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Summary: Unraveling the mechanisms of home‐field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking.To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool‐temperate forests.Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome‐wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss.The results indicated that the unique relationships between plant litter and soil microbes through plant–soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land‐use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land‐use change on decomposition processes in forest ecosystems. See also the Commentary on this article by Keiser, 243: 2048–2049. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Purple Napier grass (PNG), a widely used grass rich in anthocyanin, is commonly employed in the production of silage. However, there is currently limited research on the retention of anthocyanin with or without additives during ensiling. Therefore, this study aimed to investigate the effect of different additives (Lactiplantibacillus plantarum CCZZ1 (LP), glucose, acetic acid, and dried soybean curd residue) on fermentation quality, anthocyanin content, and microbial community structure of PNG silage.Ensiling PNG without additives led to poor fermentation quality and rapid degradation of anthocyanin, resulting in a decline in antioxidant activity and the persistence of harmful microorganisms with high relative abundance. The use of additives, especially LP, effectively increased the relative abundance of L. plantarum, enhancing fermentation quality, the retention of anthocyanin (up to 166% increase rate) and antioxidant activity, while reducing the relative abundance of harmful microorganisms during ensiling for 30 days. Additionally, prolonged ensiling negatively affected the preservation of anthocyanin. Based on both fermentation quality and bioactivity, PNG should be ensiled for 30 days with LP inoculation.The employment of additives, especially LP, improved the fermentation quality, anthocyanin retention, and microbial community structure in PNG silage. To optimize both fermentation quality and bioactivity, it is recommended that PNG be ensiled for 30 days with LP inoculation. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Numerous Treponema species are prevalent in the dysbiotic subgingival microbial community during periodontitis. The major outer sheath protein is a highly expressed virulence factor of the well‐characterized species Treponema denticola. Msp forms an oligomeric membrane protein complex with adhesin and porin properties and contributes to host–microbial interaction. Treponema maltophilum and Treponema lecithinolyticum species are also prominent during periodontitis but are relatively understudied. Msp‐like membrane surface proteins exist in T. maltophilum (MspA) and T. lecithinolyticum (MspTL), but limited information exists regarding their structural features or functionality. Protein profiling reveals numerous differences between these species, but minimal differences between strains of the same species. Using protein modeling tools, we predict MspA and MspTL monomeric forms to be large β‐barrel structures composed of 20 all‐next‐neighbor antiparallel β strands which most likely adopt a homotrimer formation. Using cell fractionation, Triton X‐114 phase partitioning, heat modifiability, and chemical and detergent release assays, we found evidence of amphiphilic integral membrane‐associated oligomerization for both native MspA and MspTL in intact spirochetes. Proteinase K accessibility and immunofluorescence assays demonstrate surface exposure of MspA and MspTL. Functionally, purified recombinant MspA or MspTL monomer proteins can impair neutrophil chemotaxis. Expressions of MspA or MspTL with a PelB leader sequence in Escherichia coli also demonstrate surface exposure and can impair neutrophil chemotaxis in an in vivo air pouch model of inflammation. Collectively, our data demonstrate that MspA and MspTL membrane proteins can contribute to pathogenesis of these understudied oral spirochete species. [ABSTRACT FROM AUTHOR]

Summary Microbiota have co‐evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco‐evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota‐mediated plant functions. [ABSTRACT FROM AUTHOR]

Host‐associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from systems biased towards animal models and humans. While many studies on non‐model and wild animals have characterised the taxonomic diversity of their microbiomes, few have investigated the functional potential of these microbial communities. Functional ‘omics’ approaches, such as metagenomics, metatranscriptomics and metabolomics, represent promising techniques to probe the significance of host‐associated microbiomes in the wild. In this review, we propose to (1) briefly define the main available functional omics tools along with their strengths and limitations, (2) summarise the key advances enabled by omics tools to understand microbiome function in human and animal models, (3) showcase examples of how these methods have already brought invaluable insights into wild host microbiomes and (4) provide guidelines on how to implement these tools to address outstanding questions in the field of wild animal microbiomes. To conclude, we suggest that, building on knowledge derived from cheaper, more traditional approaches (e.g. 16S metabarcoding and qPCR), functional omics tools represent a promising approach to test hypotheses regarding the ecological and evolutionary significance of the resident microbiota in wild animals. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Co‐occurrence networks offer insights into the complexity of microbial interactions, particularly in highly diverse environments where direct observation is challenging. However, identifying the scale at which local and non‐local processes structure co‐occurrence networks remains challenging because it requires simultaneously analyzing network structure within and between local networks. In this context, the rumen microbiome is an excellent model system because each cow contains a physically confined microbial community, which is imperative for the host's livelihood and productivity. Employing the rumen microbiome of 1012 cows across seven European farms as our model system, we constructed and analyzed farm‐level co‐occurrence networks to reveal underlying microbial interaction patterns. Within each farm, microbes tended to close triangles but some microbial families were over‐represented while others under‐represented in these local interactions. Using stochastic block modeling we detected a group structure that reflected functional equivalence in co‐occurrence. Knowing the group composition in one farm provided significantly more information on the grouping in another farm than expected. Moreover, microbes strongly conserved co‐occurrence patterns across farms (also adjusted for phylogeny). We developed a meta‐co‐occurrence multilayer approach, which links farm‐level networks, to test scale signatures simultaneously at the farm and inter‐farm levels. Consistent with the comparison between groups, the multilayer network was not partitioned into clusters. This result was consistent even when artificially disconnecting farm‐level networks. Our results show a prominent signal of processes operating across farms to generate a non‐random, similar (yet not identical) co‐occurrence patterns. Comprehending the processes underlying rumen microbiome assembly can aid in developing strategies for its manipulation. More broadly, our results provide new evidence for the scale at which forces shape microbe co‐occurrence. Finally, the hypotheses‐based approach and methods we developed can be adopted in other systems to detect scale signatures in species interactions. [ABSTRACT FROM AUTHOR]

