Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria

Abstract

Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.

In silico identification of bacterial seaweed-degrading bioplastic producers

“…Levulinic acid produced from acid pre-treated Kappaphycus (red alga) cell wall polysaccharide [26] Bacillus megaterium Acid-treated and untreated Gelidium amansii (red alga) [27] Cupriavidus necator Acid pretreatment and enzymatic saccharification of brown seaweed (Sargassum sp.) [28] Saccharophagus degradans 2-40 Gelidium amansii (red alga) [29] Hydrogenophaga UMI-18 Alginate of Macrocystis pyrifera (brown alga) [30] Cobetia sp. Alginate or waste of Laminaria sp.…”

The Structure and Function of the Sargassum fusiforme Microbiome under Different Conditions

“…Some genera were reported to decompose algal polysaccharides, such as Vibrio [40], Alteromonas [41], and Sphingomonas [42]. Vibrio is widespread in marine water, and most of them (>70%) can encode alginate lyases [13]. The isolation of Vibrio spp.…”

“…To detect candidate PDE genes distributed in Sargassum-associated bacteria, we implemented a method previously used to combine sequence alignment and domain search [13]. Reference PDE-related protein sequences were collected from the CAZyme database and literature mining [14].…”

“…Many new PDEs have been purified, and activity assays were performed from marine bacteria [12]. Genome mining can also detect candidate PDEs by a curated reference database [13]. The CAZy database is a knowledge-based resource widely used for annotating carbohydrate-active enzymes [14].…”

Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata

“…In marine pelagic systems or coastal ecosystems, fungi have received far less attention than in terrestrial systems (∼1,900 documented marine species compared to over 100,000 documented terrestrial species) ( Hyde et al, 1998 ; Ortega-Arbulú et al, 2019 ), and marine fungal degradation has received far less attention than marine bacterial OM degradation. Fungal pathways for kelp degradation are yet to be explored, whereas kelp degradation by bacteria (Bacteroidetes, Verrucomicrobia, Planctomycetes, Gammaproteobacteria, and Chlamydiae) has been intensively investigated ( Sakai et al, 2003 ; Bengtsson et al, 2011 ; Silchenko et al, 2013 ; Sichert et al, 2020 ; Sun et al, 2021 ). Bacteria account for 60% ( Sichert et al, 2020 ) to 90% ( Koop et al, 1982 ) of kelp detritus degradation.…”