Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment

Abstract

Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.

Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

“…Protein sequences from the 14 available type-strain genomes of Leisingera, Phaeobacter, Ruegeria and outgroup ( Oceanibulbus, Roseobacter , and Sediminimonas ) species (Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Riedel et al, 2013; Breider et al, 2014) were retrieved from the IMG website (http://img.jgi.doe.gov/cgi-bin/w/main.cgi) ( L. aquimarina DSM 24565 T , ID 2516653083 = AXBE00000000; L. methylohalidivorans MB2 T , ID 2512564009 = CP006773/CP006774/CP006775; L. nanhaiensis NH52F T , ID 2512047090 = AXBG00000000; P. arcticus DSM 23566 T ; ID 2516653081 = AXBF00000000; P. caeruleus 13 T , ID 2512047087 = AXBI00000000; P. daeponensis TF-218 T , ID 2516493020 = AXBD00000000; P. inhibens T5 T , ID 2516653078 = AXBB00000000; Sediminimonas qiaohouensis DSM 21189 T , ID 2523533612 = AUIJ00000000) or from NCBI ( Oceanibulbus indolifex HEL-45 T , ABID00000000; P. gallaeciensis CIP105210 T , AOQA01000000; Roseobacter denitrificans Och 114 T , CP000362, CP000464, CP000465, CP000466, CP000467; Roseobacter litoralis Och 149 T , CP002623, CP002624, CP002625, CP002626; Ruegeria lacuscaerulensis ITI-1157 T , ACNX00000000; ACNX00000000; Ruegeria pomeroyi DSS-3 T , CP000031, CP000032).…”

“…The values were taken from previous studies (Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Riedel et al, 2013; Breider et al, 2014; Frank et al, 2014). …”

“…Recently, Phaeobacter strains retrieved a lot of interest because of their production of various secondary metabolites (e.g., Berger et al, 2011). Analyses of the 16S rRNA gene and in some publications also preliminary genomic analyses were in conflict with the current classification (Jin et al, 2011; Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Gaboyer et al, 2013; Riedel et al, 2013; Breider et al, 2014; Liu et al, 2014; Park et al, 2014). These analyses mostly showed that P. aquaemixtae, P. caeruleus, P. daeponensis, Leisingera methylohalodivorans , and L. aquimarina form a clade, P. arcticus and P. leonis comprise a distinct monophyletic group, and P. gallaeciensis and P. inhibens form a third clade.…”

“…Phylogenetic trees for the trimethylamine monooxygenase ( tmm ) and the gamma-glutamyl-methylamine synthetase (Chen, 2012) showed that L. nanhaiensis is more distantly related to the other Leisingera species. This was confirmed by recent 16S rRNA gene sequence analyses (even though largely unresolved) and preliminary genomic analyses using the Genome-to-Genome Distance Calculator (GGDC; Auch et al, 2010a,b; Meier-Kolthoff et al, 2013) of diverse Phaeobacter and Leisingera type strains (Beyersmann et al, 2013; Buddruhs et al, 2013a; Dogs et al, 2013a,b; Freese et al, 2013; Riedel et al, 2013; Breider et al, 2014), suggesting the need for reclassification of L. nanhaiensis . Digital DNA:DNA hybridization (DDH) estimates as delivered by the GGDC were preferred over Average Nucleotide Identity (ANI) estimates because they provide higher correlations with traditional DDH results than do any of the ANI implementations (Auch et al, 2010b; Meier-Kolthoff et al, 2013).…”

Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

“…Lineages with type strain genome sequencing projects registered in GOLD [40] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [21]. The genomes of six more Leisingera and Phaeobacter species are published in the current issue of Standard in Genomic Science [41-46]. The 16S rRNA sequences of P.…”