Microbial communities are ubiquitous in nature and play an important role in ecology and human health. Cross-feeding is thought to be core to microbial communities, though it remains unclear precisely why it emerges. Why have multi-species microbial communities evolved in many contexts and what protects microbial consortia from invasion? Here, we review recent insights into the emergence and stability of coexistence in microbial communities. A particular focus is the long-term evolutionary stability of coexistence, as observed for microbial communities that spontaneously evolved in the E. coli long-term evolution experiment (LTEE). We analyze these findings in the context of recent work on trade-offs between competing microbial objectives, which can constitute a mechanistic basis for the emergence of coexistence. Coexisting communities, rather than monocultures of the 'fittest' single strain, can form stable endpoints of evolutionary trajectories. Hence, the emergence of coexistence might be an obligatory outcome in the evolution of microbial communities. This implies that rather than embodying fragile metastable configurations, some microbial communities can constitute formidable ecosystems that are difficult to disrupt. This Review discusses recent insights into the emergence and stability of coexistence in microbial communities. [ABSTRACT FROM AUTHOR]

Gut microbial communities confer protection against natural pathogens in important pollinators from the genera Bombus and Apis. In commercial species B. terrestris and B. impatiens, the microbiota increases their resistance to the common and virulent trypanosomatid parasite Crithidia bombi. However, the mechanisms by which gut microorganisms protect the host are still unknown. Here, we test two hypotheses: microbiota protect the host (1) through stimulation of its immune response or protection of the gut epithelium and (2) by competing for resources with the parasite inside the gut. To test them, we reduced the microbiota of workers and then rescued the microbial community by feeding them with microbiota supplements. We then exposed them to an infectious dose of C. bombi and characterised gene expression and gut microbiota composition. We examined the expression of three antimicrobial peptide genes and Mucin‐5AC, a gene with a putative role in gut epithelium protection, using qPCR. Although a protective effect against C. bombi was observed in bumblebees with supplemented microbiota, we did not observe an effect of the microbiota on gene expression that could explain alone the protective effect observed. On the other hand, we found an increased relative abundance of Lactobacillus bacteria within the gut of infected workers and a negative correlation of this genus with Gilliamella and Snodgrassella genera. Therefore, our results point to a displacement of bumblebee endosymbionts by C. bombi that might be caused by competition for space and nutrients between the parasite and the microbiota within the gut. [ABSTRACT FROM AUTHOR]

Environmental microbes routinely colonize wildlife body surface microbiota. However, animals experience dynamic environmental shifts throughout their daily routine. Yet, the effect of ecological shifts in wildlife body surface microbiota has been poorly explored. Here, we sequenced the hypervariable region V3–V4 of the 16S rRNA gene to characterize the body surface microbiota of wild Magellanic penguins (Spheniscus magellanicus) under two ecological contexts: (1) Penguins walking along the coast and (2) Penguins sheltered underground in their nest, across three subantarctic breeding colonies in the Magellan Strait, Chile. Despite ecological contexts, our results revealed that Moraxellaceae bacteria were the most predominant and abundant taxa associated with penguin body surfaces. Nevertheless, we detected colony‐specific core bacteria associated with penguin bodies. The most abundant were: Deinococcus in the Contramaestre colony, Fusobacterium in the Tuckers 1 colony, and Clostridium sensu stricto 1 in the Tuckers 2 colony. Our results give a new perspective on the niche environmental hypothesis for wild seabirds. First, the ecological characteristics of each colony were associated with the microbial communities from the nest soil and the body surface of penguins inside the nests. For example, in the colonies with heterogenous vegetation cover (i.e. the Tuckers Islets), there was a similar microbial composition between the nest soil and the body surface of penguins. In contrast, on the more arid colony (Contramaestre), we detected differences in the microbial communities between the nest soil and the body surface of penguins. [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]

BACKGROUND: The microbial community plays a crucial role in Chinese strong‐flavor baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing. RESULTS: The results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. The influence of seasons on fungal communities was found to be more significant than on bacterial communities. The diversity of bacteria was higher during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Stochastic processes maintained their dominance in microbial assembly throughout all four seasons but the significance of heterogeneous selection increased during summer for both bacteria and fungi, whereas homogeneous selection became more pronounced during winter for fungi. The pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate. CONCLUSION: These findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality‐control measures for SFB brewed in different seasons. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Coral mucus, teeming with organic matter, releases nutrients and microorganisms, affecting element cycling and microbial communities in coral reefs. While terrestrial ecosystems exhibit well‐studied priming effects from root exudates, the influence of mucus in marine environments, particularly in coral reefs, remains underexplored. We hypothesize that coral mucus, through its nutrients and microbes, stimulates the surrounding microorganisms, regulating carbon metabolism and thus contributing to high coral reef productivity. Initially, natural samples (Acropora pruinosa mucus, seawater, and sediment) were collected for metagenomic assessment of microbial communities and functions. Results showed significant differences in microbial diversity, community structures, co‐occurrence modes, and unique functions among mucus, seawater, and sediment. Subsequent laboratory experiments demonstrated mucus's substantial influence on surrounding microorganisms. Analyses, including 16S rRNA sequencing and Eco‐plate results, revealed that mucus regulates microbial composition and activities. Quantitative gene‐chip analysis showed significant increase in the functional genes related to carbon fixation (e.g., the 3‐hydroxypropionate cycle) and degradation (e.g., pectin and hemicellulose hydrolysis) by 55.81% and 65.48%, respectively. Partial least squares path modeling identified mucus nutrients and microbial community composition as key contributors to carbon metabolic potential. This research confirms that mucus acts as a trigger, reshaping microbial profiles around corals and enhancing carbon utilization efficiency, highlighting its essential role in carbon metabolism and the maintenance of high productivity in coral reef ecosystems. [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]

Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post‐diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post‐diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole‐community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post‐diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees. [ABSTRACT FROM AUTHOR]

Bean paste is a traditional Chinese fermented condiment, which is loved by consumers for its pleasant flavor and nutritional properties. However, the microbial communities and related flavor compounds in bean paste remain unclear. We studied the correlation between the core functional microorganisms and flavor compounds in bean paste samples at different fermentation stages. Bacterial and fungal communities changed significantly during fermentation. The results indicated that the dominant bacterial genera were Staphylococcus, Lactococcus, and Bacillus. The dominant fungi were Aspergillus and Lichtheimia. During the early and late stages of bean paste fermentation, alcohols, hydrocarbons, esters, and phenols were the main flavor compounds detected. The types and proportions of alcohols and esters in the bean pastes fermented for different durations were similar, whereas the relative contents of phenols and hydrocarbons were higher in the later stages of fermentation. Correlation analysis revealed that core functional microorganisms played a key role in the fermentation process, and the potential correlation between bacterial genera and flavors was stronger than that of fungal genera. Staphylococcus abundance was significantly correlated with the flavor levels of ethyl oleate, ç‐pinene, diallyl disulfide, á‐myrcene, D‐limonene, and tetradecanoic acid, ethyl ester. The abundance of Aspergillus and Lichtheimia was significantly correlated with the flavor levels of á‐myrcene, ç‐pinene, and DL‐3‐phenyllactic acid. This study explored the relationship between microorganisms and flavor compounds in bean paste to deepen our understanding of the mechanism of flavor formation for bean paste. [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]

Wetlands are the largest natural source of CH4 globally, yet our understanding of how environmental parameters and microorganisms affect the production and emission of CH4 in emergent plant–sediment systems remains limited. In this study, CH4 fluxes were investigated in a wetland with Canna indica for 42 d, as well as nutrients and microbial community. It was found that the chimney effect formed by aerenchyma in roots, stems, and leaves of C. indica promoted the emission and oxidation of CH4 in the wetland and reduced the CH4 concentration in sediments. Canna indica reduced the nutrient release from surface sediments into the overlying water. Pearson correlation analysis showed that temperature, pH, and oxidation–reduction potential were the main influencing factors for CH4 production and oxidation in the wetland. Canna indica inhibited the diversity of archaeal community but promoted the diversity of bacterial community in the rhizosphere. Stochastic processes had a greater impact on bacterial and archaeal succession trajectories in wetland sediments. Network analysis showed that C. indica promoted interactions among bacteria and archaea that enhanced their ability to resist environmental interference. The well‐developed aerenchyma of C. indica provided an important passage for the transport of CH4 from sediments to the atmosphere and shaped the microbial community structure in the rhizosphere. Meanwhile, CH4 emissions were also constrained by several variables, such as temperature and physiological adaptation in the long term. Thus, it is necessary to plant emergent plants in areas with low CH4 emissions and optimize plant configuration in the context of global warming. [ABSTRACT FROM AUTHOR]

The analysis of meta‐omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta‐omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta‐omics bioinformatics pipeline, Meta‐Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre‐processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta‐omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities. [ABSTRACT FROM AUTHOR]

Invasions are commonly found to benefit from disturbance events. However, the importance of the relative timing of the invasion and disturbance for invader success and impact on community composition remains uncertain. Here, we experimentally test this by invading a five‐species bacterial community on eight separate occasions—four before a disturbance and four after. Invader success and impact on community composition was greatest when the invasion immediately followed the disturbance. However, the subsequent invasions had negligible success or impact. Pre‐disturbance, invader success and impact was greatest when the invader was added just before the disturbance. Importantly, however, the first three pre‐disturbance invasion events had significantly greater success than the last three post‐disturbance invasions. Moreover, these findings were consistent across a range of propagule pressures. Overall, we demonstrate that timing is highly important for both the success and impact on community composition of an invader, with both being lower as time since disturbance progresses. [ABSTRACT FROM AUTHOR]

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region‐specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production. Highlights: A catalog of microbial genes and metagenome‐assembled genomes from the duck gut microbiome.The microbiota within different duck intestinal segments exhibits both similarities and distinctive taxonomic and functional differences.Significant shifts in microbiota composition have been observed in newly hatched ducks at 3 days of age, followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days).Ducks with free access to water have shown an increased bacterial capacity for lipopolysaccharide biosynthesis, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. [ABSTRACT FROM AUTHOR]

Carbon dioxide can be relatively easily reduced to organic matter in a bioelectrochemical system (BES). However, due to insufficient reduction force from in‐situ hydrogen evolution, it is difficult for nitrogen reduction. In this study, MoS2 was firstly used as an electrocatalyst for the simultaneous reduction of CO2 and N2 to produce microbial protein (MP) in a BES. Cell dry weight (CDW) could reach 0.81±0.04 g/L after 14 d operation at −0.7 V (vs. RHE), which was 108±3 % higher than that from non‐catalyst control group (0.39±0.01 g/L). The produced protein had a better amino acid profile in the BES than that in a direct hydrogen system (DHS), particularly for proline (Pro). Besides, MoS2 promoted the growth of bacterial cell on an electrode and improved the biofilm extracellular electron transfer (EET) by microscopic observation and electrochemical characterization of MoS2 biocathode. The composition of the microbial community and the relative abundance of functional enzymes revealed that MoS2 as an electrocatalyst was beneficial for enriching Xanthobacter and enhancing CO2 and N2 reduction by electrical energy. These results demonstrated that an efficient strategy to improve MP production of BES is to use MoS2 as an electrocatalyst to shift amino acid profile and microbial community. [ABSTRACT FROM AUTHOR]

