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

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.

Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment

“…An interaction network analysis showed that Bacteroidetes , Nitrospirae , Planctomycetes , Cyanobacteria , Firmicutes , Zixibacteria , and Calditrichaeota were significantly related to the sediment phosphorus and nitrogen cycles (Figure B). Bacteroidetes , Nitrospirae , Cyanobacteria , Planctomycetes , Chloroflexi , and Firmicutes were the dominant gates in sediments (Figure S7) and were mainly involved in sediment carbon, nitrogen, and sulfur metabolism. , Chloroflexi , Planctomycetes , Bacteroidetes , and Cyanobacteria degraded organic pollutants and participated in organic carbon turnover. − Nitrospirae , an important microbial component of the nitrogen cycle in sediments, were mainly involved in nitrification and denitrification processes. , Our study findings agreed with these previous reports, indicating that tritium and carbon-14 exposure affected the sediment nitrogen cycle function by changing the sediment abundance of nitrogen cycle-related microorganisms.…”

Denitrification, anammox, and DNRA in oligotrophic continental shelf sediments

“…The lower abundance of Proteobacteria could be related to the higher relative abundance of Planctomycetota (14.8 ± 5.1%), a phylum in which both denitrifiers and anammox bacteria have been identified. Curiously, previous studies on shelf sediments found a relatively lower proportion of Planctomycetota, particularly in more eutrophic sediments (Zhu et al 2013; Suominen et al 2021). High abundances of Planctomycetota were recently detected in the deepest hadal sediments (Schauberger et al 2021).…”

“…Heterotrophic Proteobacteria are the key members of denitrification in shelf sediments (Brettar et al 2001; Liu et al 2003; Hunter et al 2006; Marchant et al 2017). However, the relative abundance of Proteobacteria (average of 18.4 ± 6.1%) in oligotrophic NE New Zealand shelf sediments was substantially lower than those in other eutrophic shelf sediments with higher nutrient and organic matter content, such as the Baltic Sea (30%), Atlantic (61%), and South China Sea (45%) (Schauer et al 2010; Zhu et al 2013; Suominen et al 2021). The lower abundance of Proteobacteria could be related to the higher relative abundance of Planctomycetota (14.8 ± 5.1%), a phylum in which both denitrifiers and anammox bacteria have been identified.…”

Organic sulfur from source to sink in low‐sulfate Lake Superior

“…Organic matter mineralization is conducted by many phyla that are extremely metabolically diverse and are not uncommon in lake sediments (Davis et al 2011). Chloroflexi, especially classes observed here like Anaerolineae and Dehalococcoidia, are important initial fermenters for complex compounds (Suominen et al 2021). Members of Verrucomicrobiota may be specialists (Williams et al 2021), for example, by consuming sulfated polysaccharides (Orellana et al 2022) that appear to be concentrated in Lake Superior (Fig.…”