Abstract Understanding microbial responses to environmental gradients is important for ecosystem assessment in estuarine environments. Here, we integrated time-series samples and shotgun metagenomics with association network inference, to examine patterns of taxonomic and functional co-variation. We collected and sequenced eDNA from two sediment time series from neighbouring but environmentally contrasting Basque estuaries, and compared the resulting taxonomic and functional association networks, based on Metagenome Assembled Genomes (MAGs) and KEGG Orthologous Groups (KOs), respectively. Networks inferred using 16S rRNA gene metabarcoding data were also included in this comparison. Several topology-based network properties differed strongly between the two sites, although differences were not always consistent when comparing the networks based on MAGs, KOs and metabarcoding. KO-based networks revealed distinct sets of associated Ortholog groups between sites, consistent with known environmental differences. Contrary to our expectations, metabolically related genes rarely formed complete pathway modules in gene networks, likely due to functional redundancy, gene copy number variation, synchronized pathway dynamics, or algorithmic constraints of correlation-based inference. Overall, the results illustrate both the potential and interpretative limitations of metagenome-based time association networks for functional ecosystem assessment, and support their use as hypothesis-generating tools that require further validation across a larger range of sites following environmental gradients.
Abstract The foliar mycobiome plays an important role in tree health and stress resilience, yet factors shaping foliar fungal communities in boreal conifer seedlings remain poorly understood. We investigated how geographic region, seedling origin (planted vs. naturally regenerated), needle nitrogen status, and local stand structure influence needle-associated fungal communities of Scots pine (Pinus sylvestris) seedlings. Needle samples were collected from seedlings without visible disease symptoms across 23 forest stands in southern Finland. Fungal communities were characterized using Illumina ITS2 amplicon sequencing and clustered into operational taxonomical units (OTUs). Alpha diversity was analyzed via linear mixed models (LMMs), and community composition via PERMANOVA and NMDS using Bray–Curtis dissimilarity. Geographic region was the strongest driver of fungal community composition among stands, whereas within stands, community composition was primarily associated with seedling height and birch abundance. Alpha diversity was higher in the Southeastern region compared to the Southwest, and tended to be lower in planted than naturally regenerated seedlings. Moreover, diversity decreased with higher proportions of birch and spruce but increased with higher needle C:N ratios. These findings suggest that early foliar mycobiomes reflect regional conditions and local forest structure, highlighting potential forest management impacts on fungal communities.
Abstract Bark and ambrosia beetles are associated with various filamentous fungi, whose roles range from mutualists to antagonists. Mutualists can provide various benefits and are typically selectively dispersed by these wood-boring beetles. However, it is currently unknown how such bark and ambrosia beetles distinguish their fungal mutualists from other fungal associates, including insect pathogens. We hypothesized that volatile organic compounds might help maintain the mutualisms between beetles and specific fungal partners. Here, we compared the volatiles emitted by 30 fungi known to act as mutualists, commensals or antagonists for their beetle hosts. GC-MS analysis showed that all the fungi had characteristic volatile profiles with beneficial fungi emitting a greater diversity of volatiles than other fungal species. The volatile profiles of beneficial fungi were dominated by aliphatic and aromatic alcohols and esters in terms of both diversity and abundance. Furthermore, we demonstrated that the larvae and adults of two ambrosia beetle species can distinguish their mutualistic fungi from others based on volatile cues. Our results highlight the importance of aliphatic and aromatic alcohols and esters as recognition cues for mutualist fungi by wood-boring beetles. Volatiles likely play key roles in maintaining beetle associations with fungi that are essential to their insect host.
Abstract The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs) are known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.
Abstract Tropical montane forests are undergoing rapid climate change, with declining cloudiness and warming in higher elevations. While impacts on vegetation are increasingly documented, effects on belowground microbial communities and ecosystem processes remain poorly studied. We investigated how experimental drought and warming influence soil microbial communities and decomposition across a 900-m elevation gradient in the tropical montane forests of the Dominican Republic. Precipitation exclusion shelters simulated drought at high (2250 m a.s.l.) and low elevation (1350 m a.s.l.) and high elevation soils were translocated to the lower elevation to simulate warming. Fungal and bacterial communities were measured by DNA sequencing over 11 months, in addition to soil properties and litter decomposition. Fungal richness increased under drought but was unchanged following translocation, whereas bacterial richness and abundance were largely unaffected by either treatment. Decomposition was consistently faster at the lower (warmer) site but slowed under intense drought at both elevations. Soil carbon was higher at high elevation, consistent with slower decomposition. Overall, these results indicate cooler and wetter conditions promote structurally and functionally complex fungal communities. As temperature and precipitation patterns change, fungal communities are more likely to shift in response, altering decomposition and nutrient cycling, with implications for carbon storage in tropical montane ecosystems, especially at high elevations.
