Environmental Microbiome最新文献

Background: Plants can recruit specific microbes to help them defend themselves against phytopathogens in a process known as "cry for help". In this study, we investigated whether a plant species modulates its root-associated microbiome differently - i.e. "cries out differently" - depending on the diversity of fungal pathogens attacking its leaves. To address this question, we monitored changes in the root microbiome of Oryza sativa cv. Nipponbare following infection with two fungal pathogens: Pyricularia oryzae (leaf blast) and Bipolaris oryzae (brown spot), under controlled conditions and using the same soil.

Results: Our results support the "cry for help" hypothesis, suggesting that pathogen-induced stress drives the recruitment of beneficial microbes. While the composition of the root-associated microbiota remained globally stable after infection, subtle but significant taxonomic shifts were observed. Alpha diversity was unaffected, but changes in beta diversity occurred in micro-eukaryotic communities one week after brown spot infection and in bacterial communities two weeks after blast infection. Notably, beneficial taxa such as the bacterial genera Lentzea and Streptomyces, as well as the fungi Cladosporium halotolerans and Rhizophagus irregularis, were enriched in the below-ground microbiome of leaf-infected plants. The biocontrol potential of Rhizophagus irregularis was confirmed against blast but not brown spot infection.

Conclusions: These results advance our understanding of the "cry for help" hypothesis in rice and provide potential candidates for biocontrol. They highlight the complexity of plant-microbe interactions and suggest that rice plants specifically modulate their root microbiome in response to fungal infections, potentially shaping microbial communities to enhance defence strategies.

Background: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.

Method: The entire DNA sample was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.

Results: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.

Conclusion: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.

Background: The identification of complex spatial patterns of microbial communities in relation to their ecological niches is fundamental to understanding the mechanisms of ecological interactions among diverse organisms. This study introduces a novel three-dimensional (3D) sampling approach to examine the spatial dynamics of microbial populations and niche differentiation influenced by plant-mediated effects in natural ecosystem.

Results: Microbial communities across horizontal and vertical dimensions were systematically mapped, and we found that the total microbial diversity, particularly among eukaryotes, increased more than ten-fold compared to that obtained via single-grid sampling, emphasizing the importance of spatial heterogeneity in shaping microbial dynamics. Moreover, the 3D framework enabled us to identify taxa specifically associated with particular plants, offering insights into plant-microbe interactions, pathogen prevalence, and ecological consequences of plant-driven effects on local communities.

Conclusions: Collectively, these findings demonstrate that 3D sampling approach provides a reproducible and scalable methodology for investigating microbial spatial heterogeneity, pathogen ecology, and niche differentiation in natural environments.

Background: Deep ocean blue holes are characterized by distinct physicochemical gradients and complex biological processes, and Yongle Blue Hole (YBH) in the South China Sea (SCS) is the world's deepest (301 m) underwater cavern with unique environmental characteristics. So far, studies investigated the bacterial community structure with different lifestyles of the YBH; however, our understanding of viruses in the YBH remains limited. Here, we utilized a metagenomic approach to investigate viral communities in both the "viral fraction" and "cellular fraction" of seawater samples in oxic and anoxic zones within YBH.

Results: A total of 1,730 viral operational taxonomic units (vOTUs) were identified, with over 70% affiliated with the classes Caudoviricetes and Megaviricetes, particularly within the families Kyanoviridae, Phycodnaviridae and Mimiviridae. Gene-sharing network analyses indicated that the deeper anoxic layers contain a high proportion of novel viral genera, while the oxic layer's viral genera overlap with those found in the open water samples from SCS. Virus-linked prokaryotic hosts predominantly belong to the phyla Patescibacteria, Desulfobacterota, and Planctomycetota. Notably, the detected putative auxiliary metabolic genes (AMGs) suggest that these viruses may influence photosynthetic and chemosynthetic pathways, as well as methane, nitrogen, and sulfur metabolisms, especially with several high-abundance AMGs potentially involved in prokaryotic assimilatory sulfur reduction.

Conclusions: Together, these findings highlight the potential ecological roles and diversity of viral communities within YBH and shedding light on niche-separated viral speciation.

Background: Rapid urbanization has profoundly impacted soil fungal dynamics and thus soil health, however, it remains poorly addressed due to lack of ideal experimental region. Taking Shenzhen of China, a megacity built within 30 years, as the study region, we analyzed the effects of rapid urbanization on soil fungal diversity, species composition, and community stability from the perspective of urbanization stages (within 10, 10-20, 20-30, 30-40, and over 40 years of urbanization), and original (forests, paddy fields, and drylands) and present (parks, streets, and residential areas) urban land-use types.

Results: Results showed that soil fungi of urban areas had significantly lower Chao1 and phylogenetic diversity (PD) than that of natural ecosystem (P < 0.05), i.e., forests in this study, with the lowest PD in street. The urbanization-induced higher phosphorus (P) content and thus lower soil N/P may explain the lower PD in city areas (P < 0.05). As the urbanization proceeded, soil fungal species composition shifted and resilience stability reduced significantly within 10 years (P < 0.05) compared with forests, but then the composition gradually transitioned to a consistent state while stability recovered to a certain extent for the rest of the urbanization stages. Key phyla driving these results included Ascomycota and Mortierellomycota. Original land-use types did not significantly affect urban soil fungal diversity or composition (P > 0.05). However, SparCC-based network analysis revealed no significant differences (P > 0.05) in fungal co-occurrence patterns or stability across different land-use types and urbanization stages, suggesting that urbanization may not strongly restructure fungal interaction networks.

