Environmental Microbiome最新文献

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.

Background: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.

Results: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p < 0.001) in summer than in winter while the community maturity index was higher (p < 0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p < 0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p < 0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p < 0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R = 0.222, p = 0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R²=0.64-0.72 for key paths) than in winter (R²=0.52-0.63).

Conclusions: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.

Background: Yeasts are ubiquitous microorganisms thriving in diverse environments. They are prevalent members of the phyllosphere microbiome, but genomic studies of plant-associated yeasts remain limited.

Results: We established a taxonomically diverse yeast culture collection from flag leaves of field-grown wheat. This collection captured between 48-56% of the genus-level diversity detected by ITS amplicon sequencing conducted over two consecutive years, including the core members Aureobasidium, Dioszegia, Filobasidium, Papiliotrema, Sporobolomyces, and Vishniacozyma. De novo sequencing of 96 high-quality genomes from this collection, representing 14 yeast genera, and comparative genomics revealed specific signatures associated with life in the phyllosphere, the aboveground part of the plant. These adaptive traits encompass enriched carbohydrate metabolism, secondary metabolite biosynthetic pathways, and pectin degradation. The substantially smaller genomes of the phyllosphere yeast genera Candida and Metschnikowia suggest niche specialization via prioritizing metabolic pathways that are essential for survival in the nutrient-limited phyllosphere.

Conclusions: This study represents a significant advancement in our understanding of the diverse and largely unknown genomic traits of environmental yeasts and their adaptation to life in the phyllosphere environment. Our findings highlight their untapped functional potential for biotechnological applications in sustainable crop production.

Background: Understanding how agricultural practices affect soil bacterial communities is vital to mitigating the negative impacts of intensive agriculture on soil health and preventing further deterioration of arable land. Increasing pressure on agricultural land necessitates careful management of our productive soil. This study investigates the interaction between organic amendments and soil texture in agricultural soils (n = 93) used for arable production, using a 16S rRNA-sequencing based microbial community analysis. Amendments include slurry, digestate, and farmyard manure. Additionally, soil physicochemical parameters were collected to explore the drivers of patterns of soil microbial diversity.

Results: Microbial community composition was significantly influenced by organic amendments and soil texture, which both exerted distinct selective pressures. Analysis using 16S rRNA-sequencing and advanced modelling identified significant factors affecting community structure, including soil calcium levels, the crop grown one year previously, loss on ignition (LOI), and farm ID. The genus Candidatus Nitrosotalea was found to be positively associated with application of farmyard manure, while genus AD3 (phyla Chloroflexi) was found to be negatively associated with application of digestate and slurry.

Conclusions: The results highlight the importance of considering multiple, interacting factors when trying to establish how agricultural practice affects soil microbial communities. Our findings underscore the need for tailored management strategies - specific to the local environment and available resources - to promote soil health.

Background: Viruses are fundamental to many aspects of life influencing ecosystem functions. The `number of lenses´ we use for exploring the viral diversity has expanded, yet each has limitations that constrain our view of the uncultured virosphere. It is fundamental to evaluate the different viromic approaches and sequencing methods on their ability to recover the extant viral diversity and microdiversity present in a sample. The differences in genome recovery between technologies have downstream impacts on subsequent estimates of viral diversity and function within a sample that can limit our comprehension of natural viral assemblages and their interactions with their microbial hosts.

Results: Here, using the same surface seawater sample, we compare short- and long-read viromics (i.e., Illumina, PacBio-HiFi and MinION sequencing) along with high-throughput single-virus genomics (sequencing of 700 uncultured single-viruses) to explore the consensus between approaches to uncover the extant viral diversity (sequencing effort ≈1.6 Tbp). Overall, ≈42,000 viral contigs (> 10 kb) were obtained, resulting in ≈12,500 and ≈23,400 viral OTUs at the genus and species levels, respectively, infecting mostly Flavobacteriaceae and Pelagibacteracea. At the viral family level, single-virus genomics (SVG) recovered viruses with a more distinct taxonomic profile compared to other methods. At lower taxonomic resolution, only < 1% of all species and genera, including some of the most abundant viruses, were captured by all methods; reaching a value of ≈2% when only viromics excluding SVG were considered. The highest pairwise diversity consensus was observed between PacBio-HiFi and Illumina, with approximately ≈11% of PacBio-HiFi species-level vOTUs also detected by Illumina. To understand how different methods resolve the co-occurring genomic microdiversity within species, we used one of the most abundant and microdiverse viruses -the uncultured pelagiphage vSAG 37-F6, proposed to be classified as Pelagimarinivirus ubique- originally discovered by single-virus genomics, as a reference. None of the methods alone were able to assemble the complete genome, which was only achieved by combining all datasets. Similarly, none of the viral clusters at the strain level were recovered by all methods.

Conclusions: Our study suggests that the inherent bias of each method still represents a challenge for the recovery of marine viral diversity and potentially for other environmental viral samples. Nevertheless, regarding standard viromic techniques, PacBio HiFi in combination with Illumina seem to perform the best in absolute recovery of viral species and genera.

