Soares, D. M. | bioRxiv Science

bioRxiv2025

Microbial diversity of Atlantic Rainforest ponds assessed by nanopore sequencing

Despite their limited size, ponds are ecologically important habitats that harbor rich microbial communities and play key roles in global biodiversity and biogeochemical cycling. In this study, we conducted a metagenomic survey of microbial diversity in three ponds - Vermelha, Grande, and Furnas - situated within the Atlantic Rainforest biome in Brazil. Vermelha and Grande are natural, remote, and minimally impacted by human activity, whereas Furnas is an artificial pond with greater human accessibility. Using a long-read nanopore shotgun metagenomics approach, we sequenced DNA extracted from pond water, assembled metagenomes, and performed taxonomic classification and functional annotation. Furthermore, 21 metagenome-assembled genomes (MAGs) were recovered. Our results reveal striking biodiversity contained within ponds, with pond-specific microbial community structures and functional profiles. In addition to bacterial communities, some dsDNA bacteriophages and eukaryotic viruses were also detected. Functional annotation identified putative antimicrobial resistance genes (ARGs), most of them in Furnas, potentially reflecting human impact. Cyanotoxin biosynthesis genes were detected as well, predominantly in Vermelha. Our findings underscore the ecological distinctiveness of each pond and demonstrate the utility of nanopore-based metagenomics for investigating microbial biodiversity in understudied freshwater ecosystems, with implications for conservation and biotechnological exploration. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/660208v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1941bd9org.highwire.dtl.DTLVardef@b06d66org.highwire.dtl.DTLVardef@de6df3org.highwire.dtl.DTLVardef@1048bbd_HPS_FORMAT_FIGEXP M_FIG Through nanopore metagenomic sequencing, this work uncovered the microbiome of the 3 analysed freshwater ponds of the Brazilian Atlantic Forest. Results include the taxonomic profile present in each sample, countless genes identified and 21 MAGs recovered. C_FIG

bioinformatics↗

bioRxiv2024

Velamins: the first green-light emitting class of wild-type Ca2+-regulated photoproteins isolated from the ctenophore Velamen parallelum

Ca2+-regulated photoproteins (CaPhs) consist of single-chain globular proteins to which coelenterazine, a widely distributed marine luminogenic substrate (the luciferin), binds along with molecular oxygen, producing a stable peroxide. Upon Ca2+ addition, CaPhs undergo conformational changes leading to the cyclization of the peroxide and the formation of a high-energy intermediate. Subsequently, its decomposition yields coelenteramide in an excited state and results in the emission of a flash of light. To date, all CaPhs reported produce blue light ({lambda}max 465-495 nm). Here, we report the cloning and functional characterization of a novel class of wild-type CaPhs capable of emitting green light: velamins, isolated from the bioluminescent ctenophore Velamen parallelum. Ten unique photoprotein-like sequences were recovered and grouped in three main clusters. Representative sequences were cloned, expressed, purified, and regenerated into the active His-tagged -, {beta}-, and {gamma}-velamins. Upon injection of a calcium-containing buffer into the velamin, a flash of green light ({lambda}max 500-508 nm) was observed across pH values ranging from 7 to 9. Whilst -velamin isoforms exhibited the highest light emission activity, {beta}- and {gamma}-velamins were found to be more thermostable at higher temperatures. Velamins are the only known wild-type Ca2+-regulated photoproteins that exhibit the longest wavelength in light emission, making them a promising model for studying spectral modulation. As a result, velamins hold potential for enhancing the sensitivity of signal detection in analytical systems, particularly when dealing with complex biological matrices.

biochemistry↗