Chemosynthetic microorganisms facilitate microbialite development in many caves throughout the world. In Youqin Cave and Tian'e Cave, located in the Carboniferous–Triassic carbonates on the South China Block, five Quaternary speleothems (stalagmite, stalactite and cave pearl) that are 2.3 to 11.0 cm long were examined for their petrographic, geochemical and microbiological features to reveal how chemotrophs contribute to microbialite growth. In the speleothems, millimetre‐sized stromatolites, thrombolites and calcified microbial mats are characterized by alternating light, calcitic microlaminae and dark, clay and organic‐rich calcite microlaminae. Filamentous (reticulate, smooth, nodular and helical), coccoid and bacilliform microbes, originally carried into the caves from surface soils, are more common in the dark microlaminae/clots than in the light microlaminae. 16S rRNA gene sequencing shows that the biotas in the microbialites are dominated by chemoorganotrophic heterotrophic bacteria, including primarily Sphingomonas, Crossiella and Acinetobacter, and rare Archaea. Diverse metabolic pathways of these prokaryotes, including ureolysis, denitrification and nitrite ammonification, contributed to increases in localized pH and/or dissolved inorganic carbon in these microenvironments, prompting carbonate precipitation. Development of the cave microbialites was probably controlled by the evolution of the cave microbial community as environmental conditions changed. Microbialite growth was probably mediated by the microorganisms that flourished on the speleothem surfaces during periods of low drip water rates and slow calcite precipitation. The change from microstromatolites to microthrombolites was probably linked to a decrease in cell populations in the microbial communities. These cave microbialites provide clear insights regarding the biogenicity and growth mechanisms of chemosynthetic microbialites. Given their association with chemolithotrophic activities that can date back to the Meso‐Archean, cave microbialites provide insights into the biogenicity and growth mechanisms of chemosynthesis‐based microbialites throughout geological history. [ABSTRACT FROM AUTHOR]

This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three‐domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host‐specific, while the assembly of the midgut was more influenced by the environmental microorganisms. [ABSTRACT FROM AUTHOR]

Plastic waste, especially positively buoyant polymers known as polyolefins, are a major component of floating debris in the marine environment. While plastic colonisation by marine microbes is well documented from environmental samples, the succession of marine microbial community structure over longer time scales (> > 1 month) and across different types and shapes of plastic debris is less certain. We analysed 16S rRNA and 18S rRNA amplicon gene sequences from biofilms on polyolefin debris floating in a flow‐through seawater tank in Hawai'i to assess differences in microbial succession across the plastic types of polypropylene (PP) and both high‐density polyethylene (HDPE) and low‐density polyethylene (LDPE) made of different plastic shapes (rod, film and cube) under the same environmental conditions for 1 year. Regardless of type or shape, all plastic debris were dominated by the eukaryotic diatom Nitzschia, and only plastic type was significantly important for bacterial community structure over time (p = 0.005). PE plastics had higher differential abundance when compared to PP for 20 bacterial and eight eukaryotic taxa, including the known plastic degrading bacterial taxon Hyphomonas (p = 0.01). Results from our study provide empirical evidence that plastic type may be more important for bacterial than eukaryotic microbial community succession on polyolefin pollution under similar conditions. [ABSTRACT FROM AUTHOR]

Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free‐living (FL) and particle‐associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring–summer than in autumn‐winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time‐decay curves confirmed a high degree of predictability in both fractions. Yet, 'seasonal' Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities. [ABSTRACT FROM AUTHOR]

Ciliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is enhanced through interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here, we modify the microbial community by varying the forage‐to‐concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil the potential role of ciliates in shaping rumen metabolism. [ABSTRACT FROM AUTHOR]

Denitrification is of great significance for low C/N wastewater treatment. In this study, pyrite autotrophic denitrification (PAD) was coupled with a three‐dimensional biofilm electrode reactor (BER) to enhance denitrification. The effect of current on denitrification was extensively studied. The nitrate removal of the PAD‐BER increased by 14.90% and 74.64% compared to the BER and the PAD, respectively. In addition, the electron utilization, extracellular polymeric substances secretion, and denitrification enzyme activity (NaR and NiR) were enhanced in the PAD‐BER. The microbial communities study displayed that Dokdonella, Hydrogenophaga, Nitrospira, and Terrimonas became the main genera for denitrification. Compared with the PAD and the BER, the abundance of the key denitrification genes narG, nirK, nirS, and nosZ were all boosted in the PAD‐BER. This study indicated that the enhanced autotrophic denitrifiers and denitrification genes were responsible for the improved denitrification in the PAD‐BER. Practitioner Points: PAD‐BER displayed higher nitrate removal, EPS, NAR, and NIR activity.The three types of denitrification (HD, HAD, and PAD) and their contribution percentage in the PAD‐BER were analyzed.HAD was dominant among the three denitrification processes in PAD‐BER.Microbial community composition and key denitrification genes were tested to reveal the denitrification mechanisms. [ABSTRACT FROM AUTHOR]

Since the advent of next‐generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia. [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]

Soil microbial traits and functions play a central role in soil organic carbon (SOC) dynamics. However, at the macroscale (regional to global) it is still unresolved whether (i) specific environmental attributes (e.g., climate, geology, soil types) or (ii) microbial community composition drive key microbial traits and functions directly. To address this knowledge gap, we used 33 grassland topsoils (0–10 cm) from a geoclimatic gradient in Chile. First, we incubated the soils for 1 week in favorable standardized conditions and quantified a wide range of soil microbial traits and functions such as microbial biomass carbon (MBC), enzyme kinetics, microbial respiration, growth rates as well as carbon use efficiency (CUE). Second, we characterized climatic and physicochemical properties as well as bacterial and fungal community composition of the soils. We then applied regression analysis to investigate how strongly the measured microbial traits and functions were linked with the environmental setting versus microbial community composition. We show that environmental attributes (predominantly the amount of soil organic matter) determined patterns of MBC along the gradient, which in turn explained microbial respiration and growth rates. However, respiration and growth normalized for MBC (i.e., specific respiration and growth) were more linked to microbial community composition than environmental attributes. Notably, both specific respiration and growth followed distinct trends and were related to different parts of the microbial community, which in turn resulted in strong effects on microbial CUE. We conclude that even at the macroscale, CUE is the result of physiologically decoupled aspects of microbial metabolism, which in turn is partially determined by microbial community composition. The environmental setting and microbial community composition affect different microbial traits and functions, and therefore both factors need to be considered in the context of macroscale SOC dynamics. [ABSTRACT FROM AUTHOR]

