Biology subjects

Modolon, F.

Publications and source records attributed to Modolon, F..

3 recordsLinked to original sources

bioRxiv2026

HiFiTaxa: a reproducible analysis pipeline for full length 16S rRNA gene and ITS amplicon sequencing from PacBio reads

Long-read amplicon sequencing profiles communities at high resolution, but taxonomic accuracy depends on the reference, classifier and the parameters used. Here, we present HiFiTaxa, a reproducible, single command Nextflow pipeline for PacBio HiFi 16S rRNA gene and fungal ITS amplicons. It builds versioned references from current GTDB and UNITE releases and supports Bayesian lowest common ancestor (BLCA) and naive Bayes (NB) classifiers and the read level profilers Emu (16S rRNA gene) and EMITS (ITS). We benchmarked them on mock communities and on holdouts with 10% of GTDB or UNITE databases sequences withheld. On the 16S rRNA gene mock of 20 species, BLCA detected all 20 species and reported two false positives, NB detected 17 and reported none, and Emu detected all 20 and reported eight. In the GTDB holdout, for taxa represented in the reference, BLCA reached 80.0% species level accuracy against 48.1% for the exact matching species step of NB. However, NB produced fewer incorrect assignments for taxa absent from the reference. On fungal ITS, BLCA had slightly higher holdout accuracy at species level(54.7%) against 52.2% for NB. NB was more conservative for novel taxa, and EMITS detected the most mock species. HiFiTaxa therefore offers a single reproducible workflow that uses current GTDB and UNITE releases and enables users to choose between different classifier algorithms depending on their needs.

bioinformatics↗

bioRxiv2025

A Machine Learning Approach Elucidates Spatial Patterns of Environmental Properties Driving Microbial Composition Over Santos Basin, South Atlantic

Microbial communities in marine ecosystems play a pivotal role in global biogeochemical cycles, with particular relevance in ecologically and industrially significant regions such as the Santos Basin (SB), Brazils largest marine sedimentary basin and a hub for oil and gas exploration. Yet, our capacity of predicting the microbial community structure and function remains limited for marine ecosystems. This study investigated the structure of microbial communities across different depths in the SB, using amplicon sequencing data and quantitative cell counts obtained via flow cytometry. Using a hybrid machine learning framework combining Self-Organizing Maps and Random Forest, we identified five distinct microbial assemblages (named microbial associations) in the SB predicted with 86% accuracy. These associations were primarily driven by temperature, water density, salinity, and nutrients such as phosphate and nitrate. Our findings showed a clear stratification of microbial communities across pelagic zones, with temperature as the main factor driving the structure in epipelagic and mesopelagic layers, while salinity and density exerted greater influence in the deeper bathypelagic communities. Temporal and spatial variations, particularly between 2019 and 2021, in regions influenced by the Cabo Frio upwelling and Rio de la Plata plume, further highlighted the impact of regional and local oceanographic processes on community dynamics. The associations from deeper waters harbored more diverse microbial assemblages, and shallow waters, on the other hand, possess higher absolute abundance of microbial cells, suggesting niche specialization across depths. This study underscores the importance of environmental gradients as well as local oceanographic processes in shaping microbial diversity, providing valuable insights into the ecological dynamics of the SB, which are essential for understanding the potential impacts of human activities, such as oil and gas exploration and production, on these critical marine ecosystems.

microbiology↗

bioRxiv2025

Promiscuous endosymbionts in deep-sea corals and crinoids are shaped by nitrogen cycling

Crinoids are commonly associated with corals, but whether they physiologically interact is unclear. Like corals, crinoids host symbiotic microorganisms but little is known about the crinoid microbiome. Here, we reveal the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and, notably, their associated feather star crinoid, Koehlermetra (of the family Thalassometridae) in the Campos Basin, Brazil. We showed that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae interchangeably inhabit the internal and external structures of the corals and crinoid, indicating promiscuity in symbioses. The metagenome-assembled genome of the novel and dominant Endozoicomonas promiscua sp. nov. suggest that these symbionts may drive dissimilatory nitrate reduction to ammonia, which could be a source of energy for ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae. Thus, nitrogen cycling may determine the microorganisms that are hosted by deep-sea corals, which may be provided by their associated crinoids. These findings provide important insight about the complex ecological interactions that could lead to promiscuous symbiosis. TeaserDeep-sea corals and crinoids share symbiotic microbes that cycle nitrogen, potentially supporting each other in the nutrient-poor deep sea.

microbiology↗