Genomic insight into Aquimarina longa SW024T: its ultra-oligotrophic adapting mechanisms and biogeochemical functions

Abstract

BackgroundSouth Pacific Gyre (SPG) is the largest and clearest gyre in the world, where the concentration of surface chlorophyll a and primary production are extremely low. Aquimarina longa SW024T was isolated from surface water of the SPG center. To understand how this bacterium could survive in this ultra-oligotrophic oceanic environment and its function in biogeochemical cycle, we sequenced the genome of A. longa SW024T and performed extensive genomic analyses.MethodsGenomic DNA was extracted and sequenced using Illumina Hiseq 2000 and Miseq platform. Genome annotation, genomic comparison and phylogenetic analyses were performed with the use of multiple bioinformatics tools like: BLAST+ 2.2.24, Glimmer3.0, RAST server, Geneious 4.8.5, ClustalW2 and MEGA5. Physiological and morphological features were tested by bacterial culture, electron microscopy, fluorescence microscopy and exopolysaccharides extraction.ResultsAnalysis of seven Aquimarina genomes and 30 other genomes of Flavobacteriaceae isolated from seawater showed that most of the strains had low DNA G + C contents, and Aquimarina had larger genomes than other strains. Genome comparison showed varying genomic properties among seven Aquimarina genomes, including genome sizes and gene contents, which may warrant their specific adaptive strategies. Genome of A. longa SW024T was further compared with the genomes of two other Aquimarina species which were also isolated from the SPG and A. longa SW024T appeared to have much more genes related to replication, recombination and repair. As a copiotroph, A. longa SW024T is long in length, and possesses large genome size and diverse transporters. However, it has also evolved many properties to survive in the oligotrophic marine environment. This bacterium grew better on solid medium than in liquid medium, suggesting it may be liable to attach to particle surfaces in order to survive in the nutrient-limiting environment. Gliding motility and the capacity to degrade various polymers possibly allow the bacterium to grow on detritus particles and use polymeric substances as carbon and energy sources. Moreover, genes related to carbon, nitrogen, and sulfur metabolisms were identified, which showed that A. longa SW024T might be involved in various elemental cycles.ConclusionsGenomic comparison of Aquimarina genus exhibits comprehensive capabilities of the strains to adapt to diverse marine environments. The genomic characteristics of A. longa SW024T reveal that it evolves various strategies to cope with both copiotrophic and ultra-oligotrophic marine environment, which provides a better understanding of the survival abilities of bacteria in prevalent and even extreme oceanic environments. Furthermore, carbon, nitrogen and sulfur utilization of A. longa SW024T may represent its potential functions in the global biogeochemical cycle.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2005-3) contains supplementary material, which is available to authorized users.

Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata

“…Aquimarina sp. EL33 possesses several genes involved in nutrient cycling (C, N, and S), suggesting versatile nutrient acquisition and utilization, in line with observations made for Aquimarina longa SW024 ( 11 ). For example, 19 chitinase-encoding genes (endochitinases EC 3.2.1.14) were found, indicating that strain EL33 is capable of degrading chitin, the most abundant polysaccharide in the oceans.…”

“…For example, 19 chitinase-encoding genes (endochitinases EC 3.2.1.14) were found, indicating that strain EL33 is capable of degrading chitin, the most abundant polysaccharide in the oceans. Indeed, in vitro chitinolytic activity was shown for A. longa SW024 ( 11 ), which possesses seven chitinase-encoding genes.…”

Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

“…Genomic evidence suggests that Flavobacteriales are involved in carbon cycling in marine environments through the degradation of biopolymers such as chitin. Genes for a complete denitrification pathway as well as sulphate reduction have been found in Flavobacteriales genomes suggesting these organisms are involved in nitrogen and sulphur cycling [ 85 ]. Flavobacteriales may also help mediate biofouling through the production of algicidal substances [ 86 ].…”

Aquimarina sp. Associated With a Cuticular Disease of Cultured Larval Palinurid and Scyllarid Lobsters

“…Multiple genes encoding chitinases were detected in Aquimarina sp. TRL1, and this feature is common among members of Aquimarina recovered from S. serrata ( Midorikawa et al, 2020 ), H. americanus ( Ranson et al, 2018 ), and seawater ( Xu et al, 2015 ). Encoded genes for haemolysin, metalloprotease, and iron uptake mechanisms were also described as virulence factors for Aquimarina sp.…”

“…TRL1 likely facilitated attachment to phyllosoma appendages, as shown for larvae of S. serrata and P. trituberculatus larvae ( Midorikawa et al, 2020 ). Genes encoding glycosyltransferase may secrete extracellular polysaccharides that help the formation of aggregates, as proposed for A. longa ( Xu et al, 2015 ). The Aquimarina sp.…”