Diversity Of Bacterial Communities Research Articles

Immobilization of Heavy Metals by Phosphorus-solubilizing Bacteria and Inhibition of Cd and Pb Uptake by Wheat

Phosphorus-solubilizing microorganisms convert insoluble phosphorus in the soil into phosphorus that can be absorbed by plants. Soluble phosphate combines with heavy metals to form precipitation, reducing the content of available heavy metals, thereby reducing the absorption of heavy metals by crops, which plays an important role in the remediation of heavy metal-contaminated soil. The effects of the immobilization of Cd and Pb and the release of PO43- by the phosphorus-solubilizing bacterium Klebsiella sp. M2 were studied through solution culture experiments. In addition, the effects of strain M2 on wheat uptake of Cd and Pb and its microbiological mechanism were also explored through pot experiments. The results showed that strain M2 reduced the concentrations of Cd and Pb and increased the concentration of PO43- in the solution through cell wall adsorption and induced phosphate precipitation. Pot experiments showed that compared to those in the CK group and inactivated strain M2 group, inoculation with live strain M2 significantly increased （123%-293%） the contents of Ca2-P and Ca8-P in rhizosphere soil, decreased the content of DTPA-Cd （34.48%） and DTPA-Pb （36.72%） in wheat rhizosphere soil, and thus hindered the accumulation of Cd and Pb in wheat grains. Moreover, high-throughput sequencing results showed that strain M2 significantly increased the diversity of wheat rhizosphere bacterial communities； increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidota in wheat rhizosphere soil； and increased the proportion of heavy metal-immobilizing and phosphorus-promoting bacteria in wheat rhizosphere soil （mainly Sphingomonas, Nocardioides, Bacillus, Gemmatimonas, and Enterobacter）. These bacterial genera played an important role in immobilizing heavy metals and preventing wheat from absorbing heavy metals. These results provide bacterial resources and theoretical basis for the bioremediation of heavy metal-contaminated farmland.

Effects of Different Microbial Fertilizers on Soil Quality and Maize Yield in Coastal Saline Soil

Microbial fertilizers have the characteristics of high efficiency and environmental protection in improving saline soils, and the application of functional microbial fertilizers is of great significance for the green abatement of saline barriers and the improvement of soil quality in coastal areas. The experiment was based on moderately saline soil in the coastal area of Hebei Province, with corn as the indicator crop, on the basis of conventional chemical fertilizer application. Different microbial fertilizer treatments, namely, T1 （conventional chemical fertilizer 750 kg·hm-2 + compound microbial agent 75 kg·hm-2）, T2 （conventional chemical fertilizer 750 kg·hm-2 + Bacillus megaterium 300 kg·hm-2）, T3 （conventional chemical fertilizer 750 kg·hm-2 + B. mucilaginosus 300 kg·hm-2）, T4 （conventional chemical fertilizer 750 kg·hm-2 + organic silicon fertilizer 600 kg·hm-2）, T5 （conventional chemical fertilizer 750 kg·hm-2 + bio-organic fertilizer 600 kg·hm-2）, T6 （conventional fertilizer 750 kg·hm-2 + active microalgae 15 kg·hm-2）, and CK （only fertilizer 750 kg·hm-2）, were used for these seven treatments, to study the effects of different microbial fertilizers on soil nutrients, salinity, bacterial community, and corn yield and economic efficiency during two critical periods （V12 stage and maturity stage） of corn. The results showed that compared with that in CK, T1 significantly increased soil total nitrogen （TN） and available phosphorus （AP） contents during the whole growth period. Over the whole reproductive period, soil organic matter （OM） at maturity increased by 10.35% over the V12 stage compared to that in CK, but there was no significant difference between treatments. Compared with that in CK, T5 and T6 significantly reduced soil total salinity and Ca2+ content during the whole growth period by an average of 14.51%-18.48% and 24.25%-25.51%. T1 significantly increased the bacterial diversity index over the whole growth period by 45.16% compared to that in CK. The dominant soil phyla were Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, and the dominant genera were Bacillus and Geminicoccaceae. The most abundant functions of the bacterial community in the study area were chemoheterotrophy and aerobic chemoheterotrophy, with average relative abundances of 28.89% and 27.11%, and T3 and T6 significantly improved soil N cycling function. The results of redundancy analysis （RDA） indicated that Na+, SO42-, pH, and EC were important factors driving the structure of the bacterial community, and correlation heatmaps showed that Na+, SO42-, pH, and EC were significantly and positively correlated mainly with the phylum Planctomycetota, whereas soil OM and TN were significantly and positively correlated with Cyanobacteria. Compared with that in CK, T6 increased the relative abundance of Cyanobacteria and optimized the bacterial community structure during the whole growth period. Using recommended dosages of bacterial fertilizers T1 and T6 increased maize yield by 7.31%-24.83% and economic efficiency by 9.05%-23.23%, respectively. The preliminary results of soil chemical properties and yield correlation analysis revealed that EC, AP, HCO3-, and Mg2+ were the obstacle factors limiting soil productivity in coastal areas. In conclusion, the use of the compound bacterial agent （T1） and active microalgae （T6） at the recommended dosage can significantly enhance soil nutrients, reduce salinity, and improve the structural diversity of soil bacterial communities, which not only ensures the increase in maize yield and efficiency but also realizes the efficient use of microbial fertilizers and the improvement of soil quality.

