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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.

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.

Boundaries between environments provide important insight into how ecological communities are structured across broader landscapes. Of particular interest is how communities assemble within the transition zone constituting the boundary (i.e., where the transition in environmental variables occurs) and whether transitions in community composition parallel transitions in environmental variables. While ecological boundaries have a long history in classic ecology, similar concepts have recently emerged in microbiota literature. Currently, however, most studies of microbial ecological boundaries focus on environmental microbiota, rather than host-associated (HA) microbiota. This is likely because it is unclear what constitutes an ecological boundary in HA microbiota systems. We propose hybrid hosts as an HA analog for environmental ecological boundaries. Specifically, we outline how different types of hybrid hosts serve as models for different types of ecological boundaries. We then outline how the ecological boundary framework can be used to interpret HA microbial community coalescence (i.e., mixing) across host species. Finally, we suggest that many hybrid hosts reside within the transition zones of larger scale ecological boundaries. When this happens, hybrid hosts can be used to examine a novel phenomenon that we term a “multiscale ecological boundary.”

Understanding the spatial distribution of biodiversity is a fundamental goal in ecology, yet most microbial studies focus on single domains. This study provides a comprehensive comparison of bacteria, archaea, fungi, and protists along an ~18,000 km latitudinal gradient in intertidal mudflats. We reveal that these microbial domains do not follow a unified diversity pattern but are instead governed by distinct ecological drivers. Bacteria and archaea are strongly influenced by regional species pools, whereas fungal and protist communities are primarily shaped by local stochastic processes such as dispersal limitation. These findings highlight the importance of organismal traits (e.g., body size) in shaping community assembly. This work emphasizes the necessity of establishing a multi-domain framework to accurately predict how Earth’s complex microbiomes respond to environmental changes.

Background For in vitro batch fermentation or fecal microbiota transplantation, preparation of inoculum was recommended by pooled feces to minimize inter-individual variation. However, the impact of pooling on microbiota variability remains unclear. The present study investigated the changes in inter-sample variation of microbial community in fecal samples after pooling from different numbers of donors, and verified the hypothesis that the variation of microbiota in feces affects the fermentation outcomes in vitro using fecal inoculum. Results The pooled feces from different pigs increased the microbial richness (Sobs and Ace indexes, P  < 0.05). The PCoA indicated that the microbiota composition was not distinct among the treatments, however, the distance of the sample within group was reduced as the incremental number of feces in the mixed samples. Microbial composition analysis indicated the variation of microbiota abundance was reduced with the increasing number of feces in mixed samples. The in vitro fermentation results suggested that the coefficient variation (CV), especially inter-bath and total CV, the kinetic parameters of gas production, in vitro fermentability of dry matter (IVDMF), and SCFA production reduced as the number of mixture donors increased. Conclusions Collectively, pooled feces originating from different donors can reduce the variation of microbiota between samples, and it is proposed that the fecal samples should be mixed, derived from 5 to 10 pigs, and then prepared as an inoculum to improve the reproducibility of in vitro fermentation.

Background Low salinity is a crucial environmental stressor that affects estuarine coral ecosystems considerably. However, few studies have focused on the effects of low-salinity conditions on coral-associated microorganisms and the adaptability of coral holobionts. Methods We explored the community structure of coral symbiotic Symbiodiniaceae and associated bacteria in low-salinity conditions using samples of six coral species from the Pearl River Estuary and analyzed the adaptability of coral holobionts in estuaries. Results The symbiotic Symbiodiniaceae of all six studied coral species were dominated by Cladocopium, but, the Symbiodiniaceae subclades differed among these coral species. Some coral species (e.g., Acropora solitaryensis ) had a high diversity of symbiotic Symbiodiniaceae but low Symbiodiniaceae density, with different adaptability to low-salinity stress in the Pearl River Estuary. Other coral species (e.g., Plesiastrea versipora ) potentially increased their resistance by associating with specific Symbiodiniaceae subclades and with high Symbiodiniaceae density under low-salinity stress. The microbiome associated with the coral species were dominated by Proteobacteria , Chloroflexi , and Bacteroidetes ; however, its diversity and composition varied among coral species. Some coral species (e.g., Acropora solitaryensis ) had a high diversity of associated bacteria, with different adaptability owing to low-salinity stress. Other coral species (e.g., Plesiastrea versipora ) potentially increased their resistance by having minority bacterial dominance under low-salinity stress. Conclusions High Symbiodiniaceae density and high bacterial diversity may be conducive to increase the tolerance of coral holobiont to low-salinity environments. Different coral species have distinct ways of adapting to low-salinity stress, and this difference is mainly through the dynamic regulation of the coral microbiome by corals.

