Environmental Microbiome最新文献

Background: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.

Results: We propose a computational framework for the simulation of the metabolic potential of microbiomes, as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and species from six contrasting soil samples across the Talabre Lejía transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or sensitive to environmental shifts, through putative cooperation events.

Conclusion: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.

Background: Since recent years, German sea buckthorn (SBT) cultivation is increasingly affected by dieback. Wildly growing plants from dunes and cultivated plants from plantations show symptoms of wilt, lesions and discolorations in shoot cross sections. The cause of final plant death is not yet resolved and asymptomatic plants are rare to find. Our aim was to investigate the associated fungal communities of visibly dieback affected plants. A culture-dependent isolation approach in parallel with a culture-independent sequencing approach by metabarcoding of ITS1 was used to investigate SBT shoot fungal communities. Evaluation of the sequencing data was supported with random forest modelling.

Results: Results of both approaches complement each other and are consistent. Members of the ascomycete genera Hymenopleella and Diaporthe were most frequently isolated from symptomatic samples. Alternaria, Aureobasidium, Cladosporium, Epicoccum and Penicillium could be identified in both sample types, i.e. symptomatic and asymptomatic plants, with high frequencies. Sequencing of shoot samples revealed that the fungal community composition differs significantly between symptomatic and asymptomatic plants. Pielou's evenness was significantly reduced for symptomatic plants indicating a dominance of few fungal taxa in symptomatic samples pointing to a dysbiosis in fungal communities. In a random forest modelling approach, abundance of Capnocheirides amplicon sequence variants had the highest relative importance for the model and high relative abundance is considered as predictor for absence of SBT symptoms. In symptomatic plants, Hymenopleella and Diaporthe had high relative abundances and were suggested as predictors.

Conclusions: Overall, our combined approach has revealed an increased abundance of Hymenopleella and Diaporthe in symptomatic sea buckthorn in Germany along with changes in the total fungal community. The relative abundances derived from amplicon sequencing were reflected by the isolation frequencies of the respective taxa.

Green manure crops are increasingly recognized not only for their contributions to soil fertility but also for their role in shaping plant-associated microbiome. Astragalus sinicus, a widely used leguminous green manure in East Asian paddy fields, harbors distinct microbial assemblages across plant compartments, yet the ecological processes driving microbiome assembly along its phyllosphere-rhizosphere continuum remain unclear. In this study, we profiled microbiome composition across the rhizospheric, phyllospheric, and soil compartments of A. sinicus using 16S rRNA gene amplicon sequencing targeting the region south of the Yangtze River, analyzing 315 samples collected from seven rice-growing regions. We found that Proteobacteria predominated all sampled compartments, with Mesorhizobium (75.85-96.93%) constituting the predominant taxon in the root microbiome. The leaf microbiome showed higher variability, dominated by Vibrionimonas (0.31-46.6%), Pantoea (0.71-46.61%), Pseudomonas (0.07-24.6%) and Bradyrhizobium (0.06-8.45%). Co-occurrence networks revealed a distinct gradient, including expansive yet weakly connected soil networks, moderately sized and highly modular leaf networks, and compact, highly robust root consortia, delineating a shift from environmentally driven complexity to host-filtered stability. Root and leaf microbiome assembly was primarily governed by stochastic processes (- 2 < β-NTI < 2, NCM r² > 70%) and plant- mediated selection (DI = 0.01/0.02, DSI = 0.09/0.14), with soil nutrient conditions, particularly total nitrogen, organic carbon, available phosphorus, and available potassiu, playing significant roles in shaping microbiome composition (p < 0.05). These core plant-associated ASVs were selectively enriched by the plant from the soil in over 70% of the sampled regions. Among these, Mesorhizobium in roots and Methylobacterium-Methylorubrum in leaves were found to be critical for nitrogen fixation and nutrient cycling, as evidenced by previous studies. Our results highlight the intricate interactions between plants, microbes, and their environment, underscoring the importance of plant-mediated selection and soil nutrient conditions in shaping the microbiome of A. sinicus, with significant implications for sustainable agricultural practices.

