Next Article in Journal
Genetic Diversity and Excretion Kinetics of Enteroviruses Excreted by Patients with Primary Immunodeficiency in Tunisia over a Five-Year Period (2020–2024)
Previous Article in Journal
Dopamine Is a Key Regulatory Molecule for Escherichia coli and May Serve as a Xenosiderophore
Previous Article in Special Issue
Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members

1
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia
2
Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si 56212, Republic of Korea
3
A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia
*
Authors to whom correspondence should be addressed.
Microorganisms 2026, 14(2), 328; https://doi.org/10.3390/microorganisms14020328
Submission received: 17 December 2025 / Revised: 23 January 2026 / Accepted: 26 January 2026 / Published: 30 January 2026
(This article belongs to the Collection Feature Papers in Environmental Microbiology)

Abstract

Two marine bacteria, designated strains 4Alg 33Tand 3Alg 14/1, were isolated from brown (Saccharina japonica) and green (Ulva fenestrata) macroalgae, respectively. These isolates were aerobic Gram-negative rods exhibiting a gliding motility. The 16S rRNA gene phylogenetic analysis clearly showed their belonging to the genus Formosa, the family Flavobacteriaceae, and the phylum Bacteroidota. The closest relatives of the new strains were Formosa undariae KCTC 32328T (99.05%), Formosa arctica IMCC 9485T (99.05%) and Formosa agariphila KMM 3901T (98.96%). The ANI and dDDH values between the two new strains were 97.9% and 85.3%, respectively. The AAI values between 4Alg 33T and Formosa type strains ranged from 80.1% (Formosa haliotis MA1T) to 91.4% (F. undariae KCTC 32328T). The cellular fatty acid and polar lipid profiles of the new isolates were generally similar to those of the type strains of Formosa species. The genomes of 4Alg 33T and 3Alg 14/1 are represented by a circular chromosome of 4,157,724 bp and 4,316,096 bp in size with 3536 and 3879 protein-coding genes, respectively. They shared a DNA G+C content of 34.3 mol% and comprised four rrn operons. The pangenome of the genus Formosa belongs to the open type and is characterized by an abundance of CAZymes. The proportion of CAZyme genes in novel genomes was more than 5%, with a prevalence of glycoside hydrolase genes, suggesting great potential for utilizing marine-derived polysaccharides. Based on the results of polyphasic characterization, the two algal isolates represent a distinct species lineage within the genus Formosa, for which we propose the name Formosa bonchosmolovskayae sp. nov. with the type strain 4Alg 33T (= KMM 3963T = KCTC 72008T). In addition, we have proposed to transfer Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 to the genus Xanthomarina Vaidya et al. 2015 as Xanthomarina maritima comb. nov. and Xanthomarina arctica comb. nov. based on a combination of the genomic and phenotypic characteristics.

1. Introduction

The genus Formosa, a member of the family Flavobacteriaceae (phylum Bacteroidota), was first identified by Ivanova et al. (2004) to denote Gram-negative, aerobic, rod-shaped and cytochrome-oxidase-negative marine bacteria isolated from an enrichment community degrading the brown alga Fucus evanescens [1]. Later, Nedashkovskaya et al. [2] amended this genus due to newly obtained phenotypic and genotypic data including the presence of gliding motility, budding fission, oxidase activity, phosphatidylethanolamine as the only phospholipid, and a DNA G+C content of 34–36 mol%. In 2015, Shakeela et al. [3] proposed a revised description of the genus based on the inability of Formosa species to utilize Tween 20 and the addition of aminolipids and lipids to their polar lipid profile. At last, based on the comparative phylogenomic analysis of the type strains of the phylum Bacteroidota, the genus Formosa was further emended by assigning a new DNA G+C content value of 31–40 mol% and adding a genome size parameter of 2.9–4.6 Mb [4].
To date, the genus Formosa includes seven species with a correct and validly published name (https://lpsn.dsmz.de/genus/formosa, accessed on 15 December 2025). All Formosa species have been isolated exclusively from marine habitats, most of them found in association with green and brown algae [1,2,5]. Other species were recovered from sediments and seawater [6,7,8]. One species was isolated from the abalone gut [9]. It is worth noting that a comprehensive genomic analysis of the type strain Formosa agariphila KMM 3901T revealed a large number of genes encoding proteases and glycoside hydrolases, indicating a key role in polymer decomposition and strong specialization to the algal lifestyle [10].
During the research of the cultivable microbial diversity of green and brown algae, common in the coastal waters of the Sea of Japan, two aerobic, yellow-pigmented and gliding-motile bacterial strains were isolated. The new algal isolates were subsequently examined through a polyphasic taxonomic approach, which confirmed their classification within the genus Formosa and indicated that they represent a novel species.

2. Materials and Methods

2.1. Isolation and Maintenance of Bacterial Strains

Strains 4Alg 33T and 3Alg 14/1 were isolated from the brown alga Saccharina japonica and the green alga Ulva fenestrata, respectively, collected from Troitsa Bay (42.622754, 131.121671), Gulf of Peter the Great, the Sea of Japan, Russia, using the dilution plating technique. For strain isolation, 0.1 mL of the seaweed homogenate was spread onto marine agar 2216 (MA; BD DifcoTM, Sparks, MD, USA) plates. Following primary isolation and subsequent purification, the obtained strains were cultivated on the same medium at 28 °C and preserved at −70 °C in marine broth (MB; BD DifcoTM, Sparks, MD, USA) supplemented with 20% (v/v) glycerol. Strains 4Alg 33T and 3Alg 14/1 were deposited in the Collection of Marine Microorganisms (KMM), Russia, under numbers of KMM 3963T and KMM 6136, respectively. The type strains Formosa algae KMM 3553T and F. agariphila KMM 3901T were provided by the KMM, whereas Formosa maritima KCTC 72531T, F. undariae KCTC 32328T and Xanthomarina spongicola KCTC 22662T were obtained from the Korean Collection for Type Cultures (KCTC), Republic of Korea. These strains were used as the reference strains in the parallel assays during this study. In addition, data from other type strains belonging to the neighboring genera on the genomic tree were included in tables as reference strains.

2.2. Phenotypic Characterization

The physiological, morphological, and biochemical characteristics of strains 4Alg 33T and 3Alg 14/1 were investigated using established standard methods. The novel isolates were further analyzed with API 20NE, API 20E, API 50CH, and API ZYM test kits (bioMérieux, Marcy-l’Étoile, France) following the manufacturer’s protocols. All assays were carried out at 28 °C. Cell morphology was observed using a Zeiss Axio Scope.A1 light microscope (Zeiss, Jena, Germany) after 48 h of growth on MA at 28 °C. Gram-staining was performed as recommended by Gerhardt et al. [11]. Gliding motility was investigated as described by Bowman [12]. Oxidative or fermentative utilization of glucose was determined on Hugh and Leifson’s medium modified for marine bacteria [13]. Catalase activity was assessed by adding a 3% (v/v) H2O2 solution to bacterial colonies and observing for gas formation. Oxidase activity was determined using N,N,N,N-tetramethyl-p-phenylenediamine. The hydrolysis of agar, starch, casein, gelatin, chitin, DNA, L-tyrosine, urea, and Tweens 20, 40, and 80, as well as acid production from carbohydrates, nitrate reduction, and hydrogen sulfide formation, were examined following standard procedures [14]. The temperature range for growth was evaluated on MA between 4 °C and 42 °C at 1 °C intervals. Tolerance to NaCl was tested in medium containing (per liter of distilled water) 5 g of Bacto Peptone (BD DifcoTM), 2 g of Bacto yeast extract (BD DifcoTM), 1 g of glucose, 0.02 g of KH2PO4, and 0.05 g of MgSO4·7H2O supplemented with 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3, 4, 5, 6, 8, 10, and 12% (w/v) NaCl. Growth within the pH range 5.0–11.0 was determined at 0.5 pH unit intervals. The presence of flexirubin-type pigments was examined as described previously [15]. Antibiotic susceptibility was determined using the standard disc diffusion plate method. Unless otherwise stated, discs contained the following antibiotics (µg per a disc): ampicillin (10), benzylpenicillin (10U), carbenicillin (100), cefalexin (30), cefazolin (30), chloramphenicol (30), erythromycin (15), doxycycline (10), gentamicin (10), kanamycin (30), lincomycin (15), nalidixic acid (30), neomycin (30), ofloxacin (5), oleandomycin (15), oxacillin (10), polymyxin B (300 U), rifampicin (5), streptomycin (30), tetracycline (5), and vancomycin (30).

2.3. Chemotaxonomic Characterization

Fatty acid methyl esters and polar lipids of strains 4Alg 33T and 3Alg 14/1, together with their closest phylogenetic relatives, F. undariae KCTC 32328T, F. maritima KCTC 72531T, and X. spongicola KCTC 22662T, were extracted and analyzed as previously described using cells cultivated on MA at 28 °C [2]. Isoprenoid quinones were extracted with chloroform/methanol (2:1, v/v) and purified by TLC, employing n-hexane/diethyl ether (85:15, v/v) as the solvent system. Isoprenoid quinone composition was determined by HPLC on a Shimadzu LC-10A system (Shimadzu, Kyoto, Japan) equipped with a reversed-phase Supelcosil LC-18 column (15 cm × 4.6 mm; Supelco, Bellefonte, PA, USA). Acetonitrile/2-propanol (65:35, v/v) served as the mobile phase with a flow rate of 0.5 mL min−1 as described previously [16], and the column temperature was maintained at 40 °C. Quinones were detected by monitoring absorbance at 270 nm.

