- Open Access
Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill
BMC Microbiology volume 21, Article number: 288 (2021)
Extremophiles have attracted much attention in the last few decades, as they possess different properties by producing certain useful metabolites. However, the secondary metabolism of the extremophiles of Antarctic krill has received little attention.
In this study, a new bacterial strain MSAK28401T from Antarctic krill was isolated and identified. The results of analysis on phenotypic, chemotaxonomic, and genomic characteristics showed that the strain MSAK28401T belongs to the genus Planococcus. Cells of this strain were coccoid (0.89–1.05 μm) and aerobic. The majority of the fatty acid content was C15:0 anteiso (37.67 ± 0.90%) followed by C16:1 ω7c alcohol (10.37 ± 1.22%) and C16:0 iso (9.36 ± 0.71%). The calculated average nucleotide identity and DNA–DNA hybridization values between the strain MSAK28401T and type strains P. citreus DSM 20549T and P. rifietoensis M8T were lower than 91 and 70%, respectively. The strain MSAK28401T (=KCTC 43283T and MCCC 1k05448T) represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov. Moreover, genes involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were found in the genome, implying that strain MSAK28401T has an aromatic compound as its potential metabolite. This work will help us understand the genomic characteristics and potential metabolic pathway of Planococcus from Antarctic krill.
This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401T isolated from Antarctic krill, and provided the genome information of Planococcus strains for further studying the function roles in aromatic compound metabolism.
The genera Planococcus was initially found and proposed by Migula and has been continuously revised . It was classified as Planococcaceae of Firmicutes, and 30 species had been published to date. Recently, the species P. okeanokoites and P. mcmeekinii , P. psychrophilum , P. stackebrandtii, and P. alkanoclasticum [4, 5] were reclassified to the genera Planomicrobium based on phenotypic properties, G + C content in DNA, fatty acid composition, and menaquinone profiles. P. halophilus was classified under the genera Marinococcus [6, 7]. These changes indicated that genus Planococcus and Planomicrobium have a close phylogenetic relationship. Usually, the main splitting points of the 16S rRNA sequence between the genera Planococcus and Planomicrobium were located at sites 183 and 190 (E. coli counting), which in the Planococcus are T and A, whereas in the Planomicrobium are C and G .
Planococcus has the following known features: Gram-positive, multicellular morphology (cocci, short rod, or rod), aerobic, and no sporulation . Representative strains of genus Planococcus usually grow in cold and/or saline-alkali soil with high salt concentrations, e.g., Arctic, Antarctic, and marine environments [9,10,11]. Planococcus has attracted much attention, because they can produce carotenoids of biotechnological significance; this metabolite has potential applications as the ingredient of cosmetics, food or feed additives, and antioxidants . Planococcus can also degrade and process various contaminants, such as heavy metals and phenols, and play an important role in the bioremediation of extreme environments [13, 14].
In the present study, a new strain P. alpniumensis MSAK28401T of the genus Planococcus from Antarctic krill was isolated and identified using taxonomic, phylogenetic, chemotaxonomic, whole-genomic, and comparative genomic analysis.
Isolation, identification, and phylogenetic analysis
The single-bacterial MSAK28401T was obtained by mixing culture on Luria-Bertani (LB) agar. The 16S rRNA sequence alignment against GenBank revealed that the strain MSAK28401T belonged to the genus Planococcus, and it showed 98.62, 98.55, 98.43, 98.20, and 97.79% similarity with the corresponding gene sequences of P. citreus DSM20549T, P. rifietornsis M8T, P. maitriensis S1T, P. dechangensis NEAU-ST10-9T, and P. maritimus DSM17275T, respectively (additional File 1: Table S1). The 16S rRNA phylogenetic tree showed that strain MSAK28401T was clustered with four species of the genus Planococcus, and placed in an independent branch (Fig. 1). These results suggested that strain MSAK28401T belongs to the genus Planococcus.
The transmission electron microscopy observations showed that cell coccoid and the diameter of strain MSAK28401T was 0.89–1.05 μm with a thick cell wall (Fig. 2A). The isolates could grow in the range of 4–50 °C, and the optimal growth temperature was 30 °C (Fig. 2B). The phenotypic characteristics of strain MSAK28401T and related species as shown in Table 1. Strain MSAK28401T differed from the type strains of P. citreus DSM20549T, P. rifietornsis M8T, and P. maitriensis S1T in the assimilation of β-methyl-D-glucoside, D-aspartic acid, L-arginine, quinic acid, D-glucuronic acid, and L-malic acid. Strain MSAK28401T was distinguished from other species of the genus Planococcus by using some carbon sources and by producing acids from certain sugars. Phenotypic characteristics suggested that the strain MSAK28401T may represent a new Planococcus species and was named P. alpniumensis sp. nov.