Marine heatwaves (MHWs) are increasing in frequency, duration and intensity, disrupting global marine ecosystems. While most reported impacts have been in tropical areas, New Zealand experienced its strongest and longest MHW in 2022, profoundly affecting marine sponges. Sponges are vital to rocky benthic marine communities, with their abundance influencing ecosystem functioning. This study examines the impact of this MHW on the photosynthetic sponge Cymbastella lamellata in Fiordland, New Zealand. We describe the extent, physiological responses, mortality, microbial community changes and ecological impact of this MHW on C. lamellata. The Fiordland MHW reached a maximum temperature of 4.4°C above average, lasting for 259 days. Bleaching occurred in >90% of the C. lamellata Fiordland population. The population size exceeded 66 million from 5 to 25 m, making this the largest bleaching event of its kind ever recorded. We identified the photosynthetic symbiont as a diatom, and bleached sponges had reduced photosynthetic efficiency. Post‐MHW surveys in 2023 found that over 50% of sponges at sampling sites had died but that the remaining sponges had mostly recovered from earlier bleaching. Using a simulated MHW experiment, we found that temperature stress was a driver of necrosis rather than bleaching, despite necrosis only rarely being observed in the field (<2% of sponges). This suggests that bleaching may not be the cause of the mortality directly. We also identified a microbial community shift in surviving sponges, which we propose represents a microbial‐mediated adaptive response to MHWs. We also found that C. lamellata are key contributors of dissolved organic carbon to the water column, with their loss likely impacting ecosystem function. We demonstrate the potential for MHWs to disrupt key marine phyla in temperate regions, highlighting how susceptible temperate sponges globally might be to MHWs. [ABSTRACT FROM AUTHOR]

Host diet is one of the key factors that shapes insect associated microbial communities, and the impact of dietary shift on abundance of microbial communities and insect fitness is poorly understood. Cigarette beetle (Lasioderma serricorne (F.)) are in close association with yeast symbionts for nutritional and defence benefits. The present study highlights that dietary source determines the yeast abundance in cigarette beetle and any change in diet induces a shift in yeast abundance. A general trendline of increase in yeast abundance during larval and pupal stage followed by a drop in adult stages of cigarette beetle was observed among all diet sources. The yeast abundance varied among diet sources and was significantly higher on natal (wheat) and reverted colonies compared to other exposed dietary sources. Yeast abundance in reverted colonies of soybean and bengal gram increased to the levels of those that were originally feeding on wheat suggesting a similar microbial structure among those diet sources. The correlation between yeast abundance and beetle biomass among diet guilds suggest a predictable relationship between yeast symbionts and diet source. The investigation can provide further insights on yeast symbiont abundance and food source specificity in cigarette beetle biology and management. [ABSTRACT FROM AUTHOR]

Premise: Whole‐genome duplication (neopolyploidy) can instantly differentiate the phenotype of neopolyploids from their diploid progenitors. These phenotypic shifts in organs such as roots and leaves could also differentiate the way neopolyploids interact with microbial species. While some studies have addressed how specific microbial interactions are affected by neopolyploidy, we lack an understanding of how genome duplication affects the diversity and composition of microbial communities. Methods: We performed a common garden experiment with multiple clones of artificially synthesized autotetraploids and their ancestral diploids, derived from 13 genotypes of wild strawberry, Fragaria vesca. We sequenced epiphytic bacteria and fungi from roots and leaves and characterized microbial communities and leaf functional traits. Results: Autotetraploidy had no effect on bacterial alpha diversity of either organ, but it did have a genotype‐dependent effect on the diversity of fungi on leaves. In contrast, autotetraploidy restructured the community composition of leaf bacteria and had a genotype‐dependent effect on fungal community composition in both organs. The most differentially abundant bacterial taxon on leaves belonged to the Sphingomonas, while a member of the Trichoderma was the most differentially abundant fungal taxon on roots. Ploidy‐induced change in leaf size was strongly correlated with a change in bacterial but not fungal leaf communities. Conclusions: Genome duplication can immediately alter aspects of the plant microbiome, but this effect varies by host genotype and bacterial and fungal community. Expanding these studies to wild settings where plants are exposed continuously to microbes are needed to confirm the patterns observed here. [ABSTRACT FROM AUTHOR]

The arrival order of species can strongly influence the early assembly of ecological communities. Such events, known as priority effects, are documented in various ecological settings, but remain understudied within the context of the gut microbiome. Given the fundamental link between the gut microbiome and host health, exploring the potential role of priority effects in shaping the assembly and development of microbial communities within the gut becomes imperative. Using the freshwater planktonic crustacean Daphnia magna as a model system, we manipulated the immigration order of three bacterial strain pairs in two germ‐free genotypes and quantified gut microbiome composition and host fitness at two time points, namely day 8 and day 12. Priority effects were observed; however, their presence, amplitude, and direction (suppressive or facilitative) were found to be contingent on the identity of bacterial strain and host genotype. These findings were accompanied by notable differences in Daphnia life history traits across inoculation order treatments, shedding light on the tangible consequences of priority effects triggered by the sequence of bacterial strain arrival in the gut environment, for host fitness. Our results thus highlight the complex nature of priority effects in gut community assembly, their strain/genotype specificity, and their potential impact on the host. [ABSTRACT FROM AUTHOR]

