Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment

Abstract

The marine environment contains a large diversity of sulfated polysaccharides and other glycopolymers. Saccharolytic microorganisms degrade these compounds through hydrolysis, which includes the hydrolysis of sulfate groups from sugars by sulfatases. Various marine bacteria of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum have exceptionally high numbers of sulfatase genes associated with the degradation of sulfated polysaccharides. However, thus far no sulfatase-rich marine anaerobes are known. In this study, we aimed to isolate marine anaerobes using sulfated polysaccharides as substrate. Anoxic enrichment cultures were set up with a mineral brackish marine medium, inoculated with anoxic Black Sea sediment sampled at 2,100 m water depth water and incubated at 15°C ( in situ T = 8°C) for several weeks. Community analysis by 16S rRNA gene amplicon sequencing revealed the enrichment of Kiritimatiellaeota clade R76-B128 bacteria in the enrichments with the sulfated polysaccharides fucoidan and iota-carrageenan as substrate. We isolated two strains, F1 and F21, which represent a novel family within the order of the Kiritimatiellales . They were capable of growth on various mono-, di-, and polysaccharides, including fucoidan. The desulfation of iota-carrageenan by strain F21 was confirmed quantitatively by an increase in free sulfate concentration. Strains F1 and F21 represent the first marine sulfatase-rich anaerobes, encoding more sulfatases (521 and 480, 8.0 and 8.4% of all coding sequences, respectively) than any other microorganism currently known. Specific encoded sulfatase subfamilies could be involved in desulfating fucoidan (S1_15, S1_17 and S1_25) and iota-carrageenan (S1_19). Strains F1 and F21 had a sulfatase gene classification profile more similar to aerobic than anaerobic sulfatase-rich PVC bacteria, including Kiritimatiella glycovorans , the only other cultured representative within the Kiritimatiellaeota . Both strains encoded a single anaerobic sulfatase-maturating enzyme which could be responsible for post-translational modification of formylglycine-dependent sulfatases. Strains F1 and F21 are potential anaerobic platforms for future studies on sulfatases and their maturation enzymes.

Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea

“…However, it should be noted these gene clusters, that formed very long branches in the inferred phylogenetic tree, are in a badly resolved region of the tree also containing MBNT15, Acidobacteria, Actinobacteria and Verrucomicrobia (Supplementary Figure S1 for full description), which precludes a safe identification at present. Although, Kiritimatiellaeota phylum is not well described (Spring et al, 2016), strains from this group were recently identified as anaerobic degraders of sulfated polysaccharides compounds (Van Vliet et al, 2019). Such compounds are produced by marine algae and are generally abundant in marine waters (Helbert, 2017).…”

Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers

“…Kiritimatiellae are widespread and abundant in anoxic environments such as the intestinal tract of vertebrate animals [10,11] and marine or hypersaline sediments [9,12]. Our marine isolates, strains F1 T and F21 T , were found to represent a novel family-level Kiritimatiellae lineage [8] previously marked as ubiquitous yet uncultured (R76-B128) [13]. Currently, the only described species of the Kiritimatiellae class is Kiritimatiella glycovorans L21-Fru-AB T , a moderate halophile isolated from a hypersaline microbial mat [9].…”

“…K. glycovorans L21-Fru-AB T was ordered from the DSMZ (Braunschweig, Lower Saxony, Germany). Strains F1 T and F21 T were cultured in a basal anoxic bicarbonate-buffered marine medium described previously [8] containing 25 g L −1 NaCl for optimum salinity for growth, with 10 mM L-fucose as the substrate, unless mentioned otherwise. K. glycovorans was cultured in the same basal medium except for containing 60 g L −1 NaCl, with 5 mM D-glucose as the substrate.…”

“…In a previous study, we isolated two anaerobic marine bacteria from anoxic Black Sea sediment, strains F1 T and F21 T , which grew on sulfated polysaccharides and belonged to the Kiritimatiellae class of the Verrucomicrobiota phylum [8]. This class was formerly known as Verrucomicrobiota subdivision 5 and initially proposed to represent a novel phylum [9].…”

“…Like several PVC bacteria described before [5,6,14,15], K. glycovorans was proposed to degrade sulfated polysaccharides in situ based on the presence of glycoside hydrolase and sulfatase genes in the genome, although stable growth could not be achieved in vitro [9]. In contrast, strains F1 T and F21 T were able to grow on complex sulfated polysaccharides, such as fucoidan, and notably encoded exceptionally high numbers of sulfatases (521 and 480, respectively) [8]. Here, we present a comprehensive characterization of both strains.…”