were collected 0, 3, and 6 weeks after transplanting, and 16S rRNA gene amplicon sequencing revealed significant differences in bacterial community composition diversity between the sake and table rice cultivars. The root endophytic bacterial communities at the transplanting differed significantly between the rice cultivars, indicating differences in each seed-derived endophytic community. After an overall dominance of Pantoea and Methylobacterium-Methylorubrum at the transplanting, the endophytic community was gradually replaced by soil-derived bacteria that varied by the rice cultivars. Notably, PERMANOVA results showed that the rice endophytic bacterial community composition differed significantly between the sake and table rice cultivars (p < 0.001). These results highlight the distinct root endophytic bacterial composition in the sake rice cultivars compared to those in the table rice cultivars, supporting our hypothesis.

Variations of soil metal content, soil enzyme activity and soil bacterial community in Rhododendron delavayi natural shrub forest at different elevations

BackgroundRhododendron delavayi is a natural shrub that is distributed at different elevations in the karst region of Bijie, China, and that has an important role in preventing land degradation in this region. In this study, we determined the soil mineral element contents and soil enzyme activities. The composition of the soil bacterial community of R. delavayi at three elevations (1448 m, 1643 m, and 1821 m) was analyzed by high-throughput sequencing, and the interrelationships among the soil bacterial communities, mineral elements, and enzyme activities were determined.ResultsThe Shannon index of the soil bacterial community increased and then decreased with increasing elevation and was highest at 1643 m. Elevations increased the number of total nodes and edges of the soil bacterial community network, and more positive correlations at 1821 m suggested stronger intraspecific cooperation. Acidobacteria, Actinobacteria and Proteobacteria were the dominant phyla at all three elevations. The Mantel test and correlation analysis showed that Fe and soil urease significantly affected bacterial communities at 1448 m; interestingly, Chloroflexi was positively related to soil urease at 1448 m, and Actinobacteria was positively correlated with Ni and Zn at 1821 m. Fe and soil urease significantly influenced the bacterial communities at lower elevations, and high elevation (1821 m) enhanced the positive interactions of the soil bacteria, which might be a strategy for R. delavayi to adapt to high elevation environments.ConclusionElevation significantly influenced the composition of soil bacterial communities by affecting the content of soil mineral elements and soil enzyme activity.

Source and variation of the amazing live Sea-Monkey microbiome.

An embryonic diapause in unfavourable conditions has allowed brine shrimp to thrive in hypersaline environments and, unexpectedly, mail-order sachets and small, novelty tanks. Marketed as Sea-Monkeys®, each kit involves a 3-step process to generate adult Artemia within a matter of weeks. Whether these kits also allow for the maintenance of a host-associated microbiome is unclear. Therefore, comparing five replicate tanks under the same culture conditions, we sequenced the 16S ribosomal small subunit (SSU) gene to analyse bacterial community compositions in adults, their surrounding tank water, and their feed. Adult Sea-Monkeys® harboured a bacterial microbiome that was clearly distinguishable from the tank water and food. Furthermore, individual tanks had a notable effect on fine-scale microbiome variation. Several Sea-Monkey bacterial variants appeared absent in environmental samples and included genera (Leucobacter and Microbacterium) known to confer desiccation resistance in other hosts. Although Sea-Monkeys® taxonomy is unclear, phylogenetic inference of the cytochrome c oxidase I (COXI) gene from the host animal suggests Sea-Monkeys® belong to the Artemia franciscana 'superspecies'. Overall, Sea-Monkeys® kits appear to be a convenient and scalable mesocosm for the study of host-microbiome interactions and could serve as a useful tool for future invertebrate microbiome research, outreach, and education.

Global patterns in the growth potential of soil bacterial communities

Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.

Characteristics and assembly mechanisms of bacterial and fungal communities in soils from Chinese forests across different climatic zones

Forest soils are intricate ecosystems that harbor a diverse array of microorganisms, yet our current understanding of the characteristics and environmental implications of forest soil microbiomes remains limited. Here we present a continental-scale study on soil microbiomes of ten forests in China, spanning latitudes from 18°54′N to 50°48′N, resulting in a comprehensive catalog of bacterial and fungal operational taxonomic units (OTUs). Both bacterial and fungal communities exhibited discernible spatial variations in taxonomic and phylogenetic diversity. The composition of bacterial communities varied distinctively due to climatic zones—cold temperate, temperate, subtropical, and tropical—whereas fungal communities did not exhibit such pronounced distinctions. The co-occurrence network complexity of bacterial communities displayed a decremental trend along the cold temperate, temperate, subtropical, and tropical zones, whereas that of fungal communities displayed an incremental pattern. These results may be attributed to the facts that low temperatures sustain a high biomass of bacteria and foster increased interactions, while high temperatures and precipitation stimulate fungi-plant interactions. Furthermore, community assembly modeling revealed that forest soil microbial communities were dominated by stochastic processes. The bacterial community structure was mainly driven by homogeneous selection (26–41%) and dispersal limitation (35–44%), whereas dispersal limitation (51–56%) had the greatest impact on fungal community structure. Notably, bacterial functional genes associated with carbon fixation were more abundant in cold temperate soils compared to tropical soils. This study sheds light on spatial variations of forest soil microbiomes in China, enhancing further understanding of their response to global changes and implications for soil organic carbon cycles.