To clarify the diversity of glyphosate-degrading bacteria and genes in arid and alkaline soil environments, an efficient bacterial community, named CW, was enriched from the long-term continually cropped saline-alkali cotton soil in Xinjiang. This community could degrade 500 mg/L of glyphosate within 36 h in MSM medium with a pH of 8.0. The CW community was mainly composed of over 20 genera belonging to the phyla Pseudomonadota, Bacillota, and Bacteroidota. Notable genera include Hyphomicrobium, Pseudoxanthomonas, and Aquamicrobium. From this community, twenty-four strains showing glyphosate-degrading ability, representing 9 different genera, were successfully isolated. Notably, 14 strains belonging to six specific genera- Aquamicrobium (6), Shinella (2), Pseudoxanthomonas (2), Nocardioides (1), Chitinophaga (1), and Pseudomonas (2)- displayed complete degradation (100%). In addition, this study marks the first report confirming Aquamicrobium and Shinella as novel genera degrading glyphosate. During the degradation of glyphosate by the bacterial community CW, intermediate metabolites such as AMPA and phosphate were detected. Besides, sarcosine was detected during the degradation by the bacterial strain W6/W7. A detailed analysis of the glyphosate-degrading genes revealed that, besides the thiO, GAT, and phnY gene sequences, the genome of bacterial strain W6/W7 also harbors sequences with high similarity to the previously reported glyphosate-degrading genes soxA, aroA, dadA, phnJ, phnD, and phnA. Notably, the community CW efficiently expressed all the genes. Additionally, genes associated with phosphonate, hypophosphonate, oxalate, and dicarboxylate metabolism were co-expressed during glyphosate degradation. This study reveals that, even in the unique soil environment of Xinjiang, there exists a highly diverse bacterial community which can completely and efficiently degrade glyphosate.

Background: Perennial cropping systems are increasingly recognized for their potential to enhance microbial biodiversity and beneficial soil functions compared to annual crops. The impact of perennialization on the rhizomicrobiome and endophyte community was assessed by comparing intermediate wheatgrass (Thinopyrum intermedium, commercialized as Kernza®, hereafter called 'Kernza') and annual wheat (Triticum aestivum) associated communities across a north-south European agroclimatic gradient (Sweden, Belgium, and France) over two growing seasons and at two depths.

Results: Between the 2 years, the Kernza-associated rhizomicrobiome was more stable and exhibited greater homogeneity across depths compared to annual wheat. Kernza harboured a significantly more diverse set of crop-associated amplicon sequence variants (ASVs) and had a higher number of core ASVs than annual wheat. Furthermore, Kernza had a significantly higher proportion of rhizobacterial populations in root tissues than annual wheat. Environment-wide association analyses revealed that the Kernza rhizosphere had higher proportions of grassland-associated and rhizosphere-dwelling microbiomes compared to annual wheat. Despite these noteworthy differences, the greatest variation in the rhizomicrobiome composition was driven by factors such as country, year, and depth, rather than crop type. For instance, Actinobacteriota dominated rhizobacterial communities in both Kernza and annual wheat.

Conclusions: Overall, Kernza conferred modest yet clear improvements in rhizomicrobiome community stability and selective endophyte recruitment, supporting its ability to enhance sustainable, microbially-mediated soil functions. Moreover, Kernza hosted significant grassland-associated taxa, suggesting a similarity between Kernza fields and grassland ecosystems.

Background: Rice is a major food crop in China as well as Asia, yet its production is threatened by microbial diseases including blast disease caused by fungal pathogen (Magnaporthe oryzae) and bacterial blight caused by several bacterial pathogens. To screen for bacterial microbiota associated with rice blast occurrence, and/or contributing to disease resistance, we performed microbiota analysis with rhizosphere soil, root, stem, and leaf samples of blast susceptible (CO39) and resistant (Y33R) rice grown in a blast disease nursery garden.

Results: Our result showed no significant difference in microbiota of rhizosphere soil, root, or leaf between these two rice cultivars, but stem microbiota were significantly different. Pantoea spp. were enriched in stem of blast susceptible rice, suggesting that it may play a role after fungal infection. A total of 822 bacterial strains were isolated from the phyllospheric (including leaf and stem) samples of Y33R and CO39 rice. Based on 16S rRNA amplicon sequencing, and phylogenic analysis using 16S rRNA, gyrB, leuS, and rpoB gene sequences, the 3 isolated strains and 1 strain were identified as P. ananatis and P. dispersa, respectively. The strains A25-H1 and B10-A1 were selected for genome sequencing, and based on Average Nucleotide Identity (ANI) analysis, we confirmed that A25-H1 was P. ananatis and B10-A1 was P. dispersa. The P. ananatis consortium (A25-F1, A25-G1, and A25-H1 combination) A25-11 and P. dispersa strain B10-A1 displayed suppressive effect on blast disease when they were applied to the susceptible rice CO39. Although a P. ananatis strain SC7 has been reported to cause bacterial blight in rice, A25-11 or B10-A1 was non-pathogenic to rice under experimental conditions. Furthermore, they could also suppress bacterial blight caused by SC7 or Xanthomonas oryzae pv. oryzae strain Pxo99A. A25-11 and B10-A1 did not affect the growth of M. oryzae mycelia in confrontation culture analysis, but induced transcription of rice immunity genes and promoted ROS accumulation, suggesting that the biocontrol effect of A25-11 or B10-A1 may lie on immunity priming. We further showed that A25-11 and B10-A1 possessed growth promoting capacity including indole 3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and siderophore production. Under field condition, the consortium A25-11 and strain B10-A1 could effectively suppress leaf and panicle blast.

Conclusions: Overall, this study established a microbiome method for identifying the rice bacterial communities of agricultural significance, with capacity of rice disease management and/or growth promotion.

