Bacterial Community Composition Research Articles

Disentangling Shifts in the Soil Microbiome of Potatoes Infected with Rhizoctonia solani Anastomosis Group 3-PT in Search of Potential Biocontrol Agents

Rhizoctonia solani anastomosis group (AG) 3-PT is a devastating pathogenic fungus that causes several diseases in potatoes both in South Africa and globally. The removal of various fungicides from the market and strict regulations on the use of synthetic chemicals make disease management difficult. Therefore, alternative, environmentally safe control measures are being considered, such as the use of biological control agents (BCAs). BCAs are an attractive alternative for improving plant and soil health of economically important crops. To identify key microbial indicators of disease suppression against R. solani AG 3-PT, a greenhouse pot trial experiment was conducted using soil from a potato-growing region in KwaZulu-Natal, South Africa. High-throughput sequencing of fungal internal transcribed spacer and bacterial 16S ribosomal RNA was used to characterize the respective fungal and bacterial community composition in the soil with and without artificial inoculation with R. solani AG 3-PT. Results indicated that the pathogen caused dysbiosis in the potato soil microbiome, leading to a shift in fungal and bacterial community composition. Differentially abundant microbial taxa in R. solani AG 3-PT inoculated soils suggest a promising potential for disease-suppressive activity. Network analysis also confirmed the presence of key taxa involved in the microbial community shifts, which could support their role in the suppression of R. solani AG 3-PT. The identification of key microbial indicators against Rhizoctonia diseases can contribute to the development of environmentally sustainable potato production systems, which are particularly important considering the implementation of the European Green Deal.

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.

Litter Mass Loss of the Invasive Rhus typhina L. and Native Koelreuteria paniculata Laxm. Trees Alters Soil N-Fixing Bacterial Community Composition under Different N Forms

Soil N-fixing bacterial (NFB) community may facilitate the successful establishment and invasion of exotic non-nitrogen (N) fixing plants. Invasive plants can negatively affect the NFB community by releasing N during litter decomposition, especially where N input from atmospheric N deposition is high. This study aimed to quantitatively compare the effects of the invasive Rhus typhina L. and native Koelreuteria paniculata Laxm. trees on the litter mass loss, soil physicochemical properties, soil enzyme activities, and the NFB. Following N supplementation at 5 g N m−2 yr−1 in four forms (including ammonium, nitrate, urea, and mixed N with an equal mixture of the three individual N forms), a litterbag-experiment was conducted indoors to simulate the litter decomposition of the two trees. After four months of decomposition, the litter cumulative mass losses of R. typhina under the control, ammonium chloride, potassium nitrate, urea, and mixed N were 57.93%, 57.38%, 58.69%, 63.66%, and 57.57%, respectively. The litter cumulative mass losses of K. paniculata under the control, ammonium chloride, potassium nitrate, urea, and mixed N were 54.98%, 57.99%, 48.14%, 49.02%, and 56.83%, respectively. The litter cumulative mass losses of equally mixed litter from both trees under the control, ammonium chloride, potassium nitrate, urea, and mixed N were 42.95%, 42.29%, 50.42%, 46.18%, and 43.71%, respectively. There were antagonistic responses to the co-decomposition of the two trees. The litter mass loss of the two trees was mainly associated with the taxonomic richness of NFB. The form of N was not significantly associated with the litter mass loss in either species, the mixing effect intensity of the litter co-decomposition of the two species, and NFB alpha diversity. Litter mass loss of R. typhina was significantly higher than that of K. paniculata under urea. The litter mass loss of the two trees under the control and N in four forms mainly affected the relative abundance of numerous NFB taxa, rather than NFB alpha diversity.

Potential contributions of keystone species to intestinal ecosystem in patients with Crohn's disease.