A bacteria-based index of biotic integrity indicates aquatic ecosystem restoration

Intensive ecological interventions have been carried out in highly polluted shallow lakes to improve their environments and restore their ecosystems. However, certain treatments, such as dredging polluted sediment and stocking fish, can impact the aquatic communities, including benthos and fishes. These impacts can alter the composition and characteristics of aquatic communities, which makes community-based ecological assessments challenging. Here we develop a bacteria-based index of biotic integrity (IBI) that can clearly indicate the restoration of aquatic ecosystems with minimal artificial interventions. We applied this method to a restored shallow lake during 3-year intensive ecological interventions. The interventions reduced nutrients and heavy metals by 27.1% and 16.7% in the sediment, while the total organic carbon (TOC) increased by 8.0% due to the proliferation of macrophytes. Additionally, the abundance of sulfur-related metabolic pathways decreased by 10.5% as the responses to improved ecosystem. The score of bacteria-based IBI, which is calculated based on the diversity, composition, and function of benthic bacterial communities, increased from 0.62 in 2018 to 0.81 in 2021. Our study not only provides an applicable method for aquatic ecological assessment under intensive artificial interventions but also extends the application of IBI to complex application scenarios, such as ecosystems with significantly different aquatic communities and comparisons between different basins.

Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination

Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.

High dosage of exogenous glycine in cross-feeding breaks the equilibrium of anammox system

Strategies to break the cross-feeding equilibrium by dosing essential metabolites and thus enriching and isolating anammox bacteria (AnAOB) have been proposed, but amino acids have not been investigated as important cross-feeding pathways in anammox consortia. In this study, long-term experiments were designed to verify the effect of exgenous glycine on anammox consortia and changes in the bacterial community and metabolic activity after the addition of glycine in a highly active anammox system were investigated. The results showed that the impact of glycine on the activity of anammox highly depended on glycine concentrations, which was manifested as a promotive effect at low concentrations (0–150 mg/L) and an inhibitory effect at high concentrations (300–600 mg/L). The addition of low concentrations of glycine not only enhanced the diversity and richness of bacterial communities but also promoted the enrichment of Candidatus Kuenenia. The qPCR results showed that the content of functional genes Hzs, NirS and anammox 16S rRNA increased while the expression of amoA and NrfA genes was suppressed when glycine acted positively on AnAOB; Hzs and amoA were suppressed when glycine acted negatively on AnAOB, while the expression of NirS and NrfA genes increased dramatically. Specific anammox activity (SAA) experimental results show that 50–150 mg/L glycine was the optimal amount for promoting the activity of AnAOB. Analysis of community metabolic functions indicated that the addition of exogenous glycine resulted in a imbalance of glycine cross-feeding and promoted AnAOB enrichment mainly by affecting pathways such as other glycan degradation and Lysosome. Overall, this study provided new insights into understanding the glycine cross-feeding, which is essential for improving anammox-based technologies.

Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing

The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.

