Novel approaches in genetics and systems biology of marine Roseobacter group bacteria

Introduction

Roseobacter group bacteria are a large and diverse group of Alphaproteobacteria that are abundant across marine ecosystems. They are known for their versatile metabolism and genome plasticity. Frequently, these bacteria interact with other marine organisms, especially algae. Therefore, they are thought to play an important role in mediating the marine carbon cycle. Since Roseobacter group bacteria have only been investigated in the past 30 years, many aspects of their physiology, ecology, and evolution are still unknown. Consequently, further studies on different Roseobacter group bacteria are required to better understand this important group of bacterioplankton.

Goals

Here, we aim to establish novel genetic tools and to investigate the metabolic network of three model strains from the Roseobacter group, with the dual goal of 1) enabling more sophisticated approaches for genetic modification and 2) improving our understanding of the physiology of these abundant marine bacteria.

Materials & methods

We focused our investigations on the three model strains Ruegeria pomeroyi, Phaeobacter inhibens, and Dinoroseobacter shibae. Using molecular cloning, transformation or conjugation, and high-throughput screening experiments, we tested different genetic constructs in all three bacteria. Furthermore, we generated comprehensive proteomics datasets for D. shibae grown under different conditions. Finally, we compared this dataset to proteomics datasets of P. inhibens to identify shared and divergent traits in the proteomes of these Roseobacter group bacteria.

Results

We generated a vector suite with different constitutive and inducible promoters that is functional across the three tested model strains. Furthermore, we characterized changes in the proteome of D. shibae on rich medium and minimal medium with different carbon sources. Finally, we identified the core and accessory proteomes of P. inhibens and report new insights on the regulation of catabolic and anabolic pathways in response to nutrient availability.

Summary

The establishment of novel genetic tools and the comparative analysis of comprehensive proteomics datasets highlight that Roseobacter group bacteria continue to be an exciting field of study and pave the way for further investigations on the fundamental biology and the application potential of these marine microorganisms.