Environmental Microbiome最新文献

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.

Despite over three decades of research into the composition and distribution of microbial communities, gaps remain in our mechanistic understanding of microbial community assembly processes, especially in benthic communities in coastal zones continuously exposed to anthropogenic pressures. We analyzed the microbial communities (prokaryotes, fungi, and protists) in sediment samples from ports and bays located along the Adriatic coast chronically exposed to chemical and nutrient pollution, and explored how selective pressures (pollutants, nutrients, and environmental conditions) and dispersal shape these communities. We found that biogeographic factors (i.e. location) play a key role in structuring microbial communities, with benthic fungi also being shaped by the presence of pollutants and nutrients. Strong correlations between nutrient loads and pollutants were observed, along with weakened interactions between microbial communities, particularly between prokaryotes and protists, in the presence of specific pollutants (bismuth, cadmium, copper, zinc, mercury). These results are an important step in disentangling the complex interactions between pollutants and microbial community dynamics in aquatic ecosystems. Further research is needed to assess how these shifts in microbial community dynamics may affect ecosystem services in vulnerable coastal zones.

Background: Arctic warming is driving uneven greening across high-latitude regions, leading to the development of unusually productive tundra ecosystems that remain poorly understood. Here, we investigated the soil physicochemical properties and multi-kingdom microbial communities (bacteria, fungi, and micro-eukaryotes) in the rhizosphere of dominant plant species in a highly productive tundra ecosystem in the central part of North Greenland (above 82°N).

Results: A strong correlation between the normalized difference vegetation index (NDVI) and soil moisture content underscores the critical role of moisture in determining vegetation patterns. Plant species was a key determinant of microbial community structure across all microbial groups, but the strength and nature of these associations varied. Fungal communities were most affected by plant species identity, with distinct associations between mycorrhizal taxa and specific plant species observed in wetter sites. In contrast, bacterial communities were more strongly linked to vegetation-driven changes in soil geochemistry, while micro-eukaryotic communities exhibited comparatively weaker responses to both plant species and soil properties. Additionally, a positive association between nematodes and mushroom-forming fungi (mainly Agaricomycetes) suggests the presence of a functionally interconnected soil food web, and parasitic protists of the Apicomplexan order Eugregarinorida were widespread across most sites, though their ecological roles remain unclear.

Conclusions: Taken together, our findings suggest a possible role of soil water availability in shaping plant species-specific rhizosphere microbial communities in this highly productive High Arctic tundra ecosystem. Furthermore, the multi-kingdom community data provide a valuable baseline for future research on the ecological functioning and climate sensitivity of increasingly productive Arctic ecosystems.

Background: Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.

Results: Elevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.

Conclusions: We emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.

Background: Indoor microbial communities play a critical role in influencing indoor environmental quality and human health and are shaped by occupant activity, surface characteristics, and environmental conditions. While previous studies have examined these factors individually, systematic evaluations of their combined interactions, particularly involving Heating, Ventilation, and Air Conditioning (HVAC) and drainage systems, remain limited. This controlled, long-term (1.5-year) investigation assessed how human occupancy, surface moisture (dry vs. wet), aquaponics (soilless plant-aquarium systems), and environmental parameters (humidity, ventilation, and seasonal variations) influence bacterial and eukaryotic dynamics in tightly sealed residential units.

Results: Continuous air-conditioner operation without fresh-air intake led to elevated CO₂ levels during occupancy and pronounced seasonal humidity fluctuations, emphasizing the need for improved ventilation and adaptive humidity control in compact urban residences. Amplicon sequencing revealed higher microbial diversity on dry surfaces (aerosols, air-conditioner filter dust, and floor dust) than on wet surfaces (waste drains and showerheads). Wet environments supported biofilm-associated taxa adapted to moist conditions (e.g., Methylobacterium, Vermamoeba). Human occupancy significantly enriched air-conditioner filter dust with opportunistic bacteria (e.g., Finegoldia and Streptococcus), underscoring occupant-driven microbial accumulation via recirculated air. Additionally, the small-scale aquaponic system had minimal measurable influence on microbial composition at the room scale, suggesting limited aerosolization or dispersal under typical usage conditions. Indoor relative humidity was significantly correlated with microbial diversity in air systems, notably enhancing moisture-adapted taxa such as Sphingomonas during humid seasons. Seasonal variations markedly influenced eukaryotic communities (e.g., pollen influx), whereas bacterial communities were more strongly influenced by human occupancy.

Conclusions: These findings highlight the critical role of human-driven microbial accumulation in air-conditioner filters and the distinct microbial profiles associated with dry and wet indoor surfaces. Although small-scale aquaponics demonstrated minimal room-wide microbial impact, its potential localized influence warrants further exploration. These insights offer practical guidance for targeted hygiene protocols, HVAC system maintenance, and building design strategies aimed at improving indoor microbial quality and supporting occupant health.