Metaproteomics Reveals Similar Vertical Distribution of Microbial Transport Proteins in Particulate Organic Matter Throughout the Water Column in the Northwest Pacific Ocean.

Ling-Fen Kong,Yan-Bin He,Ke-Qiang Yan,Lin Lin,Da-Zhi Wang,Hong-Kai Xu,Zhang-Xian Xie,Si-Qi Liu

doi:10.3389/fmicb.2021.629802

Abstract

Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach. The proportion of transport proteins was relatively high at the bottom of the euphotic zone (200 m), indicating that this layer was the most active area of microbe-driven POM remineralization in the water column. In the upper-twilight zone, the predicted substrates of the identified transporters indicated that amino acids, carbohydrates, taurine, inorganic nutrients, urea, biopolymers, and cobalamin were essential substrates for the microbial community. SAR11, Rhodobacterales, Alteromonadales, and Enterobacteriales were the key contributors with the highest expression of transporters. Interestingly, both the taxonomy and function of the microbial communities varied among water layers and sites with different environments; however, the distribution of transporter types and their relevant organic substrates were similar among samples, suggesting that microbial communities took up similar compounds and were functionally redundant in organic matter utilization throughout the water column. The similar vertical distribution of transport proteins from the euphotic zone to the upper twilight zone among the contrasting environments indicated that solubilized POM rather than DOM was the preferable carbon and energy sources for the microbial communities.

Highlights

The global carbon cycle is strongly driven by the biological pump in the ocean, which involves a series of processes transferring carbon from surface waters to the ocean interior in the form of particulate organic matter (POM, >0.7 μm) (Jiao et al, 2010; Giering et al, 2014)
12 POM samples from both euphotic and upper-twilight zones were collected in three contrasting environments in the northwest Pacific Ocean (Supplementary Figure 1)
We focused on the transport proteins from bacteria and archaea due to their important roles in the utilization of solubilized POM

Summary

Introduction

The global carbon cycle is strongly driven by the biological pump in the ocean, which involves a series of processes transferring carbon from surface waters to the ocean interior in the form of particulate organic matter (POM, >0.7 μm) (Jiao et al, 2010; Giering et al, 2014). The solubilized POM in the oceanic water column represents DOM freshly solubilized from POM by microbes within the microenvironment of POM while the labile DOM, turned over by bacteria within days, is referred as the vast pool of DOM in the deep ocean (Bergauer et al, 2018). A recent study suggests that the heterotrophic microbes (size between 0.2 and 0.8 μm) rely largely on solubilized POM rather than on autochthonous DOM as the carbon and energy sources in the mesopelagic and bathypelagic waters (Bergauer et al, 2018)

Methods

Results

Conclusion