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The variation in the soil microbial community composition over time was assessed at monthly time steps for 1 year in three neighboring Mollisols spanning a drainage gradient. This was done to distinguish between natural oscillations in the community composition versus lasting adaptations to environmental factors such as soil water availability. To isolate soil water availability as a controlling factor, we selected three soils sharing the same soil order (fine‐silty, superactive Argixerolls/Argialbolls); slope (0%–1%); temperature regime (mesic); moisture regime (xeric); and land use history (continuous grassland for the past 10 years) but differing in drainage class (well‐drained vs. moderately well‐drained vs. poorly drained). Changes in microbial diversity were quantified by monitoring the bacterial community at monthly intervals for 1 year. Within individual soils, α‐diversity varied little with season and drainage classes. Despite the three soils experiencing the same climate regime and vegetation/land use, they exhibited distinct community composition and turnover, which we attribute to differences in moisture availability across drainage and seasons. We posit that a seasonal recurring drop in soil redox potential induced by seasonal water saturation in the poorly drained soil is the most probable cause setting the microbial community of that soil apart from those in the better drained soils. Our investigation suggests that not all indicators of microbial diversity share the same sensitivity to seasonal and drainage‐related soil moisture variations. [ABSTRACT FROM AUTHOR]

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high‐throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia‐oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS‐type denitrifying community co‐varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities. Additionally, biotic interactions drove ammonia‐oxidizing and nirS‐type denitrifying communities by influencing species co‐occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N‐cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective Methods Results Conclusion To study the association between dietary patterns and subgingival microbiota.Participants (n = 651) who were enrolled in the Oral Infections, Glucose Intolerance, and Insulin Resistance Study (ORIGINS) with subgingival plaque sampling (n = 890 plaques) and a dietary assessment were included. 16S rRNA gene amplicon sequences of subgingival plaque from sites with either probing depth <4 or ≥4 mm were processed separately and used to obtain α‐diversity metrics (Faith, Shannon, Simpson, Observed) and taxa ratios (Red Complex to Corynebacterium [RCLR], Treponema to Corynebacterium [TCLR], and Treponema to Neisseria [TNLR]). Food frequency questionnaires (FFQs) were processed to calculate Alternate Healthy Eating Index (AHEI) and A Priori Diet Quality Score (APDQS) scores. Mixed regression models examined the mean levels of microbial metrics across quartiles of diet quality. Means ± standard errors are reported along with p‐values.In multivariable models assessing the association between diet scores and α‐diversity metrics, higher AHEI values were significantly associated with lower Faith (p‐value = 0.01) and Observed (p‐value = 0.04) diversity values; similar findings were observed for APDQS (p‐value = 0.01, p‐value = 0.04). In multivariable models assessing the association between diet scores (AHEI and APDQS) and taxa ratios (RCLR, TCLR and TNLR), as the AHEI quartile increased, all taxa ratios decreased significantly as follows: −1.06 ± 0.093 in Q1 to −1.34 ± 0.099 in Q4 (RCLR), −0.43 ± 0.077 in Q1 to −0.64 ± 0.083 in Q4 (TCLR) and −0.09 ± 0.083 in Q1 to −0.38 ± 0.089 in Q4 (TNLR), respectively. In contrast, as the APDQS quartiles increased, only TNLR decreased significantly from −0.08 ± 0.085 in Q1 to −0.34 ± 0.091 in Q4.Diets rich in fruits, vegetables, whole grains and other nutritionally rich plant foods are associated with lower oral microbial diversity and favourable ratios of pathogenic to commensal microbiota. [ABSTRACT FROM AUTHOR]

We attempt to determine the effect of the dietary switch from a native to non‐native prey on the gut microbiota in the predaceous ladybird Harmonia axyridis larvae and adults and examine how the dietary effect may vary across generations. We fed H. axyridis with different diets, native aphid Megoura japonica (Matsumura) versus non‐native mealybug Phenacoccus solenopsis (Tinsley), for 5 generations and sequenced microbes in the gut of the 3rd instar larvae and adults of the 1st, 3rd, and 5th generations. In addition, we identified microbes in M. japonica and P. solenopsis. The 2 prey species differed in microbial community as measured by abundances of prevalent microbial genera and diversity. In H. axyridis, abundances of some prevalent microbial genera differed between the 2 diets in the 1st and 3rd generations, but the difference disappeared in the 5th generation; this tendency is more obvious in adults than in larvae. Overall, gut microbial assemblages became gradually cohesive over generations. Microbial diversity differed between diets in the 1st and 3rd generations but became similar in the 5th generation. Major prevalent gut microbial genera are predicted to be associated with metabolic functions of H. axyridis and associated genera are more abundant for consuming the mealybug than the aphid. Our findings from this study suggest that the gut microbiota in H. axyridis is flexible in response to the dietary switch, but tends toward homogeneity in microbial composition over generations. [ABSTRACT FROM AUTHOR]

Biodiversity changes and habitat shifts are two phenomena substantially reshaping marine life on our present and future planet. Although those phenomena are well recognized on the macrobial level, they currently do not receive similar attention on the microbial level. Generally, microbiome diversity and function, associated with and governing the health and fitness of their host organisms, are neglected in conservation efforts. This is especially problematic as previous research has highlighted that host‐associated microbes (microbiomes) may display distribution patterns that are not only correlated with host animal biogeographies but also with other factors such as prevailing environmental conditions. Here, marine spatial planning for socio‐ecological management of animal‐associated microbiomes is discussed, using deep‐sea sponge and coral‐associated microbiomes as an example of how to incorporate microbial diversity into conservation planning. We advocate for a holistic and integrative approach to marine spatial planning that incorporates the larger habitat, the host, the microbiome, as well as the socio‐economic and cultural perspective, throughout the whole decision‐making process. A general workflow containing the needed steps to establish microbiome‐integrated marine protected areas is presented, as well as the analytical steps and results underlying the implementation of the world's first microbiome‐considered marine conservation network on the Scotian Shelf off eastern Canada. [ABSTRACT FROM AUTHOR]

Background: Nanofertilisers can enhance the efficiency of nutrient utilization in crop production. Nevertheless, it is unclear how soil microbial and enzyme activities are affected by the application of nanofertilisers to wheat inter‐root soil. Aims: The study aims to investigate the influences of nanocarbon (NC) and nano‐calcium carbonate (NCC) on soil enzyme activities and microbial community in the open field setting. Methods: The effects of nanofertilisers on soil wheat rhizosphere soil were studied through the evaluation of soil microbial quantity, enzyme activity, and microbial diversity. Results: The findings revealed that the combined utilization of nanofertilizers and compound fertilizers (CF) led to an augmentation in the diversity of the soil microbial community. When comparing the effects of 100% composite nanofertilizers (100% CF + 50% NC + 50% NCC) with the control (CK) (100% CF), it was observed that the activities of urease (EC 3.5.1.5), catalase (EC 1.11.1.6), alkaline phosphatase (EC 3.1.3.1), sucrase (EC.3.2.1.26), as well as the number of fungi, actinomycetes, and bacteria, increased by 22.4%, 7.7%, 17.8%, 9.3%, 35.9%, 27.7%, and 26.0%, respectively. Similarly, the employment of 70% composite nanofertilizers (70% CF + 35% NC + 35% NCC) also resulted in an enhancement of these aforementioned indicators. The magnitude of increase over the 100% CF was 19.0%, 6.6%, 13.6%, 6.2%, 26.8%, 21.3%, and 23.5%, respectively. Notably, there was no significant difference observed between 100% CF + 50% NC + 50 % NCC and 70% CF + 35% NC + 35% NCC within the 0–35 d after anthesis. Furthermore, both 100% CF + 50% NC + 50% NCC and 70% CF + 35% NC + 35% NCC contributed to an improvement in the species uniformity and operational taxonomic unit abundance of wheat rhizosphere microorganisms, while also increasing the abundance of Proteobacteria and Actinobacteria compared to the CK. The relative abundance of Bacteroidetes and Actinobacteria was found to be elevated in the nanomaterials‐treated groups, both at 0–7 d and 14–21 d after anthesis, and positively correlated with soil enzyme activities and soil microbial populations. Conclusions: These results indicate that the application of composite nanofertilizers can enhance the soil microenvironment in wheat fields, particularly under reduced fertilization conditions. [ABSTRACT FROM AUTHOR]

Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood.We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach.Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality.Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

This study aimed to characterize the taxonomic composition of intraradicular multispecies biofilms (IMB) formed in situ in a model to reproduce clinical conditions. Twelve palatal roots of maxillary molars had its canals prepared. Two roots were randomly selected to sterility control. Ten intraoral prosthetic appliances with lateral slots were fabricated. The roots were positioned in the slots with the canal access open to the oral cavity. Eight volunteers wore the appliance for 21 days, and two wore it at two different time points. One root from each appliance was removed and stored at −20°C until DNA extraction and sequencing (n = 10). Biofilm was analyzed using next‐generation sequencing and bioinformatics. The V4 hyper‐variable region of the 16SrRNA gene was amplified and sequenced. For data analyses, the mothur pipeline was used for 16SrRNA processing, and subsequent analyses of the sequence dataset were performed in R using the Microbiome Analyst R package. The taxonomy‐based analysis of bacterial communities identified 562 operational taxonomic units (OTUs), which belonged to 93 genera, 44 families, and 8 phyla. Bacterial colonization was different for each biofilm, and samples did not have the same group of bacteria. Alpha and beta diversity analysis revealed some general patterns of sample clustering. A core microbiome of prevalent OTUs and genera was identified. IMBs were heterogeneous when analyzed individually, but some diversity patterns were found after sample clustering. The experimental model seemed to reproduce the actual biofilm composition in endodontic infections, which suggests that it may be used to evaluate disinfection protocols. [ABSTRACT FROM AUTHOR]

Despite the diversity of microbiota in birds is similar to that of other animals, there is a lack of research on the gut microbial diversity of nondomesticated bird species. This study aims to address this gap in knowledge by analyzing the bacterial communities present in the gut of two important game bird species, the Ring‐necked pheasant (Phasianus colchicus) and the Green pheasant (Phasianus versicolor) to understand the gut microbial diversity of these species. The gut microbiome of 10 individual pheasants from two different species was studied using pooled fecal samples. We used 16S rRNA gene sequencing on the Ion S5 XL System next‐generation sequencing with Mothur and SILVA Database for taxonomic division. An average of 141 different operational taxonomic units were detected in the gut microbiome. Analysis of microbial classification revealed the presence of 191 genera belonging to 12 different phyla in both pheasants. Alpha diversity indices revealed that P. colchicus exhibited most prevalence firmicutes with bacillus species microbial community than P. versicolor. Alpha diversity indices indicated that P. colchicus had a more diverse community and P. versicolor had a greater diversity of evolutionary lineages, while both species had similar levels of species richness and sample inclusiveness. These findings may have implications for the health and well‐being of pheasants, serving as a reference for their bacterial diversity. Additionally, they provide a baseline for future research and conservation efforts aimed at improving the health and well‐being of these and possibly other avian species. Research Highlights: Our research highlights a gap in understanding nondomesticated bird species' gut microbes, despite similarities across animals. It could impact the health of game birds and provide a reference for pheasant bacterial diversity. [ABSTRACT FROM AUTHOR]

The purpose of this study was to evaluate the effects of potentially toxic elements (PTEs) on soil microbial community functionality and structure. Charcas and Cedral in San Luis Potosí, Mexico, are sites with ancient mining activity. This activity has generated heavy metals (HMs) polluted soils that provoke deleterious effects on microbial community. Sampling was conducted in sites with and without aged mining activity. The parameters analysed were physicochemical properties and PTE concentrations. Functional diversity was evaluated with a community‐level physiological profiling (CLPP) analysis, diversity was evaluated using the richness (S), and the indices of Shannon's diversity (H), Simpson's dominance (D) and Pielou's evenness (J) were for the structure evaluation, based on relative substrate utilisation. CLPP results of set of soils indicated the following substrate utilisation pattern: carbohydrates > polymers (POL) > carboxylic/ketonic acids > amino acids (AmA) > amine/amides (A/A). In Cedral, the AmA utilisation favoured the increase of J value. In addition, it was observed that the utilisation of these compounds decreases at a higher concentration of Al and organic matter (OM) but increases at a higher concentration of Cu, Pb, Zn, Fe, Mn, and Ni, a phenomenon opposite to that was observed in Charcas. The results of set of soil indicated that AmA utilisation increases the values of S, J, D, and H. These results indicate that the microorganisms in soil are resistant to high PTE concentrations, in that condition they need accessible carbon sources as energy and as nutrients, however, they adapted to use complex carbon sources (POL). Furthermore, it presented low OM mineralisation despite high values of H, or J, then some metabolic processes could be compromised. Therefore, an intervention for soil conservation and monitoring is required. [ABSTRACT FROM AUTHOR]

One of the most talked about issues of the 21st century is climate change, as it affects not just our health but also forestry, agriculture, biodiversity, the ecosystem, and the energy supply. Greenhouse gases are the primary cause of climate change, having dramatic effects on the environment. Climate change has an impact on the function and composition of the terrestrial microbial community both directly and indirectly. Changes in the prevailing climatic conditions brought about by climate change will lead to modifications in plant physiology, root exudation, signal alteration, and the quantity, makeup, and diversity of soil microbial communities. Microbiological activity is very crucial in organic production systems due to the organic origin of microorganisms. Microbes that benefit crop plants are known as plant growth‐promoting microorganisms. Thus, the effects of climate change on the environment also have an impact on the abilities of beneficial bacteria to support plant growth, health, and root colonization. In this review, we have covered the effects of temperature, precipitation, drought, and CO2 on plant–microbe interactions, as well as some physiological implications of these changes. Additionally, this paper highlights the ways in which bacteria in plants' rhizosphere react to the dominant climatic conditions in the soil environment. The goal of this study is to analyze the effects of climate change on plant–microbe interactions. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions To explore the role of gut microbiota in preterm infants at high risk of developing retinopathy of prematurity (ROP).Preterm infants with gestational age (GA) < 32 weeks and/or birth weight (BW) < 1500 g born between 2020 and 2021 were prospectively enrolled. Their faecal samples were collected and analysed at different postnatal ages of life using 16S rRNA gene sequencing on the Miseq platform. The main outcome measures were the microbial diversity, taxonomy, relative abundance, bacterial predicted functional analysis, and their associations with different ROP groups. Subgroup analyses were performed by matching their GA and BW across different ROP groups.A total of 268 stool samples were collected from 110 preterm infants, including 13 with type 1 ROP, 44 with type 2 or mild ROP, and 53 without ROP. Type 1 ROP showed no significant difference in microbial diversity up to 8 postnatal weeks (p = 0.057), while type 2 and no ROP groups displayed increased diversity (p = 0.0015 and p = 0.049, respectively). Bifidobacterium genera was notably less abundant in type 1 ROP group at first postnatal week (p = 0.022) and remained low in subsequent weeks. Predicted functional analysis revealed enriched pathways in membrane transport, carbohydrate metabolism, amino acid metabolism, and replication and repair.Reduced gut microbial diversity may be associated with ROP development in high‐risk preterm infants. Further research is needed to comprehend how early‐life Bifidobacterium reduction affects metabolism and how targeting microbiome may help for ROP prevention and management. [ABSTRACT FROM AUTHOR]

