Abstract
The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T to public available genomes of Flavobacterium species to reveal the genomic traits and ecological roles of IK-1T. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1T belongs to a terrestrial clade of Flavobacterium. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1T genome. The IK-1T genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1T may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system FaRpfC-FaYpdB was identified in the IK-1T genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of Flavobacterium spp. reveal that IK-1T has adapted to a terrestrial niche. Further functional characterizations of IK-1T secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.
Highlights
The genus Flavobacterium belongs to the phylum Bacteroidetes and has been known for almost one hundred years, which was proposed in the first edition of Bergey’s Manual of Determinative Bacteriology in 1923 [1]
Our findings reveal that IK-1T belongs to a terrestrial clade of Flavobacteria and has adapted to plant host
To investigate whether IK-1T is a terrestrial bacterium associated with plant, we identified the gene families of carbohydrate-active enzymes (CAZy) in the genome, according to the previously reported method [5]
Summary
The genus Flavobacterium belongs to the phylum Bacteroidetes and has been known for almost one hundred years, which was proposed in the first edition of Bergey’s Manual of Determinative Bacteriology in 1923 [1]. More than 130 species have been identified in the genus Flavobacterium, which are isolated from terrestrial and aquatic environments. Most Flavobacterium spp. are commensal bacteria isolated with greater abundances from rivers and oceans [2]. Microorganisms are natural resources of chemicals such as biopigments and biosurfactants that have promising potentials in biotechnological and industrial applications. The genus Flavobacterium yields carotenoids, a huge family of pigments, displaying various colors, including yellow, orange, pink, red, and brown. Screening for biosurfactant-producing microorganisms identified one Flavobacterium strain as a biosurfactant-producing microbe [13]. Structure analyses revealed the Flavobacterium strain produced at least 37 flavolipids as a new class of biosurfactants [7]. Identification and characterization of Flavobacterium species and strains may help reveal biotechnological applications of this genus
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