2.4. 16S rRNA Gene Sequence and Phylogenetic Analysis

Genomic DNA from strains 4Alg 33T and 3Alg 14/1 was isolated using a NucleoSpin Tissue kit (Macherey–Nagel, Düren, Germany). The extracted DNA was subsequently used for PCR amplification of the 16S rRNA gene following a previously described protocol [17]. The obtained PCR fragments were sequenced and compared with the 16S rRNA gene sequences of validly published type strains using the EzBioCloud server, accessed on 13 October 2024 [18]. The phylogenetic relationships between the novel isolates and closely related type strains were analyzed through the GGDC web server (http://ggdc.dsmz.de/, accessed on 7 August 2025) [19] employing the DSMZ phylogenomics pipeline [20]. Maximum likelihood (ML) and maximum parsimony (MP) trees were constructed from aligned sequences using RAxML [21] and TNT [22], respectively, with 1000 bootstrap replications to assess branch robustness.

2.5. Whole-Genome Sequencing and Genome-Based Phylogenetic Analysis

The DNA libraries of strains 4Alg 33T and 3Alg 14/1 were prepared using a Nextera DNA Flex kit (Illumina, San Diego, CA, USA) and sequenced on an Illumina MiSeq platform. For nanopore sequencing, the library was constructed with an SQK-NBD114.96 kit (Oxford Nanopore Technologies, Oxford, UK) and run on a MinION device equipped with a FLO-MIN 114 flow cell (Oxford Nanopore Technologies, Oxford, UK). Base calling was conducted using Dorado (v. 1.0.2). The obtained short and long reads were quality-filtered and trimmed with Trimmomatic (v. 0.39, quality > 30, length > 100) [23] and chopper (v. 0.10.0, quality > 16, length > 2000 for 3Alg14/1 and quality > 10 for 4Alg33) [24], respectively. The quality of processed reads was assessed with FastQC v. 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed on 15 July 2024) and NanoPlot v. 1.42.2 [25]. The hybrid assembly of the genomic sequences was performed using Unicycler v0.4.8 [26] with default parameters. The genome completeness and contamination were evaluated using CheckM v. 1.1.3 [27]. Sequencing depth was estimated utilizing SAMtools v. 1.3 [28]. Gene annotation was performed with RAST [29], PGAP [30], and Prokka [31].
Genome-based phylogenetic relationships were inferred with PhyloPhlAn v. 3.0.1 [32] employing the default set of 400 conserved proteins. An ML phylogenetic tree was reconstructed using RAxML v. 8.2.12 [21] under the LG + Γ substitution model, with 100 non-parametric bootstrap replicates. Pairwise average Nucleotide Acid Identity (ANI), Amino Acid Identity (AAI), and digital DNA–DNA hybridization (dDDH) values were calculated using FastANI [33], EzAAI [34], and TYGS platforms [35], respectively.

2.6. Functional Genomic Analysis

Pan-genome analysis of Formosa type strains, including metabolic profiling, was performed using the Anvi’o workflow v. 8 following the protocol described at https://merenlab.org/2016/11/08/pangenomics-v2/, accessed on 18 November 2024 [36]. Carbohydrate-active enzymes (CAZymes) and CAZyme-associated gene clusters were identified and annotated automatically using the dbCAN3 v.10 web server (http://dbcan-hcc.unl.edu/, accessed on 21 November 2025) [37,38]. Only CAZymes detected by at least two of the three search algorithms in dbCAN3 (HMMER, DIAMOND, and eCAMI) were retained for subsequent analysis. Biosynthetic gene clusters associated with secondary metabolite production were identified and annotated with antiSMASH v.8 with relaxed detection strictness (https://antismash.secondarymetabolites.org, accessed on 10 December 2025) [39]. Components of secretion systems were detected using MacSyFinder v.2.1.4 (TXSScan-1.1.3) [40]. Heatmaps and bar plots were generated using the R packages pheatmap v.1.0.12 and ggplot2 v.3.5.1 in RStudio v.2024.09.1+394 with R v.4.4.2. Figure fonts and layout were manually adjusted in Adobe Photoshop CC 2018 to improve clarity. Functional and ecological analyses were conducted using the Protologger web tool (https://www.protologger.de/, accessed on 1 December 2025) [41].

3. Results and Discussion

3.1. Phylogenetic Analyses

Analysis of the 16S rRNA gene sequences showed that the two new strains 4Alg 33T (1159 bp long) and 3Alg 14/1 (1389 bp long) have 99.6% identity to each other and 98.9–99.1% identity to F. undariae WS-MY3T. The sequence identity values between 4Alg 33T and other relatives of the genus Formosa ranged from 96.6% with F. maritima 1494T to 99.0% with Formosa arctica IMCC 9485T, as well as 96.7% with Bizionia arctica SM1203T. The 16S rRNA gene sequences of strains 4Alg 33T and 3Alg 14/1 were submitted to the GenBank under PQ573828 and PQ573827, respectively. They were 99.9–100% identical to those of four copies of the 16S rRNA gene retrieved from genome sequences of the strains.
Phylogenetic analysis based on 16S rRNA gene sequences showed that strains 4Alg 33T and 3Alg 14/1 cluster together, representing a distinct lineage within the genus Formosa (Figure 1). Among the type strains of the genus Formosa, only the type strain of F. maritima lies outside the Formosa clade.
To date, the genus Formosa comprises seven species with validly published and correct names (https://lpsn.dsmz.de/genus/formosa, accessed on 15 December 2025), although genomic sequences are currently available for only six type strains, excluding F. arctica. Here, genomic sequences of type strains belonging to the genera Formosa and Xanthomarina, as well as [Bizionia] arctica, were subjected to a phylogenomic analysis. The genomic characteristics of Formosa species are presented in Table 1, whereas those of Xanthomarina type strains together with reclassified strains are listed in Table S1.
A phylogenomic tree was reconstructed by the PhyloPhlAn method [32] from the concatenated sequences of 400 conserved proteins derived from the genomes of Formosa type strains and closely related genera (Figure 2). In this tree, the new strains 4Alg 33T and 3Alg 14/1 occupy a separate taxonomic position, forming a common clade with the type strains F. agariphila KMM 3901T and F. undariae KCTC 32328T. The ANI/AAI values between strains 4Alg 33T and 3Alg 14/1 were 97.9%/98.6%, while the dDDH value was 85.3% (formula d4). The ANI/AAI values between 4Alg 33T and type strains of the genus Formosa ranged from 80.8%/80.1% (F. haliotis MA1T) to 88.2%/91.4% (F. undariae KCTC 32328T), and the dDDH values were less than 40%. Despite the very high sequence similarity (99.1%) between the 16S rRNA gene sequences of strains 4Alg 33T and F. undariae KCTC 32328T, ANI and dDDH values were lower than the generally accepted species delineation thresholds of 95–96% for ANI and 70% for dDDH. Therefore, in this case, genomic criteria are more decisive for species delimitation than criteria based on the 16S rRNA gene.
It is noteworthy that both type strains F. maritima 1494T and B. arctica CGMCC 1.12751T fall into the clade Xanthomarina with 100% branch support (Figure 2). Each strain forms its own distinct species-level lineage. The type strain F. maritima 1494T shared AAI values of 86.1% with X. spongicola DSM 22637T, 83.4% with X. gelatinilytica AK20T and less than 71.5% with Formosa type strains. The type strain B. arctica CGMCC 1.12751T shared AAI values of 83.1% with X. gelatinilytica AK20T, 82.2% with X. spongicola DSM 22637T and less than 72.8% with Bizionia type strains. The AAI value between F. maritima 1494T and B. arctica CGMCC 1.12751T was 82.1%. Therefore, both species should be transferred to the genus Xanthomarina.
Thus, the analysis combining the phylogenetic tree results and genome-relatedness indices clearly supported new strains 4Alg 33T and 3Alg 14/1 as a novel species of the genus Formosa in the family Flavobacteriaceae.