Decadal scale lake drying in interior Alaska results in lake margin colonization by willow shrub and graminoid vegetation, but the effects of these changes on plant production, biodiversity, soil properties, and soil microbial communities are not well known. We studied changes in soil organic carbon (SOC) and nitrogen (N) storage, plant and microbial community composition, and soil microbial activities in drying and non‐drying lakes in the Yukon Flats National Wildlife Refuge. Historic changes in lake area were determined using Landsat imagery. Results showed that SOC storage in drying lake margins declined by 0.13 kg C m−2 yr−1 over 30 years of exposure of lake sediments, with no significant change in soil N. Lake drying resulted in an increase in graminoid and shrub aboveground net primary production (ANPP, +3% yr−1) with little change in plant functional composition. Increases in ANPP were similar in magnitude (but opposite in sign) to losses in SOC over a 30‐year drying trend. Potential decomposition rates and soil enzyme activities were lower in drying lake margins compared to stable lake margins, possibly due to high salinities in drying lake margin soils. Microbial communities shifted in response to changing plant communities, although they still retained a legacy of the previous plant community. Understanding how changing lake hydrology impacts the ecology and biogeochemistry of lake margin terrestrial ecosystems is an underexamined phenomenon with large impacts to landscape processes. Plain Language Summary: Lake dominated ecosystems in Alaska have experienced periods of widespread lake drying in the past. We understand little of what occurs on these new nearshore habitats following lake drying, especially changes in soil properties and soil microbial communities. Using a combination of remote sensing and field sampling on hundreds of lakes in the Yukon Flats National Wildlife Refuge, we learned that lake margin soils lose significant quantities of soil C in the decades following lake drying, and at the same time soils become increasingly saline and soil microbial activites are reduced. Overall, lake drying has large impacts on the surrounding ecosystems and it is important to understand these changes for management. Key Points: Lake drying in the Yukon Flats National Wildlife Refuge triggers a succession of plant and microbial communities and losses of lake margin soil organic carbon (SOC)Lake drying also results in increases in the salinity of lake margin soils, slowing rates of microbial activitiesAlthough lake drying resulted in losses of SOC, increases in Aboveground Net Primary Production (ANPP) compensated for these losses [ABSTRACT FROM AUTHOR]

Soils in forested ecosystems are extremely heterogeneous and represent a critical component of terrestrial ecosystems. Despite their substantial ecological value, the geographic characteristics, ecological processes, and coexistence of microbial communities in forest soils remain poorly understood. Here, we investigated the biodiversity dynamics, environmental influences, community assembly, and co‐occurrence patterns of bacterial and fungal communities in surface and subsurface soils across 47 Chinese forest sites. The biogeographic characteristics determined using high‐throughput sequencing data sets revealed evident spatial patterns of bacterial and fungal α and β diversity, assembly processes, and co‐occurrence relationship, with greater variation in the bacterial than in fungal communities. Both fungal and bacterial communities showed significant spatial separations regulated by community assembly processes, co‐occurrence patterns, and soil variables. The microbial dissimilarity was lower in high latitudes than in low latitudes, which was consistent with the lower deterministic processes and relatively higher co‐occurrence associations in high latitudes than in low latitudes. Additionally, there were significant associations of soil dissolved organic matter (DOM) characteristics (e.g., its content, aromaticity, and molecular weight) with biodiversity dissimilarities, microbial assembly process balances, and microbial co‐occurrence relationships in bacterial and fungal communities; they clearly indicate the key role of DOM in regulating microbial biogeographic patterns in forest soil ecosystems. Collectively, our study enhances the understanding of biogeographic patterns and coexistence theories in forest soil microbial ecosystems. Plain Language Summary: Our study revealed an intrinsic link between microbial spatial variation, environmental impacts, community assembly processes, and species coexistence patterns. Understanding the mechanisms of microbial community diversity is a prerequisite for recognizing the environmental functions of microbes in forest soil ecosystems. To sum up, this study illustrates the critical influence of DOM in microbial spatial variation, assembly processes, and species coexistence of microbial communities in Chinese forest soils. Our study contributes to management strategies for microbial communities in forest ecosystems to better adapt to habitat fragmentation and climate change. Key Points: The spatial dissimilarities of bacterial and fungal communities associated with soil DOMBacterial and fungal community assembly and co‐occurrence relationships shaped microbial biogeographyBacterial and fungal community assembly and species coexistence correlated with DOM [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]

This study aims to examine the nitrogen removal characteristics and microbial community variation at low hydraulic retention time (HRT) in a shallow constructed wetland (SCW) using iron–carbon (Fe–C) porous filter material (PFM) as substrate. Effects of influent nitrogen forms and chemical oxygen demand (COD)/N ratio on nitrogen removal performance at HRT of 1 day were investigated. Results showed that total nitrogen (TN) removal declined with the decrease of influent NH4+‐N‐to‐NO3−‐N ratio. When the influent NH4+‐N/NO3−‐N ratio was 0.1, TN removal decreased by 15.4% compared with that at ratio of 2.0. The increase of influent COD/N ratio enhanced NO3−‐N reduction, and TN removal reached 74.5% at influent COD/N ratio 7.0. The microbial community was analyzed for the biofilm samples on Fe–C PFM at front (WF), middle (WM), and back (WB) of SCW. Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were dominant bacteria phyla. The relative abundance of genera involved in the nitrification and denitrification decreased with the influent flow. The iron autotrophic denitrifying and macromolecular organics degrading bacteria were abundant in the middle and back of SCW. Microbial nitrification and denitrification, plant uptake, and plant synergism contributed to 86.3%, 7.41%, and 19.9% of N removal, respectively. These results demonstrated that the SCW with Fe–C PFM as substrate was efficient in nitrogen removal at low HRT. [ABSTRACT FROM AUTHOR]

