Microbial Ecology最新文献

The distribution of diversity in function of climate has been largely studied in plants and animals, leading to a large body of literature on macroecological rules applied to large geographic scales. However, the applicability of these rules to microbes has almost never been tested at local scales. Arcellinida are a diverse group of protists known to be narrow ecological specialists and constitute therefore an excellent group to test general rules validated on "macrobes", like the water-energy balance that stipulates that biodiversity peaks with humidity and temperature. In order to test that hypothesis, we collected 122 samples from four cedar forests situated along an elevation gradient in Lebanon, spanning different local climates. We evaluated their diversity using an Arcellinida-specific metabarcoding approach based on the cytochrome oxidase subunit I gene. Our study shows that Arcellinida richness and phylogenetic diversity follow a unimodal distribution, peaking at mid-elevations. β-diversity was chiefly the product of turnover, illustrating the high spatial heterogeneity of the forests. Precipitation and actual evapotranspiration were identified as key drivers of diversity, thus supporting the water-energy balance hypothesis. Communities situated at higher or lower elevation were, to a large extent, subsets of more diverse mid-elevation assemblages, which designates the latter as biodiversity sources. These results suggest that, under the increasing aridification of the Middle East due to climate change, Arcellinida communities will lose diversity and will undergo a process of homogenisation, with possible consequences on ecosystem functioning.

Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.

Weathering of sulphur-bearing rocks leads to acid rock drainage (ARD), which decreases water pH, mobilizes heavy metals, and forms coloured coatings of metal precipitates on riverbeds. This study assessed the effects of ARD on microbial biofilm biodiversity and community structure in alpine streams across two Pyrenean regions (Núria and Chistau). Biofilms were sampled from acidic (pH < 5.5) and non-acidic (pH > 6.5) streams, and at their confluence, where metal precipitates occur (white-coated streams). We characterised bacterial and eukaryote communities by molecular tools and specifically analysed the diatom communities by morphology approach. Their respective community composition varied with stream category for both bacteria and eukaryotes, but only bacteria exhibited a loss in diversity in acidic and white-coated streams. Diatom communities and diversity differences were driven mainly by region. In acidic and white-coated streams, bacteria which can use metals and sulphurs in their metabolic processes increased, together with fungi and some photosynthetic groups (Chlorophyta, Streptophyta) among eukaryotes. Amplicon Sequence Variants (ASVs) assigned to acidophilic and psychrotolerant bacteria were highly associated with acidic streams, and Cyanophyceae ASVs were highly associated with white-coated ones. As for eukaryotes, ASVs of Chrysophyceae were associated with both acidic and white-coated streams. Nonetheless, the regional factor remained consistently significant across microbial communities. This study indicates that ARD-affected streams can support microbial communities adapted to their extreme conditions, with the communities in white-coated rivers differing markedly from those in acidic rivers.

The cloud forest harbors the highest amphibian diversity in Mexico, particularly among plethodontid salamanders. However, the expansion of agricultural and cattle ranching activities has significantly impacted this ecosystem and their native species. Beyond direct effects on cloud forest-dwelling species, effects of land-use change on free-living and salamander skin associated bacterial assemblages are underexplored in the cloud forest and in plethodontid salamanders specifically. This study examines how historical land-use changes may influence environmental and salamander skin bacterial communities, focusing on two types of previous land-use and six sympatric plethodontid salamanders from the cloud forest. Furthermore, we explored the presence of the pathogenic fungus Batrachochytrium dendrobatidis (Bd), due to its potential interaction with salamander skin bacterial communities. We found that skin bacterial communities varied with land-use history: in habitats formerly used for agriculture salamanders exhibited higher bacterial diversity, and communities' dispersion varied depending on the previous land-use. We found a very low Bd prevalence throughout the study area. Our findings suggest that bacterial communities associated with the skin of plethodontid salamanders may be influenced by land-use history in cloud forest fragments.

Temporary ponds, characterized by periodic or intermittent hydroperiods, are globally widespread in all the biogeographical regions and host peculiar biotic communities. Here we investigated shifts in diatom community assemblages across two contrasting biogeographical regions in Italy, the Mediterranean and the Alpine. The study focused on 24 temporary ponds, with 12 ponds sampled at Castelporziano (CP) and 12 at Campo Imperatore (GS). Our results highlighted that γ diversity varied significantly between the two study sites, indicating a notably greater species richness in GS compared to CP. In GS, functional richness values were generally higher, whereas no significant differences were detected for functional distance and functional divergence. Species composition differed significantly between CP and GS indicating that the two sites host distinct communities, with species turnover (0.904) which contributed most to total beta diversity (0.926), while nestedness (0.021) was negligible. CP communities were characterized by pronounced functional clustering in specific sites while GS exhibited both clustering and slight overdispersion. However, although GS communities occupy slightly larger trait space, both regions shared most functional strategies, reflecting substantial redundancy in functional traits across the two environments. Overall, diatom communities in the GS were characterized by higher frequencies of small, mobile, low-profile, and mucilaginous-tube taxa, whereas CP ponds displayed relatively higher representation of larger or motile forms. Although our study is a starting point, large-scale analyses of diatom communities are crucial, as climate change may rapidly and irreversibly alter taxonomic and functional diversity, profoundly affecting the ecology of these temporary habitats and surrounding landscapes.

