Environmental Microbiome最新文献

Background: Plants evolve as holobionts, ecological and evolutionary units made up of the host plant and its associated microbiota, which shape plant fitness and adaptive capacity. Isolated ecosystems with low biodiversity and plant cover, such as the fellfields of the remote sub-Antarctic Kerguelen Islands, represent ideal open-air laboratories to disentangle the drivers affecting plant-microbiome interactions. In such pristine environments, endemic plant species and their microbiota have coevolved in isolation possibly since the last ice age. In this study, we investigated the bacterial and fungal communities associated with different soil-plant compartments of two phylogenetically distant endemic plants, the Poaceae Poa kerguelensis and the Brassicaceae Pringlea antiscorbutica, in fellfields with contrasted pedoclimatic conditions.

Results: Using 16S rRNA gene and Internal Transcribed Spacer (ITS) region metabarcoding, we identified a strong soil-plant compartment effect affecting microbial communities, with bacterial and fungal α-diversity higher in bulk and rhizospheric soils and progressively decreasing in roots and above-ground compartments. The microbiota of the different soil-plant compartments studied differ in their recruitment patterns. The bacterial communities of the aerial parts of P. antiscorbutica were less dependent on those of the underground parts compared to those of P. kerguelensis. We also showed that the microbiota of distinct plant species and their different soil-plant compartments respond differently to pedoclimatic variables, with a greater impact of climatic variables over soil ones on aboveground bacterial microbiomes than on belowground microbiomes.

Conclusions: Our results highlight the dual role of environmental variability and of the identity of the host on the recruitment and diversity of plant microbiomes in the isolated studied ecosystems. As plant holobionts are part of the global biogeochemical ecosystem functioning, our results suggest that plant species-specific microbial recruitment strategies and differential vulnerability to environmental factors should be included in predicting sub-Antarctic ecosystem response to global warming.

Background: Intensive agriculture can disrupt adjacent stream ecosystems by increasing nutrient runoff, suspended and dissolved organic matter, and pesticide loads. Freshwater biofilms are surface-attached microbial communities that host complex interaction networks and play a key role in nutrient cycling and bioremediation. If adjacent land use drastically shifts microbial community composition and assembly, the functional resilience and adaptive capacity of biofilms under changing conditions may be impaired. In this study, we compared developing and mature biofilm samples from three sites along the Otterbach and two sites along the Perlenbach stream (Bavaria, Germany). The Otterbach sites, located in an area with agriculture and a nearby village, were adjacent to an intensively managed cropland, an extensively managed grassland, and a forest, while the Perlenbach flows through an area free of cropping and fertilization, with sites adjacent to an extensively managed grassland and a forest. Bacterial community composition was assessed through 16S rRNA gene amplicon sequencing. Bacterial diversity, differential abundance, community assembly and co-occurrence network analyses were performed.

Results: Adjacent intensive land use increased bacterial alpha diversity in both developing and mature biofilms. Moreover, adjacent intensive and extensive land use shaped bacterial community composition and increased the relevance of deterministic processes in bacterial community assembly, especially in developing biofilms, increasing the presence of key responding taxa such as Arenimonas, Blastocatella, Gemmatimonas, Flectobacillus, Leptothrix, Flavobacterium or Rhodoferax. These taxa were also detected in the co-occurrence networks of agriculturally influenced sites, displaying strong connectivity and centrality. These effects were limited to the Otterbach stream, which exhibited higher overall nutrient concentrations.

Conclusions: Agricultural land use strongly influenced bacterial richness, composition, and assembly in biofilms from adjacent stream ecosystems, particularly in developing biofilms from the most anthropogenically impacted stream, driven by the proliferation of key responding taxa. This showcased how anthropogenic nutrient inputs can redirect biofilm development pathways and potentially alter the ecological role of biofilms in stream ecosystems.

Background: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community.

Results: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival.

Conclusions: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.