Fatty acid analysis
The details of the fatty acid profiles of the strain MSAK28401T and three related species of P. citreus DSM 20549T, P. rifietoensis M8T, and P. maitriensis S1Twere described (Table 2). These major fatty acids (> 5%) of strain MSAK28401T were C15:0 anteiso (37.67 ± 0.90%), C16:1 ω7c alcohol (10.37 ± 1.22%), and C16:0 iso (9.36 ± 0.71%). The main fatty acid with the highest content is C15:0 anteiso. The other major fatty acids that were the most abundant in strain MSAK28401T, namely, C16:0 iso (9.36 ± 0.71%), C16:1 ω7c alcohol (10.37 ± 1.22%), and C14:0 iso (7.80 ± 0.15%), showed quantitative differences with those in the two related type species. Results of comparing fatty acid types and proportions suggested that the strain MSAK28401T can be distinguished from the two species of a cluster in the phylogeny.
Genome properties and mining
The genome of strain MSAK28401T formed from 10 contigs, and the genomic length was 3,930,779 bp. The G + C content was 47.15%. We identified 3998 genes and 3897 codifying sequences (Table 3 and Fig. 3A) and assigned them to 27 subsystems with SEED viewer using the RAST pipeline (Fig. 3B and additional File 2: Table S2). Nevertheless, only 26% (1150, genes) of this genome was annotated, and the other 74% was not assigned to the RAST subsystems. The most represented subsystem features were amino acids and derivatives (266), carbohydrates (214), protein metabolism (203), cofactors, vitamins, prosthetic group, and pigments (138). Notably, several genes involved in dormancy and sporulation were also found in strain MSAK28401T.
Carbohydrate-related enzymes and activity annotations of presumed genes showed that 24 genes encoded glycosyl transferases (GT) and 21 genes encoded glycosyl hydrolases (GH) (Fig. 4A and additional File 3: Table S3). KofamKOALA analysis results showed that almost all of the major metabolic pathways of bacteria were found in the genome of strain MSAK28401T (Fig. 4B and additional File 4: Table S4). Most genes were related to amino acid and carbohydrate metabolism, suggesting that MSAK28401T might possess the efficient nutrient uptake systems. In-depth analysis of the metabolic pathways of the strain MSAK28401Trevealed that genes related to aromatic hydrocarbon degradation pathways, such as catechol 2,3-dioxygenase (gene 0402), 4-oxalocrotonate tautomerase (gene 2794), and S-(hydroxymethyl) glutathione dehydrogenase / alcohol dehydrogenase (gene 2852) (Additional File 5: Table S5). Notably, 4-oxalocrotonate tautomerase (EC 5.3.2.-4-OT) is an enzyme that forms part of a bacterial metabolic pathway that oxidatively catabolizes toluene, o-xylene, 3-ethyltoluene, and 1,2,4-trimethylbenzene into intermediates of the citric acid cycle. In addition, we mapped the relevant pathways of aromatic hydrocarbons that the isolate may be involved in degradation (Fig. 4C). Above results indicated this isolate have a potential for application to the process of aromatic hydrocarbon metabolism.
Genetic relatedness and Pan-genome analysis
The phylogenetic tree of GBDP determined the phylogenetic position of strains, and it showed that the strain MSAK28401T was clustered with P. citreus DSM 20549T and P. rifietoensis M8T (Fig. 5). The DDH and ANIb values between the strain MSAK28401T and related species P. citreus DSM 20549T and P. rifietoensis M8T were less than 70 and 91%, respectively (Table 4 and Table 5), which were below the threshold for species delineation. The above results support the affiliation of the strain MSAK28401T to a new species of the genus Planococcus.
The pan-genome analysis of strains P. alpniumensis MSAK28401T, P. citreus DSM 20549T, and P. rifietoensis M8T was depicted in a Venn diagram (Fig. 6). The three strains of Planococcus possessed 3363 gene families, whereas a “core” genome comprised 2853 clusters of orthologous, accounting for 84.5% of all gene families. Most of the annotation functions of homologous clusters were involved in biological process, hydrolase activity, ion binding, molecular function, and transferase activity. A total of 63 unshared protein clusters were found in the strain MSAK28401T, whereas 6 and 4 unshared protein clusters were found in the strains of P. citreus DSM 20549T and P. rifietoensis M8T, respectively. Remarkably, the number of unshared clusters of the strain MSAK28401T was higher than those of these related species. Approximately 84% of unshared clusters involved biological processes, such as those involving nucleobase-containing compounds, cellular aromatic compounds, macromolecules, nitrogen compounds, and heterocycle metabolism, thereby indicating the unique advantages in its biological process compared with the other related strains.