Metabolic dysfunction‐associated steatotic liver disease (MASLD) represents an impending global health challenge. Current management strategies often face setbacks, emphasizing the need for preclinical models that faithfully mimic the human disease and its comorbidities. The liver disease progression aggravation diet (LIDPAD), a diet‐induced murine model, extensively characterized under thermoneutral conditions and refined diets is introduced to ensure reproducibility and minimize species differences. LIDPAD recapitulates key phenotypic, genetic, and metabolic hallmarks of human MASLD, including multiorgan communications, and disease progression within 4 to 16 weeks. These findings reveal gut‐liver dysregulation as an early event and compensatory pancreatic islet hyperplasia, underscoring the gut‐pancreas axis in MASLD pathogenesis. A robust computational pipeline is also detailed for transcriptomic‐guided disease staging, validated against multiple harmonized human hepatic transcriptomic datasets, thereby enabling comparative studies between human and mouse models. This approach underscores the remarkable similarity of the LIDPAD model to human MASLD. The LIDPAD model fidelity to human MASLD is further confirmed by its responsiveness to dietary interventions, with improvements in metabolic profiles, liver histopathology, hepatic transcriptomes, and gut microbial diversity. These results, alongside the closely aligned changing disease‐associated molecular signatures between the human MASLD and LIDPAD model, affirm the model's relevance and potential for driving therapeutic development. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Xianju wheat paste, a traditional condiment in Hubei Province, China, possesses nutritional value and a distinctive taste profile. Nevertheless, there remains a dearth of comprehensive comprehension regarding the intricate interplay between the microbial population and its nutritional profile in Xianju wheat paste.It was determined that Xianju wheat paste harbors predominant microbial genera such as Bacillus, Staphylococcus and Aspergillus. The findings from high‐throughput sequencing analysis revealed the presence of 11 bacterial genera in Xianju wheat paste, with relative abundances exceeding 1%. These genera included Bacillus, Staphylococcus, Brevibacterium, Lactobacillus, Allorhizobium‐Neorhizobium‐Pararhizobium‐Rhizobium, Enterobacteriaceae, Pantoea, Brachybacterium, Klebsiella, Escherichia‐Shigella and Ochrobactrum. Furthermore, six fungal genera were identified with relative abundances greater than 1%, specifically Aspergillus, Zygosaccharomyces, Cutaneotrichosporon, Candida, Millerozyma and Rhizopus. The correlation analysis indicated a significant impact of the microbial community and nutritional flavor on the second phase of fermentation in Xianju wheat paste. The predominant bacterium Bacillus in Xianju wheat paste facilitated the production of free amino acids, whereas Staphylococcus exhibited a negative correlation with free amino acid levels. The quantity of volatile compounds in Xianju wheat paste progressively increased during fermentation, with the presence of typical aroma compounds 4‐vinyl‐2‐methoxyphenol significantly associated with Bacillus. This indicated Bacillus notably enhanced the production of aromatic substances. Furthermore, a strong correlation was observed between Staphylococcus and the 18 volatile organic compounds, highlighting their substantial contribution to these aroma compounds.This research indicates that the presence of microbial communities significantly contributes to the development of the nutritional flavor profile in Xianju wheat paste. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above‐ground (vegetation) and below‐ground factors (soil properties), which together create habitat‐specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode‐associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi‐arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode‐associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species‐specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above‐ and below‐ground effects to assess community structure in terrestrial habitats, and how fine‐scale analyses are critical for understanding patterns of host‐associated microbiomes. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions Previous local‐scale research (within plots or landscapes) has shown that invasive plants can alter the composition and diversity of soil microbial communities, with potential feedback effects on their own invasion success. However, the broader ecological patterns of these interactions across different invasion timescales and geographic regions remain poorly understood. This study investigated whether the composition and diversity of soil microbial communities associated with Solidago canadensis (Canada goldenrod) invasion vary across both population residence times and geographic locations.South‐eastern China.Soil fungal and bacterial communities and S. canadensis.We collected rhizospheric soil of S. canadensis, nonrhizospheric soil and adjacent uninvaded soil from each of 36 populations of S. canadensis with varying residence times (8–89 years), totalling 108 samples. We extracted DNA from these samples and sequenced the V3–V4 region of the bacterial 16S rRNA gene and the ITS2 region of the fungal rDNA. We analysed the DNA sequences to assess whether variation in α‐diversity, β‐diversity, arbuscular mycorrhizal fungi (AMF) richness and the ratio of AMF to plant pathogens in the soil microbial communities varied with S. canadensis population residence time, latitude and longitude.The α‐diversity and β‐diversity of soil fungal and bacterial communities significantly varied with S. canadensis residence times, latitude and longitude. In locations where S. canadensis had been established for longer periods, there was an increase in AMF richness and a decrease in plant pathogens in the rhizospheric soil. Fungal diversity in rhizospheric soils was positively correlated with longitude, while bacterial diversity in rhizospheric and nonrhizospheric soils was positively correlated with both latitude and longitude.These findings indicate that the time since invasion and geographical location can both significantly influence the composition and diversity of soil microbial communities associated with invasive plant species. [ABSTRACT FROM AUTHOR]

Though sterile diet, post‐transplantation surgery is a clinical strategy for patient care to prevent the infiltration of gut pathogens, less is known about its effects on the gut microbiome. Here, the gut microbiome dynamics of leukemia patients following a 120‐day "sterile‐normal" diet strategy posthematopoietic cell transplantation are examined. In contrast to the traditional idea, a sterile diet leads to the lowest gut microbiota diversity (p < 0.05) and short‐chain fatty acids, promoted the proliferation of potential pathogens such as Streptococcus (up by 16.93%) and Lactobacillus (up by 40.30%), and 43.32% reduction in nodes and an 85.33% reduction in edges within the microbial interaction's network. Interestingly, a normal diet allows the gut microbiome recovery and significantly promotes the abundance of beneficial bacteria. These results indicate that a sterile diet leads to a collapse of the patient's gut microbiome and promoted the proliferation of potential pathogens. This assay is a starting point for a more sophisticated assessment of the effects of a sterile diet. The work also suggests a basic principle for the re‐establishment of microbial equilibrium that supplementation of microbial taxa may be the key to the restoration of the degraded ecosystem. [ABSTRACT FROM AUTHOR]