Mildew invasion: Deciphering its influence on primary metabolites and microbial dynamics in fermented cigar tobacco ecosystems

This study aimed to elucidate the impact of mildew on the quality of fermented cigar tobacco leaves (CTLs) and identify potential biomarkers. Chemical constituents, microbial communities and metabolites in healthy CTLs (HCTLs) and mildewed CTLs (MCTLs) were systematically analyzed. Compared with HCTLs, the moisture, reducing sugar and total nitrogen contents of MCTLs increased, but the levels of starch, protein, total sugar and carbon-nitrogen ratio decreased. Mildew significantly altered flavor profiles, with 31 volatile flavor compounds (VFCs) and 9 free amino acids (FAAs) showing significant differences. Furthermore, the richness and diversity of bacterial and fungal communities decreased with mildew. The core functional microorganisms, including Pseudomonas, Pectobacterium, Aerococcus, Aspergillus, Alternaria, and Colletotrichum were screened. Notably, 2 chemical components (total acid, reducing sugar), 3 VFCs (2-undecanone,6,10-dimethyl, myosmine, 1-(5-methylfuran-2-yl)ethenone), and 4 FAAs (Asp, Ile, Val, Gly) were proposed as biomarkers indicating mildew tendency in fermented CTLs. These findings provide theoretical foundation for optimizing cigar production.

Bacterial community in the buckwheat rhizosphere responds more sensitively to single microplastics in lead-contaminated soil compared to the arbuscular mycorrhizal fungi community

Soil pollution by microplastics (MPs), defined as plastic particles <5 mm, and heavy metals is a significant environmental issue. However, studies on the co-contamination effects of MPs and heavy metals on buckwheat rhizosphere microorganisms, especially on the arbuscular mycorrhizal fungi (AMF) community, are limited. We introduced low (0.01 g kg−1) and high doses of lead (Pb) (2 g kg−1) along with polyethylene (PE) and polylactic acid (PLA) MPs, both individually and in combination, into soil and assessed soil properties, buckwheat growth, and rhizosphere bacterial and AMF communities in a 40-day pot experiment. Notable alterations were observed in soil properties such as pH, alkaline hydrolyzable nitrogen (AN), and the available Pb (APb). High-dose Pb combined with PLA-MPs hindered buckwheat growth. Compared to the control, bacterial Chao1 richness and Shannon diversity were lower in the high dose Pb with PLA treatment, and differentially abundant bacteria were mainly detected in the high Pb dose treatments. Variations in bacterial communities correlated with APb, pH and AN. Overall, the AMF community composition remained largely consistent across all treatments. This phenomenon may be due to fungi having lower nutritional demands than bacteria. Stochastic processes played a relatively important role in the assembly of both bacterial and AMF communities. In summary, MPs appeared to amplify both the positive and negative effects of high Pb doses on the buckwheat rhizosphere bacteria.

Root endophytic bacterial communities are shaped by the specific microbiota associated to mycorrhizal symbionts

Abstract Background and aims Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms establishing mutualistic symbioses with most crop plants and promoting plant growth and health. AMF beneficial activities are complemented by their associated microbiota, leading to synergistic interactions positively affecting plant performance. In this work we assessed whether AMF may act as drivers of root bacterial endophytes, facilitating root colonization of host plants by their associated bacteria. Methods Two AMF isolates were used, Funneliformis mosseae from Indiana (USA) and Septoglomus sp. from Tuscany (Italy) in an original experimental microcosm system, utilizing micropropagated plants of Prunus persica x Prunus amygdalus inoculated with either intact or mechanically crushed AMF spores, the former able and the latter unable to establish the symbiosis. Spore and root endophytic bacterial communities diversity were analysed by Illumina Miseq sequencing. Results This study revealed that AMF with their associated bacteria can shape the root endophytic bacterial communities, inducing differential recruitment depending on the composition of spore-associated microbiota. Such data were consistent between two AMF isolates, associated with diverse bacterial communities, as shown by PERMANOVA, Bray Curtis dissimilarity, hierarchical clustering and indicator species analyses. Moreover, specific bacterial taxa were found exclusively in mycorrhizal roots. Our findings suggested also a differential recruitment depending on the ability of AMF to establish mycorrhizal symbioses. Conclusion This work revealed that AMF represent drivers of the endophytic bacterial communities diversity and composition, facilitating root colonization of host plants by their associated bacteria, that become an integral part of the root microbiome as endophytes.