Screening the genes of secondary metabolites showed two different genes clusters, which both belong to the terpene biosynthesis-related clusters (Fig. 7A). Cluster 1 displayed orphan Biosynthetic gene clusters (BGCs), which were unable to identify the known homologous gene cluster. Cluster 2 (3,001,607-3,022,437 nucleotides) was 66% similar to the known BGC (BGC0000645), which was a gene cluster comprising carotenoids biosynthetic carotenoids. Nevertheless, the low similarity of predicted gene clusters may represent the production of new metabolites.
Islands of genome
Thirty-seven genomic islands were predicted in this new strain MSAK28401T by IslandViewer 4, and the localization of the predicted genomic islands is shown in Fig. 7B. The 37 genomic islands were made up of 971 genes from the range of 4000–320,000 bp. Among these, 581 genes were hypothetical proteins with no function, 29 genes were mobile element protein, but genes producing secondary metabolites were not found within the genomic islands.
The species of Planococcus are the dominant species in many marine environments, e.g., deep sea, salt marshes, and intertidal zones . These aerobic heterotrophic bacteria degrade a variety of hydrocarbons, so they can make a significant contribution to the reduction of hydrocarbon contamination in the marine environment [5, 15]. Thirty species of Planococcus have been characterized. Notably, six typical strains have been found in the Antarctic, namely, P. faecalis , P. versutus , P. maitriensis , P. antarcticus, P. psychrophilus , and P. mcmeekinii . In this work, we isolated and identified a new species strain MSAK28401T belonging to the genus Planococcus from Antarctic krill.
Defining a new species involves two consecutive steps, namely, 16S rRNA gene analysis and calculation of several parameters of the genome . In conformity to this scheme, we analyzed the 16S rRNA sequence of strain MSAK28401T and found that the similarity between the corresponding gene sequence and related stains within genus Planococcus was less than 98.7%. This finding supported the idea that this strain might be a new species, because some species recently proposed in the genus Planococcus had similar or highly similar values in the 16S rRNA gene [17, 21, 22]. Chun et al. proposed a minimum standard to the taxonomy of prokaryotes using genomic data . The whole-genome analysis results showed that the threshold values of ANI for species differentiation were 95–96%, which were generally accepted. The calculated ANI values of the genome of related strains of Planococcus were less than 91%, thereby indicating that the strain belongs to a novel species within the genus Planococcus. Furthermore, the morphology, phenotype, and whole-genome analysis of the strain MSAK28401T showed that it represented a new member of the genus Planococcus and was named P. alpniumensis sp. nov.
Genus Planococcus is a halophilic bacterium known for producing various secondary metabolites , which are often referred to as anti-inflammatory, antimicrobial, pharmaceutically significant, and chemotherapeutic . Ganapathy et al. identified a new carotenoid (methyl glucosyl-3,4-dehydro-apo-8-lycopenoate) with antioxidant activity from P. maritimus MKU009 . Nevertheless, two clusters of genes that may be involved in the synthesis of terpenes were discovered by scanning potential secondary metabolites in strain MSAK2840T. Cluster 2 had 66% similarity with the gene cluster of the carotenoid biosynthesis of Halobacillus halophilus DSM 2266, which can help the strain resist oxidative stress. Genes associated with aromatic compound metabolism, one of the most common and persistent contaminants in environments , were found. In general, degradation of hydrocarbons, e.g., salicylate, gentisate, and quinate degradation, was a function of Planococcus .
By identifying vertical genetic homologous gene clusters from unique common ancestors, comparative analysis can help clarify the relationship between different species and the evolution and adaptability of the genome [23, 27]. The strain MSAK28401T shared 2853 gene clusters with P. citreus DSM 20549T and P. rifietoensis M8T, and had 63 unshared protein clusters. The functional distribution of homologous gene families in core genomes showed that most homologous gene families encode the basal metabolism of bacteria, such as protein processing, folding, and secretion and DNA and RNA metabolism . Notably, the number of unshared clusters in strain MSAK28401T was significantly higher than these related species among themselves (Fig. 6). The biological processes of unshared clusters of strain MSAK28401T are aromatic compound, nitrogen compound, macromolecule, and heterocycle metabolic processes, indicating the unique advantages in its biological process than other related strains.