Background: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

Results: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

Conclusion: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.

Background: The primary source of carbon is one of the most fundamental questions regarding the development of microbial communities in serpentinite-hosted systems. The hydration of ultramafic rock to serpentinites releases large amounts of hydrogen and creates hyperalkaline conditions that deplete the environment of dissolved inorganic carbon. Metagenomic studies suggest that serpentinite-hosted microbial communities depend on the local redissolution of bicarbonate and on small organic molecules produced by abiotic reactions associated with serpentinization.

Methods: To verify these bioinformatic predictions, microbial consortia collected from the Prony Bay hydrothermal field were enriched under anoxic conditions in hydrogen-fed bioreactors using bicarbonate, formate, acetate, or glycine as the sole carbon source.

Conclusions: With the exception of glycine, the chosen carbon substrates allowed the growth of microbial consortia characterized by significant enrichment of individual taxa. Surprisingly, these taxa were dominated by microbial genera characterized as aerobic rather than anaerobic as expected. Our results indicate the presence of both autotrophic and heterotrophic taxa that may function as foundation species in serpentinite-hosted shallow subsurface ecosystems. We propose that an intricate feedback loop between these autotrophic and heterotrophic foundation species facilitates ecosystem establishment. Bicarbonate-fixing Meiothermus and Hydrogenophaga, as well as formate-fixing Meiothermus, Thioalkalimicrobium, and possibly a novel genotype of Roseibaca might produce organic compounds for heterotrophs at the first trophic level. In addition, the base of the trophic network may include heterotrophic Roseibaca, Acetoanaerobium, and Meiothermus species producing CO₂ from acetate for a more diverse community of autotrophs. The cultivated archaeal community is expected to recycle CH₄ and CO₂ between Methanomicrobiales and Methanosarcinales with putative Woesearchaeales symbionts.

Background: The Genome Taxonomy Database (GTDB) initiative aims to modernize prokaryotic taxonomy by aligning it with the great amounts of full-length genomes available today. Unfortunately, there is a poor link between the GTDB and the historically widely used 16S rRNA gene-based taxonomy. The current study explores the within and between divergence of the 16S rRNA gene sequences under GTDB taxonomy, refining our understanding of the 16S gene's resolution under this new taxonomic system. The analysis focuses on the divergence of 16S sequences collected from the GTDB genomes to identify optimal clustering thresholds for taxonomic resolution. Generalized linear mixed models (GLMMs) were fitted to estimate divergences within taxonomic ranks, correcting for the variable quality of the GTDB genomes.

Results: To achieve GTDB species-level resolution, 16S sequences need clustering at a divergence threshold of around 0.01 (99% identity), while genus-level resolution requires thresholds of 0.04-0.08 (92-96% identity), optimal thresholds vary significantly across branches, highlighting the limitations of using a fixed divergence threshold.

Conclusions: The results suggest a more adaptive approach to taxonomic assignment from 16S data is needed, tailored to the diversity and complexity of the samples. These findings are fundamental for an improved taxonomic classification of environmental 16S data.

Background: Aquatic plants play key roles in ecosystems, serving as primary producers and providing habitat for other aquatic life. While many are ecologically important, some invasive species, often introduced through the ornamental plant trade, pose threats to various aquatic ecosystems. Although viral infections have been documented to some extent in aquatic crops, the viral diversity in wild and ornamental aquatic plants remains largely unexplored. Investigating the viral communities of aquatic plants is important, as their direct contact with water allows for the potential long-distance transmission of stable viruses released from infected individuals. Invasive aquatic plants exacerbate this issue by introducing novel microbes, including viruses, to new regions, increasing the potential threat to native plant populations.

Results: Here, we investigated the viral communities of diverse aquatic plants by mining publicly available transcriptome data of 79 wild aquatic species and sequencing the RNA from 14 plant species (some of them of different ornamental varieties), sourced from hobby aquascaping stores. Plant viruses from various families were detected in taxonomically diverse aquatic plants, ranging from algae to angiosperms. Alongside sequences of known crop pathogens, such as turnip yellows virus, cucumber mosaic virus, and lettuce chlorosis virus, we identified contigs of putative novel viral species belonging to several plant-infecting viral families. Most notably, we discovered sequences of known and novel begomoviruses, which may be causing observed ornamental phenotypes in two different aquatic plants. Further, we identified a novel potyvirus that appears to be globally present in multiple ornamental plants from the genus Sagittaria. We detected it in three plants sourced from online stores in Slovenia, as well as six plants intercepted during the import process into the UK.

Conclusions: Our findings expand on the so far limited knowledge of aquatic plant viruses, revealing known and putative novel plant viral species across diverse aquatic plant taxa. The detection of crop viruses, including regulated pathogens, in ornamental aquatic plants highlights the risks associated with their unregulated global trade. Further research into viruses of aquatic plants may provide insights into their role in ecosystems as well as their potential impact on agriculture.