Gut microbiota mediates ambient PM2.5 exposure-induced abnormal glucose metabolism via short-chain fatty acids

PM2.5 exposure has been found to cause gut dysbiosis and impair glucose homeostasis in human and animals, yet their underlying biological connection remain unclear. In the present study, we aim to investigate the biological significance of gut microbiota in PM2.5-induced glucose metabolic abnormalities. Our results showed that microbiota depletion by antibiotics treatment significantly alleviated PM2.5-induced glucose intolerance and insulin resistance, as indicated by the intraperitoneal glucose tolerance test, glucose-induced insulin secretion, insulin tolerance test, insulin-induced phosphorylation levels of Akt and GSK-3β in insulin sensitive tissues. In addition, faecal microbiota transplantation (FMT) from PM2.5-exposed donor mice successfully remodeled the glucose metabolism abnormalities in recipient mice, while the transplantation of autoclaved faecal materials did not. Faecal microbiota analysis demonstrated that the composition and alpha diversity of the gut bacterial community were altered by PM2.5 exposure and in FMT recipient mice. Furthermore, short-chain fatty acids levels analysis showed that the circulating acetate was significantly decreased in PM2.5-exposed donor and FMT recipient mice, and supplementation of sodium acetate for 3 months successfully improved the glucose metabolism abnormalities induced by PM2.5 exposure. These results indicate that manipulating gut microbiota or its metabolites could be a potential strategy for preventing the adverse health effects of ambient PM2.5.

Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.

Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community? A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. Pseudomonas aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200mg l-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbon-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide-producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas, and Arcobacter. Culture-based and sequence-based analyses reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.

Estructura de la comunidad bacteriana asociada con raíces de Pinus montezumae Lamb. inoculado con hongos ectomicorrízicos comestibles y bacteria auxiliar de la micorriza

Tree roots are associated with a high diversity of microorganisms that play key roles in soil fertility and plant nutrition and health. Here we examine the composition and diversity of bacterial community in ectomycorrhizal root (ECR) and their ectomycorrhizosphere (EMR) of the Neotropical tree Pinus montezumae inoculated with Laccaria laccata and Hebeloma mesophaeum, applied alone or co-inoculated with Azospirillum brasilense. For this, we used a 16S rRNA gene metabarcoding-sequencing approach in samples of ECR and EMR that were collected nine-months after inoculation in greenhouse. A total of 943 Operational Taxonomic Units (OTU) were differentiated and grouped in 32 bacterial phyla. The most abundant phyla were Proteobacteria (67%) and Actinobacteria (20.7%). Bacterial communities were structured in ECR and EMR (Anosim, R=0.77, P≤0.005), and were more diverse in EMR than ECR (Shannon-Weaver of 4.2 and 3.6, and Simpson inverse of 33.7 and 16.7, respectively). The abundance of Pseudomonas, Actinoplanes and Salinibacterium were promoted with L. laccata, while with H. mesophaeum an OTU from Burkholderiaceae was prominent. Our results showed that the ectomycorrhizal fungi strongly shaped the composition of the bacterial communities associated with roots of P. montezumae.

Preceding crop rotation systems shape the selection process of wheat root-associated bacterial communities

Wheat-maize (WM) and wheat-soybean (WS) double-cropping rotation systems are predominant in the North China Plain, with implications for national agricultural output and sustainability. As rotation systems exert legacy effects on soil health and crop productivity, the role of crop rotation in shaping the root-associated microbiome of the succeeding crops has emerged as a pivotal aspect of crop management research. Here, the effects of the preceding two cycles of WM and WS rotations on the recruitment and filtering of wheat root-associated bacterial communities across wheat developmental stages were investigated. Our results revealed that bacterial community diversity and composition were primarily influenced by compartment and developmental stage, while the preceding rotation systems had a slight but significant effect on wheat root-associated bacterial communities. The co-occurrence networks under WM were more complex in the wheat rhizosphere and rhizoplane, with the OTUs related to cellulolysis showing greater connectivity. The co-occurrence networks under WS were simple but stable in the rhizosphere and complex in the rhizoplane and endosphere, with the OTUs related to ureolysis and nitrogen fixation showing greater connectivity. While both stochastic and deterministic processes contributed to the assembly of wheat root-associated bacterial communities, the contributions of deterministic processes under WS were 19.4–38.5% higher than those under the WM rotation across the root-associated compartments, indicating the substantial impact of a soybean legacy effect on wheat root selection of microbes. Plant growth-promoting rhizobacteria with the potential to fix nitrogen, produce indole-3-acetic acid, and inhibit diseases such as Betaproteobacteriales, Azospirillales and Dyella sp., were identified within the OTUs that were consistently enriched across all the wheat root-associated compartments and developmental stages, which were also important predictors of wheat yield. This study elucidates the role of crop rotation in modulating the dynamics of crop root-associated bacterial communities, and underscores the potential of targeted microbiome manipulation for optimizing wheat production and enhancing soil health.