Ravelling the central but poorly understood issue that potential contributions of keystone species to intestinal ecosystem functioning of patients with certain life-altering diseases including Crohn's disease (CD). In this study, a combination of 16S rRNA gene amplicon sequencing and amplicon-oriented metagenomic profiling was applied to gain insights into the shifts in bacterial community composition at different stages of CD course, and explore the functional roles of identified keystone species in intestinal microecosystem. Our results showed significant alterations in structure and composition of gut microbiota between CD patients and healthy control (HC) (P<0.05), but was no difference at active and remission stages. Whole-community-based comprehensive analyses were employed to identify the differential species such as Escherichia coli, Anaerostipes hadrus, and Eubacterium hallii in CD patients, with healthy populations as the control. Metagenome-wide functional analyses further revealed that the relative abundance of specialized metabolism-related genes such as cynS, frdB, serA, and gltB from these bacterial species in CD group was significantly different (P<0.05) from that in HC, and highlighted the potential roles of the keystone species in regulating the accumulation of important metabolites such as succinate, formate, ammonia, L-glutamate, and L-serine, which might have an effect on homeostasis of intestinal ecosystem. The findings identify several potential keystone species that may influence the intestinal microecosystem functioning of CD patients and provide some reference for future CD treatment.

Effects of biochar immobilization of Serratia sp. F4 OR414381 on bioremediation of petroleum contamination and bacterial community composition in loess soil

Petroleum hydrocarbons pose a significant threat to human health and the environment. Biochar has increasingly been utilized for soil remediation. This study investigated the potential of biochar immobilization using Serratia sp. F4 OR414381 for the remediation of petroleum-contaminated soil through a pot experiment conducted over 90 days. The treatments in this study, denoted as IMs (maize straw biochar-immobilized Serratia sp. F4), degraded 82.5% of the total petroleum hydrocarbons (TPH), 59.23% of the aromatic, and 90.1% of the saturated hydrocarbon fractions in the loess soils. During remediation, the soil pH values decreased from 8.76 to 7.33, and the oxidation-reduction potential (ORP) increased from 156 to 229 mV. The treatment-maintained soil nutrients of the IMs were 138.94 mg/kg of NO3- -N and 92.47 mg/kg of available phosphorus (AP), as well as 11.29% of moisture content. The activities of soil dehydrogenase (SDHA) and catalase (CAT) respectively increased by 14% and 15 times compared to the CK treatment. Three key petroleum hydrocarbon degradation genes, including CYP450, AJ025, and xylX were upregulated following IMs treatment. Microbial community analysis revealed that a substantial microbial population of 1.01E+ 09 cells/g soil and oil-degrading bacteria such as Salinimicrobium, Saccharibacteria_genera_incertae_sedis, and Brevundimonas were the dominant genera in IMs treatment. This suggests that the biochar immobilized on Serratia sp. F4 OR414381 improves soil physicochemical properties and enhances interactions among microbial populations, presenting a promising and environmentally friendly approach for the stable and efficient remediation of petroleum-contaminated loess soil.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes.

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Characteristics of DOM and bacterial community in rural black and odorous water bodies under different dimensions

Analysis of dissolved organic matter (DOM) composition and microbial characteristics is crucial for tracing the sources of rural black and odorous water bodies (BOWB). The aim of this study was to explore the DOM and microbial diversity and identify the primary environmental factors in BOWB from various pollution sources during different periods using EEMs-PARAFAC and Illumina sequencing. It was found that the physicochemical properties vary widely across different pollution types of BOWB, with higher overall content during the high-water period compared to the normal-water period. The types of dissolved organic matter in BOWB are Tyrosine proteins, Fulvic acid, Dissolved microbial metabolites, and Humic acid. During the normal-water period, DOM originates primarily from terrestrial sources in various water bodies. However, DOM affected by livestock and poultry waste and industrial effluents is influenced by both internal and external sources during periods of high water levels. In industrial waste-type BOWB, the biological sources of water are weak. Proteobacteria, Actinobacteria, Chloroflexi, Firmicutes were the dominant bacterial phyla. According to the redundancy analysis, pH (p = 0.047), Total nitrogen (TN) (p = 0.045), Organic carbon (OC) (p = 0.044), and Nickel (Ni) (p = 0.047) are the primary environmental factors influencing the composition of bacterial communities.

Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort

Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.

Assessing the effects of microwave heat disturbance on soil microbial communities in Australian agricultural environments: A microcosm study

Weeds reduce agricultural productivity by competing for resources intended for crops. Recently, the deactivation of weed seedbanks by microwave (MW) radiation has been developed as a chemical-free weed management practice. It is unknown, if these extreme heat disturbances permanently alter the soil microbiome of different farming systems. We performed a microcosm experiment to quantify the immediate and short-term effect of MW heating on the soil microbiome. We exposed three different soil types (representing dryland, temperate and irrigated farming systems) to MW heating, and monitored the fungal and bacterial communities over a month of recovery. Bacterial and fungal community composition were strongly dependent on the soil of origin. Following MW heating, bacterial and fungal richness decreased in all soils and did not recover during the period studied (four weeks). Notably, in all soils, bacterial communities became more dissimilar to each other following disturbance, but in fungi, this depended on the soil of origin. These results highlight the importance of considering the resistance and recovery of the resident soil microbiota in developing long-term sustainable MW-based weed management system.

Effect of Forest Fires on the Alpha and Beta Diversity of Soil Bacteria in Taiga Forests: Proliferation of Rare Species as Successional Pioneers

Forest fires are among the most influential drivers of changes in forest soil bacterial diversity. Nevertheless, little is known regarding the effects of forest fires on maintaining the complex interactions that preserve forest ecosystem stability. Therefore, this study characterized alterations in soil bacterial community composition and diversity within taiga forests subjected to varying disturbance intensities. Particularly, this study examined the bacterial community within a Larix gmelinii fire-burnt site in Daxinganling, analyzing the changes in bacterial community structure and function across light, moderate, and heavy fire-burnt sites, as well as a control sample site, utilizing Illumina MiSeq technology. Through an assessment of bacterial community diversity and soil physicochemical properties (moisture content (MC), pH, microbial biomass carbon (MBC), organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AP)), we explored the influence of the soil microenvironment on the soil bacterial community structure at the burnt site under different disturbance intensities. Our findings demonstrated that (1) there was no significant change in the Chao index of soil bacteria in the burnt site under different disturbance intensities, whereas the Shannon index decreased significantly (p &lt; 0.05) and the Simpson index increased significantly (p &lt; 0.05) in the burnt site under light and moderate disturbance. (2) The relative abundance of dominant phyla, such as Proteobacteria, Proteobacteria, and Actinobacteriota, did not change significantly in the fire-burnt site under different disturbance intensities, whereas rare species, such as Acidipila, Occallatibacter, and Acidibacter, experienced a significant increase in relative abundance at the genus level. (3) The results of principal coordinates analysis (PCoA) and canonical correlation analysis (CCA) revealed significant differences in the Beta diversity of soil bacteria in the fire-burnt site under varying interference intensities. The Beta diversity of soil bacteria exhibited significant differences (p = 0.001), with MC, pH, TN, AN, and AK identified as significant influencing factors. (4) FAPROTAX functional prediction analyses were conducted to assess the changes in soil bacteria involved in Cellulolysis, Chemoheterotrophy, and Aerobic_Chemoheterotrophy in the fire-burnt site, with the relative abundance of bacteria involved in Chemoheterotrophy being significantly increased (p &lt; 0.05) under different disturbance intensities. Collectively, our findings demonstrated that different disturbance intensities caused by fires significantly affected the Alpha diversity, Beta diversity, and functional abundance of soil bacterial communities in taiga forests, with MC, pH, TN, AN, and AK being identified as key influencing factors. Additionally, the presence of numerous rare species suggests their role as pioneer communities in the succession of soil bacterial communities.

Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao

Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, − Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.