Cyanobacteria play a key role in aggregating cryoconite granules on glacier surfaces, creating stable microhabitats that support diverse microbial communities, which influence glacier albedo and melting. However, their contribution to bacterial diversity and community stability is not well understood. This study explores their impact on bacterial diversity and interactions within three cryoconite-related environments: sediments and overlying water in cryoconite holes, and surface cryoconites across four Tibetan glaciers. Our study revealed that Cyanobacteria contributed the most (15-21%) to the differences in community compositions between these three habitats within each glacier. Cyanobacteria were abundant only in cryoconite sediments and surface cryoconites, accounting for 31-37% and 12-38% of all sequences, respectively, and contributing 6-10% and 5-9% to bacterial richness. Cyanobacteria genera such as Chamaesiphon and Pseudanabaena were key taxa, interacting closely with Bacteroidetes genera (e.g., Flavobacterium and Ferruginibacter) and Proteobacteria genera (e.g., Rhodoferax and Polaromonas). Metabolic analysis suggests that Cyanobacteria may provide essential nutrients to their heterotrophic bacterial partners through carbon and nitrogen fixation. The collaboration between Cyanobacteria and these bacteria contributes to community stability. These findings suggest that Cyanobacteria may act as 'engineer taxa', influencing bacterial diversity and the structural-functional stability of cryoconite microbial communities, and providing new insights into the potential responses of glacier ecosystems to climate change.

Background: Amino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants.

Results: Amino-acid fertigation notably increased shoot biomass, plant height, and root collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts coincided with higher needle auxin, a plausible link that merits testing. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency.

Conclusions: Our findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also associated with a shift in the root mycobiome, including taxa often considered beneficial, thereby offering a sustainable pathway to nursery production of radiata pine.

Background: Microbiome research has expanded rapidly, however, lack of standardized and validated protocols for microbiome sampling and DNA extraction has hindered the reproducibility and comparability of studies. The SUS-MIRRI.IT project aimed to prepare and validate Standard Operating Procedures (SOPs) for microbiome analysis across diverse ecosystems, including fermented foods, soils, waters, and more. To validate these protocols, 15 Italian research units (RUs) participated in an interlaboratory trial on 120 samples (liquid and solid fermented foods, waters, and soils). Metataxonomic sequencing was performed using 16S rRNA gene amplicon sequencing to assess the reproducibility of the protocols. The interlaboratory trial involved distributing homogenized samples to participating RUs and evaluating performance both between and within RUs. This was done by comparing results obtained from DNA extraction and amplicon-based sequencing.

Results: The results demonstrated high reproducibility of the procedures suggested in the SOPs across different sample types, with no significant differences in microbial diversity or composition between biological replicates or research units. DNA recovery was generally consistent, with minor variations observed in solid samples.

Conclusions: This study underlines the importance of standardized protocols in microbiome research. The validated Standard Operating Procedures developed by the SUS-MIRRI.IT project demonstrate robustness and reproducibility across diverse ecosystems, providing a foundation for future microbiome studies. The adoption of these protocols will enhance data comparability and support large-scale meta-analyses in food systems microbiome research.

Drinking water distribution systems (DWDS) are low biomass biomes harboring a large variety of microorganisms. Much of the attention has been focused on bacteria, whose diversity and abundance in DWDS were repeatedly shown to be influenced by abiotic factors such as pH, temperature, growth inhibitors and water sources. However, little is known about biotic factors, such as bacteriophage presence, even though they are known to be present in DWDS and to influence bacterial dynamics. While bacteriophage impact has been assessed in natural environments such as oceans, little is known about the way they shape DWDS bacterial communities. To fill this knowledge gap and accessing bacteriophage diversity from such low biomass environment, the present study aimed to propose and compare two methods based on ultrafiltration and adsorption/elution methods, already used for the concentration of bacteria and virus from water. To this end, both methods were compared with a weekly sample collection, for one month, on the DWDS of Paris, France. Metagenomic sequencing was performed on concentrated samples to investigate the presence and diversity of bacteriophages, using a coupling of complementary bioinformatic prediction tools. Though viral fractions represented a minority of recovered contigs (1.5 to 2.5%), most were associated with Caudoviricetes class. The predicted bacterial hosts matched with the observed bacterial diversity, highlighting the robustness of host prediction tool. A total of 437 putative phages were present in all samples, constituting a core phage diversity. Among those, 380 viral contigs contained sequences showing significant non-viral matches. We leveraged this information to further refine the inference of bioinformatics pairs of bacterial hosts and their phages. In conclusion, we propose a method to simultaneously concentrate bacteriophages with bacteria from low-biomass environment. Through metagenomics, this study showed that an optimized bioinformatic pipeline could provide an overview of DWDS phage diversity. Moreover, this method allowed to detect sequence similarities between phages and bacteria, suggesting potential genetic exchanges and providing clues for host spectrum. Altogether, this study highlights the tight interactions between bacteria and bacteriophages in drinking water and the possibility to study both phages and potential hosts to better grasp their intricate interplay.

Background: The brown alga Ascophyllum nodosum and its microbiota form a dynamic functional entity named holobiont. Some microbial partners may play a role in seaweed health through bioactive compounds crucial for normal morphology, development, and physiological acclimation. However, the full spectrum of the microbial diversity and its variations according to algal life stage, season, and location have not been comprehensively studied. This study uses 208 short-read metabarcoding samples to characterize the bacterial, archaeal, and microeukaryotic communities of A. nodosum across three nearby sites, four thallus parts, and a monthly survey, aiming to explore the dynamics of ecological interactions within the holobiont.

Results: Our results revealed that A. nodosum harbors a predominantly bacterial microbiota, varying significantly across all covariables, while archaea were virtually absent. An innovative normalization using the co-amplified host reads provided an estimation of bacterial abundance, revealing a drastic decline in May, potentially linked to epidermal shedding. In contrast, fungal communities were stable, dominated by Mycophycias ascophylli and Moheitospora sp., which remained closely associated with the host year-round. We identified a core microbiome of 22 ASVs, consistently found in all samples, including Granulosicoccus, a genus consistently abundant in other brown algal microbiota. Sequence clustering revealed multiple species which vary according seasons, even in the overall stable Granulosicoccus genus. Co-occurrence network analysis revealed putative interactions between microbial groups in response to ecological niches.

Conclusions: Overall, these findings highlight the dynamic of bacterial interactions and stable fungal associations within the A. nodosum holobiont, providing new insights into the ecology of its microbiota.

Background: Host-associated microbiomes play an important role in the ecology and fitness of organisms. Given their significance, it is much debated to what extent these associations are widespread and even obligatory. Such frequent associations are captured by the concept of the core microbiome. The cladoceran Daphnia is a pivotal genus in freshwater ecosystems occupying a central position in the food webs of standing waters. With its unique standing in pelagic waters, Daphnia serves as a key grazer, regulating algal populations and nutrient cycling, making its microbiome essential to understanding ecosystem function and stability. In recent years, Daphnia has become an increasingly popular study system for exploring host‒microbiota interactions. There is, however, limited knowledge on the baseline taxa that consistently inhabit this host and potentially contribute to its fitness. Identifying whether such a host-associated "core microbiome" exists for Daphnia and, if so, which microbial taxa it comprises is important both for enhancing our ecological understanding of this genus and its ecosystem function and for interpreting future experiments.

Results: We compiled a dataset on Daphnia magna microbiome based on 12 published studies, comprising gut and whole microbiome samples of both laboratory-cultured and field-grown animals across five countries spanning three continents. To identify core taxa, we employ quantification metrics based on prevalence and a combination of prevalence and relative abundance. Our analysis demonstrates that the D. magna microbiome is highly variable, yet, a consistent association with specific taxa, notably Limnohabitans planktonicus, is observed especially under laboratory conditions. However, this pattern is tempered by the observation that field-grown animals exhibit a more diverse microbiome with a weaker presence of L. planktonicus, challenging its status as a core member.

Conclusions: Our analysis suggests that the D. magna microbiome is defined by its high variability and few conserved associations, with L. planktonicus being the most stable taxon in laboratory settings but not necessarily a core member in natural environments. These findings underscore the need for caution when using laboratory results to interpret natural microbiome compositions and emphasize the need for further research on field-grown animals to better understand the structuring of microbial communities under natural settings.