Environmental Microbiome最新文献

Background: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.

Results: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, bla_OXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (bla_NDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.

Conclusions: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.

Background: Theory predicts that biological communities can have multiple stable states in terms of their species/taxonomic compositions. The presence of such alternative stable states has been examined in classic ecological studies on the communities of macro-organisms (e.g., distinction between forest and savanna vegetation types). Nonetheless, it remains an essential challenge to extend the target of the discussion on multistability from macro-organismal systems to highly species-rich microbial systems. Identifying alternative stable states of taxonomically diverse microbial communities is a crucial step for predicting and controlling microbiome processes in light of classic ecological studies on community stability.

Results: By targeting soil microbiomes, we inferred the stability landscapes of community structure based on a mathematical framework of statistical physics. We compiled a dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from > 1,500 agroecosystem soil samples and applied the energy landscape analysis to estimate the stability/instability of observed taxonomic compositions. The statistical analysis suggested that both prokaryotic and fungal community structure could be classified into several stable states. We also found that the inferred alternative stable states differed greatly in their associations with crop disease prevalence in agroecosystems. We further inferred "tipping points", through which transitions between alternative stable states could occur.

Conclusion: Our results suggest that the structure of complex soil microbiomes can be categorized into alternative stable states, which potentially differ in ecosystem-level functioning. Such insights into the relationship between structure, stability, and functions of ecological communities will provide a basis for ecosystem restoration and the sustainable management of agroecosystems.

Background: The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").

Results: The results demonstrated that annual cumulative N₂O and CO₂ fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH₄ annual cumulative fluxes decreased from 12,669.45 ± 564.69 kg·ha^- 1 to 8,238.40 ± 207.72 kg·ha^- 1 in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50 ± 48.83 and 422.21 ± 73.59 mg·CO₂-eq·m^- 2·h^- 1, respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH₄ production. Functional genes related to CH₄ oxidation (pmoA) and gene related to N₂O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p < 0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH₄ serving as an electron donor. This suggests that Dryland may act as a CH₄ sink, despite the significant enhancement in CO₂ and N₂O fluxes.

Conclusions: In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.

Background: Urban dwellings serve as complex and diverse microbial community niches. Interactions and impact of house microbiome on the health of the inhabitants need to be clearly defined. Therefore, it is critical to understand the diversity of the house microbiota, the presence and abundance of potential pathogens, and antimicrobial resistance.

Results: Shotgun metagenomics was used to analyze the samples collected from 9 locations in 10 houses in New Delhi, India. The microbiota includes more than 1409 bacterial, 5 fungal, and 474 viral species en masse. The most prevalent bacterial species were Moraxella osloensis, Paracoccus marcusii, Microbacterium aurum, Qipengyuania sp YIMB01966, and Paracoccus sphaerophysae, which were detected in at least 80 samples. The location was the primary factor influencing the microbiome diversity in the Indian houses. The overall diversity of different houses did not differ significantly from each other. The surface type influenced the microbial community, but the microbial diversity on the cemented and tiled floors did not vary significantly. A substantial fraction of the bacterial species were potentially pathogenic or opportunistic pathogens, including the ESKAPE pathogens. Escherichia coli was relatively more abundant in bedroom, foyer, and drawing room locations. Analysis of the house microbiome antimicrobial resistome revealed 669 subtypes representing 22 categories of antimicrobial resistance genes, with multidrug resistance genes being the most abundant, followed by aminoglycoside genes.

Conclusions: This study provides the first insight into the microbiomes of houses in New Delhi, showing that these houses have diverse microbiomes and that the location within the house significantly influences the microbiota. The presence of potential pathogens and a repertoire of antimicrobial resistance genes reflect possible health risks, as these could lead to infectious disease transmission. This study builds a framework for understanding the microbial diversity of houses in terms of geographical location, environment, building design, cleaning habits, and impact on the health of occupants.

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.

Background: The variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly.

Results: Using a metabarcoding approach, we sequenced ITS2 regions from 864 samples collected from four distinct habitats-leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Generalized dissimilarity modeling (GDM) revealed that spatial distance, interacting with precipitation, was the strongest predictor of fungal turnover, particularly in the phyllosphere. Normalized Stochasticity Ratio (NST) analyses further highlighted contrasting assembly processes, with deterministic influences dominating in the phyllosphere habitat, while stochasticity prevailed in soil and litter. Random forest analysis accurately classified habitats based on ASVs' relative abundances, with strong predictors were mostly habitat-specific ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most habitat-specific ASVs. A Cladosporium sp. emerged as a keystone species, maintaining network stability across forests.

Conclusion: This study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show extremely high turnover in fungal community are present over very short distances and that local fungal taxa are strong habitat predictors. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.

Background: Soil organic matter composition and microbial communities are key factors affecting ecosystem multifunctionality (EMF) during ecosystem restoration. However, there is little information on their interacting mechanisms in degraded and restored meadows. To fill this knowledge gap, plant, root and soil samples from alpine swamp meadows, alpine Kobresia meadows, severely degraded alpine meadows, short-term restored meadows (< 5 years) and long-term restored meadows (6-14 years) were collected. We leveraged high-throughput sequencing, liquid chromatography and mass spectrometry to characterize soil microbial communities and soil organic matter composition, measured microbial carbon metabolism and determined EMF.

