# Structure and Spatial Heterogeneity of Chemosynthesis‐Based Deep‐Sea Archaeal and Bacterial Communities in Western South Atlantic

## TL;DR

This study explores deep-sea microbial communities in methane-rich cold seeps in the South Atlantic, revealing how geochemical factors shape these ecosystems.

## Contribution

The study provides the first detailed analysis of prokaryotic community structure and function in a poorly explored South Atlantic cold seep.

## Key findings

- Methane concentration and depth are the main drivers of archaeal and bacterial community structuring in the SMTZ.
- Sulfur- and nitrogen-related metabolisms dominate the functional potential of the microbiome.
- A core microbiome with widespread taxa, including Sulfophobococcus, accounts for a large proportion of community abundance.

## Abstract

Cold seeps are widespread deep‐sea ecosystems sustained by methane‐rich fluid seepage and host dense chemosynthesis‐based biological communities. In 2016, a methane‐driven chemosynthetic system was discovered on the Rio Grande Cone, in the Western South Atlantic Ocean, but the structure and drivers of its prokaryotic communities remained poorly understood. Here, we investigated archaeal and bacterial communities associated with deep‐sea sediments across three geographic areas (A, C, and E) and a vertical gradient of up to 18 m below the seafloor, encompassing sediment layers within and below the sulfate–methane transition zone (SMTZ). Community composition was assessed using high‐throughput sequencing of the 16S rRNA gene (V3‐V4 region), processed into amplicon sequence variants (ASVs), and related to local geochemical gradients using multivariate analyses. To disentangle the ecological responses of methane‐cycling taxa from the broader microbiome, the prokaryotic community was analyzed by contrasting the ANME‐SRB consortium with the remaining archaeal and bacterial taxa. Both groups exhibited significant spatial structuring across areas and sediment layers. Methane concentration and depth were the dominant drivers shaping both ANME‐SRB and the remaining prokaryotic community, with conductivity further influencing the latter. Core microbiome analysis revealed a small number of widespread taxa accounting for a large proportion of total community abundance, including an atypical dominance of the archaeal genus Sulfophobococcus. Functional predictions indicated a predominance of sulfur‐ and nitrogen‐related metabolisms, with no clear depth‐structured metabolic profiles across the SMTZ. Overall, our results highlight how local geochemical gradients shape both methane‐cycling and non‐methane‐cycling prokaryotic assemblages in a poorly explored South Atlantic cold seep, providing a baseline for future genome‐resolved investigations of microbial functioning in this system.

We report an extensive investigation of prokaryotic communities from a methane cold‐seep area in the Western South Atlantic Ocean (Southern Brazil) employing a broad sample set, including three distinct geographic areas (A, C and E) across a depth gradient (up to 18 m below the seafloor) related to the sulfate–methane transition zone (SMTZ). Results indicated differences in community composition among the surveyed areas, and from shallow to deeper sediment layers related to the SMTZ, which were mainly influenced by the methane gradients. Functional predictions revealed that bacterial and archaeal communities are predominantly involved in sulfur and nitrogen cycles, although no depth‐structured metabolic profiles were detected, revealing undescribed roles of microbial communities occurring in this poorly explored area, contributing to a deeper understanding of cold seeps' microbiota diversity and functioning.