Environmental Microbiome最新文献

Background: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

Results: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

Conclusion: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.

Background: Entomopathogenic fungi are increasingly used as bio-inoculants to enhance crop growth and resistance. When applied to rhizosphere soil, they interact with resident soil microbes, which can affect their ability to colonize and induce resistance in plants as well as modify the structure of the resident soil microbiome, either directly through interactions in the rhizosphere or indirectly, mediated by the plant. The extent to which such direct versus indirect interactions between bio-inoculants and soil microbes impact microbe-induced resistance in crops remains unclear. This study uses a split-root system to examine the effects of direct versus indirect (plant-mediated) interactions between an entomopathogenic fungus, Metarhizium brunneum, and resident soil microbes on induced resistance in tomato against two-spotted spider mites. Additionally, the study explores how these interactions influence the composition and diversity of soil fungal and bacterial communities.

Results: Resident soil microbes reduced the efficacy of M. brunneum to induce resistance against spider mites. This reduction occurred not only when resident microbes directly interacted with the bio-inoculant but also when they were spatially separated within the root system, indicating plant-mediated effects. M. brunneum inoculation did not affect rhizosphere microbial diversity but led to changes in fungal and bacterial community composition, even when these communities were not in direct contact with the inoculant.

Conclusions: This research highlights the impact of both direct and plant-mediated interactions between bio-inoculants and resident soil microbes on bio-inoculant-induced pest resistance in crop plants and underscores the importance of assessing potential adverse effects of fungal bio-inoculants on native soil communities.

Background: The anthosphere, also known as the floral microbiome, is a crucial component of the plant reproductive system. Therefore, understanding the anthospheric microbiome is essential to explore the diversity, interactions, and functions of wildflowers that coexist in natural habitats. We aimed to explore microbial interaction mechanisms and key drivers of microbial community structures using 144 flower samples from 12 different wild plant species inhabiting the same natural environment in South Korea.

Results: The microbial diversity of the anthosphere showed plant dependence, with the highest diversity observed in Forsythia koreana, indicating microbial dynamics in relation to plant species. Caulobacter, Sphingomonas, Achromobacter, Epicoccum, Cladosporium, and Alternaria were anthosphere generalists, suggesting that the local plant anthosphere had a similar microbial composition. Ecological network analysis revealed that anthosphere generalists were tightly coupled to each other and constructed core modules in the anthosphere. Functions associated with parasites and pathogens were commonly observed in the anthosphere, particularly in Capsella bursa-pastoris and Brassica juncea.

Conclusion: Overall, the anthosphere depends on the plant species and microbial generalists function as keystone species to support and connect the anthospheric microbiome in natural habitats.

Background: Viruses that infect prokaryotes (phages) constitute the most abundant group of biological agents, playing pivotal roles in microbial systems. They are known to impact microbial community dynamics, microbial ecology, and evolution. Efforts to document the diversity, host range, infection dynamics, and effects of bacteriophage infection on host cell metabolism are extremely underexplored. Phages are classified as virulent or temperate based on their life cycles. Temperate phages adopt the lysogenic mode of infection, where the genome integrates into the host cell genome forming a prophage. Prophages enable viral genome replication without host cell lysis, and often contribute novel and beneficial traits to the host genome. Current phage research predominantly focuses on lytic phages, leaving a significant gap in knowledge regarding prophages, including their biology, diversity, and ecological roles.

Results: Here we develop and describe Prophage-DB, a database of prophages, their proteins, and associated metadata that will serve as a resource for viral genomics and microbial ecology. To create the database, we identified and characterized prophages from genomes in three of the largest publicly available databases. We applied several state-of-the-art tools in our pipeline to annotate these viruses, cluster them, taxonomically classify them, and detect their respective auxiliary metabolic genes. In total, we identify and characterize over 350,000 prophages and 35,000 auxiliary metabolic genes. Our prophage database is highly representative based on statistical results and contains prophages from a diverse set of archaeal and bacterial hosts which show a wide environmental distribution.

Conclusion: Given that prophages are particularly overlooked and merit increased attention due to their vital implications for microbiomes and their hosts, we created Prophage-DB to advance our understanding of prophages in microbiomes through a comprehensive characterization of prophages in publicly available genomes. We propose that Prophage-DB will serve as a valuable resource for advancing phage research, offering insights into viral taxonomy, host relationships, auxiliary metabolic genes, and environmental distribution.

Background: Seed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed-associated microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. In this study we investigated the composition and functional potential of seed-associated bacterial epiphytes associated with stored and freshly collected seeds of a native plant, Acacia ulicifolia, using both 16S rRNA gene sequencing and culture-based approaches.