While traditionally perceived as yield‐reducing elements in rice (Oryza sativa L.) cultivation, weed communities in paddy fields play a crucial role in the ecosystem. These communities, when selectively retained, can significantly enhance ecosystem services. This review examines the impact of various weed communities on rice in different paddy fields, their response to field nutrients, and the ecological benefits they offer. These benefits include nitrogen retention, promotion of microbial diversity, and reduction of diseases, pests, and weed proliferation. Examples of such benefits are seen in weeds like Lemna minor L. and Azolla imbricata (Roxb.) Nakai, which help in nitrogen fixation and act as biocontrol agents against harmful pests. However, current research in this area faces challenges, including the lack of intelligent and precise weed control technologies, comprehensive green control strategies, and expertise in weed management. Our findings suggest a strategic approach to weed control in paddy fields, emphasizing the importance of preserving weed species that have minimal impact on rice yields but offer significant ecological advantages. These practices can lead to grass‐mediated weed control and enhanced nutrient absorption, thereby reducing fertilizer loss. Ultimately, this approach could reduce the reliance on chemical fertilizers and herbicides in paddy fields, laying the groundwork for greener rice cultivation and sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

Diverse native plant communities resist non‐native plants more than species‐poor communities, in part through resource competition. The role of soil biota in diversity–invasibility relationships is poorly understood, although non‐native plants interact with soil biota during invasions. We tested the responses of non‐native plants to soil biota generated by different native plant diversities. We applied well‐watered and drought treatments in both conditioning and response phases to explore the effects of 'historical' and 'contemporary' environmental stresses. When generated in well‐watered soils, the microbial legacies from higher native diversity inhibited non‐native growth in well‐watered conditions. In contrast, when generated in drought‐treated soils, the microbial legacies from higher native diversity facilitated non‐native growth in well‐watered conditions. Contemporary drought eliminated microbial legacy effects on non‐native growth. We provide a new understanding of mechanisms behind diversity–invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota and non‐native plants. [ABSTRACT FROM AUTHOR]

Shelter‐building insects are important ecosystem engineers, playing critical roles in structuring arthropod communities. Nonetheless, the influence of leaf shelters and arthropods on plant–associated microbiota remains largely unexplored. Arthropods that visit or inhabit plants can contribute to the leaf microbial community, resulting in significant changes in plant–microbe interactions. By artificially constructing leaf shelters, we provide evidence that shelter‐building insects influence not only the arthropod community structure but also impact the phyllosphere microbiota. Leaf shelters exhibited higher abundance and richness of arthropods, changing the associated arthropod community composition. These shelters also altered the composition and community structure of phyllosphere microbiota, promoting greater richness and diversity of bacteria at the phyllosphere. In leaf shelters, microbial diversity positively correlated with the richness and diversity of herbivores. These findings demonstrate the critical role of leaf shelters in structuring both arthropod and microbial communities through altered microhabitats and species interactions. [ABSTRACT FROM AUTHOR]

Summary: Oral tolerance promotes the suppression of immune responses to innocuous antigen and is primarily mediated by regulatory T cell (Tregs). The development of oral tolerance begins in early life during a "window of tolerance," which occurs around weaning and is mediated by components in breastmilk. Herein, we review the factors dictating this window and how Tregs are uniquely educated in early life. In early life, the translocation of luminal antigen for Treg induction is primarily dictated by goblet cell‐associated antigen passages (GAPs). GAPs in the colon are negatively regulated by maternally‐derived epidermal growth factor and the microbiota, restricting GAP formation to the "periweaning" period (postnatal day 11–21 in mice, 4–6 months in humans). The induction of solid food also promotes the diversification of the bacteria such that bacterially‐derived metabolites known to promote Tregs—short‐chain fatty acids, tryptophan metabolites, and bile acids—peak during the periweaning phase. Further, breastmilk immunoglobulins—IgA and IgG—regulate both microbial diversity and the interaction of microbes with the epithelium, further controlling which antigens are presented to T cells. Overall, these elements work in conjunction to induce a long‐lived population of Tregs, around weaning, that are crucial for maintaining homeostasis in adults. [ABSTRACT FROM AUTHOR]

Studies have shown that the microbiome of saline‐tolerant plants plays a significant role in promoting salt stress in non‐saline‐tolerant plants, but the microorganisms are still unclear. In the present study, the microbial diversity changes in Suaeda salsa (L.) Pall. in the Yellow River Delta region were investigated. In the bacterial community, the dominant bacteria in the rhizosphere soil of the low‐saline soil (YDL), moderate‐saline soil (YDM), and high‐saline soil (YDH) groups were Proteobacteria, Chloroflexi, Bacteroidota, and Actinobacteriota (at the phylum level), while Ascomycota and Basidiomycota were the dominant fungi in the fungal community. At the family level, with the increase of salinity, the relative abundance of Rhodobacteraceae (bacterial community), Thermoascaceae, and Phaffomycetaceae (fungal community) gradually increased; and to the best of our knowledge, there are no reports on the relationship between Thermoascaceae and Phaffomycetaceae families with salt stress. At the genus level, Salinimicrobium (bacterial community) was the dominant bacterium in the rhizosphere soil of the YDL, YDM, and YDH groups, while with the increase of salinity, the relative abundance of Byssochlamys and Wickerhamomyces (fungal community) gradually increased, and to the best of our knowledge there are no reports on the relationship between Byssochlamys and salt stress. Salinity mainly affected the bacterial community abundance, but it had little effect on the fungi community abundance. The bacterial community of the YDH group was dominated by bacteria of unknown origin (52.76%), while bacteria of unknown origin accounted for 26.46% and 20.78% of the bacterial communities in the YDM and YDL groups, respectively. The fungi community of the YDH group was dominated by YDL group fungi (relative abundance of 44.44%), followed by YDM group fungi (29.42%) and fungi of unknown origin (26.14%). These results provide a better understanding of the rhizosphere microbial diversity of saline–alkali‐tolerant plants, laying a foundation for developing a saline–alkali‐tolerant plant microbiome. Studies have shown that the microbiome of saline‐tolerant plants plays a significant role in promoting salt stress in non‐saline‐tolerant plants, but the microorganisms and their mechanisms are still unclear. In this study, the Suaeda salsa (L.) Pall. in Yellow River Delta region was selected to study the changes of microbial diversity. These results can provide valuable information for understanding the rhizosphere microbial diversity of saline–alkali‐tolerant plants, and lay a foundation for developing saline–alkali‐tolerant plant microbiome. [ABSTRACT FROM AUTHOR]