Advanced sustainable processes via functionalized Fe–N co-doped fishbone biochar for the remediation of plasticizer di-(2-ethylhexyl) phthalate-contaminated marine sediment

Sediments are important sinks for di-(2-ethylhexyl) phthalate (DEHP), a plasticizer, and thus, maintaining the sediment quality is essential for eliminating plasticizers in aqueous environments and recovering the sediment ecological functions. To mitigate the potential risks of endocrine-disrupting compounds, identifying an effective and eco-friendly degradation process of organic pollutants from sediments is important. However, sustainable and efficient utilization of slow pyrolysis for converting shark fishbone to generate shark fishbone biochar (SFBC) has rarely been explored. Herein, SFBC biomass was firstly produced by externally incorporating heteroatoms or iron oxide onto its surface in conjunction with peroxymonosulfate (PMS) to promote DEHP degradation and explore the associated benthic bacterial community composition from the sediment in the water column using the Fe-N-SFBC/PMS system. SFBC was pyrolyzed at 300–900 °C in aqueous sediment using a carbon-advanced oxidation process (CAOP) system based on PMS. SFBC was rationally modified via N or Fe–N doping as a radical precursor in the presence of PMS (1 × 10−5 M) for DEHP removal. The innovative SFBC/PMS, N-SFBC/PMS, and Fe-N-SFBC/PMS systems could remove 82%, 65%, and 90% of the DEHP at pH 3 in 60 min, respectively. The functionalized Fe3O4 and heteroatom (N) co-doped SFBC composite catalysts within a hydroxyapatite-based structure demonstrated the efficient action of PMS compared to pristine SFBC, which was attributed to its synergistic behavior, generating reactive radicals (SO4•–, HO•, and O2•–) and non-radicals (1O2) involved in DEHP decontamination. DEHP was significantly removed using the combined Fe-N-SFBC/PMS system, revealing that indigenous benthic microorganisms enhance their performance in DEHP-containing sediments. Further, DEHP-induced perturbation was particularly related to the Proteobacteria phylum, whereas Sulfurovum genus and Sulfurovum lithotrophicum species were observed. This study presents a sustainable method for practical, green marine sediment remediation via PMS-CAOP-induced processes using a novel Fe-N-SFBC composite material and biodegradation synergy.

Evaluating microcystinase A-based approach on microcystins degradation during harvested cyanobacterial blooms

Addressing notorious and worldwide Microcystis blooms, mechanical algae harvesting is an effective emergency technology for bloom mitigation and removal of nutrient loads in waterbodies. However, the absence of effective methods for removal of cyanobacterial toxins, e.g., microcystins (MCs), poses a challenge to recycle the harvested Microcystis biomass. In this study, we therefore introduced a novel approach, the “captured biomass-MlrA enzymatic MC degradation”, by enriching microcystinase A (MlrA) via fermentation and spraying it onto salvaged Microcystis slurry to degrade all MCs. After storing the harvested Microcystis slurry, a rapid release of extracellular MCs occurred within the initial 8 h, reaching a peak concentration of 5.33 μg/mL at 48 h during the composting process. Upon spraying the recombinant MlrA crude extract (about 3.36 U) onto the Microcystis slurry in a ratio of 0.1% (v/v), over 95% of total MCs were degraded within a 24-h period. Importantly, we evaluated the reliability and safety of using MlrA extracts to degrade MCs. Results showed that organic matter/nutrient contents, e.g. soluble proteins, polysaccharides, phycocyanin and carotenoids, were not significantly altered. Furthermore, the addition of MlrA extracts did not significantly change the bacterial community composition and diversity in the Microcystis slurry, indicating that the MlrA extracts did not increase the risk of pathogenic bacteria. Our study provides an effective and promising method for the pre-treatment of harvested Microcystis biomass, highlighting an ecologically sustainable framework for addressing Microcystis blooms.

