Proteome Analyses of Soil Bacteria Grown in the Presence of Potato Suberin, a Recalcitrant Biopolymer

Abstract

Suberin is a complex lipidic plant polymer found in various tissues including the potato periderm. The biological degradation of suberin is attributed to fungi. Soil samples from a potato field were used to inoculate a culture medium containing suberin as the carbon source, and a metaproteomic approach was used to identify bacteria that developed in the presence of suberin over a 60-d incubation period. The normalized spectral counts of predicted extracellular proteins produced by the soil bacterial community markedly decreased from day 5 to day 20 and then slowly increased, revealing a succession of bacteria. The population of fast-growing pseudomonads declined and was replaced by species with the ability to develop in the presence of suberin. The recalcitrance of suberin was demonstrated by the emergence of auxotrophic bacteria such as Oscillatoria on the last days of the assay. Nevertheless, two putative lipases from Rhodanobacter thiooxydans (I4WGM2) and Myxococcus xanthus (Q1CWS1) were detected in the culture supernatants, suggesting that at least some bacterial species degrade suberin. When grown in suberin-containing medium, R. thiooxydans strain LCS2 and M. xanthus strain DK 1622 both produced three lipases, including I4WGM2 and Q1CWS1. These strains also produced other proteins linked to lipid metabolism, including fatty acid and lipid transporters and β-oxidation enzymes, suggesting that they participate in the degradation of suberin. However, only the R. thiooxydans strain appeared to retrieve sufficient carbon and energy from this recalcitrant polymer in order to maintain its population over an extended period of time.

“Omics” Technologies for the Study of Soil Carbon Stabilization: A Review

“…More recalcitrant biopolymers such as lignin, cutin, and suberin persist in soils as they take longer to degrade, where degradation requires specific enzymes produced by unique members of the microbial population, typically attributed fungi (Kramer et al, 2016;Arcand et al, 2017;Müller et al, 2017). Sidibé et al (2016) conducted an incubation study and characterized the soil metaproteome to evaluate whether addition of recalcitrant suberin to the soil can enrich specific bacterial members of soil microbial communities. Counts of protein spectral features indicated a decline in the proportion of fast-growing bacteria and enrichment of particular bacterial constituents of the soil microbial community that can specifically degrade suberin (as suggested by the observation of putative bacterial lipases and other proteins linked to lipid metabolism), providing new insight into this fundamental process in carbon-cycling in soils (Sidibé et al, 2016).…”