Environmental Microbiome最新文献

Background: Soil denitrification mediated by microbial communities is a major source of nitrous oxide (N₂O), a potent greenhouse gas. However, the regulatory roles of keystone taxa in this process remain poorly understood, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N₂O emission potentials, offering an ideal model for exploring microbial mechanisms driving soil-specific denitrification dynamics.

Results: We integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the two soil types. Structural equation modeling (SEM) and correlation analyses revealed strong associations between keystone taxa and denitrification rates and N₂O emission patterns. Ensifer ASV205 was identified as a conserved keystone taxon in both soils and exhibited strain-level niche specialization. Comparative genomic analysis revealed that variations in denitrification gene composition and carbon-nitrogen metabolic pathways enabled Ensifer strains to act either as N₂O producers or reducers, depending on environmental conditions.

Conclusions: Our findings demonstrate that soil-specific denitrification processes and N₂O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study provides new insights into the microbial mechanisms regulating N₂O emissions and lays the groundwork for developing microbiome-informed strategies to mitigate greenhouse gas emissions in agricultural soils.

Background: Karst rocky desertification poses a serious threat to the ecosystems of southwest China, where Hypnum leptothallum plays a crucial role in forming microbial crusts essential for restoration. However, the use of native microbial applications in this area remains largely unexplored.

Results: In this study, the host-associated microbial communities of H. leptothallum from four severely desertified regions in Guizhou Province were characterized using high-throughput sequencing. The results revealed conserved α- and β-diversity, with dominant bacterial phyla being Pseudomonadota (34-47%) and Actinomycetota (23-35%), and fungal phyla being Ascomycota (57-83%) and Basidiomycota (14-32%). Subsequent carbon-source preference analysis guided the formulation of specialized media (e.g., α-D-lactose, N-acetyl-D-glucosamine) to isolate culturable strains, with cross-referencing identifying 14 bacterial and 36 fungal species consistently shared between sequencing and cultivation. Functional evaluation demonstrated bacterial dominance in inorganic phosphorus solubilization (68% of strains), protease synthesis (76%), ammonia production (56%), and indole-3-acetic acid biosynthesis (62%), while fungi excelled in organophosphorus solubilization. Further drought tolerance and gametophyte co-culture assays identified 10 drought-resistant bacterial strains and 16 strains significantly enhancing H. leptothallum growth within 7 days.

Conclusions: These functionally validated strains, particularly drought-adapted and growth-stimulating species closely related to Rhodococcus erythropolis, provide targeted microbial resources for developing synthetic inoculants to optimize artificial crust propagation in karst restoration.

Background: The Barrancas Blancas (BB) plain, situated in the high-altitude Atacama region, is a cryogenic, hyper-arid, poly-extreme environment. The seasonal formation of a temporary freshwater lake under these harsh conditions provides a unique opportunity to examine how liquid water influences the metabolic responses of desert microbial communities. Using a metatranscriptomic approach, we characterised microbial community responses along a 70-meter natural moisture gradient.

Results: Along the gradient, the most active sites (8-23 m from the lake) exhibited high RNA recovery and diverse metabolic functions. Bacillariophyta (diatoms) drove oxygenic phototrophy, while Pseudomonadota contributed to anoxygenic phototrophy and nitrogen fixation. Additionally, Pseudomonadota, Actinomycetota, and Bacteroidota expressed genes for the oxidation of nitrate, sulfide, thiosulfate, and trace gases (H₂, CO). The energy derived from these processes was reflected in the high capacity for carbon fixation by these taxa. Moreover, network analysis revealed that these primary producers co-occurred with a diverse range of heterotrophic prokaryotic and eukaryotic groups. In contrast, at the driest site, hydrogen oxidation was the primary energy-conserving process, predominantly associated with Actinomycetota, which also contributed to hydrogenotrophic carbon fixation. Notably, even at this site, heterotrophic eukaryotes co-occurred with these chemolithotrophic primary producers.

Conclusions: This study presents the first transcriptomic analysis from the high-altitude Atacama Desert, facilitated by the favourable moisture conditions. Furthermore, these findings highlight a moisture-driven transition in microbial energy acquisition strategies and emphasise the ecological significance of both photoautotrophy and chemolithotrophy, which likely vary depending on the dynamics of temporary lakes. The BB plain and its lake thus offer a robust model for understanding microbial resilience, functional plasticity, community assembly, and trophic interactions in extreme environments, providing novel insights into life at the edge of habitability.

Background: In viticulture, temporary cover crops and organic mulching are sustainable practices that enhance biodiversity, improve soil fertility, and strengthen grapevine health/resilience, particularly in Mediterranean regions. However, their impact on microbial communities associated with grapevines in non-irrigated vineyards remains largely unexplored. Inter-row soil management included a cereal-based cover crop (CC), a mixed cereals, legumes and brassicas cover crop (MC), and a control with alternating soil tillage and spontaneous grass (GT). In spring, cover crops were terminated to form a dry mulch under the vine rows.

Results: At veraison, under-row dry mulching significantly maintained higher soil water availability and reduced soil temperature by approximately 2.5 °C compared to the GT treatment. CC, in particular, enhanced grapevine physiological performances. These different soil conditions positively shaped the rhizosphere microbiome by maintaining higher microbial richness and promoting nutrient-cycling microorganisms (e.g., Bradyrhizobium sp., Nitrospira japonica) in both CC and MC. In contrast, the GT treatment selectively favored drought-tolerant plant growth-promoting rhizobacteria (PGPR) taxa such as Bacillus zanthoxyli, Gaiella occulta, Roseiflexus sp., Pseudarthrobacter sp., and Paenibacillus sp. In the phyllosphere, the abundance of Erysiphe necator, the powdery mildew agent, was lower in CC and MC, which also showed a higher presence of Aureobasidium pullulans, a species reported in the literature as a potential biocontrol agent.

