Environmental Microbiome最新文献

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.

Background: Octocoral gorgonians are the engineer species of the Mediterranean coralligenous assemblages, but they are threatened with collapse due to recurring marine heat waves. These extreme events disrupt their symbiotic relationship with their associated microbes, promoting pathogen proliferation and tissue-degrading diseases. While the effects of seawater warming on microbial taxonomic diversity have been extensively studied, the functional response of bacterial symbionts and opportunists to thermal stress in Mediterranean octocorals has not yet been investigated. To fill this gap, we investigated a unique and very stable symbiosis between the emblematic red coral Corallium rubrum and its Spirochaetota symbionts. Although the relative and absolute abundances of Spirochaetota are not affected by heat stress, these symbionts may lose their functions within the coral holobiont.

Results: Our results infer that the Spirochaetota bacterial symbionts of C. rubrum underwent only limited functional changes in response to thermal stress, consistent with their stable abundance in coral tissue. These symbionts may play a role in enhancing the tolerance of C. rubrum to temperature fluctuations by maintaining essential amino acid and vitamin biosynthesis. However, thermal stress affected other groups of bacteria, with Gammaproteobacteria showing reduced functionality (with the exception of Vibrionales, which may contribute to the deterioration of coral health) and Alphaproteobacteria showing increased opportunistic activity. In addition, many differentially expressed genes were associated with the sulfur cycle, highlighting its key role in shaping coral-associated bacterial communities under thermal stress.

Conclusions: The stability of the bacterial symbionts of C. rubrum, especially Spirochaetota, despite thermal stress, is consistent with their constant presence in octocoral tissues. These symbionts contribute to coral resilience by maintaining essential biosynthetic processes. However, the increased activity of opportunistic and pathogenic bacteria such as Vibrio suggests that C. rubrum may be susceptible to the recurring heat waves of the summer season.

Background: Soil microbes play a central role in nutrient recycling in soils: however, the genetic mechanisms governing their responses to long-term fertilization remain poorly understood. While the agronomic benefits of long-term fertilization are well-documented, the genetic mechanisms and ecological processes underlying microbial community responses to different fertilization regimes remain poorly understood, particularly in unique soil systems such as black soils (Mollisols), which are critical for global food security. A deeper insight into how organic and inorganic fertilizers influence microbial assembly, functional potential, and community stability is essential for developing sustainable soil management practices.

Results: This study deciphers microbial assembly mechanisms, functional gene dynamics, and community restructuring in black soils subjected to 44 years of chemical fertilizer (CF), manure amendment (M), and integrated chemical fertilizer with manure (CFM) treatments. Results revealed that CF significantly enhances functional gene abundance related to carbon (C) degradation (e.g., starch, cellulose, chitin and lignin) and nitrification, accelerating the conversion of recalcitrant C to labile C pools and ammonium to nitrate. Conversely, M and CFM treatments promote microbial diversity and stability while decelerating nutrient transformation processes. In addition, microbial assembly mechanisms shift from stochastic to deterministic processes with long-term fertilizer application in CF. The structural equation modeling (SEM) indicated that soil chemical properties shape both the diversity and composition of taxonomic and functional gene communities which subsequently regulate microbial -mediated nutrient cycling processes and crop yield.

Conclusions: Our findings highlight the trade-offs between microbial functional potential and community stability under contrasting fertilization strategies, emphasizing the need to integrate microbial metrics into sustainable land management frameworks.

Background: To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.

Results: Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~ 60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.

Conclusions: Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.

Fungi are key drivers of biogeochemical processes, yet marine fungi remain understudied and under-characterized due to primer biases and database gaps. In this study, we conducted a metabarcoding survey targeting the small and large subunit rRNA genes and the internal transcribed spacer region of fungi (18S, 28S, and ITS2) in the sediment and surface water of salt and brackish marshes in the North Inlet-Winyah Bay estuarine system (Georgetown, South Carolina, USA). The universal 18S/16S primer set (515F-Y and 926R) identified few fungal taxa. The ITS2 primer set (ITS3mix and ITS4) revealed high diversity among Dikarya but failed to capture the full extent of early diverging fungi (EDF). In contrast, the 28S primer set (LR0R and LF402) excelled at identifying EDF lineages, including Chytridiomycota, Mucoromycota, Zoopagomycota, and Blastocladiomycota, many of which dominated the brackish marsh sampling site but were less prevalent in the salt marsh sampling sites. Over half of the fungal OTUs identified by the 28S primer set were from EDF lineages. Copy-normalized 28S qPCR showed that EDF were more abundant in brackish sediments than in the salt marsh. Several putative denitrifying fungi, primarily species from Trichoderma and Purpureocillium, were also detected, suggesting overlooked functional guilds that may contribute to estuarine nitrogen cycling. A FUNGuild analysis found that most lineages were saprotrophic. Overall, our findings show that EDF are key contributors to community differences across salinity gradients and may play more important functional roles in coastal biogeochemistry than is currently understood. The 28S primer set is ideal for marine fungal metabarcoding because it provides comprehensive taxonomic coverage and enables phylogenetic analysis.