Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative β-agarase

Agarose Degrading Potential and Whole Genome Sequence Analysis of Marine Bacterium Aliagarivorans sp. Strain DM1 Isolated from the Arabian Sea

In recent years, agar-degrading bacteria have gained significant interest due to their biotechnological, environmental, microbiological, and industrial applications. Agar poses challenges such as marine waste accumulation, difficult industrial processing, limited natural degradability, and sustainability concerns due to high demand and overharvesting of red algae. The present study addresses the need for efficient agar-degrading microorganisms by isolating Aliagarivorans sp. strain DM1 from biofilm on fabric surfaces in the intertidal regions of the Arabian Sea, India. Phylogenetic analysis revealed that strain DM1 is closely related to Aliagarivorans taiwanensis AAT1T, and it exhibited significant agar-degrading activity on Zobell marine agar plates. Whole genome sequencing of Aliagarivorans sp. strain DM1, conducted using the Illumina NovaSeq platform, yielded a genome size of 4,898,415 bp with an average G + C content of 53.3%. The genome includes 4,518 predicted protein-coding genes (CDS), 86 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes, with thirteen predicted agarases identified. The highest enzyme activity recorded was 51.00 U mL-1 on the 6th day of incubation using 10% inoculum, with optimal conditions of pH 8-9, 0.8 M NaCl, and temperatures between 50 and 60 °C. These findings underscore the promise of Aliagarivorans sp. strain DM1 in developing efficient enzymatic processes that can be applied in various biotechnological and industrial fields, including waste management and agaro-oligosaccharide production. Furthermore, strain DM1 possesses several key characteristics that enhance its adaptability and utility in marine and industrial applications, surpassing closely related strains in enzyme stability, environmental tolerance, and industrial versatility.

Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer

This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.

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.

Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria

Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.