# Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays

## TL;DR

This study explores how microbial communities in two bays adapt to environmental changes through metabolic flexibility and functional redundancy.

## Contribution

The paper provides new insights into how environmental factors shape functional redundancy and metabolic potential in estuarine microbiomes.

## Key findings

- Microbial communities show high metabolic flexibility to utilize diverse energy sources.
- Functional redundancy varies with seasons, microbial lifestyles, and environmental factors like salinity and temperature.
- Gene expression patterns are influenced by environmental drivers such as phosphate and chlorophyll a levels.

## Abstract

Functional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbations.