Environmental microbiology最新文献

Resolving the spatial organisation of microbial populations in environments shaped by steep thermal and geochemical gradients remains a challenge in environmental biogeochemistry. Conventional molecular biomarker or gene-based approaches typically require large volumes of homogenised samples, limiting their ability to depict spatially structured microbial ecosystems, where critical microbial processes occur on millimetre scales. To overcome these limitations, we applied high-resolution mass spectrometry imaging (MSI) to an 11.5 cm long sediment section from the hydrothermal Cathedral Hill mat complex in the Guaymas Basin, known for its extreme temperatures and sharp geochemical gradients. The μm-scaled spatial resolution unveiled a nuanced lipidome zonation tightly compressed to a narrow 5-cm segment below the sediment–water interface. The surface layer (above 1.1 cmbsf) hosts molecular patterns primarily shaped by opposing oxygen and sulphide gradients, followed by a near-seamless transition to an anoxic zone dominated by anaerobic methane-oxidising archaea (ANME) and sulphate-reducing bacteria (SRB). At greater depth, molecular signals indicative of active microbial communities remained below the detection limit except for diverse, potentially ANME- and SRB-related lipids concentrated within a siliceous concretion. The sharp transitions in lipid zonation hint at persistent redox zones and resilient microbial niches under intense fluid flow and dynamic geochemical gradients.

Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.

Crustose coralline algae (CCA) and their bacterial communities can emit chemical cues favoring coral larval settlement. Indeed, larvae of Eunicella singularis (white gorgonian) preferentially settle on CCA. Here, we investigated the effect of two Mediterranean CCA holobionts, Macroblastum dendrospermum and Lithophyllum stictiforme, on E. singularis larvae settlement and their bacterial communities, after warming and acidification treatments. We exposed CCA to temperature and pH expected for 2100 (SSP5-8.5) and to a marine heatwave event. Larval settlement increased 1.8–2.7 times in the presence of CCA exposed to warming and acidification compared to non-exposed CCA. High abundance of bacteria belonging to the Pirellulaceae family was observed in all CCA, while a higher abundance of monosaccharides was found in exudates of exposed CCA. Based on CCA-related 16S rDNA metabarcoding and metabolomics results, we hypothesize that the enhanced larval settlement was driven by the Pirellulaceae breakdown and utilization of CCA polysaccharides, in combination with polysaccharide release through the CCA cell walls likely augmented by decalcification. Furthermore, CCA acted as sources of bacterial taxa that may establish and persist in the adult E. singularis holobiont, independently of climate change effects. We conclude that CCA are key for E. singularis recruitment success, especially under future climate conditions, and contribute to their microbiome development.

Habitat fragmentation is a critical issue for biodiversity conservation, disrupting ecological processes and species interactions. While its effects on many organisms are well studied, impacts on symbiotic systems remain poorly understood. Lichen symbioses, in particular, have been widely investigated, but most work has focused on the fungal partner. To our knowledge, this is the first study to assess how forest fragmentation and structure influence photobiont diversity in epiphytic lichen communities. We analysed over 2000 thalli from 44 mycobiont species across 28 genera in a fragmented Mediterranean forest using high-throughput sequencing. We identified 33 algal species across three genera, including two putative undescribed taxa. Several lineages were newly recorded for Europe and the Iberian Peninsula, highlighting that green algal photobiont diversity remains substantially underestimated. Mycobiont identity emerged as the primary driver of photobiont community structure. In addition, forest structure and fragmentation variables were significantly associated with photobiont diversity. However, it remains possible that these effects drive photobiont diversity by directly influencing lichen holobionts. Overall, our results indicate that variation in green algal photobiont diversity is closely linked to the richness of their fungal partners, with any effects of fragmentation likely mediated through changes in mycobiont communities.

The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.

Getting insights into the quantitative and qualitative contribution of different DNA states, i.e., extracellular (exDNA) and intracellular DNA (iDNA), to the total environmental DNA (eDNA) pool requires reliable methods for their separation. Even though a multitude of respective extraction protocols has been published, their validation is often missing. Here, we selected four protocols for the state-specific extraction of eDNA and traced the separation of exDNA and iDNA within natural environments using previously designed spike-and-recovery controls. Besides accounting for the different eDNA states, the spike-ins also distinguished different bacterial origins (gram-positive, gram-negative). Following their quantification by digital PCR, the recovery of exDNA and iDNA spike-ins in both the target as well as nontarget eDNA states differed among the selected extraction protocols and environmental matrices, albeit the effect of the former was far more decisive. While the recovery of exDNA spike-ins was mainly affected by the chemical composition of the washing buffer and the duration of each washing step, the lysis method determined the recovery of spiked iDNA. These aspects were further combined within an optimised protocol, providing a valuable step towards a more concise understanding of factors governing the state-specific extraction of eDNA and hence their relevance in molecular microbial ecology.

In cold seeps, anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria (SRB) oxidise methane to inorganic carbon (IC) coupled to sulphate reduction. While catabolic pathways are well resolved, carbon flow into biomass as well as the functional roles of lipid biomarkers remain unclear. We conducted lipid stable isotope probing (lipid-SIP) experiments with Astoria Canyon sediments dominated by ANME-2/SRB consortia and incubated samples with either ¹³C-labelled methane (¹³CH₄) or dissolved IC (DI¹³C). Lipid-specific δ¹³C analysis showed higher ¹³C incorporation from DI¹³C than from ¹³CH₄. After 30 days, δ¹³C values were up to +417‰ in SRB-specific fatty acids (e.g., C_16:1ω5c, cyC_17:0ω5,6) and +126‰ in ANME-2-specific isoprenoid lipids (e.g., archaeol, crocetane). Based on these values, we calculated carbon assimilation rates and found that both partners primarily assimilate IC. Remarkably, IC assimilation in SRB lipids was eight times higher than in ANME lipids, suggesting that ANME may use additional yet-to-be-identified carbon sources, potentially produced by their partner SRB. By examining the stepwise ¹³C-enrichment of ANME- and SRB-derived lipids, we further delineate biosynthetic pathways for archaeal and bacterial diether lipid formation and highlight crocetane as a bilayer-modulating isoprenoid hydrocarbon potentially affecting membrane fluidity and proton permeability.

Arctic warming is leading to permafrost thawing which modifies, in cascade, hydrosystems at diverse levels. This study aimed to compare prokaryotic community structure and methane (CH₄) dynamics across 16 sub-Arctic waterbodies, and to assess how these features are shaped by permafrost thaw. The sampled waterbodies, located in an ice-rich discontinuous permafrost region (Southwestern Yukon, Canada) differed in size, depth, stratification and degree of thaw influence. Prokaryotic communities were characterised through 16S rRNA gene sequencing and qPCR targeting mcrA (methanogenesis) and pmoA (methanotrophy) genes. Community structures differed significantly between shallow stratified, deep stratified and non-stratified waterbodies. Methanogens, predominantly represented by the Methanobacterium genus, were mostly detected in shallow non-stratified waterbodies. Methanotrophs, primarily represented by the Methylacidiphilaceae family, were more abundant in oxic layers whereas bacteria of Crenothrix and Methylobacter genera dominated in anoxic conditions. Our results showed that non-stratified waterbodies directly affected by permafrost thaw harboured distinct prokaryotic communities, including specific methanogens and methanotrophs. The two sites with the highest CH₄ emissions were affected by permafrost thaw, with fluxes reaching up to 1.7 × 10⁻¹ mg m⁻² s⁻¹. Future investigations should address gaps in CH₄-related processes in thaw-affected systems, as they are hotspots for methane emissions and harbour different microbial communities.