Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column

Abstract

The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.

The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

“…Although P. otitidis was initially isolated from a patient with an ear infection, this species is also widespread in nonclinical environments, as was MrB4, isolated from the near-shore area of Lake Biwa in Japan [73]. In agreement with these results, a recent study showed that a pair-wise comparison of P. alcaligenes OT69 against several type-strain genomes indicated P. otitidis DSM 17224 as its closest relative, rather than the type P. alcaligenes strain NBRC 14159, suggesting that OT69 should be included in a potentially new species [74]. In addition, these authors reported that P. alcaligenes OT69 and the other two oyster-associated Pseudomonas spp.…”

A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

“… 80 Our previous studies along with several others have demonstrated pseudomonads to be a major bacterial group in the oysters. 44 , 45 , 46 Notably, some pseudomonads can be opportunistic pathogens and have been found in spoiled oysters. 1 , 53 , 81 To provide further insights into the metabolic traits of Pseudomonas species from the eastern oysters, we conducted whole genome sequencing (WGS), comparative genomic analysis and BIOLOG-based physiological assessments on isolates obtained from the eastern oysters.…”

“…were found to be the dominant oyster-associated bacteria. 43 , 44 , 45 , 46 More recently, our metagenomics survey of the eastern oysters indicated the dominance of Lactobacillus, Burkholderia , Bradyrhizobium , Afipia, and Delfitia bacterial groups with lower representations of Psychrobacter spp. Additionally, Mycoplasma , which has been previously suggested as one of the autochthonous bacteria in eastern oysters, was also identified (unpublished data).…”

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

“…One reason for the interest in the denitrification potential of bacteria associated with the Eastern oyster is that oyster aquaculture is associated with low greenhouse gas emissions [38]. Metagenomics sequencing technologies have aided in the identification of archaea and bacteria associated with oyster anatomical parts including the gills, gut, hemolymph, mantle, pallial fluid, stomach, and shell [37,[39][40][41][42][43]. In studies with a focus on the denitrification potential of the oyster microbiome [37,42], the bacteria genera identified include Clostridium, Endozoicomonas, Erythrobacter, Mycoplasma, Neptunibacter, Pleurocapsa, Psychrobacter, Pseudomonas, Pseudoalteromonas, Shewanella, Synechococcus, and Vibrio.…”