Arbuscular mycorrhizal fungal interactions bridge the support of root-associated microbiota for slope multifunctionality in an erosion-prone ecosystem.

The role of diverse soil microbiota in restoring erosion-induced degraded lands is well recognized. Yet, the facilitative interactions among symbiotic arbuscular mycorrhizal (AM) fungi, rhizobia, and heterotrophic bacteria, which underpin multiple functions in eroded ecosystems, remain unclear. Here, we utilized quantitative microbiota profiling and ecological network analyses to explore the interplay between the diversity and biotic associations of root-associated microbiota and multifunctionality across an eroded slope of a Robinia pseudoacacia plantation on the Loess Plateau. We found explicit variations in slope multifunctionality across different slope positions, associated with shifts in limiting resources, including soil phosphorus (P) and moisture. To cope with P limitation, AM fungi were recruited by R. pseudoacacia, assuming pivotal roles as keystones and connectors within cross-kingdom networks. Furthermore, AM fungi facilitated the assembly and composition of bacterial and rhizobial communities, collectively driving slope multifunctionality. The symbiotic association among R. pseudoacacia, AM fungi, and rhizobia promoted slope multifunctionality through enhanced decomposition of recalcitrant compounds, improved P mineralization potential, and optimized microbial metabolism. Overall, our findings highlight the crucial role of AM fungal-centered microbiota associated with R. pseudoacacia in functional delivery within eroded landscapes, providing valuable insights for the sustainable restoration of degraded ecosystems in erosion-prone regions.

Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Correlation between the bacterial community succession and purine compound changes during Huangjiu fermentation

Purine is mainly culprit of hyperuricemia (HUA) and gout, which is widely present in Huangjiu in the form of free bases. Bacterial succession plays an important role in quality control in Huangjiu. The correlation between the purine compound content and the bacterial communities during the fermentation process has not yet been evaluated. In this study, high-throughput sequencing (HTS) technology was used to monitor the bacterial community composition of Huangjiu at different fermentation stages. The correlation between the bacterial community and the contents of physicochemical properties and purine compounds were evaluated using the Spearman analysis method. The key enzymes of purine metabolism pathway in the microbial community were analyzed by bioinformatics using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The results showed that the purine content in Huangjiu increased gradually in 0∼9d of fermentation (21.05–65.71 mg/L), and stabilized gradually in 12∼18d (65.63–69.55 mg/L), while the abundance of lactic acid bacteria (LAB) of bacterial microbial flora were increased (0∼9d) and then stabilized (12∼18d). Moreover, Lactobacillus acetotolerans and Lactobacillus helveticus were highly correlated positively with purine contents, while Limosilactobacillus fermentum and Lactiplantibacillus plantarum were correlated negatively. In addition, the dominant strains of bacteria were involved in the metabolism of purine, and the key enzymes for purine compound synthesis were more abundant than that for purine degradation. This study is helpful to scientifically understand the formation mechanism of purines, providing a basis for screening functional strains of purine degrading to accurately regulate purine level in Huangjiu.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by ‘Candidatus Phytoplasma pini’ as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, ‘Ca. Phytoplasma pini’ is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

Pseudostellaria heterophylla improves intestinal microecology through modulating gut microbiota and metabolites in mice.

Pseudostellaria heterophylla is a Chinese medicine and healthy edible that is widely used to for its immunomodulatory, antioxidant, antidiabetic and antitussive properties. However, the potential function of P. heterophylla in intestinal microecology remains unclear. In this study, we investigated the impact of P. heterophylla on immune functions and evaluated its potential to regulate the gut microbiota and metabolome. The results showed that P. heterophylla significantly increased the content of red blood cells, total antioxidant capacity and expression of immune factors, and decreased platelet counts when compared to the control under cyclophosphamide injury. In addition, P. heterophylla altered the diversity and composition of the gut bacterial community; increased the abundance of potentially beneficial Akkermansia, Roseburia, unclassified Clostridiaceae, Mucispirillum, Anaeroplasma and Parabacteroides; and decreased the relative abundance of pathogenic Cupriavidus and Staphylococcus in healthy mice. Metabolomic analyses showed that P. heterophylla significantly increased the content of functional oligosaccharides, common oligosaccharides, vitamins and functional substances. Probiotics and pathogens were regulated by metabolites across 11 pathways in the bacterial-host co-metabolism network. We demonstrated that P. heterophylla increased the abundance of probiotics and decreased pathogens, and further stimulated host microbes to produce beneficial secondary metabolites for host health. Our studies highlight the role of P. heterophylla in gut health and provide new insights for the development of traditional Chinese medicine in the diet. © 2024 Society of Chemical Industry.

