Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus

Abstract

Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1T and 59MF3M-4T, for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.

Microbial communities colonising plastics during transition from the wastewater treatment plant to marine waters

“…S9) and have been categorised as Most Abundant Taxonomic Groups (MATGs). Members of hydrocarbon-degrading genus Oleibacter , which was recently [ 64 ] merged with the genus Thalassolituus, the type strain of which was originally described by Yakimov et al [ 65 ] as an obligate hydrocarbonoclastic bacterium with a high affinity to hydrophobic compounds, were predominant (> 10%) taxa on PET, which was also supported by 16S rRNA amplicon sequencing (Additional file 1 : Fig. S9B).…”

Vanadium-dependent haloperoxidases from diverse microbes halogenate exogenous alkyl quinolone quorum sensing signals

“…To further interrogate AQ halogenation enzymology, four novel VHPOs that exhibited strong in vitro lysate activity were selected for protein purification, including homologs from: marine myxobacterium Enhygromyxa salina (esVHPO); soil acidobacteria Luteitalea pratensis H33-S (lpVHPO); freshwater betaproteobacterium Rubrivivax albus (raVHPO); and marine gammaproteobacterium Oleibacter marinus (omVHPO) (recently recommended to be renamed to Thalassolituus maritimus 39 ). Despite previously reported solubility and purification challenges with Microbulbifer sp.…”

Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis

“…The limitation of nutrients in ecosystems is a significant constraint on the vitality of microbial life [1]. Numerous microorganisms that thrive in nutrient-poor environments, including freshwater lakes, deserts, plateaus, and oceans, have been identified [2][3][4][5]. Among these microorganisms, nutrient-poor bacteria can be classified as specialized or parthenogenetic.…”