First Draft Genome Sequence of a Strain from the Genus Citricoccus

Abstract

Bacteria of the genus Citricoccus have been isolated from ecological niches characterized by diverse abiotic stress conditions. Here we report the first genome draft of a strain of the genus Citricoccus isolated from the extremely oligotrophic Churince system in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico.The Micrococcaceae family is comprised of the genera Citricoccus, Kocuria, Micrococcus, Renibacterium, Nesterenkonia, and Rothia (8) within the class Actinobacteria (2). The genomes of four members of this family have been sequenced to date, namely, Arthrobacter aurescens TC1 and Arthrobacter sp. strain FB24, Kocuria rhizophylla, and Renibacterium salmoninarum (10); however, there is no genome information available for the genus Citricoccus. Members of this genus have been isolated from different environments, such as a desert soil, a sandy seashore sediment, a medieval wall painting, a mold-colonized wall, a saline wastewater bioreactor, and a wastewater treatment plant at a pesticide factory. Some of these strains are capable of utilizing aromatic compounds as a sole source of carbon (9, 7) and produce the hydroxamate siderophore desferrioxamine E (6). Here we present the draft genome sequence of Citricoccus strain CH26A, isolated from the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico. The CCB is a system of subterranean water streams and ponds characterized by high endemism and biodiversity of macro-and microorganisms and an extremely oligotrophic aquatic environment, poor in NaCl and carbonates and rich in magnesium, calcium, and sulfates (1). Therefore, analysis of the CH26A genome would help us to gain insight into the evolution and adaptation of the actinomycete metabolism to the CCB.CH26A was identified as a member of the genus Citricoccus by 16S rRNA gene phylogenetic analysis. Sequencing of the CH26A genome was performed using the 454 FLX system and Titanium platforms (454 Life Sciences). A total of 826,643 reads were generated and assembled de novo with the Newbler assembler, v. 2.5, yielding 67 contigs with an N 50 of 121 kb and the largest contig of 299.376 kb. We then produced a genome scaffold using the r2cat software program (5), taking as a reference the genome sequence of Micrococcus luteus (12). The Newbler-estimated size of the Citricoccus CH26A genome is 3.7 Mb, with a mean GC content of 70.96%. Gene prediction and annotation carried out using the RAST server (3) and further manually curated identified 3,030 coding sequences, grouped into 23 categories. We then carried out a genome-scale metabolic reconstruction (GSMR) of central metabolic pathways using an actinomycete-focused metabolic database (P. Cruz-Morales, unpublished results) and an in-house pipeline. This analysis showed the presence of all genes for the glycolytic and pentose phosphate pathways, as well as those for the biosynthesis of amino acids and nucleotides. Since no homolog of the malate dehydrogenase was identified, the conversion catalyzed by this enzyme in the tricarboxylic acid cycle is probably bypassed vi...

Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits

“…Similarly, none of the two Citrococcus strains tested for siderophore production, including strain CH26A isolated previously from the CCB, and whose genome includes the desABCD genes (Hayano-Kanashiro et al. 2011 ), were positive for the CAS assay under the conditions used. Given that the CAS assay may potentially give false negatives, as emphasized by the case of Citrococcus CH26A that contains the des genes, we randomly selected three CAS-negative strains and checked for their ability to produce DFOs under the iron-limited conditions used for original isolation, by means of HPLC profiling (see also next subsection).…”

Iron acquisition in the marine actinomycete genusSalinisporais controlled by the desferrioxamine family of siderophores

“…The lack of amphiphilic siderophores produced by Salinispora may therefore be a limiting factor in its proliferation into other environmental niches, such as the water column. Interestingly, the recently reported genome sequence of aquatic Citricoccus strain CH26A predicted a novel acylation mechanism in its production of DFO (Hayano‐Kanashiro et al ., ). This biosynthetic pathway may therefore be evolutionarily distinct from other reported DFO pathways.…”

Capacity of Aromatic Compound Degradation by Bacteria from Amazon Dark Earth

“…Most genera have great industrial interest, such as Arthrobacter, Rhodococcus and Gordonia, which are associated with saturated aliphatic and aromatic hydrocarbons [35][36][37], in addition to Citricoccus [38] and Microbacterium. Methylobacterium is methane utilizing and degrades explosive compounds in association with plants [39].…”