3.2. Genomic Characteristics and Pan-Genome Analysis

The complete circular genomes of 4Alg 33T (=KMM 3963T) and 3Alg 14/1 (=KMM 6136) were assembled de novo for each strain (Figure 3). The obtained genomic characteristics aligned with the revised recommended minimal standards for the application of genomic data in prokaryotic taxonomy [42]. The genomes of 4Alg 33T and 3Alg 14/1 are 4,157,724 bp and 4,316,096 bp in size, encoding 3570 and 3686 proteins, respectively, and with an overall G+C content of 34.5 mol% (Table 1).
The Proksee server was used to construct and visualize the chromosome maps of 4Alg 33T and 3Alg 14/1 [43] (Figure 3a). To carry out genome annotations, the RAST [29] and Prokka [31] tool kits were utilized. Due to the chromosomal-level completeness of the genome assemblies, the number of rrn operons in each strain could be determined precisely, with all four operons located on the leading strands (Table 1, Figure 3a). It is noteworthy that the CRISPR-Cas system was detected in the 3Alg14/1 strain, while this system was absent in the type strain 4Alg33T. The ANI between the new strains amounted to 97.98%.
To determine genus-related features, a pan-genome analysis of Formosa species (Table 1) was performed using orthologous clustering and metabolic pathway reconstruction with the anviὸ platform [36]. The Formosa pan-genome (Figure 4A) was composed of 7052 gene clusters (Euclidean distance; Ward’s linkage) with 25,680 gene calls. A total of 2386 core gene clusters were included in the core genome, covering 17,017 genes, among which 1917 were identified as single-copy genes (SCGs) with 13,419 gene calls. Composing the accessory shell and cloud, there were 513 (2553 genes) and 1255 (3135 genes) clusters, respectively. The singleton portion of the pan-genome included 2898 gene clusters (2975 genes). The largest number of singletons was observed in the genome of F. haliotis MA1T (755 gene clusters), while the smallest number was found in 4Alg 33T (157 clusters). All predicted gene clusters were annotated using COGs database (Figure 4B,C). Among the core cluster, the most represented functional classes were translation (J, 10.8%) and cell wall/membrane/envelope biogenesis (M, 9.5%). The most abundant COG classes in the accessory genome were carbohydrate metabolism and transport (G, 13.6%), inorganic ion transport and metabolism (P, 13.5%), general functional prediction only (R, 11%), cell wall/membrane/envelope biogenesis (M, 9.5%), and transcription (K, 8.3%) (Figure 4B). Most of the unique genes did not belong to any COG category. However, genes of categories G, M, P, V, and R prevailed (Figure 4C).
The observed gene patterns suggest that core functions support conserved cellular processes within the genus Formosa, while the accessory genome, in particular due to the enrichment of enzymes involved in carbohydrate metabolism and various transport proteins, reflects flexible adaptation to heterogeneous marine niches such as different algal hosts or particle-associated microenvironments. The prevalence of unassigned singletons further implies ongoing specialization toward lineage-specific substrates or interactions that remain to be elucidated.
Genes involved in central carbohydrate metabolism, including the Embden–Meyerhof pathway, gluconeogenesis, PRPP biosynthesis, pentose phosphate pathway, tricarboxylic acid cycle, pyruvate oxidation, and electron transport chain, were identified as complete metabolic pathways in all genomes, whereas the Entner–Doudoroff pathway was only partially represented. Protologger-based functional genome analysis [41] identified 3510 and 3580 coding sequences in strains 4Alg 33T and 3Alg 14/1, respectively, including 108 transporter genes, 17 and 18 genes associated with secretion systems, and 726 and 724 unique enzyme genes. The genomes of both strains contain metabolic pathways associated with environmental adaptation, including folate (vitamin B9) biosynthesis from 7,8-dihydrofolate (EC 1.5.1.3), as well as pathways for the production of acetate (EC 2.3.1.8, 2.7.2.1), propionate (EC 2.3.1.8, 2.7.2.1), and L-glutamate (EC:6.3.1.2, 1.4.1.-). The predicted ability to synthesize zeaxanthin likely accounts for the yellow pigmentation observed in bacterial cells. In addition, the presence of a cbb3-type cytochrome c oxidase, inferred from the detection of subunits I/II (ccoNO), III, and IV, suggests adaptation to microaerobic conditions typical of benthic and host-associated marine environments.

3.3. In Silico Analysis of Hydrolytic and Biosynthetic Potentials

Coastal ecosystems with macroalgae and seagrasses are recognized as “blue carbon ecosystems” because of their capacity to capture and store substantial amounts of organic carbon [44]. Complex polysaccharides such as laminarin, alginate, ulvan, and others are primarily present in the cell walls of seaweeds, which can be degraded by marine bacteria. These bacteria synthesize polysaccharide-degrading enzymes that facilitate the depolymerization of algal polysaccharides. The resulting oligosaccharides are subsequently broken down into various intermediates, which are then used for energy conversion pathways [45]. Since both new strains, 4Alg 33T and 3Alg 14/1, were isolated from different macroalgae, it is of interest to predict their hydrolytic potential and determine whether their genome reflects adaptation to the algal source.
Based on annotation using the dbCAN3 server [37], members of the genus Formosa encode a diverse repertoire of carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs), many of which were predicted to participate in the degradation of macroalgal polysaccharides. The proportion of genes encoding CAZymes in the analyzed genomes ranged from 4.55% to 5.92%, with the highest value predicted for F. haliotis MA1T. In the genomes of the novel strains 4Alg 33T and 3Alg 14/1, CAZyme-related genes accounted for approximately 5.35% of the predicted coding sequences and were predominantly represented by glycoside hydrolases, followed by glycosyltransferases and polysaccharide lyases (Figure 5).
Formosa strains were enriched in glycoside hydrolase (GH) families associated with the degradation of diverse polysaccharides. GH29 and GH95, commonly linked to the hydrolysis of fucose-containing polysaccharides, were consistently represented across all analyzed genomes. Similarly, GH3, GH13, GH31, and GH97, associated with the degradation of α-glucans and related oligosaccharides, were prevalent. GH30 and GH43, which are associated with the degradation of xylan and related hemicellulosic polysaccharides, were widely detected in the novel strains. In addition, strains 4Alg 33T, 3Alg 14/1, and KCTC 32328T uniquely encoded GH27, which includes α-galactosidases involved in the degradation of galactose-containing algal polysaccharides. Interesting to note, GH28, commonly associated with polygalacturonase activity and pectin-like substrate degradation, was detected exclusively in strain 4Alg 33T.
Glycosyltransferases (GTs), particularly families GT2, GT4, and GT51, were consistently detected in all strains, with GT2 and GT4 occurring in high copy numbers (up to 34 per genome), suggesting an important role in the biosynthesis of exopolysaccharides, cell wall polymers, and glycoproteins.
The majority of annotated polysaccharide lyases (PLs) were assigned to families PL6, PL7, and PL40, which are commonly associated with the depolymerization of alginate and ulvan, the predominant structural polysaccharides of brown and green algae, respectively. Among carbohydrate esterases (CEs), family CE20 was most frequently detected and is linked to the deacetylation of algal xylans, a modification that may increase polysaccharide accessibility in marine environments. Furthermore, the genomes of strains 4Alg 33T and MA1T encoded CAZymes belonging to families GH28, PL10, CE8, and CE12 that are predicted to be involved in pectin degradation. The presence of these enzymes suggests a potential capacity to utilize plant-derived polymeric substrates in coastal habitats influenced by terrestrial inputs. Approximately half of the annotated GH, PL, and CE proteins predicted by dbCAN3 contained a signal peptide, suggesting their targeting to the periplasmic or extracellular space and supporting a role in the extracellular processing and turnover of complex polysaccharides in marine environments.
A large number of PULs were detected within the Formosa genus, comprising genes related to the modification and degradation of various marine polysaccharides; however, the majority of these loci could not be functionally annotated, indicating substantial unexplored metabolic potential.
It is known that laminarin is widely distributed in brown algae but is often found in diatoms and golden algae [46]. The macroalgal polysaccharide laminarin primarily consists of a linear backbone of 20–30 β-1,3-linked D-glucopyranose residues, with branching chains formed by β-1,6-linked D-glucopyranose units. Using the dbCAN server, PULs capable of degrading beta-glucan were identified in both strains 4Alg 33T and 3Alg 14/1. A detailed analysis of these loci revealed genes encoding GH16, GH17, and GH30, responsible for laminarin utilization [47]. Another polysaccharide-utilizing cluster, found in both strains 4Alg 33T and 3Alg 14/1, was predicted to be an alginate-degrading cluster. Alginate is a linear, anionic polysaccharide from brown algae, made of repeating units of two uronic acids: β-D-mannuronic acid and α-L-guluronic acid linked by (1→4) bonds. These PUL genes, encoding PL-6, -7, and -17, are well-characterized alginate lyases [48,49,50].
Ulvan-utilizing PUL was detected in 3Alg 14/1 and absent from 4Alg 33T. This difference is not surprising, as strain 3Alg 14/1 was isolated from the green alga Ulva fenestrata. Ulvan is a branched sulfated polysaccharide consisting of repeating disaccharide units, where D-glucuronic acid or L-iduronic acid is linked to L-rhamnnose 3-sulfate through β-1,4 and α-1,4-bonds, respectively, the last residues form an α-1,4-linked backbone, giving the polymer its characteristic branched configuration. GH105 and PL28 enzymes were shown to be key enzymes for the degradation of ulvan [51]. The ulvan-degrading cluster of strain 3Alg 14/1 was compared with the same cluster previously described in F. agariphila KMM 3901T isolated from the green alga Acrosiphonia sonderi (Figure 6). Both clusters have a similar structure, but the KMM 3901T strain contains genes encoding the additional SusCD transporter. The 4Alg 33T genome also contained three enzymes belonging to the GH105 family, but these were predicted to be related to pectin utilization. Furthermore, PL28 was absent from the 4Alg 33T genome, indicating that this strain is unable to utilize ulvan.
Thus, despite the high sequence similarity between strains 4Alg 33T and 3Alg 14/1, their genomes differ at several PULs, determined by different substrate preferences in their ecological niche, namely, green or brown algae. It also indicates the ecological importance of the new Formosa species in the global carbon cycle in marine ecosystems.
Analysis using TXSScan [40] predicted the presence of two types of secretion systems (TSSs) in all studied Formosa genomes (Figure 5C). An almost complete gene set encoding the type IX secretion system (T9SS), a hallmark of members of the phylum Bacteroidota, was identified. The mandatory gene sprA was not detected due to low sequence similarity to known homologues. The T9SS is essential for the secretion of cell-surface and extracellular proteins, including some CAZymes, and is also required for gliding motility. In agreement with these genomic predictions, gliding motility was observed in Formosa strains during phenotypic characterization. In addition to T9SS, T1SS was detected in all analyzed genomes. T1SS is commonly found in Gram-negative bacteria and facilitates the direct, one-step transport of substrates from the cytoplasm to the extracellular environment. The genomes of strains 4Alg 33T and 3Alg 14/1 encoded up to ten copies of the core T1SS components, comprising the ATP-binding cassette transporter, membrane fusion protein, and outer membrane factor.
The biosynthetic gene cluster (BGC) repertoire of the genus Formosa was analyzed using the antiSMASH server [39]. Two types of BGCs were detected in all examined genomes and were predicted to be involved in the biosynthesis of terpenes and terpene precursors (Figure 5C). In the genomes of the novel strains, as well as strains MA1T and PS13T, an additional gene cluster (cytokinin) was identified. This cluster may play a role in microbe–host interactions or environmental signaling. No gene clusters associated with flexirubin-type pigment biosynthesis, which are common among Bacteroidota members, were detected in all analyzed genomes. This finding is supported by phenotypic characteristics of Formosa strains (Table 2). However, gene clusters putatively related to carotenoid biosynthesis were predicted in all genomes, suggesting that carotenoids may contribute to the yellow-to-orange pigmentation observed in the strains.
Ecological distribution analysis using the Protologger web tool did not identify any metagenome-assembled genomes (MAGs) corresponding to novel strains, indicating limited representation in current genomic databases [41]. However, 16S rRNA gene-based screening revealed 4Alg 33T- and 3Alg 14/1-like sequences in coral-associated metagenomes (29.6% and 27.0%, respectively), followed by marine sediment (27.2% and 21.2%) and marine (19.3% and 16.7%) datasets.
The observed distribution agrees with the isolation sources of the strains and with the known ecology of the genus Formosa, whose representatives are largely marine and commonly associated with coastal and host-related environments.