Although bold and shy behavioral phenotypes in zebrafish (Danio rerio) have been selectively bred and maintained over multiple generations, it is unclear if they are underscored by different gut microbiota. Using the microbiota–gut–brain concept, we examined the relationship between gut microbiota and the behavioral phenotypes within this model animal system to assess possible gut microbe‐mediated effects on host behavior. To this end, we amplified and sequenced 16S rRNA gene amplicons from the guts of bold and shy zebrafish individuals using the Illumina Miseq platform. We did not record any significant differences in within‐group microbial diversity nor between‐group community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiome profiles between the two phenotypes would suggest that in this species, there might exist a stable core gut microbiome, regardless of behavioral phenotypes, and possibly, a limited role for the gut microbiota in modulating this selected‐for host behavior. This study characterized the gut microbiomes of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and did not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cold chain distribution with multiple links maintains low temperatures to ensure the quality of meat products, whereas temperature fluctuations during this are often disregarded by the industry. The present study simulated two distinct temperatures cold chain distribution processes. Quality indicators and high‐throughput sequencing were employed to investigate the effects of temperature fluctuations on the quality and microbial diversity of beef meatballs during cold chain distribution. RESULTS: Quality indicators revealed that temperature fluctuations during simulated cold chain distribution significantly (P < 0.05) exacerbated the quality deterioration of beef meatballs. High‐throughput sequencing demonstrated that temperature fluctuations affected the diversity and structure of microbial community. Lower microbial species abundance and higher microbial species diversity were observed in the temperature fluctuations group. Proteobacteria and Pseudomonas were identified as the dominant phylum and genus in beef meatballs, respectively, exhibiting faster growth rates and greater relative abundance under temperature fluctuations. CONCLUSION: The present study demonstrates that temperature fluctuations during simulated cold chain distribution can worsen spoilage and shorten the shelf life of beef meatballs. It also offers certain insights into the spoilage mechanism and preservation of meat products during cold chain distribution. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

BACKGROUND: Yangjiang douchi (YD) is a traditional fermented soybean product, which is popular in Chinese cuisine for its unique flavor. However, due to its high salt content and unstable flavor, its competitiveness in the international market is gradually weakening. Microorganisms have a key role in the production process of YD because it is a fermented food but the effect of microorganisms on the volatile compounds of YD is also not currently clear. RESULTS: In this paper, aroma compounds and microbial diversity in different fermentation stages of YD were analyzed using gas chromatography–mass spectrometry/olfactometry (GC–MS/O) and IlluminaMiseq system sequencing. A total of 78 aroma‐active compounds were detected throughout the fermentation process and they influenced the formation of flavor in YD. Fungi flora were relatively single in YD, and bacteria were rich and varied. A total of 418 species of bacteria were present during fermentation, with unclassified_Staphylococcus, Staphylococcus_kloosii, and Bacillus_velezensis_Bacillus predominating. There were 25 species of fungi at the species level, and Aspergillus minisclerotigenes (OTU 4) played a dominant role in the whole fermentation process. CONCLUSION: Staphylococcus and Bacillus in the bacterial genus were strongly correlated with most flavor compounds detected, and A. minisclerotigenes in the fungi were more relevant to flavor compounds. This research provides a theoretical basis for the enhancement of the flavor of traditional fermented douchi in China. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Many research findings stated that field pea was phenotypically diverse and symbiotically effective. However, limited studies were conducted on field pea (Pisum sativum var. abysinicum) regarding biological nitrogen fixation with local varieties and races. Therefore, the current study was conducted on the synergetic efficiency of locally available inoculums on yield and yield components of Dekoko. Randomized complete block design with three replications was used at farmers field level as an experimental design. The analysis of variance result revealed that, locally isolated Rhizobium inoculants significantly influence the agronomic parameters such as plant height, number of tillers, number of seeds, grain yield, and 1000‐seed weight at p < 0.05. The highest plant height (81.87 and 87.49 cm), pod number (19.53 and 20.93 NP/P), grain yield (633.2 and 790.2 kg ha−1) and 1000‐seed weight (97.33 and 92.42 g) were recorded from field condition. The rhizobial population count of the study sites varied, and experimental site number 1 had higher population count (2.33 × 108) compared to the second experimental site (1.23 × 108). Soils having various rhizobial population have different capability to fix atmospheric nitrogen. Since Ethiopian soils harbor rhizobial populations in the soil Rhizosphere. Therefore, the authors concluded that, prior to field experimentation, assessing the microbial diversity of the study area is a primary agenda. Core Ideas: Symbiotic efficiency of field pea nodulating bacteria through inoculating new isolated strains.Validating the presence or absence of native rhizobial population on the field experiment is mandatory.Evaluating the physiological and morphological characterization of the isolated strains are senstive isues.Nodulation and yield of field pea can affect through the presence or absence of rhizobial population in the Rhizosphere. [ABSTRACT FROM AUTHOR]

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio‐indicators of aged polluted drains. [ABSTRACT FROM AUTHOR]

In large and stratified lakes, substantial methane stocks are often observed within the metalimnion. The origin of the methane (CH4) accumulated in the metalimnion during stratification, which can sustain significant emissions during convective mixing, is still widely debated. While commonly attributed to the transport of methane produced anaerobically ex situ, recent evidence suggests that oxic in situ methane production could also contribute to metalimnetic methane peaks. Here, we assessed the origin, that is, pelagic CH4 production or transport of sublittoral CH4 through the interflow, of metalimnetic methane in Lake Geneva, the largest lake in Western Europe. Microbial diversity data do not support the hypothesis of oxic methane production in the metalimnion. In contrast, both spatial and temporal surveys of methane show that maxima occur at depths and sites most affected by the Rhône River inflow. Methane δ13C values point to an anaerobic sublittoral methane source, within a biogeochemical hotspot close to the river delta region, and an efficient transport across several kilometers in a vertically well‐constrained metalimnion. Our current findings emphasize the indirect role of river interflows for the long‐range transport of CH4 produced in sediment biogeochemical hotspots, even for large lakes where sublittoral habitats represent a fairly limited fraction of the lake volume. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions The airway microbiome in severe asthma has not been characterised at species‐level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in ‘type‐2 low’, neutrophilic asthma been defined. We performed an integrated species‐level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.Sputum and nasal lavage samples were analysed using long‐read metagenomic sequencing with Nanopore and qPCR in two cross‐sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species‐level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O‐link.The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type‐1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL‐10. R. mucilaginosa associated positively with IL‐6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type‐1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.This species‐level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma. [ABSTRACT FROM AUTHOR]

Recent studies have provided new insights into the role of the microbiome in shaping host behavior. However, the relationship between the temporal division of labor among honey bees (Apis mellifera) and their gut microbial community has not been widely studied. Therefore, we aimed to evaluate the link between the gut microbiome and division of labor in honey bees by examining the microbial absolute abundance and relative composition of 7‐day‐old nurse bees and 28‐day‐old forager bees from a natural hive, as well as those of worker bees of the same 14‐day‐old age showing different behaviors in a manipulated hive. We found that forager bees had fewer core bacteria, particularly gram‐positive fermentative genera such as Lactobacillus and Bifidobacterium, with Bifidobacterium asteroides being the most sensitive to host behavioral tasks. Our results showed that forager bees have lower gut community stability compared to nurse bees, suggesting that their gut community is more susceptible to invasion by non‐core members. Furthermore, a pollen limitation experiment using caged honey bees indicated that dietary changes during behavioral shifts may be a driving factor in honey bee microbial diversity. This study contributes to a greater understanding of the interaction between the gut microbiome and behavioral tasks and provides a foundation for future assays. [ABSTRACT FROM AUTHOR]

Background: Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis. Objectives: This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis. Methods: The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist. Results: From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as‐yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 105 to 106 in primary infections and from 103 to 104 in posttreatment infections. Discussion: Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta‐analysis. Conclusions: There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type. Registration: PROSPERO CRD42021275886. [ABSTRACT FROM AUTHOR]