Behavior of Spoilage Bacterial Communities in Different Cuts of Enshi Black Pork under Refrigerated Storage (4 °C).

The Enshi black pig is a Chinese native breed known for its rich nutrition content and high quality, which has notable traction in the consumer market. In this study, the potential impact of the main commercial cuts from Enshi black pork carcasses (ham, loin, and belly) on the bacteria community of spoiled meat under refrigerated storage (4 °C) was assessed by using a high-throughput sequencing method. Moreover, the spoilage potential of isolated strains from spoiled pork was investigated. The results demonstrated significant differences (p < 0.05) in bacterial community diversity and composition among spoiled ham, loin, and belly samples. Linear discriminant analysis effect size (LEfSe) analysis revealed a total of 20 significantly different potential bacterial biomarkers, with the dominant genera of Pseudomonas, Psychrobacter, Shewanella and Carnobacterium. Additionally, C. divergens THT1-5, isolated from spoiled ham samples, displayed cold adaptation and higher spoilage potential in Enshi black pork. These findings are helpful for identifying key factors contributing to spoilage in Enshi black pork and developing strategies to inhibit bacterial growth during preservation.

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

Land use patterns influence in the soil microbial composition

Studies on the impact of land-use patterns on soil health and sustainability have indicated that land-use changes and unsuitable agricultural practices are key driving factors in the degradation of soil. However, the impact of land-use patterns on soil microbial diversity is not entirely consistent or known, and the specific effects of environmental factors need to be further considered. This study explored the impact of three different land-use patterns—rotation land (RL), garden land (GL), and uncultivated land (UL)—on soil health in a farming region by analyzing the soil physicochemical properties and the diversity of the soil bacterial and fungal communities. In this study, the results showed that the soil pH of GL was significantly lower than that of RL and UL, total nitrogen was lowest in GL, and available potassium and soil organic carbon were higher in RL and GL than in UL. The impact of the land-use patterns on microbial diversity was somewhat inconsistent, but greater on soil bacteria than fungi, with 17 bacterial and 4 fungal metabolic pathways showing significant differences. In particular, a decrease in the relative abundance of dominant bacteria was observed in GL. The land-use patterns had little impact on fungal functional genes; however, plant pathogen-related fungi were significantly higher in GL than in RL and UL. Overall, these results indicate that while the soil basic nutrients in different land-use patterns were high, long-term single planting (GL) still had a negative impact on the health and sustainability of the soil, especially owing to low soil pH. Therefore, when evaluating the effect of different planting systems on soil health, it is necessary to consider the true effect of local agricultural measures on soil properties and microbial community composition, and monitor for microbial diseases in the field to determine the impact of land-use patterns on crop production.

The diversity, composition and functions of soil bacterial communities surrounding Syowa Station, East Antarctica, under different intensities of human disturbances

Since the establishment of Syowa Station over six decades ago, the study on the terrestrial bacterial community surrounding the station has been notably lacking and inadequately documented. Using the latest sequencing technology, we revealed the soil bacterial composition from soil samples collected from the surrounding of the station. In doing so, we also assessed the effect of human disturbances brought upon by different activities in the proximity of the station, in contrast to those in less human interference and pristine areas. Our results show that human activities near the main station facilities, especially within the 100-m range, visibly changed the structure and functions of the soil microbial community. Areas with high levels of human disturbances displayed a decrease in both microbial diversity and richness, accompanied by a lower count of unique amplicon sequence variants (ASVs) compared to regions with intermediate and low human disturbances. Moreover, higher proportions of functions related to hydrocarbon degradation were also predicted from samples collected within this area. In contrast, soil microbial communities from intermediate and low human disturbances samples have higher proportions of bacterial groups and functions consistent with those in undisturbed natural habitats.

Spatial Variation of Oomycetes and Bacteria on Surfaces, Solutions, and Plants from a Commercial Hydroponic Greenhouse

