Biology subjects

Romano, R. G.

Publications and source records attributed to Romano, R. G..

4 recordsLinked to original sources

bioRxiv2025

Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean

BackgroundThe pelagic environment may present a mosaic of biogeographical domains that regional oceanographic processes can influence. Here, a coastal-to-open ocean microbiome investigation was conducted on 64 water samples from the Santos Basin (SB), South Atlantic Ocean. Using metagenomics and machine learning approaches, we assessed the diversity and distribution of pelagic microbes, identified key bacterial and archaeal taxa, and inferred their ecosystem functions. ResultsUnsupervised machine learning revealed a clear spatial and vertical (light availability) distribution pattern across SB, with some indicator taxa previously observed in other marine waters. Supervised learning further revealed that environmental variables, notably phosphate, salinity, and nitrate, which are key markers of local upwelling and the La Plata River plume, are primary drivers of microbial community structure. Furthermore, we recovered 307 metagenome-assembled genomes with 45% of Archaea and 42% of Bacteria possible new taxa. In terms of functionality, the SB dataset revealed a pelagic ecosystem resembling typical marine (e.g., Atlantic Ocean) waters, with photoautotrophs and nitrogen fixers in the photic zone and different autotrophic pathways in the aphotic environment. Surprisingly, the SB dataset revealed genes for CO bio-oxidation and algal dimethylsulfoniopropionate (DMSP) degradation at all depths. Furthermore, we observed potential non- cyanobacterial diazotrophs in dark water. ConclusionsOur results revealed that the SB represents a unique ecosystem with local oceanographic processes shaping the distribution of diverse and uncharacterized microbiomes. Additionally, these findings highlight the importance of mixotrophic microbes in SB biogeochemical cycles. This massive investigation of the SB pelagic microbiome provided knowledge-based data for understanding local ecosystem health, services, and dynamics, which are essential for future sustainable ocean management.

microbiology↗

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↗

bioRxiv2021

Diversity of free-living prokaryotes on terrestrial and marine Antarctic habitats

Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. In order to explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly by thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa in comparison to the habitats from the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.

microbiology↗

bioRxiv2020

BATHYARCHAEOTA OCCURRENCE IN SHALLOW MARINE METHANE-RICH SEDIMENTS (SACO DO MAMANGUA, RIO DE JANEIRO, BRAZIL)

Methane gas (CH4) reservoirs have previously been reported in tropical marine sediments of Saco do Mamangua ria (Rio de Janeiro, Brazil). It is known that a methane microbiome can be established in methane seeps sites; however, they are still poorly characterised. In this study, we aimed to investigate the spatial and vertical distribution of the bacterial and archaeal composition and the community structure in the sediments of Saco do Mamangua ria. For this purpose, we collected sediment samples through 100 cm long gravity corer at three different sites and performed community analysis based on 16S rRNA gene sequencing, quantification of the methyl coenzyme M reductase-encoding gene (mcrA) and geochemical analysis, including CH4 stable isotope. Our results revealed a biogenic trend for CH4 isotopic signature and a high proportion of archaeal sequences assigned as Bathyarchaeota, with a spatial distribution throughout the inner areas of the channel and the deepest strata. OTUs classified within Bathyarchaeota and Chloroflexi (Dehalococcoidia) showed positive correlation with methane concentrations, sediment depth and oxidation-reduction potential. Due to their prevalence in the microbial community, we also performed phylogenetic analysis to understand the closeness of our Bathyarchaeota OTUs with Bathyarchaeota subgroups, and the results demonstrated a close relationship particularly with Bathy-8 and Bathy-13, which possess genes for acetogenesis and methanogenesis. Although direct relations between microbial populations and the biogenic methane emissions in Saco do Mamangua cannot be assured, our results emphasize the importance of further investigations about the potential role of Bathyarchaeota in the carbon cycling in methane-rich tropical shallow ecosystems.

microbiology↗