Introduction: Stratum corneum (SC) is essential for skin barrier function, mitigating water loss and shielding against potentially harmful substances and allergens. The SC's lipid matrix, arranged in a lamellar structure, is integral to its protective role. Our study explores the restoration effects of a multilamellar cream with an acidic pH compared to a basic placebo cream on skin physiology and its interaction with the skin microbiome after stress induction via tape stripping (TS). Materials and Methods: In this double‐blind study, 14 healthy participants aged 21–58 years were assessed pre‐ and post‐tape stripping, followed by a 14 days application of a multilamellar test cream and a placebo cream with evaluations on days 7, 14 and 17 for sustained effects. Skin physiology was analysed in terms of epidermal barrier function, SC hydration and surface pH. The microbiome was analysed by 16S rRNA amplicon sequencing the 16S rRNA gene using Illumina MiSeq, with subsequent species identification. Results: Our study showed significant improvements in skin barrier repair and SC hydration with verum, particularly after 14 days of application, while both creams initially enhanced stratum corneum hydration. No significant changes in surface‐pH were detected. The skin microbiome analysis revealed that TS slightly decreased alpha diversity, a trend that verum significantly reversed, enhancing diversity beyond baseline levels after 14 days. Overall, while both creams contributed to a broader microbial phyla diversity over time, no significant changes in the abundance of specific genera or species were noted between treatments. Discussion and Conclusion: Our study delineates the efficacy of a pH‐optimized multilamellar cream in enhancing epidermal barrier recovery and SC hydration post‐sequential TS, in contrast to an unstructured basic placebo. Verum cream significantly improved skin barrier function and SC hydration at day 14, with sustained effects evident beyond the treatment period. Furthermore, the multilamellar formulation facilitated the restitution of cutaneous microbiome diversity, a key indicator of healthy skin ecology, underscoring the symbiotic relationship between barrier integrity and microbial composition. These findings underscore the importance of multilamellar emollient structures in dermatological therapeutics, with potential implications for the design of advanced skincare interventions that holistically support cutaneous resilience and homeostasis. [ABSTRACT FROM AUTHOR]

Tick vectors and tick‐borne disease are increasingly impacting human populations globally. An important challenge is to understand tick movement patterns, as this information can be used to improve management and predictive modelling of tick population dynamics. Evolutionary analysis of genetic divergence, gene flow and local adaptation provides insight on movement patterns at large spatiotemporal scales. We develop low coverage, whole genome resequencing data for 92 blacklegged ticks, Ixodes scapularis, representing range‐wide variation across the United States. Through analysis of population genomic data, we find that tick populations are structured geographically, with gradual isolation by distance separating three population clusters in the northern United States, southeastern United States and a unique cluster represented by a sample from Tennessee. Populations in the northern United States underwent population contractions during the last glacial period and diverged from southern populations at least 50 thousand years ago. Genome scans of selection provide strong evidence of local adaptation at genes responding to host defences, blood‐feeding and environmental variation. In addition, we explore the potential of low coverage genome sequencing of whole‐tick samples for documenting the diversity of microbial pathogens and recover important tick‐borne pathogens such as Borrelia burgdorferi. The combination of isolation by distance and local adaptation in blacklegged ticks demonstrates that gene flow, including recent expansion, is limited to geographical scales of a few hundred kilometres. [ABSTRACT FROM AUTHOR]

Climate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change. [ABSTRACT FROM AUTHOR]

Background: Zha cai, a pickled vegetable with unique flavors, is produced by fermenting fresh mustard tubers. In this study, the main physicochemical indices and volatile flavor compounds were determined in three fermentation periods. The bacterial and fungal communities in the three fermentation periods of zha cai were also monitored using high‐throughput sequencing. Key microbial communities were identified based on significant correlations with flavor substances. Results: Firmicutes and Proteobacteria were the main bacterial phyla found within the three fermentation periods. Lactic acid bacteria, namely Lactobacillus, was the predominant bacteria found at the genus level. Ascomycetes and Stenotrophomonas were the major fungal phyla found in the three fermentation periods. Yeast, namely Debaryomyces, was the predominant fungus found at the genus level. A total of 42 bacterial genera were negatively correlated with volatile flavor substances of zha cai, and 37 bacterial genera were positively correlated. Meanwhile, a total of 47 genera of fungi were negatively correlated with the volatile flavor substances of zha cai, while 50 genera were positively correlated. Several microbial genera were significantly correlated with volatile flavor compounds, including Lactobacillus, Halomonas, Rhodococcus, and Debaryomyces. Conclusion: This study identified the microbial classes that positively regulate the flavor of zha cai which could provide valuable help for flavor modulation in zha cai production. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Colistin is renowned as a last‐resort antibiotic due to the emergence of multidrug‐resistant pathogens. However, its potential toxicity significantly hampers its clinical utilization. Melatonin, chemically known as N‐acetyl‐5‐hydroxytryptamine, is an endogenous hormone produced by the pineal gland and possesses diverse biological functions. However, the protective role of melatonin in alleviating antibiotic‐induced intestinal inflammation remains unknown. Herein, we reveal that colistin stimulation markedly elevates intestinal inflammatory levels and compromises the gut barrier. In contrast, pretreatment with melatonin safeguards mice against intestinal inflammation and mucosal damage. Microbial diversity analysis indicates that melatonin supplementation prevents a reduction in the abundance of Erysipelotrichales and Bifidobacteriales, as well as an increase in Desulfovibrionales abundance, following colistin exposure. Remarkably, short‐chain fatty acids (SCFAs) analysis shows that propanoic acid contributes to the protective effect of melatonin on colistin‐induced intestinal inflammation. Furthermore, the protection effects of melatonin and propanoic acid on LPS‐induced cellular inflammation in RAW 264.7 cells are confirmed. Mechanistic investigations suggest that intervention with melatonin and propanoic acid can repress the activation of the TLR4 signal and its downstream NF‐κB and MAPK signaling pathways, thereby mitigating the toxic effects of colistin. Our work highlights the unappreciated role of melatonin in preventing the potential detrimental effects of colistin on intestinal health and suggests a combined therapeutic strategy to effectively manage intestinal infectious diseases. [ABSTRACT FROM AUTHOR]

Atmospheric nitrogen (N) deposition has been substantially reduced due to declines in the reactive N emission in major regions of the world. Nevertheless, the impact of reduced N deposition on soil microbial communities and the mechanisms by which they are regulated remain largely unknown. Here, we examined the effects of N addition and cessation of N addition on plant and soil microbial communities through a 17‐year field experiment in a temperate grassland. We found that extreme N input did not irreversibly disrupt the ecosystem, but ceasing high levels of N addition led to greater resilience in bacterial and fungal communities. Fungi exhibited diminished resilience compared to bacteria due to their heightened reliance on changes in plant communities. Neither bacterial nor fungal diversity fully recovered to their original states. Their sensitivity and resilience were mainly steered by toxic metal ions and soil pH differentially regulating on functional taxa. Specifically, beneficial symbiotic microbes such as N‐fixing bacteria and arbuscular mycorrhizal fungi experienced detrimental effects from toxic metal ions and lower pH, hindering their recovery. The bacterial functional groups involved in carbon decomposition, and ericoid mycorrhizal and saprotrophic fungi were positively influenced by soil metals, and demonstrated gradual recovery. These findings could advance our mechanistic understanding of microbial community dynamics under ongoing global changes, thereby informing management strategies to mitigate the adverse effects of N enrichment on soil function. [ABSTRACT FROM AUTHOR]