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]

Straw incorporation increases the amount of nutrients in soil and greatly impacts soil nitrogen and microbial communities. In this study, 15N‐labeled corn straw was used as the material, the experiment consisted of five treament (AS: placing the straw 15 cm above the soil surface, SM: using the straw to mulch the soil surface, B15: burying the straw 15 cm below the ground surface, B30: burying the straw 30 cm below the ground surface, B45: burying the straw 45 cm below the ground surface). The changes in 15N abundance in straw were analyzed. An estimation method for nitrogen release and uptake by field‐incorporated straw was proposed, and the relationships between nitrogen release and uptake and related microbes were established. The results showed that the exchange of nitrogen between maize straw buried in soil at different depths and the environment was not significant. The corn straw exposed to the air absorbed more nitrogen from the environment in the second year of decomposition, and the larger the area exposed to the air was, the more nitrogen was absorbed from the environment. The relative abundances of Burkholderiales, Flavobacteriales, Pseudomonadales, and Sphingobacteriales were significantly positively correlated with the straw decomposition rate and nitrogen release rate. The relative abundance of Rhizobiales was significantly negatively correlated with the straw decomposition rate and nitrogen release rate. The relative abundances of Sphingobacteriales, Flavobacteriales, and Pseudomonadales were significantly negatively correlated with the straw nitrogen uptake rate. [ABSTRACT FROM AUTHOR]

From the moment of birth, the newborn gastrointestinal tract is infiltrated by various bacteria originating from both maternal and environmental sources. These colonizing bacteria form a complex microbiota community that undergoes continuous changes until adulthood and plays an important role in infant health. The maturation of the infant gut microbiota is driven by many factors and follows a distinct patterned trajectory, with specific bacterial taxa establish in the intestine in accordance with developmental milestones as the infant grows. In this review, we highlight how elements such as diet and host physiology select for specific microbial functions and shape the composition of the bacterial community in the large intestine. [ABSTRACT FROM AUTHOR]

Objective Methods Results Conclusion The purpose of this study was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.Fecal samples were collected from 93 owned pet dogs. Dogs were designated as either clinically healthy or OA pain using validated methods. Metagenomic profiling was performed through shotgun sequencing using the Illumina NovaSeq platform. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance. Comparisons between healthy and OA‐pain groups were performed individually for each taxa using nonparametric tests following Benjamini and Hochberg adjustment for multiple comparisons. Permutation analysis of variance was performed using Bray‐Curtis distance matrices. All downstream analyses were completed in R.No significant differences between healthy and OA‐pain dogs were observed for alpha and beta diversity. We found 13 taxa with nominally significant (P < 0.05) associations with OA case status, but none of the associations remained significant after adjustment for multiple comparisons. No differences in alpha or beta diversities or the Firmicutes to Bacteroidetes ratio were found regarding pain severity, mobility or activity level, age, or body composition score.Similar to recent studies in humans, the present study did not demonstrate a significant difference in the fecal microbial communities between dogs with OA pain and healthy control dogs. Future research in this naturally occurring model should expand on these data and relate the gut microbiome to gut permeability and circulating proinflammatory and anti‐inflammatory molecules to better understand the influence of the gut microbiome on OA and OA pain. [ABSTRACT FROM AUTHOR]

Premise Methods Results Conclusions In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question.We described leaf‐ and root‐associated microbial communities using ITS2 and 16 S high‐throughput sequencing and investigated the stochastic‐deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities.While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall.This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change. [ABSTRACT FROM AUTHOR]

Saline‐alkali soil degradation is a significant environmental problem with a negative impact on sustainable agroforestry development. Therefore, efficient remediation methods are urgently required. A potential solution to this problem is using biochar produced from bamboo waste and inoculated with plant growth‐promoting microbes as cleaner production materials for saline‐alkali soil. The present study investigated the potential of combining biochar, microbes, and dwarf bamboo to improve saline‐alkali soil. Different application rates (1%, 3%, and 5% of soil mass) of biochar were added to coastal saline soil planted with dwarf bamboo (Pleioblastus argenteastriatus) in pot experiments. Soil physicochemical properties, microbial communities, and plant responses were systematically studied. Bamboo and microbial‐modified biochar effectively decreased soil pH and electrical conductivity and increased soil nutrient contents. Compared with untreated soil, the relative abundance of the dominant bacterial phyla Acidobacteria, Actinobacteria, and Chloroflexi, and dominant fungal phyla Basidiomycota increased after applying biochar and modified biochar. With the increase in application concentration, the antioxidant activities of modified biochar decreased, biochar peroxidase and catalase content decreased, and the malondialdehyde content of bamboo biochar and microbial‐modified bamboo biochar decreased. The biomass of bamboo with added biochar and modified biochar was significantly higher than that of untreated soil. Comprehensive correlation and redundancy analyses showed that the bacterial and fungal communities were greatly affected by soil factors, especially soil pH, electrical conductivity, total organic carbon, potassium, and sodium ions. The findings of this study suggest that 5% bamboo biochar and 3% modified biochar benefit soil remediation, improve the stress resistance of dwarf bamboo, and enhance plant growth. Therefore, combined biochar–microbe remediation has great potential for the sustainable improvement of saline‐alkali soil. [ABSTRACT FROM AUTHOR]