Terrestrial hot springs are globally distributed extreme environments, and these systems have long served as natural laboratories for studying microbial life under thermal stress. While much of the research to date has focused on thermophilic bacteria and archaea, there is a growing appreciation for the diversity and ecological significance of eukaryotic microorganisms in these habitats. In this study, we used metagenomic sequencing to assess inter-domain microbial diversity in biofilms from 47 circumneutral hot springs across East and Southeast Asia, with a specific focus on resolving eukaryotic taxa and their ecology. Whilst all biofilm communities were dominated by bacteria, the microbial eukaryotes represented approximately 10% of the taxonomic diversity and accounted for 1.3% of overall taxa abundance, indicating a small but significant presence. We provide the first comprehensive inter-domain checklist of over 14,500 microbial taxa in hot springs. Patterns in diversity were significantly correlated with temperature, hydrogen sulfide, and pH in hot springs. Fungi emerged as the most abundant and prevalent eukaryotic group, indicating an important role as eukaryotic saprotrophs, with Ascomycota yeasts comprising the most individually abundant taxa. Among other microbial eukaryotic phyla, the photosynthetic Chlorophyta and Bacillariophyta were most abundant. Predatory/grazing microbial eukaryotes were relatively less diverse and abundant. Network co-occurrence analysis was used to indicate extensive and specific biotic interactions between eukaryotes and bacteria in biofilms. We further employed metatranscriptomics to identify putatively active taxa, revealing that most detected eukaryotes were transcriptionally active. While fungi accounted for most transcripts, the highest RNA:DNA ratios were observed among predatory and photosynthetic taxa, suggesting elevated activity in these functional groups. Overall, our findings highlight the diversity, interactions, and activity of eukaryotes in Southeast Asian hot spring biofilms, underscoring their potential importance in shaping microbial community structure and function in extreme environments.

The ecological characteristics of fungal generalists (FG) and specialists (FS) in rhizosphere, as well as their impact on soil micronutrient dynamics and plant metabolic adaptability are largely unknown. Through large-scale sampling of Panax notoginseng (with saponins as the primary specialized metabolite) and ecological analysis, we demonstrated that, compared to FS, the assembly of rhizosphere FG is more strongly governed by deterministic processes and that they play more crucial roles in maintaining network stability. Further, Mantel analysis and multiple machine learning models revealed that FG, rather than FS, are significant contributors to soil micronutrient availability, particularly for iron and zinc. This was substantiated by culture-based approaches, where we confirmed the zinc- and iron-solubilizing capabilities of candidate FG isolates both in vitro and in soil. A driver analysis of plant metabolic variation identified soil micronutrient availability as the predominant factor affecting plant metabolome and saponin accumulation, underscoring the significance of the FG-driven micronutrient availability in shaping plant metabolic adaptability. Among these micronutrients, available zinc exhibited the strongest positive effect on total saponin accumulation (R² = 0.24, P < 0.001). A zinc-supplement pot experiment further validates the improving effects of zinc on root saponin accumulation, which was correlated to the upregulation of the PnCYP716A47 gene. Collectively, this study clarifies that deterministically assembled rhizosphere FG regulate plant adaptability by influencing soil micronutrient availability. These findings provide new insights for plant-microbe interactions in rhizosphere and are critical for the utilization of functional microbes to enhance plant performance.

Background: Verticillium wilt, caused by Verticillium dahliae Kleb., is a devastating soilborne disease threatening global cotton production. Intercropping is a sustainable agricultural practice known to suppress soilborne diseases, yet the microbiome-mediated mechanisms underlying its efficacy against Verticillium wilt remain poorly understood.

Results: A three-year field trial (2019-2021) showed that intercropping cotton with mustard significantly reduced Verticillium wilt severity (32.11-39.2%), increased yield (13.88-23.22%), and lowered soil microsclerotia density. Intercropping reshaped soil microbial communities and enriched a core set of beneficial taxa compared to monocropping, generating more complex and cooperative rhizosphere networks during flowering and boll stage. We then constructed an intercropping-enriched synthetic community (IC-SynCom) from the enriched core microbiotas with multiple beneficial traits; this consortium, comprising Bacillus altitudinis strain CRB-021, Lysobacter firmicutimachus strain CRB-253, Rhizobium soli strain CRB-314, Enterobacter hormaechei strain CRB-070, and Pantoea sp. strain CRB-006, achieved the highest control efficacy at 72.83 ± 1.31%, promoted cotton growth, and outperformed single-strain inoculants. qRT-PCR further showed that IC-SynCom activated systemic plant defenses by the upregulation of key defense-related genes, including phenylalanine ammonia-lyase (GhPAL), cinnamate 4-hydroxylase (GhC4H1), pathogenesis-related protein 10 (GhPR10), peroxidase (GhPOD), and β-1,3-glucanase (Ghβ-1,3-glucanase), which are involved in salicylic acid signaling and lignin biosynthesis.

Conclusions: Our findings demonstrate that intercropping enhances soil's capacity to suppress Verticillium wilt by reshaping root-associated microbiomes. A core consortium of intercropping-enriched beneficial microbes (IC-SynCom) effectively suppresses Verticillium wilt through direct antagonism and activation of plant immunity. These results highlight the potential of microbiome-based strategies for sustainable management of soilborne diseases.