# Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities

## TL;DR

This paper characterizes a cold-adapted marine bacterium and its role in promoting growth of Antarctic algae through genomic and functional analysis.

## Contribution

The study provides a detailed genomic and phylogenetic analysis of Pseudosulfitobacter pseudonitzschiae and its functional role in algal morphogenesis.

## Key findings

- The genome of P. pseudonitzschiae BPC-C4-2 contains 5,380 coding sequences and multiple RNA genes, suggesting metabolic flexibility.
- A sox gene cluster involved in sarcosine oxidation and DMSP degradation was identified, indicating functional adaptations to cold environments.
- Affinity propagation clustering improved phylogenetic placement of P. pseudonitzschiae within a taxonomically complex group.

## Abstract

Pseudosulfitobacter pseudonitzschiae is a species within the genus Pseudosulfitobacter, which belongs to the Roseobacteraceae. This family is closely associated with algae and is essential to marine ecosystems, particularly through interactions with phytoplankton. Notably, this bacterium can produce bioactive compounds that influence microbial dynamics and algal growth in marine environments. In addition to essential nutritional factors, the marine green macroalgal genus Ulva (Chlorophyta) relies on a combination of regulatory morphogenetic compounds produced by its associated epiphytic bacteria to achieve proper morphogenesis. Since P. pseudonitzschiae is rarely described and phylogenetic clustering within this genus is challenging, we conducted phylogenetic and genomic analyses to better resolve its taxonomic position and to explore its functional potential in the Antarctic environment.

P. pseudonitzschiae BPC-C4-2 was isolated and integrated into a tripartite model system alongside Maribacter sp. BPC-D8 (CP128187.1) and Ulva sp. UPC-109 (PP091299.1). This biosystem was designed to study the mechanisms of cold-water adaptation involved in the morphogenetic development of the genus Ulva.

The hybrid genome assembly of P. pseudonitzschiae BPC-C4-2 consisted of seven contigs totaling 5,450,390 bp, with a GC content of 59.0%. Genome annotation identified 5,380 coding sequences (CDSs), 6 rRNA genes, 85 tRNA genes, and 1 tmRNA. The relatively large number of coding sequences and RNA genes observed may reflect an expanded genetic toolkit that enables metabolic flexibility and stress tolerance, potentially supporting adaptation to the extreme conditions of Antarctic and cold-water environments.

Given the taxonomic complexity within the bacterial family, both 16S rRNA gene sequencing and average nucleotide identity (ANI) analyses were conducted. Using affinity propagation clustering, these analyses enabled a more robust phylogenetic placement of P. pseudonitzschiae within this challenging group, providing deeper ecological and evolutionary insights.

In this study, we searched for gene clusters associated with metabolic adaptations. Functionally, the genome harbors a modularly organized sox gene cluster involved in the sarcosine oxidation pathway and dimethylsulfoniopropionate (DMSP) degradation. Additional pathways involved in osmolyte metabolism and methylation were also identified and found to be phylogenetically distinct from closely related species.

Our findings provide the basis for a cold-water bioassay system to study the morphogenesis of Ulva collected from polar regions, in association with Maribacter sp. BPC-D8 and P. pseudonitzschiae BPC-C4-2. Genomic analyses of P. pseudonitzschiae BPC-C4-2 provide insights into its revised phylogeny based on affinity propagation clustering, along with a detailed analysis of genes involved in key metabolic pathways.

The online version contains supplementary material available at 10.1186/s12864-026-12626-w.