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Link to original content: http://pubmed.ncbi.nlm.nih.gov/34745033/
Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica - PubMed Skip to main page content
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. 2021 Oct 22:12:729977.
doi: 10.3389/fmicb.2021.729977. eCollection 2021.

Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica

Stanislava Králová  1 , Hans-Jürgen Busse  2 , Matěj Bezdíček  3   4 , Megan Sandoval-Powers  5 , Markéta Nykrýnová  6 , Eva Staňková  1 , Daniel Krsek  7 , Ivo Sedláček  1
Affiliations

Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica

Stanislava Králová et al. Front Microbiol. .

Abstract

Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.

Keywords: Antarctica; Flavobacterium flabelliforme sp. nov.; Flavobacterium geliluteum sp. nov.; cold-adaptation; phylogenomics; psychrotrophic bacteria; systematics.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic tree based on 16S rRNA gene sequences comparison showing the phylogenetic positions of Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. among their closest related species within the genus Flavobacterium. The evolutionary history was inferred by using the maximum likelihood method based on Tamura-Nei distance with the gamma model. All positions with less than 95% site coverage were eliminated. Bootstrap probability values (percentages of 1,000 tree replications) greater than 70% are indicated at branch points. Flexibacter flexilis NBRC 15060T (AB680763) was used as an outgroup. Bar, 0.02 substitutions per nucleotide position.
FIGURE 2
FIGURE 2
Phylogenomic tree inferred with FastME 2.1.6.1 (Lefort et al., 2015) from GBDP distances calculated from genome sequences. Branch lengths are scaled in terms of GBDP distance formula d5. Numbers above branches indicate GBDP pseudo-bootstrap support values from 100 replications with the average branch support of 85.1%.
FIGURE 3
FIGURE 3
Comparison of COG functional categories between F. flabelliforme sp. nov. P4023T and F. geliluteum sp. nov. P7388T. Each colored segment indicates the relative contribution of a functional category as a percentage of total COGs with the color of COG family indicated in the legend. Ring A, F. flabelliforme sp. nov. P4023T; Ring B, F. geliluteum sp. nov. P7388T.
FIGURE 4
FIGURE 4
A polyketide synthase (PKS)-non-ribosomal peptide synthetase (NRPS) hybrid BGC, Cluster 3.1, and the predicted core structure annotated by antiSMASH (Blin et al., 2021) from the genome of strain P7388T. ORFs are depicted as white arrows and the core PKS-NRPS biosynthetic domains are color coded in each ORF.
FIGURE 5
FIGURE 5
Annotation of an arylpolyene/resorcinol BGC, Cluster 5.1, from strain P7388T based on antiSMASH analysis and similarity of Cluster 5.1 to a PKS flexirubin biosynthetic gene cluster from Flavobacterium johnsoniae UW101 (BGC0000838.1).
FIGURE 6
FIGURE 6
Polar lipid profiles of strains P7388T (A) and P4023T (B) after two-dimensional thin layer chromatography at detection with 5% ethanolic molybdatophosphoric acid and development at 140°C. PE, phosphatidylethanolamine; OL, ornithine lipid; APL unidentified amino lipid; GL, unidentified glycolipid; L1-5, unidentified lipids lacking a functional group.
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