Comparative Genomics of Pseudomonas sp. Strain SI-3 Associated With Macroalga Ulva prolifera, the Causative Species for Green Tide in the Yellow Sea.

Huihui Fu,Chunhui Wu,Jin Zhao,Peng Jiang

doi:10.3389/fmicb.2018.01458

Abstract

Algae-bacteria associations occurred widely in marine habitats, however, contributions of bacteria to macroalgal blooming were almost unknown. In this study, a potential endophytic strain SI-3 was isolated from Ulva prolifera, the causative species for the world's largest green tide in the Yellow Sea, following a strict bleaching treatment to eliminate epiphytes. The genomic sequence of SI-3 was determined in size of 4.8 Mb and SI-3 was found to be mostly closed to Pseudomonas stutzeri. To evaluate the characteristics of SI-3 as a potential endophyte, the genomes of SI-3 and other 20 P. stutzeri strains were compared. We found that SI-3 had more strain-specific genes than most of the 20 P. stutzeri strains. Clusters of Orthologous Groups (COGs) analysis revealed that SI-3 had a higher proportion of genes assigned to transcriptional regulation and signal transduction compared with the 20 P. stutzeri strains, including four rhizosphere bacteria, indicating a complicated interaction network between SI-3 and its host. P. stutzeri is renowned for its metabolic versatility in aromatic compounds degradation. However, significant gene loss was observed in several aromatic compounds degradation pathways in SI-3, which may be an evolutional adaptation that developed upon association with its host. KEGG analysis revealed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification, two competing dissimilatory nitrate reduction pathways, co-occurred in the genome of SI-3, like most of the other 20 P. stutzeri strains. We speculated that DNRA of SI-3 may contribute a competitive advantage in nitrogen acquisition of U. prolifera by conserving nitrogen in form, as in the case of microalgae bloom. Collectively, these data suggest that Pseudomonas sp. strain SI-3 was a suitable candidate for investigation of the algae-bacteria interaction with U. prolifera and the ecological impacts on algal blooming.

Highlights

Substance exchange is considered the fundation of the partnership between algae and associated bacteria (Dittami et al, 2014; Cooper and Smith, 2015; Kouzuma and Watanabe, 2015)
Pseudomonas sp. strain SI-3, which was phylogenetically close to P. stutzeri, was isolated from U. prolifera, the only dominant alga of the world’s largest green tide
We reported the complete genome sequence of strain SI-3 and revealed its unique genomic characteristic as a potential endophyte based on comparison with 20 P. stutzeri strains

Summary

Introduction

Substance exchange is considered the fundation of the partnership between algae and associated bacteria (Dittami et al, 2014; Cooper and Smith, 2015; Kouzuma and Watanabe, 2015). As the primary producer in freshwater and marine environments, provide dissolved organic nutrients to phycosphere heterotrophic bacteria (Field et al, 1998; Kouzuma and Watanabe, 2015). Algae-associated bacteria have the potential to stimulate the growth of algae, similar to plant growth-promoting rhizobacteria. Algae-associated bacteria can confer the competitive advantages to their host. It has been suggested that associated bacteria promote algae bloom in the interaction between diatom and bacteria (Doucette, 1995)

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