The magnitude of terrestrial carbon (C)‐climate feedback largely depends on the temperature sensitivity of soil organic matter (SOM) decomposition (Q10). However, our understanding of determinants of Q10 for SOM fractions such as particulate and mineral‐associated organic matter (POM and MAOM, respectively) is still inadequate. Particularly, it remains unclear whether microbial effects on Q10 are fraction‐dependent, which induces large uncertainties in projecting soil C dynamics. Here, we conducted large‐scale topsoil sampling on the Tibetan Plateau, in combination with SOM fractionation and 300‐day laboratory incubation to assess SOM fraction‐dependent linkages between Q10 and microbial properties. We found that compared with MAOM, POM had larger Q10 and greater microbial diversity, and also structured distinct microbial communities as well as their co‐occurrence patterns. Furthermore, associations of Q10 with microbial properties differed between the two SOM fractions. Bacterial community composition and relative abundance of bacterial keystone taxa affected Q10 for POM and MAOM respectively, while bacterial alpha diversity showed opposite relationships with Q10 for POM and MAOM. These findings highlight the necessity of incorporating SOM fraction‐dependent microbial properties and their linkages with Q10 into Earth system models to accurately predict terrestrial C‐climate feedback. [ABSTRACT FROM AUTHOR]

Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock‐soil‐plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including Picrophilus, Ferroplasma, and Thermogymnomonas were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including Ferrimicrobium and Granulicella were abundant in the rhizoplane samples, whereas rhizosphere‐associated microbes including Pseudomonas, Pedobacter, Rhizobium, and Novosphingobium were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock‐soil‐plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions. [ABSTRACT FROM AUTHOR]

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Objective Method Results Conclusion Exploring the effects of age on microbial community structure and understanding the effects of chronological ageing as well as sun exposure on microbial community diversity.The microbial characteristics of the facial skin of 98 adult women aged 18–70 years were studied using 16S rRNA gene sequencing, and differences based on age and reported sun exposure were assessed.The cheek skin's bacterial diversity and richness increased with age. The relative abundance of Cutibacterium decreased with age, while the relative abundance of Corynebacterium, Anaerococcus, Paracoccus, Micrococcus, Kocuria, Kytococcus, and Chryseobacterium increased. In addition, an increase in Micrococcus and a decrease in Cutibacterium were observed in volunteers with more than 2 h of daily sun exposure compared to volunteers with <2 h of daily sun exposure. Under low‐sunlight conditions, Cutibacterium was more prevalent in the youth group, and Corynebacterium, Anaerococcus, and Kytococcus were more prevalent in the older group.The diversity and composition of the bacterial community on the cheeks are affected by age and extrinsic factors (sun exposure) may also play a role in this. [ABSTRACT FROM AUTHOR]

Soil erosion has become a serious ecological problem hindering the agricultural and economic development in Northeast China. Soil aggregates are basic units that regulate soil fertility and microbial activity. However, there have been few reports on the role of soil erosion in regulating the microbial diversity, multiple ecosystem services, and functions (multifunctionality) of soil aggregates. In this study, we investigated the effects of soil erosion on microbial diversity and the activities of various extracellular enzymes associated with soil aggregates by using Mollisol soil in Northeastern China at different positions of a slope, and how soil erosion affects soil multifunctionality indexes obtained by normalized calculation of soil enzyme activities. The results showed that soil erosion could reduce the physicochemical properties, soil enzyme activity, and microbial diversity of the aggregates, resulting in accumulation of aggregate nutrients and increase in microbial diversity and enzyme activity in the sedimentation area. Compared with smaller soil aggregates, larger soil aggregates had higher nutrient content, enzyme activity, and microbial diversity. However, with the intensification of soil erosion, the differences in microbial diversity and soil enzyme activities among different sizes of aggregates were reduced. Soil erosion also significantly reduced soil multifunctionality (p < 0.001). The multifunctionality of 2000–250 μm, 250–53 μm, and <53 μm aggregates respectively declined from 0.52, 0.20, and 0.08 (no erosion sites) to −0.17, −0.66, and −0.77 (heavy erosion sites). Additionally, microbial diversity was found to have a linear positive correlation with soil multifunctionality (R2 = 0.23, p < 0.01). Structural equation modeling and random forest analysis revealed that soil organic carbon and aggregate water stability are main predictors of soil multifunctionality. Furthermore, soil physicochemical properties had a greater influence on soil multifunctionality than microbial diversity. Collectively, our results demonstrate that soil erosion negatively affects the structure, resource effectiveness, and microbial activity of soil aggregates, thereby reducing to differential soil multifunctionality. [ABSTRACT FROM AUTHOR]

Although studies have explored how soil microbial diversity and soil multifunctionality respond to land‐use change at local scales, they have rarely been explored at larger scales and across different climatic and soil environmental conditions. By sampling 40 paired sites of land‐use change from natural forests to agricultural lands (including croplands and orchards) along the middle and lower Yangtze River, combined with a global meta‐analysis, we investigated the effects of land‐use change and climate on the alpha and beta diversity of soil bacterial and fungal functional groups (FGs) and their associated soil multifunctionality at a regional scale. Our results showed that land‐use change strongly changed the diversity of soil bacterial and fungal FGs and decreased multifunctionality, which was supported by our meta‐analysis at a global scale. Direct effects of land‐use change and climate and their interaction, together with changes in soil environmental variables, were the main determinants of the land‐use change‐induced changes in the diversity of soil bacterial or fungal FGs. The land‐use change‐induced decrease in multifunctionality was mainly associated with the direct effect of forest conversion, soil fertility and diversity of fungal FGs. Furthermore, climate also regulated the effects of land‐use change on multifunctionality by affecting soil fertility and fungal FGs diversity along the Yangtze River. Synthesis and applications. Taken together, our findings highlight the important effects of land‐use change, climate and their interactions on microbial diversity and multifunctionality and suggest that effective land‐use management and climate change mitigation strategies should be adopted to protect biodiversity and ecosystem function in the Yangtze River Basin. [ABSTRACT FROM AUTHOR]

