Environmental Microbiome最新文献

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.

Background: The interaction between host microbiomes, pathogen diversity, and environmental stress is a critical but understudied mechanism shaping disease outcomes in marine foundation species. Eelgrass (Zostera marina) suffering from wasting disease, caused by the protist Labyrinthula zosterae, offers a powerful system with which to probe this interaction. We conducted complementary laboratory experimentation and field surveys to examine three main questions: (1) whether thermal stress compromises the eelgrass microbiome and exacerbates disease outcomes; (2) whether different isolates of L. zosterae differ in virulence and their effects on the host microbiome; and (3) whether laboratory-derived microbiome signatures of heat stress correspond with those observed in the field. In the lab, we exposed eelgrass pieces to two temperature regimes (11 °C vs. 19 °C) and inoculated with two L. zosterae strains. We tracked lesion development, pathogen load via qPCR, and epiphytic microbiome dynamics via 16S rRNA gene sequencing. In parallel, we tagged and sampled intact intertidal eelgrass in situ at Fourth of July Beach, San Juan Island, Washington, before and after a three-day heat stress event, tracking tissue damage, growth, and microbiome dynamics.

Results: In the lab, elevated temperature significantly heightened wasting disease severity across both pathogen isolates, with no significant difference in virulence between them. High temperatures in the lab also led to more pronounced diseased-induced microbiome dysbiosis: community composition shifted, and a greater number of microbial taxa changed in abundance relative to controls, including Colwelliaceae. Both lab and field heat stress decreased microbiome diversity with intertidal eelgrass experiencing extensive tissue damage and reduced growth.

Conclusions: Warming accelerates wasting disease progression in Z. marina by some combination of microbiome disruption, enhanced pathogen virulence, or compromised host defenses. Although pathogen strain identity had limited influence, temperature emerged as a dominant driver of both disease outcomes and microbiome shifts. While temperature stress in the lab and field was not comparable in duration and intensity, we show consistent trends towards microbiome dysbiosis characterized by changes in diversity and taxon abundance. Exploring the four-way interaction among host, microbiome, pathogen, and environment promises deeper insights for forecasting disease outbreaks and bolstering resilience in eelgrass ecosystems.

Background: Soil microbial communities can affect plant nutrient uptake, productivity, and may even confer resistance to global change. Elevated atmospheric CO₂ is widely expected to stimulate plant productivity; however, this will depend on the availability of growth limiting nutrients such as nitrogen. Soil microbial communities are the main mediators of soil nitrogen cycling and should therefore play a key role in influencing plant responses to elevated CO₂.

Results: To test this, we conducted a controlled, growth chamber experiment with Pinus sylvestris to evaluate how soil microbiome variation influences plant physiology, productivity, and responses to elevated CO₂ (eCO₂; 800 ppm versus 400 ppm in the ambient treatment). Field soils were collected from six forests with varying tree growth rates and were used as an inoculant source, either sterilized or living, into a common growth medium seeded with P. sylvestris. After seven months of growth, we measured plant carbon assimilation, photosynthetic nitrogen use efficiency, above- and belowground productivity, and we measured soil microbial biodiversity using DNA metabarcoding. Our findings demonstrate that seedling productivity was stimulated under eCO₂ conditions and that this was supported by improved plant photosynthetic nitrogen use efficiency, but only in the presence of living versus sterilized soil inoculant. The magnitude of this response was also dependent on the forest soil microbial inoculant source and was linked to a 70% increase in bacterial species richness, increased relative abundances of bacteria known to have positive effects on plant growth (e.g., Lactobacillus, Bacillus, Flavobacterium), and with a concomitant shift in saprotrophic fungal community composition and root growth. Variation in inorganic nitrogen cycling which favored the accumulation of nitrate under eCO₂ was also correlated with a twofold reduction in photosynthetic nitrogen use efficiency, suggesting a decoupling of nitrogen availability and assimilation efficiency with distinct implications for plant growth responses to elevated CO₂.

Conclusions: Our results show that soil microbial community variation directly affects P. sylvestris physiology, productivity, and responses to eCO₂, and may enhance plant growth through improved nitrogen use efficiency. Surprisingly, growth with different microbial communities even more strongly impacted plant productivity than a doubling of atmospheric CO₂ concentrations. The soil microbiome therefore plays a key role in supporting plant nutrition and growth under ambient and eCO₂ conditions, and in turn, may confer increased forest resistance to climate change.

Background: Global climate change exacerbates the incidence of marine heatwaves (MHWs), which have increased in intensity and frequency over the past years, causing severe impacts on marine coastal ecosystems. MHWs have already triggered mass mortalities of habitat-forming species, including corals, sponges and gorgonians, in temperate, tropical and polar seas. In the Mediterranean, these high peaks of temperature have been shown to affect several sponge species, and likely, their symbiotic microbial communities. During the summer of 2022, populations of the sponge Petrosia ficiformis (Poiret, 1789) were conspicuously observed with signs of thermal stress linked to a MHW around the Gulf of Naples (Tyrrhenian Sea, Italy). These included depigmentation spots and tissue texture alterations, which often evolved in necrotic processes and eventual death. At the peak of the MHW, however, apparently thermoresistant sponges co-occurred with sensitive unhealthy specimens. In order to explore potential microbial drivers correlated with these divergent thermal-stress tolerances, Healthy and Unhealthy individuals were sampled along the coast of Ischia Island in early September 2022.

Results: Prokaryotic community characterization based on the 16 S rRNA gene revealed dissimilar compositions in Unhealthy versus apparently Healthy sponges. Increased alpha diversity richness and low evenness in thermosensitive sponges were due to an extensive presence of rare taxa, and to the introduction of potentially pathogenic groups (e.g., Vibrio spp.). Major microbial families regularly associated with P. ficiformis - SAR202, Caldilineaceae, Poribacteria or TK17, were replaced in thermosensitive specimens by professed opportunistic groups within Lentimicrobiaceae, Rhodobacteraceae or Flavobacteriaceae. In turn, conservancy of hub microbes and thermotolerant symbionts (e.g., Rhodothermaceae, Thermoanaerobaculaceae) in Healthy sponges were observed during this disrupting event. Unhealthy microbiomes reflected lower network stability with respect to Healthy holobionts, due to the inconsistency of functional keystone taxa and prevalence of transient microbes.

Conclusions: Dysbiotic shifts due to colonization of scavenger groups and opportunistic microbes, and interconnectivity loss characterized thermally stressed sponges. In contrast, resistant specimens retained keystone symbionts that could have ensured functional cooperation, and maintenance of prokaryotic community cohesion under thermal stress. The existence of stress-resistant phenotypes in sponge holobionts offers a glimmer of hope for species persistence, and their study may identify potential source populations for ecosystem recovery.