The analysis of genomic, chemotaxonomic, and phenotypic traits showed that the strain MSAK28401T belongs to a new species of the genus Planococcus, named P. alpniumensis sp. nov, whose type strain is MSAK28401T. Furthermore, genomic characterization and comparative analysis showed that the strain P. alpniumensis MSAK28401T contained many genes related to the metabolism and transportation of amino acids and carbohydrates, thereby suggesting that MSAK28401T might possess n efficient nutrient uptake system. Screening the secondary metabolite genes found two different types of terpene biosynthesis-related clusters. Cluster 2 was similar to carotenoids (66% of genes showed similarity), thereby indicating that these predicted gene clusters may represent the production of new metabolites. Finally, genes (catechol 2,3-dioxygenase (gene 0402), 4-oxalocrotonate tautomerase (gene 2794), and S-(hydroxymethyl) glutathione dehydrogenase / alcohol dehydrogenase (gene 2852)) involved in the degradation of aromatic compounds (e.g., salicylate, gentisate, and quinate) were identified, indicating the potential metabolism of an aromatic compound of the new species.
Description of P. alpniumensis sp. nov.
This study reported the genomic information and phenotypic characteristics of the new strain P. alpniumensis MSAK28401T isolated from Antarctic krill. Cells were Gram-stain positive, aerobic, non-motile and coccoid (0.89–1.05 μm). After 3 days of culture on LB medium at 28 °C, the colonies were orange and round, no-flagellum, no-spore, no-mobility, growth temperature range from 4 to 45 °C, and 30 °C is the optimum growth temperature, as well as anaerobic growth does not occur. Tween 40 hydrolyzes the colony, while gelatin and casein do not. The carbon sources were D-turanose, 3-methyl glucose, D-galactose, D-sorbitol, D-mannitol, D-mannose, D-lactic acid methyl ester, and D-gluconic acid, but not dextrin, β-methyl-D-glucoside, α-D-lactose, L-pyroglutamic acid, D-lellobiose, D-melibiose, D-glucose, L-aspartic acid, D-glucose-6-PO4, D-fructose, D-arabitol, L-glutamic acid, D-galacturonic acid, L-malic acid, L-alanine, L-arginine, D-aspartic acid, D-glucuronic acid, L-galactonic acid lactone, glucuronamide, and quinic acid. C15:0 anteiso, C16:1 ω7c alcohol, C15:0 iso, C16:0 iso, C17:0 anteiso, and C14:0 iso were the major fatty acids (> 5%) of the strain. Content of DNA G + C was 47.15%. The type species was P. alpniumensis, MSAK28401T (KCTC 43283T and MCCC 1k05448T).
Antarctic krill was collected from Antarctica (58°33.1″ W, 63°6.3″ S) in 2016. It was washed with sterile seawater thrice under aseptic conditions to remove superficial residual sediments and microbes. Three Antarctic krill samples from a collected site were ground and homogenized as one specimen. Then, the milled samples were diluted with approximately 1 ml of sterile water, collected in a 2 ml aseptic centrifuge tube, and centrifuged at 3500 rpm for approximately 5–10 min. An inoculation loop was used to obtain a small amount of supernatant liquid, which was spread on agar-mixed LB. Bacteria in inoculated dishes were allowed to multiply at 10 °C until the colonies became visible. The colonies were randomly isolated from the agar plates, picked, and sub-cultured almost thrice under the same conditions. The same strains were preserved in 20% glycerin liquid medium at − 80 °C for future use.
Phylogenetic tree construction
16S rRNA gene sequence of strain MSAK28401T was amplified and sequenced through the sequencing DNA service of TSINGKE Biological Technology, China and then compared with the EzBioCloud database . ClustalW program was used for sequencing against the closest type strains  to analyze phylogeny. The Neighbor-Joining phylogenetic tree was established using MEGA-X . The robustness of the phylogenetic tree was evaluated through bootstrap analysis (1000 replicates) .