Results: It emerged that the similarity of soil microorganisms in meadows decreased with increasing heterogeneity of soil properties. Dispersal limitation and ecological drift led to the homogenization of the bacterial community. Based on co-occurrence network analysis, an increase in microbial network complexity promoted EMF. Root total phosphorus and soil organic matter components were the key predictors of EMF, while organic acids and phenolic acids increased the stability of the microbial network in long-term restored meadows. Carbon metabolism did not increase in restored meadows, but the niche breadth of soil microorganisms and the utilization efficiency of small molecular carbon sources such as amino acids did increase.

Conclusions: These findings emphasize the importance of soil organic matter composition in ecological restoration and that the composition should be considered in management strategies aimed at enhancing EMF.

Background: The west Antarctic Peninsula (WAP) is a region of rapid environmental changes, with regional differences in climate warming along the north-south axis of the peninsula. Along the WAP, Palmer corresponds to a warmer region with lesser sea ice extent in the north compared to Rothera ~ 400 km to the south. Comprehensive and comparative, year-round assessments of the WAP microbial community dynamics in coastal surface waters at these two locations are imperative to understand the effects of regional climate warming variations on microbial community dynamics, but this is still lacking.

Results: We report on the seasonal diversity, taxonomic overview, as well as predicted inter-and intra-domain causal effects (interactions) of the bacterial and microbial eukaryotic communities close to the Palmer station and at the Rothera time-series site between July 2013 and April 2014. Our 16S- and 18S-rRNA gene amplicon sequencing data showed that across all seasons, both bacteria and microbial eukaryotic communities were considerably different between the two sites which could be attributed to seawater temperature, and sea ice coverage in combination with sea ice type differences. Overall, in terms of biotic drivers, causal-effect modelling suggests that bacteria were stronger drivers of ecosystem dynamics at Palmer, while microbial eukaryotes played a stronger role at Rothera. The parasitic taxa Syndiniales persevered at both sites across the seasons, with Palmer and Rothera harbouring different key groups. Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. Article note: Kindly check first page article notes are correct.

Conclusions: Our research has shed light on the dynamics of microbial community composition and correlative interactions at two sampling locations that represent different climate regimes along the WAP.

The shade avoidance response triggers a dramatic promotion of elongation growth, accompanied by a significant reprogramming of metabolic pathways as plants seek to prevent overtopping and adapt to vegetative shade. Here we demonstrate that simulated vegetative shade results in significant changes in the structure and composition of the phyllosphere bacterial microbiome. Our study uncovered significant shifts in the diversity, occurrence, abundance and activity of bacteria within the phyllosphere microbiome. A comparison of responses in both wild-type plants and phytochrome mutants, which inherently exhibit a shade-avoidance phenotype, revealed both indirect responses to host plant physiology and direct responses to light among the microbiota. Hierarchical clustering of response patterns further suggested that over a third of the taxa constituting the core phyllosphere microbiome in our assay show some degree of response to vegetative shade. Bacteria that increased in abundance on plants with a shade-avoidance phenotype corresponded to genera associated with beneficial traits such as enhanced disease resistance and growth promotion. Our findings suggests that plants manipulate their phyllosphere microbiome under shade conditions as a strategy to optimise fitness when competing for light. We discuss the implications of our findings in terms of furthering our understanding of plant-microbe signalling in the shaping of the phyllosphere microbiome and the possibility of manipulating the phyllosphere microbiome for plant health in an agricultural setting at high planting densities.

Background: Members of the Campylobacterota phylum are dominant key players in sulfidic environments, where they make up a stable portion of sulfide-oxidizing bacterial communities. Despite the significance of these bacteria in primary production being well recognised in several ecosystems, their genomic and metabolic traits in sulfidic deep hypersaline anoxic basins (DHABs) remain largely unexplored. This knowledge gap not only hampers our understanding of their adaptation and functional role in DHABs but also their ecological interactions with other microorganisms in these unique ecosystems.

Results: Metabolic reconstructions from metagenome-assembled genomes (MAGs) of sulfide-oxidizing Campylobacterota were conducted at 10 cm spatial resolution within the halocline of the brine-seawater interface (BSI, salinity 91-155 PSU) of the 1466 m deep sulfidic Kebrit Deep in the Red Sea. Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. They are stratified along the BSI and utilise the reductive tricarboxylic acid cycle to fix carbon dioxide, acting as primary producers. Their energy generation processes include aerobic or anaerobic-nitrate-dependent sulfide oxidation, as well as hydrogen oxidation. In addition to the osmoprotectant pathways commonly observed in Campylobacterota, such as the synthesis and uptake of proline and glutamate, the two Kebrit Deep Sulfurovum species exhibit genomic signatures for ectoine synthesis, further aiding their adaptation to high salinity. This combination of metabolic redundancy and specialisation within the confined spatial boundaries (~1 m) of the BSI is pivotal in governing microbial interactions, including those with sulfate-reducers, heterotrophs, and other primary producers.

Conclusions: These results show how the selective pressures mediated by the sulfidic and hypersaline conditions of Kebrit Deep have resulted in novel, adapted and metabolically redundant Sulfurimonas and Sulfurovum species that contribute to the energy coupling, nutrient turnover and metabolic continuity along the physico-chemical gradient of the BSI.