Environmental Microbiome最新文献

Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.

Background: Continuous monocropping obstacles are common in plants, especially medicinal plants, resulting in disease outbreaks and productivity reductions. Foliar disease, mainly caused by Fusarium oxysporum, results in a severe decrease in the yield of Pseudostellaria heterophylla annually. Determining an effective biomethod to alleviate this disease is urgently needed to improve its productivity and quality.

Results: This study screened thirty-two keystone bacterial genera induced by pathogens in P. heterophylla rhizosphere soil under continuous monocropping conditions. Pseudomonas, Chryseobacterium, and Flavobacterium, referred to as the beneficial microbiota, were significantly attracted by pathogen infection. The P. palleroniana strain B-BH16-1 can directly inhibit the growth and spore formation of seven primary pathogens of P. heterophylla foliar disease by disrupting fusaric acid production via the emission of volatile organic compounds (VOCs). In addition, strain B-BH16-1 enhances the disease resistance of P. heterophylla by obliterating the pathogen and assembling beneficial microbiota.

Conclusion: Pathogen-induced Pseudomonas reshaped phyllosphere microbial communities via direct antagonism of pathogens and indirect disruption of the pathogen virulence factor biosynthesis to enhance disease suppression and improve yields. These results show that inhibiting pathogen virulence biosynthesis to reshape the plant microbial community using disease-induing probiotics will be an innovative strategy for managing plant disease, especially under continuous monoculture conditions.

Background: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.

Results: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.

Conclusions: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.

Biocrusts represent associations of lichens, green algae, cyanobacteria, fungi and other microorganisms, colonizing soils in varying proportions of principally arid biomes. The so-called grit crust represents a recently discovered type of biocrust situated in the Coastal Range of the Atacama Desert (Chile) made of microorganisms growing on and in granitoid pebbles, resulting in a checkerboard pattern visible to the naked eye on the landscape scale. This specific microbiome fulfills a broad range of ecosystem services, all probably driven by fog and dew-induced photosynthetic activity of mainly micro-lichens. To understand its biodiversity and impact, we applied a polyphasic approach on the phototrophic microbiome of this biocrust, combining isolation and characterization of the lichen photobionts, multi-gene phylogeny of the photobionts and mycobionts based on a direct sequencing and microphotography approach, metabarcoding and determination of chlorophyll_a+b contents. Metabarcoding showed that yet undescribed lichens within the Caliciaceae dominated the biocrust together with Trebouxia as the most abundant eukaryote in all plots. Together with high mean chlorophyll_a+b contents exceeding 410 mg m^-2, this distinguished the symbiotic algae Trebouxia as the main driver of the grit crust ecosystem. The trebouxioid photobionts could be assigned to the I (T. impressa/gelatinosa) and A (T. arboricola) clades and represented several lineages containing five potential species candidates, which were identified based on the unique phylogenetic position, morphological features, and developmental cycles of the corresponding isolates. These results designate the grit crust as the only known coherent soil layer with significant landscape covering impact of at least 440 km², predominantly ruled by a single symbiotic algal genus.

Background: In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning and single-cell sequencing. However, our ability to functionally characterize these genomes by experimental assays is orders of magnitude less efficient. Consequently, there is a pressing need for the development of swift and automated strategies for the functional classification of microbial genomes.

Results: The present work leverages a suite of supervised machine learning algorithms to establish a range of 86 metabolic and other ecological functions, such as methanotrophy and plastic degradation, starting from widely obtainable microbial genome annotations. Tests performed on independent datasets demonstrated robust performance across complete, fragmented, and incomplete genomes above a 70% completeness level for most of the considered functions. Application of the algorithms to the Biogas Microbiome database yielded predictions broadly consistent with current biological knowledge and correctly detecting functionally-related nuances of archaeal genomes. Finally, a case study focused on acetoclastic methanogenesis demonstrated how the developed machine learning models can be refined or expanded with models describing novel functions of interest.

Conclusions: The resulting tool, MICROPHERRET, incorporates a total of 86 models, one for each tested functional class, and can be applied to high-quality microbial genomes as well as to low-quality genomes derived from metagenomics and single-cell sequencing. MICROPHERRET can thus aid in understanding the functional role of newly generated genomes within their micro-ecological context.

Background: Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments -thalli, substrates, and neighboring soils- were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale.

Results: The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks.

Conclusions: The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria.

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Background: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.

Results: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.

Conclusion: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.