Global warming is resulting in increased frequency of weather extremes. Root-associated fungi play important roles in terrestrial biogeochemical cycling processes, but the way in which they are affected by extreme weather is unclear. Here, we performed long-term field monitoring of the root-associated fungus community of a short rotation coppice willow plantation, and compared community dynamics before and after a once in 100 yr rainfall event that occurred in the UK in 2012. Monitoring of the root-associated fungi was performed over a 3-yr period by metabarcoding the fungal internal transcribed spacer (ITS) region. Repeated soil testing and continuous climatic monitoring supplemented community data, and the relative effects of environmental and temporal variation were determined on the root-associated fungal community. Soil saturation and surface water were recorded throughout the early growing season of 2012, following extreme rainfall. This was associated with a crash in the richness and relative abundance of ectomycorrhizal fungi, with each declining by over 50%. Richness and relative abundance of saprophytes and pathogens increased. We conclude that extreme rainfall events may be important yet overlooked determinants of root-associated fungal community assembly. Given the integral role of ectomycorrhizal fungi in biogeochemical cycles, these events may have considerable impacts upon the functioning of terrestrial ecosystems.

A field scale experiment was performed to explore the nitrogen removal performance of the water and surface sediment in a deep canyon-shaped drinking water reservoir by operating WLAs (water-lifting aerators). Nitrogen removal performance was achieved by increasing the densities and N-removal genes (nirK and nirS) of indigenous aerobic denitrifiers. After the operation of WLAs, the total nitrogen removal rate reached 29.1 ± 0.8% in the enhanced area. Ammonia and nitrate concentrations were reduced by 72.5 ± 2.5% and 40.5 ± 2.1%, respectively. No nitrite accumulation was observed. Biolog results showed improvement of carbon metabolism and carbon source utilization of microbes in the enhanced area. Miseq high-throughput sequencing indicated that the denitrifying bacteria percentage was also higher in the enhanced area than that in the control area. Microbial communities had changed between the enhanced and control areas. Thus, nitrogen removal through enhanced indigenous aerobic denitrifiers by the operation of WLAs was feasible and successful at the field scale.

Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.

The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction of marine primary production. Here, we present quantitative niche models for these lineages that assess present and future global abundances and distributions. These niche models are the result of neural network, nonparametric, and parametric analyses, and they rely on >35,000 discrete observations from all major ocean regions. The models assess cell abundance based on temperature and photosynthetically active radiation, but the individual responses to these environmental variables differ for each lineage. The models estimate global biogeographic patterns and seasonal variability of cell abundance, with maxima in the warm oligotrophic gyres of the Indian and the western Pacific Oceans and minima at higher latitudes. The annual mean global abundances of Prochlorococcus and Synechococcus are 2.9 ± 0.1 × 10 ²⁷ and 7.0 ± 0.3 × 10 ²⁶ cells, respectively. Using projections of sea surface temperature as a result of increased concentration of greenhouse gases at the end of the 21st century, our niche models projected increases in cell numbers of 29% and 14% for Prochlorococcus and Synechococcus , respectively. The changes are geographically uneven but include an increase in area. Thus, our global niche models suggest that oceanic microbial communities will experience complex changes as a result of projected future climate conditions. Because of the high abundances and contributions to primary production of Prochlorococcus and Synechococcus , these changes may have large impacts on ocean ecosystems and biogeochemical cycles.