# Dynamics and Eco‐Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness

## TL;DR

This study explores the seasonal and environmental patterns of nitrifiers in the Baltic Sea and identifies new archaea genomes that reveal their ecological and genomic traits.

## Contribution

Recovery of five novel ammonia-oxidizing archaea genomes and insights into their ecological and genomic uniqueness in the Baltic Sea.

## Key findings

- Nitrifiers are persistently abundant in aphotic waters with seasonal peaks in surface waters from late fall to early spring.
- Genomic analysis revealed high gene conservation and variation in genes related to environmental interactions and nitrogen/phosphorus metabolism.
- Nitrifier abundance is positively correlated with nutrients and negatively with solar radiation and chlorophyll.

## Abstract

Nitrification is widespread across marine systems, yet the ecological and evolutionary drivers shaping nitrifier populations remain largely unknown. The Baltic Sea, a brackish basin with pronounced gradients in salinity, oxygen, nutrients and strong seasonality, is a valuable model environment to investigate these questions. Here, we combined metagenomics and rRNA gene sequencing to characterise the spatiotemporal dynamics and genomic diversity of nitrifiers, alongside physicochemical measurements. Nitrifiers were persistently abundant throughout aphotic waters, with vertical niche partitioning and seasonal peaks in surface waters from late fall to early spring. The seasonal peaks were positively correlated with nitrite, nitrate and diverse other prokaryotes, and negatively correlated with solar radiation and chlorophyll. To probe the genomic basis of these ecological patterns of the numerically dominant nitrifier, we recovered five novel genomes of ammonia‐oxidising archaea through metagenomics of bulk samples and selective enrichments, including the dominant taxon from aphotic depths. Comparative genomics showed high gene conservation, with variation largely in genes linked to interactions with the external environment and nitrogen and phosphorus metabolism between central surface and deep types. Together, our study provides insights into niches of Baltic Sea nitrifiers and begins the process of understanding the mechanisms and functional implications of these patterns.

Nitrifiers in the Baltic Sea show persistent abundance in aphotic waters and late‐fall to winter photic zone increases positively correlated with nutrients and negatively with light and chlorophyll. Through selective enrichment, five novel ammonia‐oxidising archaea genomes were recovered, including the dominant aphotic taxon, which revealed overall high gene conservation and uniqueness related to external environment‐facing features.