3.1 Descriptions of the morphological, taxonomic, and genomics characteristics
A strain named YPW1 was isolated from mangrove sediments in Yanpu harbor. Strain YPW1 can be cultured on 2216E solid plates with yellow color and irregular circle. Agar collapse was observed around the strain, indicating the agar degradation by YPW1. Subsequently, the sequence of the 16S rRNA gene of strain YPW1 (accession no. MZ311580) showed 99.44% of similarity with that of M. mangrovi DD-13 (NR_109105.1), and strain YPW1 was also closest to M. mangrovi DD-13 according to the phylogenetic tree of 16S rRNA genes constructed by neighborhood-joining method (Fig. 1A). Therefore, strain YPW1 was assigned into Microbulbifer genus. The whole genome of strain YPW1 without any gap was obtained (Fig. 1B and Table 1). The genome size of strain YPW1 was 4,578,595 bp, and no plasmid was found. In addition, 12 rRNA genes, 52 tRNA genes, and 13 other ncRNA genes were annotated in the genome. Six genome islands with a mean length of 2,589,666 bp were also found. Two prophages were predicted in the genome of YPW1. The maximum values of ANI and DDH of ZHDP1 genome were respectively 90.36 and 68.1 and were lower than the thresholds (ANI < 95%-96%; DDH < 70%), indicating that YPW1 was a potential new species in genus Microbulbifer.
3.2 Polysaccharide utilization abilities of strain YPW1
Strain YPW1 possessed the abilities for the degradation and utilization of different polysaccharides, including agarose, alginate, xylan, starch, pullulan, cellulose, chitin, and pectate. one agarase, one alginate lyase, two xylanases, one amylase, two cellulases, one chitinase, and one pectate lyase were located in cytoplasm. In detail, five agarases, one alginate lyase, one xylanase, two amylases, one pullulanase, one cellulase, two chitinases, and two pectate lyases were secretory proteins. One agarase, one alginate lyase, one pullulanase, and two chitinases distributed on the cell membrane of strain YPW1. These results demonstrated that strain YPW1 can degrade various polysaccharides into oligosaccharide with low polymerization degrees and further produced monosaccharides (Fig. 2A).
Ten genomes from other strains belonged to Microbulbifer genus were analyzed and compared with strain YPW1. The gene numbers of AA, GH, GT, CE, PL, and CBM of YPW1 were obviously higher than those of other Microbulbifer strains, even higher than that of M. mangrovi DD-13, the most closet strain to YPW1 (Fig. 2B). Therefore, strain YPW1 possessed more versatile abilities for polysaccharide utilization than other representative strains belonged to Microbulbifer genus.
3.3 Denitrification ability of stain YPW1
According to the genomes from Microbulbifer genus, we found that most selected genomes had the denitrification ability (Table 2). In 9/11 of the selected genomes, including M. agarilyticus GP101, M. donghaiensis CGMCC 1.7063, M. hydrolyticus IRE-31, M. mangrovi DD-13, M. marinus CGMCC 1.10657, M. pacificus LD25, M. variabilis ATCC 700307, M. yueqingensis CGMCC 1.10658, and strain YPW1, possessed the genes of nitrate and nitrite reductases that can reduce nitrate to nitrite and then to nitric oxide. M. thermotolerans DAU221 only possessed nitrate reductases that can only reduce nitrate to nitrite. In addition, M. aggregans CCB-MM1 was not able to denitrify without any nitrate or nitrite reductase. However, strain YPW1 had not only nitrate and nitrite reductases but also nitric oxide (NO) reductase that can further reduce NO to nitrous oxide (N2O). No N2O reductase was found in the genome of YPW1. Therefore, N2O served as the end-product of the denitrification process of strain YPW1 (Fig. 2A and Table 2).