Conclusions: Our results suggest that under-row dry mulching, by modifying soil conditions, can have a positive effect on grapevine microbial richness and biodiversity during the dry summer period, serving as an indicator of improved vineyard agroecosystem health and sustainability.

Background: Viscose-rayon microfibres (RFs) are cellulosic microfibres widely dispersed throughout aquatic environments. Whether ingested by or suspended in the surrounding environment, these microfibres may impact both wild and farmed animals. A previous study on European sea bass (Dicentrarchus labrax) showed that the increased presence of RFs in aquafeeds (CTRL-no RFs; RF1-0.001 g/kg; RF2-0.01 g/kg; RF3-0.1 g/kg) was linked to an exponential increase of RFs in water, intestine and skeletal muscle. This finding was associated to a fatty liver and tissue-specific transcriptional changes, depicting the up-regulation of hepatic lipogenic enzymes and intestinal/head kidney inflammatory markers. The aim of the present study was to extend this evaluation by investigating changes in associated microbial communities after the ingestion of RFs in the diet, employing a multi-layered approach for the integrative profiling of gut, skin, and environmental water microbiome using the Nanopore platform.

Results: Amplicon-sequencing identified ~2800 taxa across water, skin and gut microbiomes. Gut and skin microbiomes were more similar to each other, but increasing RF exposure shifted the skin community toward the water microbiome. Moreover, RF induced the highest taxonomic variation in water (691 taxa), followed by skin (253) and gut (99), while microbial diversity Shannon and Simpson indexes declined from 4 down to 3.3 under RF2 and RF3 in a dose-dependent manner. Major exponents of this trend were the decrease of Synechococcus and Flavobacteriales in association with the increase of starch- and hydrocarbon-degrading taxa (Ardenticatenaceae and Gracilibacteria). In both gut and skin, bacterial richness decreased in fish fed low to intermediate RF doses, whereas RF3 fish resembled controls. Thus, compositional and discriminant analyses consistently grouped CTRL and RF3 samples, suggesting the existence of a dose threshold occurring in parallel with host counter-regulatory responses. Such feature was reflected by abundant skin-associated bacteria (Exiguobacterium and Planococcus) with at least the genetic potential to be linked to vitamin B6 biosynthesis and host-driven muscle regeneration markers, whereas predominant gut taxa with the same pattern (Microbacterium and Achromobacter) was associated with polysaccharide degradation and correlated with host gene inflammatory mechanisms.

Conclusions: This study revealed a concomitant dose-dependent and dose-threshold response among the bacterial communities composing the holobiont of European sea bass in response to dietary RFs ingestion, highlighting novel bacterial taxa and pathways through which microplastic exposure may differentially reshape rearing water and host-associated microbial communities.

Microbes are integral players in plant-insect networks, and play crucial roles in host health and ecological interactions. However, the horizontal microbial transmission dynamics via flowers remain insufficiently understood, particularly in hub plants visited by diverse insect communities. Here, using 16S rRNA gene and ITS2 metabarcoding, we characterized the bacterial and fungal communities associated with open flowers, insect-excluded bagged flowers, and flower buds of bramble (Rubus spp.), a highly insect-visited hub plant. Our results show that environmental deposition and insect visitation significantly altered floral microbiota diversity and microbial load, particularly for bacterial communities. Insect visitation potentially enriched fermentative and probably also pathogenic bacteria, including Spiroplasma. While bagged flowers and open flowers both showed high within-group variation for bacterial communities, the microbial networks were more internally connected in bagged flowers, and more centralized in open flowers. The distinct network properties might be due to flower group-specific microbial hub genera introduced by different horizontal transmission routes. Moreover, cross-domain network analysis revealed hub genera unique to bacteria-fungi interactions, including Cladosporium, which was consistently detected across all flower groups. These findings highlight the dominant role of insect visitation in shaping floral microbiota and underscore the ecological significance of hub plants in horizontal microbial transmission across plant-pollinator networks.

Background: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

Results: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

Conclusions: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.

As truffle cultivation expands, growers empirically develop new agronomic management practices aimed at promoting truffle growth such as "truffle nests", localized peat amendments that are supplemented with truffle spore inoculum. Previous research showed that nests contain lower fungal diversity than the surrounding soil, which could encourage its occupation by pioneer species such as Tuber melanosporum. However, truffle nests did not quickly stimulate truffle mycelium growth. We hypothesized that the bacterial community from the soil may be the first to colonize nests and that fungal and bacterial diversity in nests would have an inverse relationship. To test this, we characterized the bacterial community of truffle nests, via 16S rRNA gene amplicon sequencing, in two orchards during the two years after establishing the nests. Unexpectedly, we did not find drastic differences in the bacterial diversity inside nests with respect to the bulk soil or the commercial substrate before being introduced in the field. However, Proteobacteria richness in nests was positively correlated to truffle mycelium abundance, which together with a higher relative abundance of Proteobacteria in nests than in bulk soil, indicates a possible underlying factor for the performance of nests in truffle plantations. Fungal and bacterial richness was positively correlated in nests, countering our hypothesis that bacterial diversity would negatively impact fungal diversity.

Background: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca₃(PO₄)₂ were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.

Results: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca₃(PO₄)₂. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.

Conclusions: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.

Background: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.

Results: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.

Conclusions: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.