Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries

Abstract

Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems. ImportanceEstuaries are dynamic transition zones where microbial communities play key roles in nutrient cycling and ecosystem functioning. This study provides new insights into the distribution of Actinobacteriota families and their responses to salinity and nutrient gradients in two major U.S. estuaries, the Chesapeake and Delaware Bays. We characterized the potential roles of Actinobacteriota in biogeochemical processes and secondary metabolite production, which may influence broad microbial interactions. These bacteria may also serve as a source of novel bioactive compounds, including antibiotics. By integrating omic and environmental data, this work advances our understanding of Actinobacteriota adaptations and their ecology in estuarine environments.