Response of bacterial and micro-eukaryotic communities to spatio-temporal fluctuations of wastewater in full scale constructed wetlands

How microbial communities respond to wastewater fluctuations is poorly understood. Full-scale surface flow constructed wetlands (SFCWs) were constructed for investigating microbial communities. Results showed that influent wastewater changed sediment bacterial community composition seasonally, indicating that a single bacterial taxonomic group had low resistance (especially, Actinobacteriota and Gammaproteobacteria). However, copy numbers of 16S rRNA, ammonia oxidizing archaea, ammonia oxidizing bacteria, nirS and nirK in the first stage SFCWs were 2.49 × 1010, 3.48 × 109, 5.76 × 106, 8.77 × 108 and 9.06 × 108 g−1 dry sediment, respectively, which remained stable between seasons. Moreover, decreases in the nitrogen concentration in wastewater, changed microbial system state from heterotrophic to autotrophic. Micro-eukaryotic communities were more sensitive to wastewater fluctuations than bacterial communities. Overall, results revealed that microbial communities responded to spatio-temporal fluctuations in wastewater through state changes and species asynchrony. This highlighted complex processes of wastewater treatment by microbial components in SFCWs.

Rehydration under extreme drought conditions affected rhizosphere microorganisms more than bulk soil in broomcorn millet farmland

Rehydration is a primary adaptation strategy for alleviating the detrimental effects of drought on crop growth. However, the effects of rehydration on microbial communities in various compartments under drought conditions remain poorly understood. Herein, we explored the response patterns of bacterial and fungal community composition, diversity, ecological network, and assembly process in the bulk soil and rhizosphere of broomcorn millet farmland at 5, 10, 20, and 30 days after rehydration during drought conditions. Compared to drought, rehydration significantly decreased the organic matter (OM), total nitrogen (TN), available potassium (AK), available phosphorus (AP), nitrate nitrogen (NO3--N), and ammonium nitrogen (NH4+-N) contents in rhizosphere, but had no obvious influences on the OM and TN contents in bulk soil on the four sampling days. In the rhizosphere of broomcorn millet field, Firmicutes and Actinobacteria were enriched in drought condition, but Proteobacteria and Bacteroidetes were enriched in rehydration regime. Compared to drought, the relative abundances of Eurotiomycetes, Dothideomycetes, Mortierellomycetes, and Leotiomycetes were enhanced, but Sordariomycetes was reduced on the 5th and 10th days after rehydration. Rehydration increased the bacterial and fungal observed ASVs and Shannon index in the rhizosphere to varying degrees, but had little effect on the bulk soil. Null-model analysis indicated that rehydration deceased the stochastic process of fungal communities in the bulk soil, whereas had no influence on deterministic process of bacterial community in the bulk soil and rhizosphere. More importantly, rhizosphere properties had a greater impact on the bacterial and fungal community composition, diversity, and assembly process than bulk soil. Network analysis revealed that rehydration improved the interconnected taxa in the rhizosphere bacterial network, but reduced microbial interactions in the rhizosphere fungal network compared to drought. This work provides a theoretical foundation for elucidating the role of rehydration regime in governing the ecological services of microbiome of broomcorn millet farmland under drought conditions.