3.4. Phenotypic Characterization of New Strains

Strains 4Alg 33T and 3Alg 14/1 were Gram-stain-negative, aerobic, rod-shaped, yellow-pigmented and motile by gliding. Both strains were positive for oxidase activity, hydrolysis of aesculin, agar and gelatin, and acid production from D-fructose, D-galactose, D-glucose, maltose, D-mannose, D-xylose and N-acetyl-glucosamine (Table 2). The new isolates shared some common features with their nearest neighbors, which supported affiliation of them with the genus Formosa (Table 2). However, unlike their closest relative species, F. undariae 32328T, strains 4Alg 33T and 3Alg 14/1 possessed a gliding motility, agar and gelatin hydrolysis as well as esterase (C4), trypsin, α-chymotrypsin, N-acetyl-β-glucosamine and α-fucosidase activities. A type of metabolism, the ability to degrade agar, to form acid from D-galactose and L-rhamnose, and to produce cysteine arylamidase, trypsin, α-chymotrypsin and α-fucosidase helped to differ the novel strains from F. algae KMM 3553T. A set of phenotypic properties, including the presence of acid formation from L-rhamnose and α-glucosidase as well as the incapability of the both strains to grow under facultatively anaerobic conditions and to utilize L-arabinose and D-lactose clearly separated them from F. agariphila KMM 3901T (Table 2). The detailed phenotypic characteristics of strains 4Alg 33T and 3Alg 14/1 are summarized in Table 2 and described in the species description section.
The cellular fatty acid profiles of strains 4Alg 33T and 3Alg 14/1 contained iso-C15:0, iso-C17:0 3-OH, iso-C16:0 3-OH, C16:1 ω7c, iso-C15:1, C16:0, C15:0 and C15:1 ω6c as the predominant fatty acids (>5%) and were similar to those of the reference strains (Table 3). Along with this, distinctiveness in the relative abundances of C16:0 and iso-C15:0 3-OH fatty acids were observed between the novel strains and their closest phylogenetic relatives, F. algae KMM 3553T and F. agariphila KMM 3901T. Also noteworthy is the presence of fatty acids C15:0 3-OH and C17:0 3-OH in the above-mentioned type strains in comparison with strains 4Alg 33T and 3Alg 14/1 (Table 3).

3.5. Reclassification of Formosa maritima and Bizionia arctica as New Xanthomarina Species

Despite the 16S rRNA gene sequence similarity between strain 4Alg 33T and X. spongicola KCTC 22662T being 97.7%, the phylogenomic tree revealed that the aforementioned strains formed different clusters (Figure 2). Moreover, the species F. maritima is closely related to species of the genus Xanthomarina, with ANI values ranging from 80.5 to 84.2% and AAI values of 82.1–83.1%. It forms a distinct evolutionary lineage within the genus Xanthomarina (Figure 2).
Indeed, consistently with the results of the phylogenetic analysis, phenotypic characteristics of F. maritima are similar to those of species of the genus Xanthomarina, including the respiratory type of metabolism, presence of gliding motility, oxidase activity, hydrolysis of gelatin and production of flexirubin-type pigments, as well as the absence of aesculin and agar hydrolysis (Table 4). However, F. maritima KCTC 72531T could be distinguished from Xanthomarina gelatinolytica AK20T by the minimal temperature for growth, arginine dihydrolase activity, urea hydrolysis, D-glucose oxidation and utilization and the DNA G+C content value. A set of such phenotypic features as nitrate reduction, hydrolysis of casein, starch, L-tyrosine and Tween 80, utilization of several sugars and acid phosphatase and α-galactosidase activities strongly supported the discrimination of F. maritima from X. spongicola (Table 3).
The fatty acid profile of strain F. maritima KCTC 72531T was in accordance with that of X. spongicola KCTC 22662T and X. gelatinolytica AK20T (Table 4). Moreover, the polar lipid composition of strain F. maritima KCTC 72531T was similar to that of X. spongicola and included PE, two unidentified aminolipids (AL 1-2) and four unidentified lipids (L1-4) (Figure S2). The above-mentioned data clarified a precise taxonomic position of the species F. maritima and strongly justified its inclusion to the genus Xanthomarina as Xanthomarina maritima comb. nov.
Recently, the phylogenomic analysis of the genus Bizionia revealed that the type strain B. arctica SM1203T is the closest relative of Xanthomarina members, as well as F. maritima KCTC 72531T [55] (Figure 2). The ANI values between B. arctica SM1203T and Xanthomarina type strains were 79.8–80.9%, whereas the AAI values were 82.1–83.1%. B. arctica had many phenotypic properties in common with the validly published species of the genus Xanthomarina, but it could be differentiated from them by the absence of gliding motility, oxidase activity and production of flexirubin-type pigments (Table 4). However, using the antiSMASH server, a flexirubin biosynthesis gene cluster was discovered in the genome of B. arctica SM1203T, similar to the Flavobacterium johnsoniae UW101 gene cluster.
The fatty acid profile of B. arctica SM1203T demonstrated some differences in the proportions of several fatty acids in comparison with those of the type strains of the genus Xanthomarina. However, all prevalent fatty acids were presented herein, including fatty acids iso-C15:0, iso-C17:0 3-OH and iso-C15:1 (Table 5). Thus, the results of the phylogenomic and phenotypic analyses clarified the precise taxonomic position of species B. arctica and strongly supported transferring the species B. arctica to the genus Xanthomarina and its reclassification as Xanthomarina arctica comb. nov.