The spatial distribution and diversity of plant pathogens and other microbial communities in commercial operations is the first step in identifying critical control points where crops may be at risk of disease. Our objective was to characterize the spatial variation of oomycete pathogens and bacteria across the production system of a greenhouse producing lettuce in hydroponics. We utilized DNA metabarcoding to identify oomycetes and 16S rRNA gene sequencing of bacteria from different production stages and sample types (surfaces, solutions, and roots) collected from a commercial greenhouse producing lettuce in deepwater culture. Pythium was the genus with the highest relative abundance (41 to 100%) across all production stages. P. dissotocum was detected in most samples, except for sowing and seedling surfaces and municipal water, where P. myriotylum was the most abundant species. Oomycete communities showed distinct clustering by production stages and sample types, where sowing and seedling surfaces and municipal water were separated from the rest. Proteobacteria had the highest relative abundance in the surfaces at the sowing (98%) and seedling (85%) stages. Municipal water was the only sample with less than 20% relative abundance of Proteobacteria and dominated by Cyanobacteria. Negative correlations between Pythium and 13 bacteria genera point to potential antagonists in hydroponics that should be further studied. Mapping the spatial variation of oomycetes and bacterial communities in a commercial greenhouse indicates that production stage and sample type influence microbial composition and potentially the risk to disease.

Gut Microbial Adaptation to Varied Altitudes and Temperatures in Tibetan Plateau Yaks.

The yak (Bos grunniens) exhibits exceptional regional adaptability, enabling it to thrive in the distinctive ecological niches of the Qinghai-Tibet Plateau. Its survival relies on the intricate balance of its intestinal microbiome, essential for adapting to harsh environmental conditions. Despite the documented significance of bacteria and fungi in maintaining intestinal homeostasis and supporting immune functions, there is still a substantial gap in understanding how the composition and functionality of yak gut microbiota vary along altitude-temperature gradients. This study aims to fill this gap by employing 16S rRNA and ITS amplicon sequencing techniques to analyze and compare the intestinal microbiome of yaks residing at different elevations and exposed to varying temperatures. The findings demonstrate subtle variations in the diversity of intestinal bacteria and fungi, accompanied by significant changes in taxonomic composition across various altitudes and temperature gradients. Notably, Firmicutes, Actinobacteriota, and Bacteroidota emerged as the dominant phyla across all groups, with Actinobacteriota exhibiting the highest proportion (35.77%) in the LZF group. Functional prediction analysis revealed significant associations between the LZF group and metabolic pathways related to amino acid metabolism and biosynthesis. This suggests a potential role for actinomycetes in enhancing nutrient absorption and metabolism in yaks. Furthermore, our findings suggest that the microbiota of yaks may enhance energy metabolism and catabolism by modulating the Firmicutes-to-Bacteroidota ratio, potentially mitigating the effects of temperature variations. Variations in gut bacterial and fungal communities among three distinct groups were analyzed using metagenomic techniques. Our findings indicate that microbial genera exhibiting significant increases in yaks at lower altitudes are largely beneficial. To sum up, our research investigated the changes in gut bacterial and fungal populations of yaks residing across diverse altitude and temperature ranges. Moreover, these results enhance comprehension of gut microbial makeup and variability, offering perspectives on the environmental resilience of dry lot feeding yaks from a microbial angle.

Changes in soil bacterial community characteristics in patches of different vegetation types under different stages of restoration in the desert of northern China.

In desert areas, the process of mobile sandy land changing to semi-fixed sandy land and eventually to fixed sandy land after undergoing vegetation restoration is inevitable. The presence of shrub patches and herb patches is common in this restoration process. No relevant studies have reported the soil bacterial community characteristics of different vegetation-type patches (shrub patches and herb patches) under different stages of restoration. Therefore, we utilized long-established experimental plots to collect soil from 0-20 cm soil layer under shrub patches (dominated by Salix psammophila) and herb patches under different stages of restoration (i.e., mobile sand land, semi-fixed sand land, and fixed sand land), by determining soil physicochemical properties, enzyme activities, and soil bacterial communities. Our results found that soil bacterial α-diversity under different restoration stages showed higher shrub patches than herb patches. The dominant bacterial communities (phyla) in shrub patches and herb patches at different recovery stages were Actinobacteria, Proteobacteria, and Bacteroidota. When the mobile sandy land returned to fixed sandy land, the relative abundance of Actinobacteria and Bacteroidota gradually decreased under shrub patches and herb patches, while the relative abundance of Proteobacteria increased significantly. In addition, herb patches significantly increased the relative abundance of bacteria (genus) relative to shrub patches at different stages of recovery. Soil nutrients, soil fine particles, and soil enzyme activities were significantly higher under shrub patches than under herb patches when fixed sandy land due to differences in life form and architecture between shrub patches and herb patches. Based on this, soil bacterial community composition and diversity under shrub patches were driven by more soil properties during the restoration of sandy land. This study complements the dynamic recovery processes and driving mechanisms of soil bacterial community structure under different vegetation patches in sandy areas, especially in the context of global climate change.