Serpentine soils are characterized by nutrient imbalances and high levels of potentially toxic metals (PTMs). These soils host depauperate plant communities of species with specialized adaptations. Initial studies showed that South African serpentine soils harbor distinct biocrust algal and cyanobacterial species compared to adjacent non‐serpentine soils, with these communities further differing based on high and low precipitation levels. Here, we investigated the bacterial and fungal diversity of biological soil crusts from serpentine and non‐serpentine soils at two precipitation levels. The bacterial and fungal communities were characterized using 16S rDNA and ITS metabarcoding, respectively. No significant differences could be found in bacterial richness and community structure. Nevertheless, bacterial taxa such as Archangium, Candidatus Solibacter, Chthoniobacter, and Microvirga were more abundant in serpentine biocrusts or biocrusts receiving lower precipitation. The fungal community structure was distinct between serpentine and non‐serpentine soils (p = 0.027) and between high and low precipitation (p = 0.018). Furthermore, fungal diversity was lowest in the drier, serpentine biocrusts compared to non‐serpentine (p = 0.001) and serpentine crusts receiving higher precipitation (p = 0.002). The fungal genera, Ramimonilia and Vishniacozyma, which are known to be resistant or tolerant to PTMs and other environmental extremes, were significantly more abundant (p = 0.036 and p = 0.016, respectively) in serpentine biocrusts, with the latter indicating serpentine habitats. This study concluded that soil type influenced the fungal alpha diversity, specifically in the serpentine soil, resulting in a decrease in fungal species richness. Furthermore, precipitation influenced fungal beta diversity by shaping distinct fungal communities found in the biocrusts of serpentine and non‐serpentine soils. [ABSTRACT FROM AUTHOR]

Soil organisms play a key role in carbon and nutrient cycling in forest ecosystems. While soil organisms are strongly influenced by litter chemistry and are highly sensitive to abiotic conditions, little is known about the interactive effects of these two factors. To address this gap in knowledge, we conducted a 10 week microcosm experiment in which we simulated the effects of climate change on soil ecology. More specifically, we studied relationships among litter nutrient concentration, microbial biomass, Collembola demographic parameters, and litter decomposition, exploring the potential impacts of increasing air temperature and decreasing soil moisture. To develop a gradient of nutrient concentrations, we created six tree litter mixtures with materials gathered from Quercus pubescens and its companion species. In contrast to microbes, we observed that Collembola abundance and litter decomposition were interactively affected by soil moisture and air temperature: the negative effect of increasing air temperature on Collembola abundance was amplified by reduced soil moisture, whereas the positive effect of increasing air temperature on litter decomposition disappeared under reduced soil moisture conditions. In contrast to fungi, the response of bacterial biomass and Collembola abundance to litter nutrient concentration was dependent on abiotic conditions. More specifically, the relationships between nutrients, especially calcium and magnesium, and bacterial biomass and Collembola abundance were less robust or disappeared under drier or warmer conditions. In conclusion, our findings underscore that ongoing climate change could affect soil organisms directly as well as indirectly, by altering their responses to litter nutrient concentrations. In addition, we found that nutrient‐rich habitats might be more affected than nutrient‐poor habitats by altered climatic conditions. [ABSTRACT FROM AUTHOR]

The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the microbiome and environment modulate these fitness benefits. Moreover, vertically transmitted bacteria might constrain the ability of both the microbiome and host to respond to changing environments. Drosophila melanogaster provides an excellent system to investigate the impacts of interactions between the microbiome and the environment. To address this question, we created field mesocosms of D. melanogaster undergoing seasonal environmental change with and without the vertically transmitted bacteria, Wolbachia pipientis. Sampling temporal patterns in the microbiome revealed that Wolbachia constrained microbial diversity. Furthermore, Wolbachia and a dominant member of the microbiome, Commensalibacter, were associated with differences in two higher‐order fitness traits, starvation resistance and lifespan. Our work here suggests that the interplay between the abiotic context and microbe–microbe interactions may shape key host phenotypes that underlie adaptation to changing environments. We conclude by exploring the consequences of complex interactions between Wolbachia and the microbiome for our understanding of eco‐evolutionary processes that shape host‐microbiome interactions. [ABSTRACT FROM AUTHOR]

The Chinese alligator (Alligator sinensis) is currently an endangered species due to a combination of factors, including climate change, anthropogenic activities, and habitat fragmentation. Captivity plays a crucial role in mitigating the decline of the Chinese alligator population. Currently, there is a lack of clarity regarding the influence of host development and captive conditions on the gut microbiota of Chinese alligators. The aim of the study was to investigate the gut bacterial communities of Chinese alligators and their surrounding environmental bacterial communities using 16S rRNA sequencing. The primary gut flora of Chinese alligators consists of Proteobacteria, Bacteroidetes, and Firmicutes. Proteobacteria is the most abundant and efficient settler in the gut, water, and sediment. PCoA and Adonis test revealed significant differences in bacterial communities across these habitats. Venn analysis revealed overlap in OTUs among the gut, water, and sediment, varying with growth stage and density stress. Different growth stages of Chinese alligator guts harbor distinct pathogenic bacteria, requiring attention. Density stress leads to an increase in pathogenic bacteria, a decrease in gut absorption efficiency. PICRUst2 predicts more abundant metabolic pathways related to gut function during high‐density stress, possibly linked to Roseburia. SourceTracker Analysis indicated that water bacteria have a greater impact on Chinese alligator gut bacteria than sediment, and density stress significantly affects the contribution of environmental microorganisms to the gut microbes of Chinese alligator. BugBase analysis identified water body microbes as the main source of "potentially pathogenic" phenotypes in the gut microbiota. RDA analysis found dissolved oxygen (DO) in water to be the most significant factor influencing water microorganisms, positively correlated with certain pathogenic strains. These findings enhance our understanding of the significance of microbial communities in the gut and surrounding aquatic environment of the Chinese alligator. Furthermore, they provide theoretical support for environmental regulation, disease control, and healthy breeding. [ABSTRACT FROM AUTHOR]

Aim: To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole‐metagenome shotgun sequencing. Methodology: Twenty‐two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole‐metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray‐Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes. Results: Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p =.001). Community composition was significantly different in primary versus secondary infection (R =.11, p =.005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol‐activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase. Conclusions: Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar. [ABSTRACT FROM AUTHOR]

Aim: Climate is widely understood to determine elevational patterns of soil microbial communities, whereas the effects of parental material are uncertain. Changes in the composition of parental materials along elevational transects could also affect soil microbial communities by influencing soil pH and nutrient availability. Here, we aim to illustrate the combined effects of climate and parental material on the biomass and composition of soil microbial communities along an elevational transect. Location: A subtropical forest on a karst mountain (Mt. Jinfo), China. Taxon: Bacteria and Fungi. Methods: We use phospholipid fatty acid analysis (PLFA) and DNA amplicon high‐throughput sequencing to determine biomass and diversity patterns of soil microbial communities along a subtropical elevational gradient with contrasting parental materials (limestone and clasolite). Results: We observed that the microbial communities were more diverse (α‐diversity) and productive (biomass) on limestone than on clasolite. Additionally, we found that parental material played a role in shaping the composition (β‐diversity) of soil microbial communities along the elevational gradient. The impact of climate on soil microbial communities was found to be significant, albeit relatively weak. Structural equation models provided evidence for both direct and indirect effects of climate and parental material on microbial biomass and α‐diversity along the elevational gradient. Notably, the changes in soil pH, influenced by both parental material and climate, were identified as a key factor driving these effects. Main Conclusions: Our results underline the importance of both climate and parental material variations in space‐for‐time studies investigating soil microbial communities along elevational gradients. [ABSTRACT FROM AUTHOR]

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress. Summary Statement: The application of melatonin to waterlogged plants significantly enhanced photosynthesis and antioxidant capacity, promoted nitrogen utilization efficiency and regulated the diversity and function of the rhizosphere microbial community, ultimately facilitating the recovery of apple plants after waterlogging stress. [ABSTRACT FROM AUTHOR]