4. Conclusions

Brown algae Saccharina japonica and green algae Ulva fenestrata are common inhabitants of the Far East’s coastal waters in the Sea of Japan. During the study of the cultured microbial diversity of these macroalgae two novel strains, 4Alg 33T and 3Alg 14/1 were identified. A comprehensive CAZyme analysis showed that strain-specific differences in PUL content can reflect the sources of their initial isolation. The strain 4Alg 33T, isolated from brown algae, carries multiple PULs for alginate and laminarin degradation, two hallmark polysaccharides of brown algal cell walls. The presence of PL6, PL7, and PL17, along with GH16 and GH17 (laminarinases), reflects its adaptation to the utilization of brown-algal detritus. In contrast, 3Alg 14/1, isolated from green algae, possesses an ulvan-degrading cluster with GH105 and PL28, which is absent from 4Alg 33T. This directly links its genomic traits to its ecological niche: the ability to utilize ulvan provides a selective advantage at or near Ulva surfaces, where such polysaccharides predominate. The presence of genes responsible for the breakdown of pectin and xylan in both genomes further indicates metabolic flexibility, possibly allowing these strains to process mixed organic matter in coastal habitats where macroalgae and terrestrial organisms converge.
Moreover, the phylogenetic analyses, taken together with chemotaxonomic data obtained in this study, suggest that strains 4Alg 33T and 3Alg 14/1 belong to the genus Formosa and represent a novel species within the genus, for which the name Formosa bonchosmolovskayae sp. nov. is proposed.
In addition, the combination of the genomic and phenotypic characteristics strongly supports the affiliation of the species Formosa maritima and Bizionia arctica with the genus Xanthomarina and permits their reclassification as Xanthomarina maritima comb. nov. and Xanthomarina arctica comb. nov.
  • Description of Formosa bonchosmolovskayae sp. nov.
Formosa bonchosmolovskayae (bonch.os.mo.lovs’ka.yae. N.L. gen. fem. n. bonchosmolovskayae, of Bonch-Osmolovskaya, in honor of famous Russian microbiologist Elizaveta A. Bonch-Osmolovskaya, who has made a significant contribution to the investigation of environmental microbiology).
Cells are Gram-negative, strictly aerobic, motile by gliding and rod-shaped (approximately 0.4–0.8 μm in diameter and 1.2–5.2 μm in length). On marine agar, colonies are 2–3 mm in diameter, circular, with entire edges, shiny, yellow pigmented and slightly sinking into agar. Growth occurs at 4–34 °C (optimum, 25–28 °C), at pH 5.5–9.0 (optimum, pH 7.5) and with 0–8% NaCl (optimum, 1–3%). Arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase and tryptophan deaminase activities are absent. Aesculin, agar and gelatin are hydrolyzed, but casein, chitin, L-tyrosine, Tween 80, DNA and urea are not degraded. Hydrolysis of starch and Tweens 20 and 40 are strain-dependent. Acid is produced from D-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, rhamnose, sucrose, D-xylose, and mannitol but not from L-arabinose, raffinose, ribose, trehalose, inositol, sorbitol, D-cellobiose, lactose, maltose, melibiose and N-acetyl-glucosamine. Acid production from glycogen is strain-dependent. Utilization of gluconate is strain-dependent. Nitrate is not reduced to nitrite. Hydrogen sulfide and indole are not produced. Production of acetoin is strain-dependent. Flexirubin-type pigments are not formed. In API 20NE gallery, positive results are obtained for aesculin, gelatin and PNPG hydrolysis and utilization of maltose, mannose and mannitol as sole carbon sources. Utilization of gluconate is strain-dependent. In API 20E, positive results are obtained for ONPG and gelatin hydrolysis and acid formation from D-glucose. Production of acetoin and acid formation from mannitol, sucrose and melibiose are strain-dependent. In API 50CH, a positive result is obtained for acid formation from D-arabinose, D-xylose, galactose, glucose, fructose, mannose, rhamnose, aesculin, amygdalin and L-fucose and utilization of N-acetylglucosamine, maltose and glycogen. Acid formation from mannitol and N-acetylglucosamine is strain-dependent. In the API ZYM gallery, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, cystine arylamidase, valine arylamidase, trypsin, α-chymotrypsin, acid phosphatase, naphtol-AS-BI-phosphohydrolase, α-glucosidase, N-acetyl-β-glucosaminidase and α-fucosidase activities are present, but lipase (C14) and β-glucuronidase activities are absent. Activity of α-galactosidase, β-galactosidase, β-glucosidase and α-mannosidase are strain-dependent. The predominant fatty acids are iso-C15:0, iso-C17:0 3-OH, iso-C16:0 3-OH, C16:1 ω7c, iso-C15:1, C16:0, C15:0 and C15:1 ω6c. The polar lipid profile consists of phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. The major respiratory quinone is MK-6. The DNA G+C content of the type strain is 34.5 mol%.
The type strain 4Alg 33T (=KCTC 72008T=KMM 3963T) was isolated from the brown alga Saccharina japonica collected from Troitsa Bay, Gulf of Peter the Great, Sea of Japan (also is known as East Sea), Pacific Ocean, Russia (42.622754, 131.121671).
The DDBJ/GenBank accession number for the 16S rRNA gene sequence of strain 4Alg 33T is PQ573828.
The GenBank accession number for the whole-genome sequence of strain 4Alg 33T is CP174605.1.
  • Description of Xanthomarina maritima comb. nov.
Xanthomarina maritima (ma.ri′ ti. ma. L. fem. adj. maritima of or belonging to the sea, maritime, referring to coastal sediment from which the type strain was isolated).
Basonym: Formosa maritima Cao et al. 2020.
The description of this species is the same as that provided by Cao et al. (2020).
The type strain 1494T (=KCTC 72531T=MCCC 1H00385T) was isolated from marine sediment collected off the coast of Weihai, PR China. The DNA G+C content of the type strain is 31.1 mol%. Genome size is 3.0 Mb.
  • Description of Xanthomarina arctica comb. nov.
Xanthomarina arctica (arc′ ti.ca. L. fem. adj. arctica northern, from the Arctic).
Basonym: Bizionia arctica Li et al. 2015.
The description of this species is the same as that provided by Li et al. (2015).
The type strain SM1203T (=CGMCC 1.12751T=JCM 30333T) was isolated from surface seawater of Kongsfjorden, Svalbard. The genomic DNA G+C content of the type strain is 33.0 mol%. Genome size is 3.9 Mb.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms14020328/s1, Table S1: Genomic features of type strains of Xanthomarina genus, F. maritima 1494T 4, and B. arctica CGMCC 1.12751T; Figure S1: Two-dimensional thin-layer chromatogram of polar lipids extracted from strain 4Alg 33T (a), 3Alg 14/1 (b), Formosa undariae KCTC 32328T (c), Xanthomarina spongicola KCTC 22662T (d) and Formosa maritima KCTC 72531T (e). PE, phosphatidylethanolamine; AL1-2, unidentified aminolipids, L1-4, unidentified lipids; Figure S2: Two-dimensional thin-layer chromatogram of polar lipids extracted from strain Formosa maritima KCTC 72531T (a) and Xanthomarina spongicola KCTC 22662T (b). PE, phosphatidylethanolamine; AL1-2, unidentified aminolipids, L1-4, unidentified lipids.

Author Contributions

Investigation, O.N., E.B., N.O., Y.S., Y.B., V.E., S.-G.K., N.Z. and M.I.; methodology, O.N., S.-G.K., N.Z. and M.I.; project administration, M.I.; resources O.N. and M.I.; software, E.B., V.E., N.O. and Y.S.; writing—original draft O.N., E.B., Y.S., Y.B. and M.I.; writing—review and editing, O.N., E.B. and M.I. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by a grant from the Ministry of Science and Higher Education, Russian Federation 15.BRK.25.14 (contract no. 075-15-2025-467).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The original data presented in the study are openly available in DDBJ/GenBank at PQ573828, PQ573827, CP174605.1, CM137262.1.

Conflicts of Interest

The authors declare no conflicts of interest.

