Abstract
Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki’s Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. A substantial number of genes encoding for extracellular polysaccharide synthesis pathways, curli fibres and attachment to surfaces could mediate adhesion in the biofilm and may contribute to the biofilm formation. In addition to aerobic respiration, the complete denitrification pathway and genes for sulphide oxidation e.g. sulphide:quinone reductase are present in the genome. sulphide:quinone reductase and denitrification may serve as detoxification systems allowing L. profundi LP1T to thrive in a sulphide and nitrate enriched environment. The information gained from the genome gives a greater insight in the functional role of L. profundi LP1T in the biofilm and its adaption strategy in an extreme environment.
Highlights
The type strain Lutibacter profundi LP1T (=DSM 100437T =JCM 30585T) belongs to the family Flavobacteriaceae within the phylum Bacteroidetes [1]
The genome of Lutibacter profundi LP1T comprises a single chromosome of 2,966 Mbp, smaller compared to other marine Bacteroidetes [21, 62, 74]
The mat consisted of long recalcitrant sugar polymers produced by the Epsilonproteobacteria Sulfurovum with Bacteroidetes attached along the filament surface [32]
Summary
The type strain Lutibacter profundi LP1T (=DSM 100437T =JCM 30585T) belongs to the family Flavobacteriaceae within the phylum Bacteroidetes [1]. Wissuwa et al Standards in Genomic Sciences (2017) 12:5 of marine isolates have revealed a large number of GHs, GTs, peptidases and adhesion proteins, as well as genes for gliding motility, supporting an organotrophic life style as HMW organic matter degraders [21,22,23,24]. Genome project history L. profundi LP1T as the type strain is the first Lutibacter isolate from a deep-sea hydrothermal vent system.
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