Metagenomics Investigation of Agarlytic Genes and Genomes in Mangrove Sediments in China: A Potential Repertory for Carbohydrate-Active Enzymes

Abstract

Monosaccharides and oligosaccharides produced by agarose degradation exhibit potential in the fields of bioenergy, medicine, and cosmetics. Mangrove sediments (MGSs) provide a special environment to enrich enzymes for agarose degradation. However, representative investigations of the agarlytic genes in MGSs have been rarely reported. In this study, agarlytic genes in MGSs were researched in detail from the aspects of diversity, abundance, activity, and location through deep metagenomics sequencing. Functional genes in MGSs were usually incomplete but were shown as results, which could cause virtually high number of results in previous studies because multiple fragmented sequences could originate from the same genes. In our work, only complete and nonredundant (CNR) genes were analyzed to avoid virtually high amount of the results. The number of CNR agarlytic genes in our datasets was significantly higher than that in the datasets of previous studies. Twenty-one recombinant agarases with agarose-degrading activity were detected using heterologous expression based on numerous complete open-reading frames, which are rarely obtained in metagenomics sequencing of samples with complex microbial communities, such as MGSs. Aga2, which had the highest crude enzyme activity among the 21 recombinant agarases, was further purified and subjected to enzymatic characterization. With its high agarose-degrading activity, resistance to temperature changes and chemical agents, Aga2 could be a suitable option for industrial production. The agarase ratio with signal peptides to that without signal peptides in our MGS datasets was lower than that of other reported agarases. Six draft genomes, namely, Clusters 1–6, were recovered from the datasets. The taxonomic annotation of these genomes revealed that Clusters 1, 3, 5, and 6 were annotated as Desulfuromonas sp., Treponema sp., Ignavibacteriales spp., and Polyangiaceae spp., respectively. Meanwhile, Clusters 2 and 4 were potential new species. All these genomes were first reported and found to have abilities of degrading various important polysaccharides. The metabolic pathway of agarose in Cluster 4 was also speculated. Our results showed the capacity and activity of agarases in the MGS microbiome, and MGSs exert potential as a repertory for mining not only agarlytic genes but also almost all genes of the carbohydrate-active enzyme family.

Diversities and potential biogeochemical impacts of mangrove soil viruses

“…Thus, the biolysis of complex polysaccharides in soils and organism debris is essential for mangrove biomass recycling and critical in local and global carbon cycles. The biodegradation of polysaccharides is a complex process that requires the participation of multiple enzymes [57, 58]. Significantly, mangrove soil viruses encode abundant genes of CAZymes, including core hydrolysis enzymes (cellobiosidase, xylanase, chitinase, alpha-amylase, mannanase and endoglucanase) and auxiliary enzymes (polysaccharide deacetylase, pectinesterase and pectate lyase), that are essential for the degradation of various polysaccharides, indicating the full-scale capabilities of mangrove soil viruses in the biolysis of complex polysaccharides (Table 1).…”

Production of Neoagaro-Oligosaccharides With Various Degrees of Polymerization by Using a Truncated Marine Agarase

“…Agarose, the cell-wall component of marine algae, is a polysaccharide that consists of alternating disaccharide units of d-galactose and 3,6-anhydro-l-galactose (Ramos et al, 2016). Hydrolysis products of agarose, namely agaro-oligosaccharides (AOS) and neoagaro-oligosaccharides (NAOS), exhibit potential uses in food, pharmaceutical, and cosmetic industries (Chen et al, 2009;(Qu et al, 2018) and characterized through heterologous expression (Di et al, 2018). In the present study, we truncated AgaM1 and found that the truncated recombinant AgaM1 (trAgaM1) could hydrolyze agarose into NAOS with various DPs (NA4, NA6, NA8, NA10, and NA12) as end-products under specific reaction conditions.…”

“…agaM1 (GenBank accession number MG280837), a β-agarase gene, was isolated from mangrove sediment microbiome ( Qu et al, 2018 ) and characterized through heterologous expression ( Di et al, 2018 ). In the present study, we truncated AgaM1 and found that the truncated recombinant AgaM1 (trAgaM1) could hydrolyze agarose into NAOS with various DPs (NA4, NA6, NA8, NA10, and NA12) as end-products under specific reaction conditions.…”

One-Step Process for Environment-Friendly Preparation of Agar Oligosaccharides From Gracilaria lemaneiformis by the Action of Flammeovirga sp. OC4

“…On the other hand, algae, an inexpensive and abundant biomass, is attracting increasing attention because it can be used for the production of algae oligosaccharides that have better physiological activity and a higher value than algae polysaccharides (such as agar, carrageenan, and alginate). However, current studies are mostly focused on agarase (Kim et al, 2017, 2018; Qu et al, 2018; Schultz-Johansen et al, 2018), and little has been done in the direct and efficient preparation process of algae oligosaccharides from algae. Currently, algae oligosaccharides are prepared by a two-step process: step 1 is the extraction of algae polysaccharides from algae, which consumes a lot of strong acids and alkalis, diatomite and perlite, and produces useless algal dregs; step 2 is the degradation of polysaccharides by expensive agarases or strong acids, which can result in great pollution to the environment.…”