Environmental Microbiome最新文献

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.

Background: Understanding soil microbial interactions is essential for developing biofertilizers in regenerative agriculture. Polyphosphate-accumulating organisms (PAOs) play a pivotal role in enhanced biological phosphorus removal (EBPR) systems by sequestering phosphorus from wastewater and storing it as intracellular polyphosphate. However, their role in terrestrial phosphorus cycling remains poorly characterized, despite their potential to serve as a reservoir of plant-available phosphorus. This study investigates PAO-enriched microbiomes in the sorghum rhizosphere, focusing on their novel interactions with arbuscular mycorrhizal fungi (AMF). By integrating PAOs derived from EBPR biosolids and compost with AMF, we assessed their synergistic effects on plant growth and nutrient uptake in Sorghum bicolor (sorghum), as well as their broader influence on rhizosphere microbial traits and functional dynamics.

Results: We employed plant biometry analysis, nutrient assays, ³¹P NMR spectroscopy, single-cell Raman microspectroscopy (SCRS), and microbiome profiling to comprehensively evaluate rhizosphere microbial interactions and their effects on plant physiology and nutrient dynamics. ³¹P NMR confirmed polyphosphate accumulation by PAOs derived from both compost and EBPR biosolids, demonstrating the soil adaptability of EBPR-derived PAOs. AMF showed enhanced synergy with EBPR-derived microbiomes, significantly enhancing sorghum growth, nutrient acquisition, and microbial diversity. Key PAOs, Thauera, Rhodanobacter, and Paracoccus, were successfully incorporated into the rhizosphere and positively correlated with improved phosphorus uptake. PICRUSt2 analysis indicated enrichment of microbial functions linked to motility and xenobiotic metabolism in EBPR-treated rhizospheres. SCRS revealed AMF-induced phenotypic shifts in EBPR-derived microbiomes, while network analysis showed that AMF reorganized community connectivity, fostering novel microbial interactions in EBPR-amended environments.

Conclusions: This study explored the interactions between AMF and microbiomes derived from EBPR biosolids, in comparison with those from compost, uncovering novel microbial synergies that enhance phosphorus uptake in Sorghum bicolor and promote plant productivity. The findings underscore the potential of targeted microbial co-inoculation such as integrating EBPR microbiomes with AMF as an innovative strategy for improving soil fertility and advancing biofertilizer development through microbial-driven nutrient recycling. By harnessing wastewater-derived phosphorus via PAOs, this approach offers a sustainable alternative to conventional fertilization, supporting regenerative agriculture, nutrient circularity, and the broader application of microbial biofertilizers in crop production.

Background: Plants evolve as holobionts, ecological and evolutionary units made up of the host plant and its associated microbiota, which shape plant fitness and adaptive capacity. Isolated ecosystems with low biodiversity and plant cover, such as the fellfields of the remote sub-Antarctic Kerguelen Islands, represent ideal open-air laboratories to disentangle the drivers affecting plant-microbiome interactions. In such pristine environments, endemic plant species and their microbiota have coevolved in isolation possibly since the last ice age. In this study, we investigated the bacterial and fungal communities associated with different soil-plant compartments of two phylogenetically distant endemic plants, the Poaceae Poa kerguelensis and the Brassicaceae Pringlea antiscorbutica, in fellfields with contrasted pedoclimatic conditions.

Results: Using 16S rRNA gene and Internal Transcribed Spacer (ITS) region metabarcoding, we identified a strong soil-plant compartment effect affecting microbial communities, with bacterial and fungal α-diversity higher in bulk and rhizospheric soils and progressively decreasing in roots and above-ground compartments. The microbiota of the different soil-plant compartments studied differ in their recruitment patterns. The bacterial communities of the aerial parts of P. antiscorbutica were less dependent on those of the underground parts compared to those of P. kerguelensis. We also showed that the microbiota of distinct plant species and their different soil-plant compartments respond differently to pedoclimatic variables, with a greater impact of climatic variables over soil ones on aboveground bacterial microbiomes than on belowground microbiomes.

Conclusions: Our results highlight the dual role of environmental variability and of the identity of the host on the recruitment and diversity of plant microbiomes in the isolated studied ecosystems. As plant holobionts are part of the global biogeochemical ecosystem functioning, our results suggest that plant species-specific microbial recruitment strategies and differential vulnerability to environmental factors should be included in predicting sub-Antarctic ecosystem response to global warming.