References

  1. Ivanova, E.P.; Alexeeva, Y.V.; Flavier, S.; Wright, J.P.; Zhukova, N.V.; Gorshkova, N.M.; Mikhailov, V.V.; Nicolau, D.V.; Christen, R. Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int. J. Syst. Evol. Microbiol. 2004, 54, 705–711. [Google Scholar] [CrossRef]
  2. Nedashkovskaya, O.I.; Kim, S.B.; Vancanneyt, M.; Snauwaert, C.; Lysenko, A.M.; Rohde, M.; Frolova, G.M.; Zhukova, N.V.; Mikhailov, V.V.; Bae, K.S.; et al. Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa. Int. J. Syst. Evol. Microbiol. 2006, 56, 161–167. [Google Scholar] [CrossRef] [PubMed]
  3. Shakeela, Q.; Shehzad, A.; Zhang, Y.; Tang, K.; Zhang, X.H. Flavirhabdus iliipiscaria gen. nov., sp. nov., isolated from intestine of flounder (Paralichthys olivaceus) and emended descriptions of the genera Flavivirga, Algibacter, Bizionia and Formosa. Int. J. Syst. Evol. Microbiol. 2015, 65, 1347–1353. [Google Scholar] [CrossRef] [PubMed]
  4. Garcia-Lopez, M.; Meier-Kolthoff, J.P.; Tindall, B.J.; Gronow, S.; Woyke, T.; Kyrpides, N.C.; Hahnke, R.L.; Goker, M. Analysis of 1000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front. Microbiol. 2019, 10, 2083. [Google Scholar] [CrossRef] [PubMed]
  5. Park, S.; Lee, J.-S.; Lee, K.-C.; Yoon, J.-H. Formosa undariae sp. nov., isolated from a reservoir containing the brown algae Undaria pinnatifida. Int. J. Syst. Evol. Microbiol. 2013, 63, 4130–4135. [Google Scholar] [CrossRef]
  6. Cao, W.R.; Lu, D.C.; Li, Y.J.; Sun, X.K.; Sun, Y.Y.; Saren, G.; Du, Z.J. Formosa maritima sp. nov., isolated from coastal sediment. Int. J. Syst. Evol. Microbiol. 2020, 70, 982–988. [Google Scholar] [CrossRef]
  7. Han, B.; Kim, M.; Lee, K.E.; Lee, B.H.; Lee, E.Y.; Park, S.J. Formosa sediminum sp. nov., a starch-degrading bacterium isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 2020, 70, 2008–2015. [Google Scholar] [CrossRef]
  8. Kwon, T.; Baek, K.; Lee, K.; Kang, I.; Cho, J.C. Formosa arctica sp. nov., isolated from Arctic seawater. Int. J. Syst. Evol. Microbiol. 2014, 64, 78–82. [Google Scholar] [CrossRef]
  9. Tanaka, R.; Cleenwerck, I.; Mizutani, Y.; Iehata, S.; Shibata, T.; Miyake, H.; Mori, T.; Tamaru, Y.; Ueda, M.; Bossier, P.; et al. Formosa haliotis sp. nov., a brown-alga-degrading bacterium isolated from the gut of the abalone Haliotis gigantea. Int. J. Syst. Evol. Microbiol. 2015, 65, 4388–4393. [Google Scholar] [CrossRef]
  10. Mann, A.J.; Hahnke, R.L.; Huang, S.; Werner, J.; Xing, P.; Barbeyron, T.; Huettel, B.; Stüber, K.; Reinhardt, R.; Harder, J.; et al. The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. Appl. Environ. Microbiol. 2013, 79, 6813–6822. [Google Scholar] [CrossRef]
  11. Gerhardt, P.; Murray, R.G.E.; Wood, W.A.; Krieg, N.R. (Eds.) Methods for General and Molecular Bacteriology; American Society for Microbiology: Washington, DC, USA, 1994. [Google Scholar]
  12. Bowman, J.P. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int. J. Syst. Evol. Microbiol. 2000, 50, 1861–1868. [Google Scholar] [CrossRef]
  13. Lemos, M.L.; Toranzo, A.E.; Barja, J.L. Modifed medium for oxidation-fermentation test in the identifcation of marine bacteria. Appl. Environ. Microbiol. 1985, 40, 1541–1543. [Google Scholar] [CrossRef]
  14. Smibert, R.M.; Krieg, N.R. Phenotypic characterization. In Methods for General and Molecular Bacteriology; Gerhardt, P., Murray, R.G.E., Eds.; American Society for Microbiology: Washington, DC, USA, 1994; pp. 607–655. [Google Scholar]
  15. Reichenbach, H. The order Cytophagales. In The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed.; Balows, A., Trüper, H.G., Dworkin, M., Harder, W., Schleifer, K.H., Eds.; Springer: New York, NY, USA, 1992; pp. 3631–3675. [Google Scholar]
  16. Komagata, K.; Suzuki, K.I. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol. 1987, 19, 161–207. [Google Scholar] [CrossRef]
  17. Romanenko, L.; Bystritskaya, E.; Savicheva, Y.; Eremeev, V.; Otstavnykh, N.; Kurilenko, V.; Velansky, P.; Isaeva, M. Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan. Microorganisms 2024, 12, 1413. [Google Scholar] [CrossRef] [PubMed]
  18. Yoon, S.H.; Ha, S.M.; Kwon, S.; Lim, J.; Kim, Y.; Seo, H.; Chun, J. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 2017, 67, 1613. [Google Scholar] [CrossRef] [PubMed]
  19. Meier-Kolthoff, J.P.; Carbasse, J.S.; Peinado-Olarte, R.L.; Göker, M. TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2021, 7, D801–D807. [Google Scholar] [CrossRef] [PubMed]
  20. Meier-Kolthoff, J.P.; Hahnke, R.L.; Petersen, J.; Scheuner, C.; Michael, V.; Fiebig, A.; Rohde, C.; Rohde, M.; Fartmann, B.; Goodwin, L.A.; et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand. Genomic. Sci. 2014, 8, 10. [Google Scholar] [CrossRef]
  21. Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30, 1312–1313. [Google Scholar] [CrossRef]
  22. Goloboff, P.A.; Farris, J.S.; Nixon, K.C. TNT, a free program for phylogenetic analysis. Cladistics 2008, 24, 774–786. [Google Scholar] [CrossRef]
  23. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114–2120. [Google Scholar] [CrossRef]
  24. De Coster, W.; D’Hert, S.; Schultz, D.; Cruts, M.; Van Broeckhoven, C. NanoPack: Visualizing and processing long-read sequencing data. Bioinformatics 2018, 34, 2666–2669. [Google Scholar] [CrossRef] [PubMed] [PubMed Central]
  25. De Coster, W.; Rademakers, R. NanoPack2: Population-scale evaluation of long-read sequencing data. Bioinformatics 2023, 39, btad311. [Google Scholar] [CrossRef] [PubMed]
  26. Wick, R.R.; Judd, L.M.; Gorrie, C.L.; Holt, K.E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 2017, 13, e1005595. [Google Scholar] [CrossRef] [PubMed]
  27. Parks, D.H.; Imelfort, M.; Skennerton, C.T.; Hugenholtz, P.; Tyson, G.W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015, 25, 1043–1055. [Google Scholar] [CrossRef]
  28. Danecek, P.; Bonfield, J.K.; Liddle, J.; Marshall, J.; Ohan, V.; Pollard, M.O.; Whitwham, A.; Keane, T.; McCarthy, S.A.; Davies, R.M.; et al. Twelve years of SAMtools and BCFtools. GigaScience 2021, 10, giab008. [Google Scholar] [CrossRef]
  29. Aziz, R.K.; Bartels, D.; Best, A.A.; DeJongh, M.; Disz, T.; Edwards, R.A.; Formsma, K.; Gerdes, S.; Glass, E.M.; Kubal, M.; et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genom. 2008, 9, 75. [Google Scholar] [CrossRef]
  30. Tatusova, T.; DiCuccio, M.; Badretdin, A.; Chetvernin, V.; Nawrocki, E.P.; Zaslavsky, L.; Lomsadze, A.; Pruitt, K.D.; Borodovsky, M.; Ostell, J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016, 44, 6614–6624. [Google Scholar] [CrossRef]
  31. Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 2014, 30, 2068–2069. [Google Scholar] [CrossRef]
  32. Asnicar, F.; Thomas, A.M.; Beghini, F.; Mengoni, C.; Manara, S.; Manghi, P.; Zhu, Q.; Bolzan, M.; Cumbo, F.; May, U.; et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 2020, 11, 2500. [Google Scholar] [CrossRef]
  33. Jain, C.; Rodriguez-R, L.M.; Phillippy, A.M.; Konstantinidis, K.T.; Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 2018, 9, 5114. [Google Scholar] [CrossRef]
  34. Kim, D.; Park, S.; Chun, J. Introducing EzAAI: A pipeline for high throughput calculations of prokaryotic average amino acid identity. J. Microbiol. 2021, 59, 476–480, Erratum in J. Microbiol. 2023, 61, 879. [Google Scholar] [CrossRef]
  35. Meier-Kolthoff, J.P.; Göker, M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 2019, 10, 2182. [Google Scholar] [CrossRef]
  36. Eren, A.M.; Esen, O.C.; Quince, C.; Vineis, J.H.; Morrison, H.G.; Sogin, M.L.; Delmont, T.O. Anvi’o: An advanced analysis and visualization platform for ‘omics data. PeerJ 2015, 3, e1319. [Google Scholar] [CrossRef] [PubMed]
  37. Zheng, J.; Ge, Q.; Yan, Y.; Zhang, X.; Huang, L.; Yin, Y. dbCAN3: Automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 2023, 51, W115–W121. [Google Scholar] [CrossRef] [PubMed]
  38. Ausland, C.; Zheng, J.; Yi, H.; Yang, B.; Li, T.; Feng, X.; Zheng, B.; Yin, Y. dbCAN-PUL: A database of experimentally characterized CAZyme gene clusters and their substrates. Nucleic Acids Res. 2021, 49, D523–D528. [Google Scholar] [PubMed]
  39. Blin, K.; Shaw, S.; Lisa, V.; Szenei, J.; Reitz, Z.L.; Augustijn, H.E.; Cediel-Becerra, J.D.D.; de Crécy-Lagard, V.; Koetsier, R.A.; Williams, S.E.; et al. antiSMASH 8.0: Extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation. Nucleic Acids Res. 2025, 53, W32–W38. [Google Scholar] [CrossRef]
  40. Neron, B.; Denise, R.; Coluzzi, C.; Touchon, M.; Rocha, E.P.; Abby, S.S. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community J. 2023, 3, e28. [Google Scholar] [CrossRef]
  41. Hitch, T.C.A.; Riedel, T.; Oren, A.; Overmann, J.; Lawley, T.D.; Clavel, T. Automated Analysis of Genomic Sequences Facilitates High-Throughput and Comprehensive Description of Bacteria. ISME Commun. 2021, 1, 16. [Google Scholar] [CrossRef]
  42. Riesco, R.; Trujillo, M.E. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 2024, 74, 006300. [Google Scholar] [CrossRef]
  43. Grant, J.R.; Enns, E.; Marinier, E.; Mandal, A.; Herman, E.K.; Chen, C.; Graham, M.; Van Domselaar, G.; Stothard, P. Proksee: In-Depth Characterization and Visualization of Bacterial Genomes. Nucleic Acids Res. 2023, 51, W484–W492. [Google Scholar] [CrossRef]
