Diversity of Culturable Bacteria from the Coral Reef Areas in the South China Sea and Their Agar-Degrading Abilities.

The South China Sea (SCS) is abundant in marine microbial resources with high primary productivity, which is crucial for sustaining the coral reef ecosystem and the carbon cycle. Currently, research on the diversity of culturable bacteria in the SCS is relatively extensive, yet the culturable bacteria in coral reefs has been poorly understood. In this study, we analyzed the bacterial community structure of seawater samples among Daya Bay (Fujian Province), Qionghai (Hainan Province), Xisha Islands, and the southern South China Sea based on culturable methods and detected their abilities for agar degradation. There were 441 bacterial strains, belonging to three phyla, five classes, 43 genera, and 101 species, which were isolated by marine agar 2216E (MA; Becton Dickinson). Strains within Gammaproteobacteria were the dominant group, accounting for 89.6% of the total bacterial isolates. To investigate vibrios, which usually correlated with coral health, 348 isolates were obtained from TCBS agar, and all isolates were identified into three phylum, three classes, 14 orders, 25 families, and 48 genera. Strains belonging to the genus Vibrio had the greatest number (294 strains), indicating the high selectivity of TCBS agar for vibrios. Furthermore, nineteen strains were identified as potentially novel species according to the low 16S rRNA gene similarity (<98.65%), and 28 strains (15 species) had agar-degrading ability. These results indicate a high diversity of culturable bacteria in the SCS and a huge possibility to find novel and agar-degrading species. Our study provides valuable microbial resources to maintain the stability of coral ecosystems and investigate their roles in the marine carbon cycle.

Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea.

Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains. Less CAZymes were organized more PULs, indicating highly efficiently polysaccharides utilization in Rossellomorea. Meanwhile, PUL0459, PUL0460 and PUL0316 related to agar degradation, and exolytic beta-agarase GH50, endo-type beta-agarase GH86 and arylsulfatase were identified in the genome of strain DA94. We verified that strain DA94 can degrade agar to form a bright clear zone around the bacterial colonies in the laboratory. Moreover, the carotenoid biosynthetic pathways were proposed, which may be responsible for orange-pigment of Rossellomorea sp. DA94. This study represents a thorough genomic characterization of CAZymes repertoire and carotenoid biosynthetic pathways of Rossellomorea, provides insight into diversity of related enzymes and their potential biotechnological applications.

Production of neoagarobiose from agar through a dual-enzyme and two-stage hydrolysis strategy.

The oligosaccharides from agar hydrolysis have special biological activities, and exhibit application prospects in cosmetic, food and pharmaceutical industry. In this study, two novel ß-agarases (AgaA and AgaB) were screened and characterized. It was found that the AgaA was an endo-type agarase which could efficiently hydrolyzed agar or agarose to form neoagarobiose (NA2), neoagarotetraose (NA4) and neoagarohexaose (NA6), while the AgaB was an exo-type and bifunctional enzyme that showed activities towards both agarose and porphyran. Based on the properties of the two enzymes, we developed modular strategy for enzymatic production of neoagarobiose through a two-stage hydrolysis reaction. The cheap substrate agar was first liquefied by AgaA at high temperature to form neoagaroligosaccharides, which together with the sulfated polysaccharides were homogenized by AgaB to form neoagarobiose as the final product. High concentration of agar (10 g/L) was almost completely converted into neoagarobiose with high purity.

Recombinant ß-agarases: insights into molecular, biochemical, and physiochemical characteristics.

Agarases (agarose 4-glycanohydrolase; EC 3.2.1.81) are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, ß-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of ß-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant ß-agarases. These recombinant ß-agarases have wide range of industrial applications due to its improved catalytic efficiency and stability in tough environments with ease of production on large scale. In this review, we have perused different types of recombinant ß-agarases in consort with their molecular, physiochemical, and kinetic properties in detail and the significant features of those agarases are spotlighted. From the literature reviewed after 2010, we have found that the recombinant ß-agarases belonged to the families GH16, GH39, GH50, GH86, and GH118. Among that, GH39, GH50, and GH86 belonged to clan GH-A, while the GH16 family belonged to clan GH-B. It was observed that GH16 is the largest polyspecific glycoside hydrolase family with ample number of ß-agarases and the families GH50 and GH118 were found to be monospecific with only ß-agarase activity. And, out of 84 non-catalytic carbohydrate-binding modules (CBMs), only CBM6 and CBM13 were professed in ß-agarases. We witnessed a larger heterogeneity in molecular, physiochemical, and catalytic characteristics of the recombinant ß-agarases including molecular mass: 32-132 kDa, optimum pH: 4.5-9, optimum temperature 16-60 °C, K M: 0.68-59.8 mg/ml, and V max: 0.781-11,400 U/mg. Owing to this extensive range of heterogeneity, they have lion's share in the multibillion dollar enzyme market. This review provides a holistic insight to a few aspects of recombinant ß-agarases which can be referred by the upcoming explorers to this area.

Isolation of a novel Saccharophagus species (Myt-1) capable of degrading a variety of seaweeds and polysaccharides.

A bacterial strain, Myt-1, was isolated in Toyama Bay in Toyama Prefecture, Japan. Myt-1 was capable of reducing the thalli of various seaweed species to single cell detritus particles. A 16S rDNA homology search revealed that the closest relative of Myt-1 was Saccharophagus degradans 2-40 (CP000282; 100% similarity), which was first isolated in Chesapeake Bay in Virginia, USA. The Myt-1 strain was capable of degrading more than 10 polysaccharides, almost all of which were also degraded by S. degradans 2-40. Analyses of alginase gene DNA sequence homology, DNA-DNA homology, and zymogram analysis of obtained polysaccharidases suggested that Myt-1 was a new species of Saccharophagus. Thus, Myt-1 is only the second species in this genus, which has contained only one strain and species since 1988, and was tentatively designated Saccharophagus sp. Myt-1. Myt-1 has considerable potential for reducing the volume of seaweed wastes, and for producing functional materials from seaweed substrate.