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While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.

Background Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning. Results Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group ( Bradyrhizobium , Streptomyces , Variovorax , Pseudomonas , and Sphingomonas ) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group ( Anaeromyxobacter , Bdellovibrio , Conexibacter , Flavobacterium , and Gemmatimonas ). D4peFR94inzfCLNbpY8QhX Video Abstract Conclusion These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.

Although we understand the ecological processes eliciting changes in plant community composition during secondary succession, we do not understand whether co-occurring changes in plant detritus shape saprotrophic microbial communities in soil. In this study, we investigated soil microbial composition and function across an old-field chronosequence ranging from 16 to 86 years following agricultural abandonment, as well as three forests representing potential late-successional ecosystems. Fungal and bacterial community composition was quantified from ribosomal DNA, and insight into the functional potential of the microbial community to decay plant litter was gained from shotgun metagenomics and extracellular enzyme assays. Accumulation of soil organic matter across the chronosequence exerted a positive and significant effect on fungal phylogenetic β-diversity and the activity of extracellular enzymes with lignocellulolytic activity. In addition, the increasing abundance of lignin-rich C 4 grasses was positively related to the composition of fungal genes with lignocellulolytic function, thereby linking plant community composition, litter biochemistry, and microbial community function. However, edaphic properties were the primary agent shaping bacterial communities, as bacterial β-diversity and variation in functional gene composition displayed a significant and positive relationship to soil pH across the chronosequence. The late-successional forests were compositionally distinct from the oldest old fields, indicating that substantial changes occur in soil microbial communities as old fields give way to forests. Taken together, our observations demonstrate that plants govern the turnover of soil fungal communities and functional characteristics during secondary succession, due to the continual input of detritus and differences in litter biochemistry among plant species.

Minimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.

A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar–one organic acid). Furthermore, sugar–acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.

• It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited. • Using 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1-yr-old aspen saplings and the associated bulk soil after a recent high-intensity prescribed fire across a burn severity gradient. • Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modeling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree. • Overall, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

Microbial fuel cells (MFCs) offer a promising alternative for sustainable wastewater treatment and energy recovery. However, the mechanisms underpinning electrogenic biofilm formation remain poorly understood. This study investigates the spatial and temporal dynamics of microbial community assembly using a novel multi-electrode MFC design under two substrate conditions: acetate and starch. Pre-inoculation of three designated electrodes led to successful current generation within 110 h in both MFCs, while a dispersed inoculation strategy failed to establish electrogenic biofilms despite equivalent inoculum volume. Electrode positioning significantly influenced start-up, with vertical alignment above inoculated electrodes facilitating faster colonisation and current generation than lateral spacing. Notably, starch-fed MFCs exhibited more rapid and widespread biofilm proliferation, suggesting that complex microbial consortia may disperse more efficiently than single-function electrogens. Community sequencing revealed spatial heterogeneity and a shift from diverse to more optimised anodic communities over time. Geobacter initially dominated, but community succession was shaped by substrate complexity, competition, and spatial structure. Interestingly, non-inoculated electrodes often outperformed inoculated ones, indicating that deterministic selection pressures favoured more efficient biofilms. However, long-term current production declined, particularly under batch conditions, suggesting that population drift and limited microbial renewal limited sustained performance. This study is the first to characterise electrogenic biofilm assembly in a multi-electrode MFC, highlighting the interplay between stochastic dispersal and deterministic selection. These findings underscore the importance of inoculation strategy, substrate selection, and continuous microbial replenishment for optimising MFC performance and real-world applicability. Key points • Substrate complexity shaped colonisation and distinct microbial communities. • Vertical electrode positioning enhanced colonisation and start-up efficiency. • Temporal succession led to specialised but less diverse electrogenic biofilms.

Microbial ecosystems are almost always dominated by only a few species, but their diversity resides in the rare biosphere. These rare members are usually considered passive passengers with little influence, yet our work reveals that they can collectively determine which species to become the most abundant taxon. We describe this process as a “nomination–voting” system: competitive traits nominate potential dominants, while rare taxa vote for the ultimate winner through their complex interactions. Recognizing this hidden but decisive role of rare microbes provides a new perspective on community assembly and underscores how subtle ecological interactions shape community outcomes. This assembly framework offers new opportunities for the prediction, manipulation, and stabilization of agriculture, health, and environmental microbiomes.

It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited. Using 16S rRNA gene and ITS region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1 y old aspen saplings and the associated bulk soil after a recent high-intensity prescribed fire across a burn severity gradient. Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modelling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree. Finally, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

Understanding the drivers of airborne microbial community structure is essential for predicting microbial dispersal, ecosystem connectivity, and responses to environmental change. This study reveals that atmospheric fungal and bacterial communities are shaped by distinct ecological and environmental factors, with fungi exhibiting stronger site-specific responses and vertical stratification than bacteria. The contrasting patterns between subalpine forest and grassland ecosystems underscore how local conditions influence microbial diversity and transport potential. Importantly, the detection of shared taxa, especially at greater sampling heights, suggests that atmospheric transport may connect distant ecosystems and that certain taxa are ubiquitous. These findings highlight the complexity of the aerobiome and its sensitivity to spatial and temporal dynamics, providing new insights into microbial distribution and the role of the atmosphere in microbial exchange across landscapes.