Honeybees encounter low environmental doses of ethanol, primarily through fermenting nectar, which can have both beneficial and detrimental effects on their functioning. Yet, ethanol traces can also be detected in the crop of caged bees with no access to environmental food sources. This raises the possibility that endogenous ethanol accumulation could occur under restricted conditions, with microbial contributions as a potential mechanism. The crop microbiota, although less diverse than that in other gut segments, plays important roles in food fermentation and pathogen defense. We hypothesized that captivity-induced shifts in crop microbiota may facilitate fermentation, resulting in measurable ethanol. To test this, we compared the crop contents of naturally foraging hive bees and caged bees reared without access to the natural environment. Ethanol levels were low in both groups and did not differ significantly, but non-zero measurements were more frequently observed in caged bees. Microbial community structure differed strongly in α- and β-diversity. Caged bees showed reduced abundance of nectar-associated genera (e.g., Apilactobacillus) and an increase in genera that include known ethanol-producing strains, such as Gilliamella and Bifidobacterium. While we did not directly assess metabolic activity, our results suggest that captivity alters microbial communities in ways that may influence ethanol levels. This raises broader questions about how microbe-host interactions modulate host phenotypes under different environmental conditions.

Phyllosphere microorganisms promote plant health, facilitate plant growth, and support ecosystem function. In this study, we compared the effects of leaf anatomy, physiological properties, and chemical composition on the diversity and abundance of epiphytic microorganisms across four forage species: wheat (Triticum aestivum), rye (Secale cereale), barley (Hordeum vulgare), and Italian ryegrass (Lolium multiflorum). The results showed that crop type significantly influenced microbial abundances on leaf surfaces and in whole leaves (P < 0.05). Specifically, wheat exhibited higher abundances of aerobic bacteria, lactic acid bacteria, molds, and yeasts in whole leaves and on leaf surfaces than those of the other three forage species. Microbial abundance on leaf surfaces was lower than that in whole leaves among the four crops. The stomatal density on the abaxial leaf surface was significantly higher than that on the adaxial surface (P < 0.0001) among the four crops. The main drivers of whole-leaf microbial abundance included soluble sugars, stomatal density, intercellular CO₂ concentration, and total water vapor conductance. Conversely, the key factors influencing surface microbial abundance were reducing sugars (affecting lactic acid bacteria and molds) and stomatal density on the adaxial surface (affecting yeasts). In conclusion, the morphology, physiology, and chemical composition of forage leaves collectively shape the colonization patterns and abundance of epiphytic microorganisms. Wheat exhibited larger microbial numbers than those of the other three forages. Soluble sugars and stomatal density emerged as key determinants of microbial community structure, whereas epidermal structure influenced the formation of specific functional microbial communities through a dual mechanism of physical selection and microenvironmental regulation.

Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe's most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils-likely involving Chloroflexota taxa-compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.

Microbe-derived antimicrobial peptides (AMPs) can shape gut community structure; however, their contribution to disease-associated dysbiosis remains poorly understood. We assembled fecal metatranscriptomes from individuals with normal weight (NW), obesity (O), and obesity with metabolic syndrome (OMS), yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms combined with stringent post-hoc bioinformatics filters identifying 51 high-confidence AMP candidates. Most matched bacterial homologs, predominantly Faecalibacterium prausnitzii, while eight mapped to plasmids or bacteriophages. Differential expression identified two and four AMPs overexpressed in O and OMS, respectively. Two of them were originated from chromosomes, three from phages, and one from plasmid. Notably, the over-expression of these AMPs was negatively correlated with healthy-associated bacteria and positively correlated with obesity-enriched taxa. Furthermore, these AMPs were broadly detectable across 372 external gut metatranscriptomes (prevalence up to 94% of the samples) indicating conservation within the human gut microbiome and highlighting mobile elements as an overlooked reservoir of transcriptionally active AMPs. Using DNA virome sequencing and prophage analyses, we suggested phage origin of the transcribed AMPs. We further synthesized a phage-encoded AMP (AMP-3020), demonstrating broad-spectrum activity against Gram-positive and Gram-negative bacteria, without detectable cytotoxicity toward human immune T cells. This supports the idea that phages could encode functional AMPs capable of shaping gut community structure by suppressing diverse bacteria without harming host immune cells. Our gut metatranscriptome-virome profiling revealed a conservative core of actively transcribed, plasmid- and phage-encoded AMPs with exploratory associations to obesity/MetS. These findings support mobile-element AMPs as candidate ecological regulators and motivate validation in larger cohorts and mechanistic models.

Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.