After incubating the MSAK28401T strain on LB-Agar-Powder plates for 48 h at 25 °C, transmission electron microscopy confirmed the morphological characteristics. Motility was examined by stab-culture in semi-solid medium according to the method of Gerhardt et al. Oxidase activity was tested using 1% (w/v) tetramethyl-p-phenylenediamine. Formation of spores was monitored by phase-contrast microscopy on cells cultured on LB agar at 30 °C for up to 7 days. Growth at different temperatures (4, 10, 16, 25, 30, 37, 45, and 50 °C) was determined and bacterial concentration was measured as optical density at 600 nm. Under manufacturer-indicated conditions, phenotypic characterization of this strain and two reference strains (P. citreus DSM20549T and P. rifietornsis M8T, which were obtained from Marine Culture Collection of China, MCCC) were identified using Biolog Gen III microstation. Strains P. citrus DSM20549T, P. rifietornsis M8T, and the strain MSAK28401T were incubated together at 25 °C for 30 h and the results were tested.
For cellular fatty acid analysis, strains MSAK28401T, P. citreus DSM20549T, and P. rifietornsis M8T were incubated together on LB-Agar-Powder at 25 °C for 2 days. Culture was harvested and prepared, and fatty acid methyl esters were separated based on the method proposed by Sasser  and were tested by the MIDI Sherlock Microbial Identification system.
Genome sequencing and mining
Total DNA of the genome was purified from a purely cultured strain MSAK28401T using a DNA extraction kit (TaKaRa, Japan) following the manufacturer’s protocol. PacBio sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China). The total DNA obtained was subjected to quality control via agarose gel electrophoresis and quantified by Qubit. The library was constructed utilizing the SMRTbell template prep kit 1.0 from Pacific Biosciences. Single-molecule real-time (SMRT) sequencing was performed on the PacBio Sequel platform. SMRT Analysis 2.3.0 was used to filter low-quality reads [34, 35]. The filtered reads were assembled into a contig without gaps. Falcon was used for the de novo assembly of these reads . This draft genome sequence of MSAK28401T was collected in GenBank and was given the accession number JAAMTH000000000.
A circular genome map of this strain MSAK28401T was generated with CGView server (http://cgview.ca/) [37, 38]. Gene prediction of the assembled genome was performed with Prodigal v2.6.3 , and an assembled genome was masked with RepeatMasker v4.0.7 . Annotation was completed with Rapid Annotation using Subsystem Technology (RAST 2.0) [2, 41, 42]. The genome-BLAST Distance Phylogeny (GBDP)  method compared these whole-genome sequences at nucleotide level, calculates DNA-DNA hybridization (dDDH) value, and a phylogenetic tree was constructed. The Average Nucleotide Identity (ANIb) value between genomes was calculated using JSpeciesWS Online Service . Predictive genes were functionally classified using e-values of 1e-5 in five databases, namely, Non-Redundant Protein Database (NR), Gene Ontology (GO) Database, Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/pathway.html) [45, 46].
Pan-genome and comparative genome-wide analysis
To compare genomes, the reference genome sequence of this bacteria was downloaded from the GenBank database. The pan-genome sequence comparative analysis of this strain MSAK28401T was performed using the GBDP method . Genomic homogeneous clustering analysis, including the genetic ontogeny of all predicted protein-coding genes, was performed using OrthoVenn2 .
Availability of data and materials
All data generated or analyzed during this study are included in this published article and its supplementary information files. The datasets presented in this study can be found in online repositories. The datasets generated and/or analyzed during the current study are available in the [NCBI] repository, [https://www.ncbi.nlm.nih.gov/] [JAAMTH000000000].
Average nucleotide identity
The Genome-Blast Distance Phylogeny
Non-Redundant Protein Database
Clusters of Orthologous Groups
Kyoto Encyclopedia of Genes and Genomes
Rapid Annotation using Subsystem Technology
Biosynthetic gene clusters
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The authors thank to Professor Li Wenjun, Dr. Liu Lan, Dr. Li Shuai, and all members of the ecological environment research team for their valuable help with classification and identification of the new species. The author also thanks to Dr. Zhang Lingyu from our laboratory for her help in the genome analysis of the new species.
This work was supported by the National Key Research and Development Program of China (Nos. 2018YFD0900504 and 2018YFD0900501), the Science and Technology Planning Project of Guangzhou (No. 201904020043), the China Agriculture Research System (No. CARS-46), the Guangdong Key Research and Development Program (No. 2019B020217001), Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Teams, and the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (No. 311021006). This work is not supported by a funder.
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The similarity of bacterial 16S rRNA.
Subsystems of genes according to SEED database (RAST server).
Carbohydrate-Active enZYmes (CAZy) database annotated classification statistics.
KEGG database annotated classification statistics.
KEGG database notes summary table.
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Wang, Y., Ma, L., He, J. et al. Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill. BMC Microbiol 21, 288 (2021). https://doi.org/10.1186/s12866-021-02347-3
- Antarctic krill
- Genomic analysis