Proteomic Assessment of Polar Bacteria Phylogeny and Functional Shifts During POM Degradation at 0°C

Polar marine bacterial community and metabolic response was tracked over a ten-day shipboard incubation experiment at 0°C, measured by high-mass accuracy tandem mass spectrometry. Planktonic bacteria were collected from Bering Strait surface waters and bottom water of the Chukchi Sea to target bacterial communities with unique metabolic capacities for particulate organic matter (POM) decomposition. From each location, resident POM was concentrated and amended as a treatment to one incubation, with the second as a control. Metagenomics was completed on both incubations and metaproteomics expression was tracked as a function of time.

The Bering Strait surface water proteomic signature was dominated by microbial classes Alphaproteobacteria (31%), Gammaproteobacteria (30%) and Flavobacteriia (22%) . TonB-dependent transporter (TBDT) receptors accounted for ~20% of the proteins that exhibited an increased abundance before incubation, a quarter of which were attributed to siderophore transport, an important iron chelator. Flavobacteriia and Gammaproteobacteria (48% and 39%, respectively) regulated expression of the TBDT receptors. ATP-binding cassette (ABC) transporter protein expression was controlled by the bacterial family Rhodobacteraceae and included functional groups specific to the transport of polyamines, peptides and branched-chain amino acids.

By day 10, 63 proteins in the POM amended incubation increased abundance relative to the control experiment. Bacterial class Flavobacteriia dominated this signature (64%) with TBDT activity, iron-sulfur binding, glutamine biosynthesis, and calcium ion binding. 88 proteins were uniquely identified in the control experiment at day 10, and the population responsible for this set of expressed proteins differed from that of the POM addition experiment. This study demonstrates the potential to use proteomics to link the structures and functions of natural marine bacterial communities.