Results: Seeds obtained from seed banking facilities were found to host significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and in community members commonly identified in freshly collected A. ulicifolia seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds.

Conclusion: Overall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds.

Background: Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

Results: The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.

Conclusions: The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.

Background: Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6-15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing.

Results: Salinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9-15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant.

Conclusions: Increasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina's interactions with the surrounding microbiota at salinity 9-15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate.

Background: Fusarium head blight (FHB) is a major disease affecting cereal crops including wheat, barley, rye, oats and maize. Its predominant causal agent is the ascomycete fungus Fusarium graminearum, which infects the spikes and thereby reduces grain yield and quality. The frequency and severity of FHB epidemics has increased in recent years, threatening global food security. Spray-induced gene silencing (SIGS) is an alternative technique for tackling this devastating disease through foliar spraying with exogenous double-stranded RNA (dsRNA) to silence specific pathogen genes via RNA interference. This has the advantage of avoiding transgenic approaches, but several aspects of the technology require further development to make it a viable field-level management tool. One such existing knowledge gap is how dsRNA spraying affects the microbiota of the host plants.

Results: We found that the diversity, structure and composition of the bacterial microbiota are subject to changes depending on dsRNA targeted and host studied, while the fungal microbiota in the phyllosphere remained relatively unchanged upon spraying with dsRNA. Analyses of fungal co-occurrence patterns also showed that F. graminearum established itself among the fungal communities through negative interactions with neighbouring fungi. Through these analyses, we have also found bacterial and fungal genera ubiquitous in the phyllosphere, irrespective of dsRNA treatment. These results suggest that although rarer and less abundant microbial species change upon dsRNA spray, the ubiquitous bacterial and fungal components of the phyllosphere in wheat and barley remain unchanged.

Conclusion: We show for the first time the effects of exogenous dsRNA spraying on bacterial and fungal communities in the wheat and barley phyllospheres using a high-throughput amplicon sequencing approach. The results obtained further validate the safety and target-specificity of SIGS and emphasize its potential as an environmentally friendly option for managing Fusarium head blight in wheat and barley.

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO₂ concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H₂ during earthquakes may provide substrates for methanogenic and chemolithoautotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 238 m deep drill core, running across six lithostratigraphic zones. We evaluated the diversity and distribution of bacterial and archaeal communities. Our investigation revealed a distinct low-biomass community, with a surprisingly diverse archaeal population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis demonstrated that ion concentrations (mostly sodium and sulfate) were highest in sediments from 50 to 100 m depth and in weathered rock below 200 m, indicating an elevated potential for ion solution in these areas. Microbial communities were dominated by common soil and water bacteria. Together with the occurrence of freshwater cyanobacteria at specific depths, these observations emphasize the heterogenous character of the sediments and are indicators for vertical groundwater movement across the Eger Rift subsurface. Our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur-cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia-oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO₂ and, when available, H₂, as a primary energy source.

Background: Crustose Coralline Algae (CCA) play a crucial role in coral reef ecosystems, contributing significantly to reef formation and serving as substrates for coral recruitment. The microbiome associated with CCAs may promote coral recruitment, yet these microbial communities remain largely understudied. This study investigates the microbial communities associated with a large number of different CCA species across six different islands of French Polynesia, and assess their potential influence on the microbiome of coral recruits.

Results: Our findings reveal that CCA harbor a large diversity of bacteria that had not been reported until now. The composition of these microbial communities was influenced by geographic location, and was also closely linked to the host species, identified at a fine taxonomic unit using the 16S rRNA gene of the CCA chloroplast. We demonstrate the usefulness of these ecologically meaningful units that we call CCA chlorotypes. Additionally, we observed a correlation between host phylogeny and microbiome composition (phylosymbiosis) in two CCA species. Contrary to expectations, the CCA microbiome did not act as a microbial reservoir for coral recruits. However, the microbial community of coral recruits varied according to the substrate on which they grew.

Conclusions: The study significantly expands the number of characterized CCA microbiomes, and provides new insight into the extensive diversity of these microbial communities. We show distinct microbiomes between and within CCA species, characterized by specific chloroplast 16S rRNA gene sequences. We term these distinct groups "chlorotypes", and demonstrate their utility to differentiate CCA. We also show that only few bacterial taxa were shared between CCA and coral recruits growing in contact with them. Nevertheless, we observed that the microbial community of coral recruits varied depending on the substrate they grew on. We conclude that CCA and their associated bacteria influence the microbiome composition of the coral recruits.