Environmental Microbiome最新文献

Background: Fungal communities play crucial roles in plant development and metabolite accumulation, especially in fully mycoheterotrophic medicinal plants like Gastrodia elata. While the importance of fungal symbiosis in G. elata is recognized, how fungal community dynamics evolve across its entire growth cycle and how they influence biomass and bioactive compound accumulation remain largely unclear.

Results: High-throughput sequencing combined with multi-omics analyses revealed that developmental progression significantly shapes fungal diversity and composition, thereby influencing biomass and metabolite accumulation in G. elata. These effects are mediated by stage-specific selective recruitment and dynamic remodeling of fungal communities in both rhizome and rhizosphere compartments. Structural equation modeling indicated that developmental stage, fungal α-diversity, and community structure exert both direct and indirect effects on biomass and the accumulation of bioactive compounds. High-resolution association network analyses further identified key functional fungal groups, particularly wood and soil saprotrophs, as major contributors to seed stem biomass regulation. Notably, the symbiotic fungus Armillaria showed the strongest positive correlation with gastrodin accumulation, while wood saprotrophs and plant pathogens also significantly influenced its levels.

Conclusions: This study systematically elucidates the dynamic changes in fungal communities across different developmental stages of G. elata and their effects on biomass and bioactive metabolite accumulation. Our findings highlight the central role of microbe-plant-metabolite interactions in regulating biomass and bioactive metabolite production, offering valuable insight for optimizing the cultivation and quality of medicinal plants through microbiome-targeted strategies.

Background: Trees and their associated microbes provide numerous ecosystem services including carbon sequestration, nutrient cycling and phytoremediation. Tree bark represents a large and seasonably stable habitat for microbial communities. However, the tree bark microbiome remains largely understudied, particularly for wetland tree species. In the Lower Mississippi River Basin, bald cypress (Taxodium distichum) are the predominant tree species in many wetlands, including lakes and streams connected to large agroecosystems dominated by row-crop agriculture. These water bodies are often managed for irrigation and drainage needs and are subject to agrochemical runoff from adjacent fields. Thus, we sought to understand how hydrology affects the bald cypress bark microbiome.

Results: We collected 278 bark samples over six months from 18 trees located in three different lakes. Using 16S rRNA gene sequencing, we found that the bald cypress tree bark microbiome was largely consistent between trees within a lake as well as between different lakes, with a core microbiome that includes bacterial taxa that were present in over 95% of samples collected. Hydrology had a significant influence on microbiome structure, with different sections of bark having distinct bacterial communities depending on if the bark was submerged, just above the water, or dry. Water quality was significantly correlated with alpha diversity of wet bark, which was more diverse than dry bark and had higher relative abundances of bacteria that may be providing relevant ecosystem services such as denitrification, methane oxidation, and pollutant degradation.

Conclusions: Wetlands are important for nutrient cycling and water quality regulation. Our study provides insights into microbial dynamics of these ecosystems and how hydrology can impact the microbial communities present, which in turn may be impacting water quality. This work is the first to the describe the bark microbiome of a wetland tree species and lays the groundwork for future studies assessing the functional role of the microbiome in wetland ecosystem services.

Lettuce, a widely consumed raw vegetable, harbors leaf-associated microbial communities whose understanding and prediction are crucial for plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated how three key plant factors -genetic distance, plant variety and leaf micro- and macronutrient content- influence the composition and diversity of lettuce leaf bacterial communities, by analyzing 131 fully-sequenced Lactuca sativa genotypes via 16S rRNA amplicon sequencing. Our findings revealed that variety, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with available and detailed shoot traits they explained 13.4% of the observed bacterial diversity. Inspection of 9 specific leaf morphological traits, with further validation by MAGs analysis, showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. These results highlight the strong relationship between leaf morphology and bacterial community structure, suggesting that phenotypic traits play an outsized but understudied role in shaping the leaf microbiota, a crucial aspect of the edible microbiome.

Introduction: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

Objectives: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

Methods: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

Results: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

Conclusion: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.

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.