  44. Lozada, M.; Diéguez, M.C.; García, P.E.; Dionisi, H.M. Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments. Sci. Total Environ. 2023, 857, 159392. [Google Scholar] [CrossRef] [PubMed]
  45. Imran, M.; Poduval, P.B.; Ghadi, S.C. Bacterial degradation of algal polysaccharides in marine ecosystem. In Marine Pollution and Microbial Remediation; Naik, M.M., Dubey, S.K., Eds.; Springer: Singapore, 2017; pp. 189–203. [Google Scholar]
  46. Chen, J.; Yang, J.; Du, H.; Aslam, M.; Wang, W.; Chen, W.; Li, T.; Liu, Z.; Liu, X. Laminarin, a major polysaccharide in stramenopiles. Mar. Drugs 2021, 19, 576. [Google Scholar] [CrossRef] [PubMed]
  47. Becker, S.; Scheffel, A.; Polz, M.F.; Hehemann, J.-H. Accurate quantification of laminarin in marine organic matter with enzymes from marine microbes. Appl. Environ. Microbiol. 2017, 83, e03389-16. [Google Scholar] [CrossRef] [PubMed]
  48. Xu, F.; Chen, X.-L.; Zhang, Y.-Z. Alginate catabolic systems in marine bacteria. Curr. Opin. Microbiol. 2025, 83, 102564. [Google Scholar] [CrossRef]
  49. Sun, X.-K.; Gong, Y.; Shang, D.-D.; Liu, B.-T.; Du, Z.-J.; Chen, G.-J. Degradation of alginate by a newly isolated marine Bacterium Agarivorans sp. B2Z047. Mar. Drugs 2022, 20, 254. [Google Scholar] [CrossRef]
  50. Chernysheva, N.; Bystritskaya, E.; Likhatskaya, G.; Nedashkovskaya, O.; Isaeva, M. Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia. Molecules 2021, 26, 2387. [Google Scholar] [CrossRef]
  51. Reisky, L.; Préchoux, A.; Zühlke, M.-K.; Bäumgen, M.; Robb, C.S.; Gerlach, N.; Roret, T.; Stanetty, C.; Larocque, R.; Michel, G.; et al. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat. Chem. Biol. 2019, 15, 803–812. [Google Scholar] [CrossRef]
  52. Li, H.; Zhang, X.Y.; Liu, C.; Liu, A.; Qin, Q.L.; Su, H.N.; Shi, M.; Zhou, B.C.; Chen, X.L.; Zhang, Y.Z.; et al. Bizionia arctica sp. nov., isolated from Arctic fjord seawater, and emended description of the genus Bizionia. Int. J. Syst. Evol. Microbiol. 2015, 65, 2925–2930. [Google Scholar] [CrossRef]
  53. Vaidya, B.; Kumar, R.; Sharma, G.; Srinivas, T.N.R.; Anil Kumar, P. Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater. Int. J. Syst. Evol. Microbiol. 2015, 65, 3926–3932. [Google Scholar] [CrossRef]
  54. Yoon, B.J.; Oh, D.C. Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia. Int. J. Syst. Evol. Microbiol. 2011, 61, 330–333. [Google Scholar] [CrossRef]
  55. Kurilenko, V.; Bystritskaya, E.; Otstavnykh, N.; Velansky, P.; Baldaev, S.; Eremeev, V.; Ageenko, N.; Kiselev, K.; Nedashkovskaya, O.; Isaeva, M. Genome-Based Reclassification of [Bizionia] algoritergicola Bowman and Nichols 2005 as Algorimicrobium algoritergicola gen. nov., comb. nov. and description of Algorimicrobium bowmanii sp. nov. Microorganisms 2026, 14, 24. [Google Scholar] [CrossRef]
Figure 1. ML/MP 16S rRNA phylogenetic tree showing the positions of the novel strains 4Alg 33T and 3Alg 14/1 (in bold) among type strains of the genus Formosa and closely related type strains of the family Flavobacteriaceae. The ML tree was constructed using the GTR + GAMMA substitution model. Bootstrap values (ML/MP) greater than 60%, based on 1000 replicates, are shown at branch nodes. The scale bar represents 0.02 substitutions per nucleotide position. GenBank accession numbers are provided alongside strain names.
Figure 1. ML/MP 16S rRNA phylogenetic tree showing the positions of the novel strains 4Alg 33T and 3Alg 14/1 (in bold) among type strains of the genus Formosa and closely related type strains of the family Flavobacteriaceae. The ML tree was constructed using the GTR + GAMMA substitution model. Bootstrap values (ML/MP) greater than 60%, based on 1000 replicates, are shown at branch nodes. The scale bar represents 0.02 substitutions per nucleotide position. GenBank accession numbers are provided alongside strain names.
Microorganisms 14 00328 g001
Figure 2. Maximum likelihood phylogenomic tree reconstructed from the concatenated sequences of 400 conserved proteins, depicting the phylogenetic placement of strains 4Alg 33T and 3Alg 14/1 among the type strains of the genera Formosa and Xanthomarina, together with type species from other phylogenetically related genera. The bootstrap values of 100 replicates were employed. Scale bar represents 0.1 substitution per amino acid position. Strain Flavobacterium aquatile NBRC 15052T was used as an outgroup.
Figure 2. Maximum likelihood phylogenomic tree reconstructed from the concatenated sequences of 400 conserved proteins, depicting the phylogenetic placement of strains 4Alg 33T and 3Alg 14/1 among the type strains of the genera Formosa and Xanthomarina, together with type species from other phylogenetically related genera. The bootstrap values of 100 replicates were employed. Scale bar represents 0.1 substitution per amino acid position. Strain Flavobacterium aquatile NBRC 15052T was used as an outgroup.
Microorganisms 14 00328 g002
Figure 3. (a) Chromosomal maps of strains 4Alg33T and 3Alg14/1 built using the Proksee server [43]. The inner scale indicates genome size in megabases (Mbp). From the innermost rings outward, the first two circles display a GC content (black) and GC skew (G−C)/(G+C) (in violet and green, respectively). The next circle shows CDSs strand. Moving outward, the blue circle shows PULs with the substrates indicated in brackets, annotated by the dbCAN3 server [37]. The figure also shows rrn operons and CRISPR-Cas system. (b) ANI visualization by FastANI. Each red line segment represents a reciprocal alignment between the two genomes, highlighting evolutionary conserved regions.
Figure 3. (a) Chromosomal maps of strains 4Alg33T and 3Alg14/1 built using the Proksee server [43]. The inner scale indicates genome size in megabases (Mbp). From the innermost rings outward, the first two circles display a GC content (black) and GC skew (G−C)/(G+C) (in violet and green, respectively). The next circle shows CDSs strand. Moving outward, the blue circle shows PULs with the substrates indicated in brackets, annotated by the dbCAN3 server [37]. The figure also shows rrn operons and CRISPR-Cas system. (b) ANI visualization by FastANI. Each red line segment represents a reciprocal alignment between the two genomes, highlighting evolutionary conserved regions.
Microorganisms 14 00328 g003
Figure 4. Pan-genome and functional COG classification in Formosa. (A) The pan-genome of Formosa genus members created using the anvi’o platform [36]. Functional classes of COG database predicted in the core and shell-cloud genomes (B) and distribution of unique genes into classes among Formosa strains (C). Circlular bars indicate the presence or absence of pan-genomic clusters across individual genomes. The heatmap in the upper right displays pairwise ANI and AAI values. The strain 4Alg 33T is shown in brown, the strain 3Alg 14/1 in green, and other Formosa species in black. Additional data integrated into the figure include COG20 functional categories and KOfam module annotations. Description of COG one-letter codes can be found at https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/, accessed on 23 January 2026.
Figure 4. Pan-genome and functional COG classification in Formosa. (A) The pan-genome of Formosa genus members created using the anvi’o platform [36]. Functional classes of COG database predicted in the core and shell-cloud genomes (B) and distribution of unique genes into classes among Formosa strains (C). Circlular bars indicate the presence or absence of pan-genomic clusters across individual genomes. The heatmap in the upper right displays pairwise ANI and AAI values. The strain 4Alg 33T is shown in brown, the strain 3Alg 14/1 in green, and other Formosa species in black. Additional data integrated into the figure include COG20 functional categories and KOfam module annotations. Description of COG one-letter codes can be found at https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/, accessed on 23 January 2026.
Microorganisms 14 00328 g004
Figure 5. Heatmaps illustrating distribution of CAZymes (A,B), PULs, BGCs, and TSS (C) in 4Alg 33T, 3Alg 14/1, and the Formosa type strains. GH, glycoside hydrolase; GT, glycosyltransferase; CE, carbohydrate esterase; PL, polysaccharide lyase; AA, auxiliary activity; PUL, polysaccharide-utilizing locus; BGC, biosynthetic gene cluster; TSS, type secretion system.
Figure 5. Heatmaps illustrating distribution of CAZymes (A,B), PULs, BGCs, and TSS (C) in 4Alg 33T, 3Alg 14/1, and the Formosa type strains. GH, glycoside hydrolase; GT, glycosyltransferase; CE, carbohydrate esterase; PL, polysaccharide lyase; AA, auxiliary activity; PUL, polysaccharide-utilizing locus; BGC, biosynthetic gene cluster; TSS, type secretion system.
Microorganisms 14 00328 g005
Figure 6. Genomic organization and genetic relatedness of ulvan-utilizing loci between 3Alg 14/1 and F. agariphila KMM 3901T strains. BLAST version 2.16.0+ identity is represented by grayscale shading ranging from 100% to 50%.
Figure 6. Genomic organization and genetic relatedness of ulvan-utilizing loci between 3Alg 14/1 and F. agariphila KMM 3901T strains. BLAST version 2.16.0+ identity is represented by grayscale shading ranging from 100% to 50%.