Conclusions: Our findings shed new lights on the scientific understanding and the urban spatial planning when considering soil health under the context of rapid urbanization. Additionally, they emphasize the need to incorporate multiple analytical approaches when studying microbial community interactions.

Background: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.

Results: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.

Conclusions: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.

Background: Hydrothermal vents along mid-ocean ridges host diverse microbial communities and are crucial to global elemental cycling. The Red Sea, known for its unique environmental conditions-including low nutrient levels, high year-round temperatures, bottom-water temperatures of 21 °C, and elevated salinity-hosts recently discovered active low-temperature hydrothermal vent fields at the axial Hatiba Mons volcano. These vents, characterized by large iron oxide mounds and abundant microbial mats, offer an extreme environment for studying the diversity and functions of prokaryotes involved in elemental cycling in this system. In this study, we used 16S rRNA sequencing and shotgun metagenomics to examine the microbial diversity and metabolic capabilities of precipitates and microbial mats from five vent sites.

Results: We recovered 314 non-redundant metagenome-assembled genomes (MAGs), including 250 bacterial and 64 archaeal MAGs, representing 34 bacterial and 11 archaeal phyla. Functional annotations revealed diverse nutrient and metal cycling potentials, with notable enrichment in iron redox genes. Key players include Bathyarchaeia and Chloroflexi in the precipitates (contributing to carbon, nitrogen, sulfur, and metal cycling potentials) and Pseudomonadota members in the microbial mats and upper precipitates (involved in iron and sulfur metabolism and carbon fixation through the CBB cycle). Carbon fixation in precipitate potentials primarily occurs through the Wood-Ljungdahl pathway. Sulfur and nitrogen cycling genes are distributed across various genomes, indicating collaborative cycling.

Conclusion: Our genome-resolved analysis positions the Hatiba Mons vents as an iron-rich system that provides new insights into oligotrophic hydrothermal environments, with potential relevance for understanding novel metabolic pathways, extremophilic adaptations, and their roles in element cycling and biotechnological applications.

Background: Salt-tolerant phosphorus solubilizing fungi (PSF) play a pivotal role in plant growth promotion and P-nutrition in saline agro-ecoregions. Isolation and characterization of salt-tolerant fungi with P-solubilizing potential and plant growth promotion of sorghum at different salinity levels were conducted.

Results: The best PSFs with inherent salt-tolerance were identified as Penicillium oxalicum (PO), Talaromyces islandicus 1 (Tal1), Talaromyces islandicus 2 (Tal2), Penicillium canescens (PC), and Penicillium setosum (PS). The PO demonstrated the highest salt-tolerance at 2% NaCl concentration. The P and Zn solubilization, ammonia, HCN, siderophore and IAA production were 1.1-10.5 times greater for the PO. The ascorbic and butyric acids were the most abundant organic acids in growth media for Tal1 and other PSF. The fungal mycelium grown on the media supplemented with tricalcium phosphate (TCP) contained 3.3-3.9 times greater P content than the mycelium from the growth medium without TCP (0.44-0.98%). The acidolysis-related genes (pqqC, gcd) and enzymolysis-related genes (phoD, ppk) in salt-tolerant fungal cultures were also present. The fungal inoculated sorghum roots had 3.8-11.0 times greater P-content than uninoculated roots. The siderophore, ammonia, HCN, organic acid and phosphatase secretion explained ~ 46-47% variability in the PSF inoculation responsiveness of P pools and plant parameters to PSF inoculation. The responsiveness of the Olsen's-P, aboveground biomass, and P uptake were strongly correlated with siderophore, ammonia, HCN and organic acid production by the PSF.

Conclusions: This study concludes that augmenting the rhizospheric assemblage of the crops with PSFs having inherent salinity tolerance can be an agronomically sound option to improve the salinity- tolerance and P-nutrition under salt-affected soils.

Metagenomic studies have significantly expanded our understanding of the bacterial communities present in bat guano. Several studies have reported the presence of common human pathogenic bacteria, including enteric foodborne species, zoonotic pathogens, unusual Gram-negative bacteria, and multidrug-resistant strains. These findings have reinforced the perception of bat guano as a potential reservoir of pathogens. Despite this, research conducted in sites with frequent human contact remains limited. Caves and tunnels such as those along the Camino del Hierro in northeastern Spain represent environments with regular human exposure, making them areas of particular interest from a public health perspective. In this study, we conducted an extensive analysis of the guano microbiome during both the breeding season and hibernation period in bats inhabiting this touristic site, using shotgun metagenomics and a comprehensive bioinformatic pipeline. Our results revealed marked differences in the relative microbial composition across samples from fresh and desiccated bat guano. The most abundant viral order detected was Herpesvirales, while among bacterial genera, Bacillus, Burkholderia, Lactobacillus, Pseudomonas, Salmonella and Streptococcus were dominant. The presence of these taxa in the tunnels poses a potential risk not only to visitors but also to park staff who are regularly exposed to bat guano, particularly due to the presence of species associated with various human viral and bacterial diseases. No significant differences were observed in the overall abundance of detected organisms between seasons. However, distinct seasonal patterns emerged when analyzing metabolic pathways and virulence factors. During the breeding season, there was a notable predominance of metabolic pathways related to cell proliferation, along with virulence factors associated with strategies for surface attachment and biofilm formation. Overall, our findings highlight an underrecognized and unmonitored risk of pathogen transmission for both visitors and personnel at this tourist site, underscoring the need for increased awareness and further investigation into the health implications of human-bat interactions in such environments.