Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments.

Saara Suominen,Jaap S Sinninghe Damsté,Daan M Van Vliet,Marcel T J Van Der Meer,Irene Sánchez-Andrea,Laura Villanueva

doi:10.3389/fmicb.2021.628301

Abstract

Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.

Highlights

Marine sediments are a living ecosystem (Parkes et al, 2014), containing roughly as many cells as found in the oceans and soils (Kallmeyer et al, 2012)
Sediments from the bottom of the sulfate-reducing zone, located in the 20–30 cm horizon below sea floor (Piker et al, 1998; Jørgensen et al, 2020), and with interesting target groups based on 16S rRNA amplicon sequencing, were selected as inocula and slurries were prepared without the addition of sulfate in order to induce highly reduced conditions (Supplementary Table S3)
We investigated the microbial communities potentially responsible for the degradation of complex algal organic matter (OM) sources originating from marine anoxic sediments

Summary

Introduction

Marine sediments are a living ecosystem (Parkes et al, 2014), containing roughly as many cells as found in the oceans and soils (Kallmeyer et al, 2012). Microbial communities living in marine sediments are responsible for driving the sedimentary biogeochemical cycles (Jørgensen, 2006), including the cycling of a large organic matter (OM) reservoir (Mackenzie et al, 2004). Most members of these microbial communities remain uncultured and the details. Initial degraders produce and export extracellular enzymes for the degradation of complex organic polymers such as carbohydrates and proteins to oligomers or monomers of sugars and amino acids (Arnosti, 2011) These monomers are fermented to intermediate compounds like volatile fatty acids (VFAs) and alcohols. In the terminal stages of OM degradation acetate or hydrogen can be oxidized by microorganisms utilizing terminal electron acceptors (TEAs) like sulfate or utilized by methanogens to produce methane (Arndt et al, 2013)

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