Reforestation after forest clear‐cutting is an effective measure to increase soil organic carbon (SOC) sequestration; still, the soil C balance under reforestation and the role of microbial communities in that process remain to be determined. Samples of organic (0–2 cm) and mineral (2–10 cm) horizons were collected from the 7‐, 15‐, 20‐, 29‐, and 36‐year‐old forest stands of Chinese fir (Cunninghamia lanceolata) after plantation clear‐cutting in subtropical zone under the condition of phosphorus limitation. Particulate organic carbon (POC), mineral‐associated organic carbon (MAOC), microbial phospholipid fatty acids (PLFAs), and enzymatic activities for C, nitrogen (N), and phosphorus (P) acquisition were analyzed. The lowest contents of POC (10%) and MAOC (13%) in the organic horizon were found in 7‐year‐old stands due to the slow tree regrowth and extensive decomposition of SOC in the first years of forest regrowth. POC (2.0×) and MAOC (0.8×) increases in the organic horizon with forest age were attributed to the stand development and accumulation of above‐ and belowground litter. The organic horizon had a higher POC:MAOC ratio than the mineral (0.7–1.1 vs. 0.2–0.5), indicating lower SOC stability in the first one. The ratio of POC:MAOC increased with the Gram‐positive to Gram‐negative bacteria (G+:G‐) ratio, pointing out that microbial communities developed a specific community structure and substrate utilization strategies of organic matter under plantation restoration. The increase of total PLFAs and the G+:G‐ ratio was closely linked with the microbial C and P limitations, indicating that microorganisms shifted community structure to slow‐growing species and increased their content to cope with the C and P restrictions. In the soils of young plantations, microorganisms were limited by C and P; however, the C limitation was alleviated in the 36‐year‐old plots in the organic horizon due to increased litter input, whereas the P limitation was not. This discrepancy between C and P limitation suppressed the decomposition of litter entering the soil, which was seen in decreased specific activity of C degrading enzymes and led to the accumulation of POC in the organic horizon. Thus, soil C sequestration under reforestation of Chinese fir can be controlled by the amount of litter entering the soil and by metabolic C, N, and P limitations that force microorganisms to shift community structure and change their activity. [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]

Many pathways of invasion have been posited, but ecologists lack an experimental framework to identify which mechanisms are dominant in a given invasion scenario. Plant–soil feedbacks (PSFs) are one such mechanism that tend to initially facilitate, but over time attenuate, invasive species' impacts on plant diversity and ecosystem function. PSFs are typically measured under greenhouse conditions and are often assumed to have significant effects under field conditions that change over time. However, direct tests of PSFs effects in natural settings and their change over time are rare. Here we compare the role of PSFs with the effects of biomass in limiting the dominance of an invasive species and impacts on resident species diversity. We characterized the effects of the invader Bromus inermis (Leyss.) on native plant communities over time and measured changes in its conspecific PSFs and vegetative growth to understand their integrated effects on community diversity. To do so, we combined data from a 6‐year field study documenting the rate and impacts of invasion with a short‐term greenhouse experiment quantifying PSF as a function of time since invasion in the field. We found that the nature and strength of B. inermis PSFs did not change over time and were not mediated by soil microbial communities. Though PSFs impacted B. inermis reproduction, they did not sufficiently limit vegetative growth to diminish the negative impacts of B. inermis biomass on native species. B. inermis experienced the full strength of its negative PSFs immediately upon invasion, but they were ineffective at reducing B. inermis vigor to facilitate the recovery of the native plant community. We recommend that conservation efforts focus on limiting B. inermis vegetative growth to facilitate community recovery. [ABSTRACT FROM AUTHOR]

Microorganisms are important associates of insect and arthropod species. Insect‐associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect‐associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect–microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect‐microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities. [ABSTRACT FROM AUTHOR]

Summary: Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant–soil interactions, such as the transition of dwarf shrub‐dominated into graminoid‐dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state.We analysed vegetation, soil microbial communities and activities as well as soil physico‐chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid‐dominated; 'shifting'; and recovered dwarf shrub‐dominated vegetation inside enclosures.Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico‐chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous.Self‐maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico‐chemical properties return back towards their predisturbance state. [ABSTRACT FROM AUTHOR]

Aim: To analyse the effect of ultrasonic irrigant activation (UIA) and the GentleWave (GW) multisonic irrigation (GW) with minimal instrumentation on the root canal microbial diversity in an ex vivo model that used extracted molars with a history of pulp necrosis. Methodology: Twenty‐three mandibular molars were prepared ex vivo for collection of superficial (surface control), pre‐treatment and post‐treatment samples 24 h after extraction. Samples were divided into two groups: UIA using 6% NaOCl (n = 11) and GW group (n = 12). All samples were processed using quantitative real‐time polymerase chain reaction (qPCR) and 16S rRNA next‐generation sequencing to measure microbial diversity before and after the antimicrobial treatment. For qPCR, a t‐test (α =.05) was used to compare the log10 reduction. The Chao1 and Shannon indices evaluated alpha diversity. Differences in community composition (beta diversity) were evaluated by analysis of similarity (ANOSIM). Kruskal–Wallis test with Bonferroni corrections was performed to evaluate the differences in abundances genera in the samples. Results: Quantitative real‐time polymerase chain reaction revealed an estimated 1.6 and 2.6 log10 reduction for UIA and GW groups respectively (p =.048). An average of 5 ± 4 and 3 ± 5 operational taxonomic units (OTUs) were found in surface's samples in the UIA and GW group respectively. These values were significantly lower (p <.001) compared to the number of preoperative OTUs in those groups (155 ± 79 and 187 ± 121). In assessing beta diversity, there were no significant differences found in pre‐treatment samples (R =.090, p =.070 ANOSIM with Bonferroni corrections). Also, no significant differences in community composition were observed in post‐treatment samples (R = −.05, p =.829). After treatment, there was a significant reduction of Eubacterium using conventional treatment with UIA and a significant reduction of Prevotella using minimal instrumentation with GW irrigation (p =.007 and p =.002 respectively). Conclusion: Quantitative PCR analysis revealed a significant reduction in microbial load for GW group. Overall, diversity changes were similar between UIA and GW irrigation in this ex vivo model that used extracted teeth with a history of pulp necrosis. OTUs obtained from the surface sample were negligible and did not affect the statistical outcome of the study. [ABSTRACT FROM AUTHOR]