Alterations in the diversity and composition of the fecal microbiota of domestic yaks (Bos grunniens) with pasture alteration-induced diarrhea

Diarrhea is a common issue in domestic yaks (Bos grunniens) that can occur with pasture alterations and significantly impacts growth performance. Previous research has examined the microbiota of diarrhetic yaks; however, the structural changes in gut bacterial community and microbial interactions in yaks with grassland alteration-induced diarrhea remain poorly understood. To explore variations in gut microbiota homeostasis among yaks suffering from diarrhea, fecal microbiota diversity and composition were analyzed using 16 S rRNA amplicon sequencing. Gut fecal microbiota diversity was lower in diarrhetic yaks than in non-diarrhetic yaks. Furthermore, the bacterial community composition (including that of Proteobacteria and Actinobacteria) in the feces of diarrhetic yaks displayed significant alterations. Co-occurrence network analysis further underscored the compromised intestinal flora stability in yaks with diarrhea relative to that in non-diarrhetic yaks. Interestingly, the abundance of beneficial bacteria, such as Lachnospiraceae_AC2044_group and Lachnospiraceae_NK4A136_group, were decreased in yaks with diarrhea, and the reductions were negatively correlated with the fecal water content. Collectively, these findings indicate that diminished microbial stability and increased abundance of certain bacteria in the gut may contribute to diarrhea occurrence in yaks.

Effects of Acid Mine Drainage Leakage on Bacterial Communities in Desert Grassland Soil Profiles

Acid mine drainage （AMD） is of great concern owing to its safety hazards and environmental risks. However, little is known about the effects of AMD leakage on soil physicochemical properties and bacterial communities in ecologically fragile desert steppe soils, especially in the soil profile. Therefore, an AMD-contaminated profile and clean profile were used as research objects respectively to investigate the effects of AMD on soil physicochemical properties and bacterial community composition, structure, and interactions in soil layers at different depths of desert grassland and, based on this, to analyze the driving factors of bacterial community changes. The results showed that AMD significantly decreased the pH and increased electrical conductivity （EC） and heavy metal content in the upper （0-40 cm） soil layer of the profile. The AMD-contaminated profile bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacterota, whereas clean profile bacteria were dominated by Firmicutes and Bacteroidota, with Thermithiobacillus and Alloprevotella being the biomarkers for the contaminated and clean profiles, respectively. AMD contamination significantly reduced bacterial diversity and significantly altered bacterial community structure in the upper soil layers of the profile. The results of redundancy analysis showed that soil physicochemical properties explained 57.21% of the variation in bacterial community changes, with EC, TP, TN, As, Zn, and Pb being the main drivers of bacterial community changes. Network analyses showed that AMD contamination increased profile complexity, modularity, and intra-community competition, thereby improving bacterial community stability and resilience. In conclusion, the study provided useful information on the effects of AMD pollution on soil physicochemical properties and bacterial communities in desert steppe soils, which may help to improve the understanding of the ecological hazards of AMD pollution on soils in extreme habitats.

Effects of bacteriocin-producing Lactiplantibacillus plantarum on bacterial community and fermentation profile of whole-plant corn silage and its in vitro ruminal fermentation, microbiota, and CH4 emissions

BackgroundSilage is widely used to formulate dairy cattle rations, and the utilization of antibiotics and methane emissions are 2 major problems for a sustainable and environmentally beneficial ruminant production systems. Bacteriocin has received considerable attention because of its potential as an alternative to antibiotics in animal husbandry. However, the impact of bacteriocin-producing lactic acid bacteria on the microbiological conversion process of whole-plant corn silage and rumen fermentation remains limited. The purpose of this study was to assess the effect of 2 class IIa bacteriocin-producing strains Lactiplantibacillus plantarum ATCC14917 and CICC24194 on bacterial community composition and ensiling profiles of whole-plant corn silage and its in vitro rumen fermentation, microbiota, and CH4 emissions.ResultsBoth bacteriocin-producing strains increased the lactic acid concentration in silage fermented for 7 d, whereas the lowest lactic acid was observed in the ATCC14917 inoculated silage fermented for 90 d (P < 0.05). The highest DM content was observed in the CICC24194 treatment (P < 0.05), and the silages treated with both strains had the lowest DM loss (P < 0.05). Bacteriocin-producing strains promoted the growth of Levilactobacillus brevis on d 60 of ensiling. In addition, treatment with bacteriocin-producing strains increased the in vitro DM digestibility (P < 0.05) and decreased the CH4 production (P < 0.05). The results of random forest and clustering analyses at the genus level showed that ATCC14917 increased the relative abundance of the influential variable Bacillus compared to that in the control group, whereas CICC24194 decreased the relative abundance of the influential variable Ruminococcaceae UCG-005. The CICC24194 treatment had the lowest total bacterial, fungal, protozoan, and methanogen populations (P < 0.05).ConclusionsBoth class IIa bacteriocin-producing L. plantarum strains improved the fermentation quality of whole-plant corn silage by regulating the bacterial community composition during ensiling, with CICC24194 being the most effective. Both bacteriocin-producing strains mitigated CH4 production and improved digestibility by modulating the interactions among rumen bacteria, protozoa, methanogens, and the composition of fibrolytic bacteria.