Environmental Microbiome最新文献

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.

Soil salinization is a critical global issue threatening agricultural productivity and significantly reducing the availability of arable land. Effective mitigation and recovery strategies are vital for sustaining food production, especially in the context of climate change. Halophytic plants, such as Atriplex nummularia, have shown potential for remediating saline soils, though their large-scale application remains limited. An alternative approach involves leveraging microorganisms adapted to saline environments to enhance plant stress tolerance. In this study, we investigated the microbiome of A. nummularia under saline and non-saline irrigation conditions to identify extremophilic microorganisms that promote salt stress tolerance. Through 16S rRNA analysis, we identified members of the genus Haladaptatus exclusively in the rhizosphere of salt-irrigated plants. These microorganisms were isolated and inoculated into maize crop systems to evaluate their ability to confer salt tolerance. Our results demonstrate that Haladaptatus strains significantly enhance salinity tolerance in maize, with a marked increase in the relative abundance of archaeal 16S rRNA in soils as NaCl irrigation levels rise. This study provides the first evidence that Haladaptatus, an archaeon isolated from the rhizosphere of a halophyte, can significantly enhance salt tolerance in an agriculturally important crop. These findings suggest a promising biotechnological application for improving crop resilience in saline environments, offering a sustainable strategy for addressing soil salinization and securing food production in the context of global climate challenges.

Background: Lignocellulose represents a primary input of organic carbon (C) into soils, yet the identity of specific microorganisms and genes which drive lignocellulose turnover in soils remains poorly understood. To address this knowledge gap, we used a 10-year grassland plant-exclusion experiment to investigate how reduced plant C inputs affect microbial communities and their lignocellulolytic potential using a combination of metagenomic sequencing and untargeted metabolomics. We specifically tested the hypothesis that microbial community function in bare fallow plots would transition towards microbiota with genes for recalcitrant biomass degradation (i.e., lignocellulose), when compared to grassland plots with high labile C inputs.

Results: Long-term plant exclusion lowered soil C and nitrogen (N) and reduced cellulose content, whilst hemicellulose and lignin were unchanged. Similarly soil microbiomes were highly distinct in long-term bare soils, along with soil extracellular enzyme profiles, though short-term plant-removal effects were less apparent. Plant exclusion resulted in a general enrichment of Firmicutes, Thaumarchaeota, Acidobacteria, Fusobacteria, and Ascomycota, with a general reduction in Actinobacteria. However, changes in bare soil lignocellulose degradation genes were more associated with discrete taxa from diverse lineages, particularly the Proteobacteria. Grouping of lignocellulose-degrading genes into broad substrate classes (cellulases, hemicellulases and lignases) revealed a possible increase in lignin degradation genes under plant exclusion confirming our hypothesis, although all other changes were at the level of the carbohydrate-active enzyme (CAZy) family. Intriguingly, untargeted metabolome profiles were highly responsive to plant exclusion, even after only one year. Bare soils were depleted in oligosaccharides and enriched in monosaccharides, fatty and carboxylic acids, supporting emerging evidence of long-term persistent C being within simple compounds.

Conclusions: Together our data show that extracellular lignin degrading enzymes increase under long-term plant exclusion. There is now a need for increased focus on the microbial metabolic mechanisms which regulate the processing and persistence of enzymatically released compounds, particularly in energy limited soils.

Background: Marine microbial communities drive global biogeochemical cycles and oceanic food webs, yet our understanding of their holistic temporal dynamics remains limited, particularly in the South China Sea. Most studies have focused on specific taxonomic groups or single temporal scales, leaving a gap in comprehensive, multi-domain, and multi-timescale analyses.

Results: Using an integrated multi-omics approach that combined metagenomic, metatranscriptomic, and metaviromic analyses, we conducted time-series sampling over 48-h periods during winter and summer to investigate microbial community dynamics in the coastal South China Sea. Seasonal transitions were identified as the primary drivers of community shifts, with diel variations playing a secondary role across all taxonomic domains. Within seasons, diel changes followed a progressive trajectory rather than recurring cyclic patterns. Eukaryotic communities exhibited the most pronounced temporal fluctuations, while prokaryotic and viral communities displayed remarkable stability. Unlike previous coastal studies, viral communities maintained high similarity between seasons, suggesting the presence of a persistent viral reservoir in this region. Gene expression analysis revealed dynamic population shifts in photosynthetic microorganisms, with Mamiellophyceae green algae and their associated Prasinovirus displaying pronounced seasonal and diel rhythmicity.