Microorganisms 14 00328 g006
Table 1. Genomic features of novel strains 4Alg 33T and 3Alg 14/1, and type strains of the genus Formosa.
Table 1. Genomic features of novel strains 4Alg 33T and 3Alg 14/1, and type strains of the genus Formosa.
Feature12345678
Assembly levelChromosomeChromosomeContigChromosomeContigChromosomeContigScaffold
Genome size (Mb)4.24.34.44.24.33.94.33
Number of contigs1149821176
G+C Content (mol%)34.534.534.133.533.53234.531
N50 (Mb)4157.74316.14407.22500108.439004300141.1
L50111113118
Coverage (x)180196150532210125644
Total genes35453663396236233693344537112838
Protein-coding genes34593579389735413613336735422775
rRNAs (5S/16S/23S)4/4/44/4/45/5/54/3/31/1/14/4/44/4/4 1/1/3
tRNA4747504541464636
checkM completeness (%)100.099.3599.0199.3599.6899.8495.0799.35
checkM contamination (%)0.111.291.8301.080.820.490.16
WGS project-JBJJID02--LMAK01-BDEL01VSFC01
Genome assembly nameASM5101608v1ASM4739746v2PRJNA1402693FAGA1ASM143966v1ASM719773v1ASM168548v1ASM808490v1
Strains: 1, 4Alg 33T; 2, 3Alg 14/1; 3, F. undariae KCTC 32328T; 4, F. agariphila KMM 3901T; 5, F. algae KMM 3553T; 6, F. sediminum PS13T; 7, F. haliotis MA1T; 8, F. maritima 1494T.
Table 2. Differential characteristics of strains 4Alg 33Tand 3Alg 14/1 compared to their closely related species of the genus Formosa.
Table 2. Differential characteristics of strains 4Alg 33Tand 3Alg 14/1 compared to their closely related species of the genus Formosa.
Feature1234
Source of isolationBrown and green algaeBrown algaBrown algaGreen alga
Type of metabolismAAFF
Gliding motility+++
Temperature range for growth (°C):4–344–304–344–33
Salinity range for growth
(% NaCl):
0–80–90–81–8
Degradation of:    
Agar++
Gelatin+++
Acid formation from:    
D-Cellobiose, D-lactose +
D-Galactose+++
L-Rhamnose++
GlycerolND+
Utilization of:    
L-Arabinose, D-lactose++
Enzyme activities (API ZYM):    
α-Glucosidase+++
Cysteine arylamidase,+++
Esterase (C4),
N-acetyl-β-glucosaminidase
+++
Trypsin, α-chymotrypsin,
α-fucosidase
++
Susceptibility to:    
Ampicillin, carbenicillin +++
Benzylpenicillin++
Oleandomycin++
Cefazolin+++
DNA G+C content (mol%)34.537.333.533.5
Oxidase++++
Catalase+++
Strains: 1, 4Alg 33T and 3Alg 14/1; 2, F. undariae KCTC 32328T; 3, F. algae KMM 3553T; 4, F. agariphila KMM 3901T. The strains were positive for the following tests: catalase and oxidase activities; hydrolysis of aesculin; acid production from D-fructose, D-glucose, maltose, D-mannose, D-xylose and N-acetyl-glucosamine; utilization of D-fructose, D-galactose, D-glucose, maltose, D-mannose, D-xylose and D-mannitol; alkaline phosphatase, esterase lipase (C8), leucine arylamidase, valine arylamidase, acid phosphatase and naphthol-AS-BI-phosphohydrolase activities; susceptibility to cefalexin, chloramphenicol, doxycycline, erythromycin, lincomycin, ofloxacin, rifampicin, tetracycline and vancomycin, and resistance to gentamicin, kanamycin, neomycin, oxacillin, polymyxin and streptomycin. The strains were negative for the following tests: nitrate reduction; hydrolysis of casein, chitin, L-tyrosine, Tween 80, DNA and urea; H2S and indole production; flexirubin-type pigments production; sucrose and citrate utilization; lipase (C14) and β-glucuronidase activities. A, aerobic; F, facultatively anaerobic; +, positive; −, negative; ND, not determined.
Table 3. Fatty acid profile of strains 4Alg 33T and 3Alg 14/1 and the type strains of the closely related members of the genus Formosa.
Table 3. Fatty acid profile of strains 4Alg 33T and 3Alg 14/1 and the type strains of the closely related members of the genus Formosa.
Fatty Acid12345
Saturated straight-chain: 
C15:05.97.66.318.513.0
C16:08.07.58.02.64.3
C18:03.92.54.3Tr1.2
Unsaturated straight-chain: 
C15:1 ω6c4.95.56.313.57.6
C16:1 ω7c7.811.58.55.86.1
Branched-chain: 
iso-C14:0Tr1.11.62.01.7
iso-C15:018.314.015.512.615.7
anteiso-C15:02.74.33.44.16.7
iso-C15:110.67.89.78.66.6
iso-C16:04.04.32.32.33.0
iso-C16:13.62.31.92.12.0
iso-C17:1 ω8c1.41.2Tr1.31.5
Hydroxy-substituted: 
iso-C15:0 3-OH2.22.72.89.210.3
iso-C16:0 3-OH8.610.85.49.010.6
iso-C17:0 3-OH15.414.521.46.48.3
Strains: 1, 4Alg 33T; 2, 3Alg 14/1; 3, F. undariae KCTC 32328T; 4, F. algae KMM 3553T [2]; 5, F. agariphila KMM 3901T [2]. Tr, trace (<1%); Summed feature 3 consists of iso-C15:0 2-OH and/or C161 ω7c that could not be separated by the microbial identification system. The polar lipid composition of strains 4Alg 33T and 3Alg 14/1 included phosphatidylethanolamine (PE), one unidentified aminolipid (AL1) and three unidentified lipids (L1-3) (Figure S1) and was in line with that of the reference strains and other type strains of the validly published species of the genus Formosa (Figure S1) [7,8,9]. However, the presence of third unidentified lipid (L3) differed the novel strains from their nearest neighbor, F. undariae (Figure S1). The major respiratory quinone of the strains studied was MK-6.
Table 4. Differential characteristics of Formosa maritima KCTC 72531T, Bizionia arctica SM1203T and Xanthomarina species.
Table 4. Differential characteristics of Formosa maritima KCTC 72531T, Bizionia arctica SM1203T and Xanthomarina species.
Feature1234
Source of isolationMarine sedimentSeawaterMarine spongeSeawater
Temperature range for growth (°C):4–37 *4–3015–35 **10–40
Salinity range for growth (% NaCl):0–8 *1–61–5 **0.5–7.5
Gliding motility+++
Oxidase+++
Arginine dihydrolase ++
Nitrate reduction++
Flexirubin-type pigment production+++
Hydrolysis of:    
Casein++
Starch+
Tween 80++
TyrosineND+ND
Urea+
Acid formation from D-glucose+++
Utilization of:    
L-Arabinose− *+ **ND
D-Glucose+ *+ **
Maltose, D-mannose− *+ **
N-acetyl-glucosamine, gluconate− *+ **ND
Enzyme activities (API ZYM):    
Acid phosphatase+ *+− **ND
α-Galactosidase− *+ **
Susceptibility to:    
Ampicillin+++
Carbenicillin, cefalexin++ND
Neomycin+
Tetracycline, vancomycin++
Streptomycin+ND
DNA G+C content (mol%) *35.5313133
Strains: 1, F. maritima KCTC 72531T (data from this study); 2, B. arctica SM1203T, data from [52]; 3, X. spongicola KCTC 22662T (data from this study); 4, X. gelatinolytica AK20T, data from [53]. * Data from [6]; ** data from [54]. The strains were positive for the following tests: the respiratory type of metabolism; alkaline phosphatase, esterase lipase (C8), cysteine arylamidase and catalase activities; hydrolysis of gelatin; susceptibility to chloramphenicol, and resistance to gentamycin, kanamycin and polymyxin. The strains were negative for the following tests: hydrolysis of agar and aesculin; utilization of D-mannitol and citrate; β-glucosidase, β-galactosidase, β-glucuronidase, N-acetyl-β-glucosaminidase and α-fucosidase activities. All data were from this study unless otherwise indicated. +, positive; −, negative; ND, not determined.
Table 5. Fatty acid profiles of strain Formosa maritima KCTC 72531T, Bizionia arctica SM1203T and Xanthomarina species.
Table 5. Fatty acid profiles of strain Formosa maritima KCTC 72531T, Bizionia arctica SM1203T and Xanthomarina species.
Fatty Acid1234
Saturated straight-chain:     
C15:04.65.3 1.7
C16:05.6Tr 6.1
C18:02.2  3.1
Unsaturated straight-chain:    
C15:1 ω6c1.2Tr Tr
C16:1 ω7c3.5 7.92.6
Branched-chain:    
iso-C14:02.73.4 1.3
iso-C15:025.025.539.325.6
anteiso-C15:04.714.2 3.8
iso-C15:115.320.329.58.6
anteiso-C15:1-3.4--
iso-C16:04.6Tr 1.7
iso-C16:12.91.2 Tr
iso-C17:1 ω8c2.3  1.8
iso-C17:1 ω9c Tr3.8 
Hydroxy-substituted:    
C15:0 2-OH-1.7--
iso-C15:0 3-OH2.42.76.12.5
iso-C16:0 3-OH5.03.9 2.5
C17:0 2-OH-1.2--
iso-C17:0 3-OH16.24.813.435.4
Strains: 1, Formosa maritima KCTC 72531T (this study): 2, Bizionia arctica SM1203T (data from [51]); 3, Xanthomarina gelatinolytica AK20T (data from [52]); 4, Xanthomarina spongiae KCTC 22662T (this study). Tr, trace (<1%); - not detected.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Nedashkovskaya, O.; Bystritskaya, E.; Savicheva, Y.; Bronnikova, Y.; Otstavnykh, N.; Eremeev, V.; Kim, S.-G.; Zhukova, N.; Isaeva, M. Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members. Microorganisms 2026, 14, 328. https://doi.org/10.3390/microorganisms14020328

AMA Style

Nedashkovskaya O, Bystritskaya E, Savicheva Y, Bronnikova Y, Otstavnykh N, Eremeev V, Kim S-G, Zhukova N, Isaeva M. Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members. Microorganisms. 2026; 14(2):328. https://doi.org/10.3390/microorganisms14020328

Chicago/Turabian Style

Nedashkovskaya, Olga, Evgeniya Bystritskaya, Yulia Savicheva, Yulia Bronnikova, Nadezhda Otstavnykh, Viacheslav Eremeev, Song-Gun Kim, Natalia Zhukova, and Marina Isaeva. 2026. "Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members" Microorganisms 14, no. 2: 328. https://doi.org/10.3390/microorganisms14020328

APA Style

Nedashkovskaya, O., Bystritskaya, E., Savicheva, Y., Bronnikova, Y., Otstavnykh, N., Eremeev, V., Kim, S.-G., Zhukova, N., & Isaeva, M. (2026). Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members. Microorganisms, 14(2), 328. https://doi.org/10.3390/microorganisms14020328

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop