Signs of biofilm formation in the genome of Labrenzia sp . PO1

Abstract

Labrenzia sp. are important components of marine ecology which play a key role in biochemical cycling. In this study, we isolated the Labrenzia sp. PO1 strain capable of forming biofilm, from the A. sanguinea culture. Growth analysis revealed that strain reached a logarithmic growth period at 24 hours. The whole genome of 6.21813 Mb of Labrezia sp. PO1 was sequenced and assembled into 15 scaffolds and 16 contigs, each with minimum and maximum lengths of 644 and 1,744,114 Mb. A total of 3,566 genes were classified into five pathways and 31 pathway groups. Of them, 521 genes encoded biofilm formation proteins, quorum sensing (QS) proteins, and ABC transporters. Gene Ontology annotation identified 49,272 genes that were involved in biological processes (33,425 genes), cellular components (7,031genes), and molecular function (7,816 genes). We recognised genes involved in bacterial quorum sensing, attachment, motility, and chemotaxis to investigate bacteria's ability to interact with the diatom phycosphere. As revealed by KEGG pathway analysis, several genes encoding ABC transporters exhibited a significant role during the growth and development of Labrenzia sp. PO1, indicating that ABC transporters may be involved in signalling pathways that enhance growth and biofilm formation.

Keywords: ABC transporter; Biofilm formation; Growth; Quorum sensing.

Fig. 1

Growth curve of Labrenzia sp. PO1.

Fig. 2

SEM image of Labrenzia sp. PO1.

Fig. 3

Labrenzia sp. PO1 subread length distribution.

Fig. 4

Correlation between the GC content and read depth distribution for Labrenzia sp. PO1. Abscissa, GC content; ordinate, average depth. The scatter plot shows a Poisson distribution of sequencing data with low GC bias.

Fig. 5

Genomic diagram of Labrenzia sp. PO1. Outer to inner: Genome (sorted by length), gene density (in 50,000 bp non-overlapping windows), ncRNA density (in 100,000 bp non-overlapping windows), GC rate (in 20,000 bp non-overlapping windows), GC skew (in 20,000 bp non-overlapping windows).

Fig. 6

Distribution of functional annotations in the GO database. The ordinate is the annotation item and the abscissa is the number of corresponding genes.

Fig. 7

Distribution of functional annotations in the KEGG database. The ordinate is the annotation item and the abscissa is the number of corresponding genes.

Fig. 8

A phylogenetic tree diagram. The evolutionary history was inferred using the neighbor-joining method. The optimal tree with the sum of branch length of 0.01309240 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) is shown next to the branches. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. The analysis involved six nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + noncoding. All ambiguous positions were removed for each sequence pair. The final dataset comprised 1,739 positions. Evolutionary analyses were conducted in MEGA7.