Conclusions: This study provides novel insights into the temporal dynamics of microbial communities and host-virus interactions in the South China Sea. The stability of viral communities, coupled with synchronised host-virus activities, highlights potential mechanisms supporting ecosystem resilience in this coastal region. These findings enhance our understanding of marine ecosystem processes and establish a robust framework for exploring microbial responses to environmental changes on both diel and seasonal scales.

Mosquito larvae develop in aquatic habitats that harbor highly variable communities of bacteria and other microorganisms, which have been well demonstrated to shape individual fitness outcomes in laboratory settings. However, relatively little is known about how this microbial variation contributes to or is influenced by mosquito population dynamics in the field. To investigate potential associations between mosquito population dynamics and microbial community assembly, we characterized bacterial communities in naturally occurring larval habitats with variable historical mosquito productivity using amplicon sequencing. We then applied a null model approach to quantify the relative importance of selection, dispersal, and drift processes in bacterial community assembly. Habitat microbiota clustered into two distinct biotypes: Biotype 1 communities were dominated by Proteobacteria, while Biotype 2 communities were dominated by Cyanobacteria. Both biotypes were shaped by a combination of selection and neutral (i.e., dispersal and drift) processes. However, selection played a more prominent role in habitats with Biotype 1 communities, whereas drift was more influential in Biotype 2 habitats. Variation partitioning further identified historical mosquito productivity and the spatial aggregation of sites with similar productivity histories as key drivers of selection. These findings suggest that mosquito population dynamics are associated with differences in microbial community structure, potentially through feedbacks between mosquito activity and habitat conditions. This study lays the foundation for future work to disentangle causal relationships and to integrate patterns of microbiota diversity and mosquito occurrence into vectorial capacity models for improved prediction of mosquito-borne disease transmission dynamics in the field.

The intensive use of agrochemicals is essential to maintain crop yields, but it has led to overexploitation of land and environmental deterioration. To promote more sustainable agriculture, this study evaluates the novel effects of biofertilizers enriched with plant growth promoting bacteria, such as Bacillus pretiosus and Pseudomonas agronomica, on Lupinus albus var. Orden Dorado, to improve the rhizospheric soil health and plant biomass as well as reducing dependence on chemical fertilizers. The organic matrix ORGAON^®PK and its sterilized version, both derived from horticultural waste, were tested compared with a traditional chemical fertilizer and a water control. After three months of treatment, metagenomic analyses (16 S rRNA gene amplicons) indicated that the strains remained in the rhizosphere, increasing metabolic diversity without altering the microbial structure (Shannon index). In addition, a significant reduction in the minimum inhibitory concentration against clinical antibiotics (p < 0.05) was observed, highlighting the potential of biofertilizers to decrease microbial resistance in the soil. Principal component analysis showed clear differences between treated and control groups, and ANCOM-BC revealed changes in non-culturable bacteria. Biometric analyses revealed increases of 70-88% in shoot weight, ~ 80% in total biomass, and up to 36% in shoot elongation compared with the control. Biofertilizers improved nutritional quality and plant biomass, suggesting their potential as a sustainable and efficient alternative to the use of chemical fertilizers.

Background: Soil microbial community plays a key role in land restoration through direct involvement in various soil biochemical processes. However, our knowledge about how different land restoration practices shape bacterial communities is limited.

Results: Soil samples were collected at 0-10 cm and 10-20 cm depths from a seven-year-old naturally restored grassland, an artificially restored grassland (restored either with grass, legume, or a mixture of two), and continuously cultivated cropland. Changes in soil biochemistry and bacterial community structure using targeted high-throughput amplicon sequencing were to identify characteristics of bacterial taxa associated with soil biochemistry altered by the grassland restoration process. The soil bacterial community composition was highly similar under the three artificial grassland management models, but significantly different from arable and naturally restored grasslands. Different grassland restoration approaches indirectly determined the composition and function of soil bacterial communities by regulating vegetation and environmental factors, which further drives the dynamic regulation of enzyme function. The structural equation modeling results indicated that soil organic carbon (SOC) may exert a direct effect on enzyme activity. Additionally, SOC may also indirectly influence enzyme activity through shifts in bacterial community composition mediated by plant biomass.

Conclusions: We found that SOC shaped the bacterial community function through multiple pathways during grassland restoration, providing an important driver for the recovery of grassland ecosystem function.