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Article

Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs

by
Katia Messner
1,
Caleb Pereira
1,
John A. Kyndt
2,
Marike Palmer
1 and
Vladimir Yurkov
1,*
1
Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
2
College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA
*
Author to whom correspondence should be addressed.
Microorganisms 2026, 14(3), 525; https://doi.org/10.3390/microorganisms14030525
Submission received: 25 January 2026 / Revised: 20 February 2026 / Accepted: 22 February 2026 / Published: 25 February 2026
(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential, 3rd Edition)
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Abstract

A pink colored, rod-shaped, prosthecate, Gram-negative bacterial strain MS644T was discovered in saline spring water near Lake Winnipegosis, Manitoba, Canada. It produces bacteriochlorophyll a, which is incorporated into its reaction center and light harvesting I complex. Alongside no anaerobic or photoautotrophic growth, these features support its designation as an aerobic anoxygenic phototroph (AAP). Unlike most AAP, the photosynthetic apparatus is produced in significantly greater amounts compared to carotenoids. Sequence of the 16S rRNA gene identified relatedness to Glycocaulis albus (96.19%), Glycocaulis alkaliphilus (96.12%) and Glycocaulis abyssi (96.07%). The DNA G + C content was 66.01 mol %. Differences in salt tolerance and photosynthesis capability, alongside low average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization compared to other Maricauaceae, support the designation of the strain as a representative of a new genus. Therefore, we propose that strain MS644T (=NCIMB 15625T = DSM 121292T) be classified as the type species of a new genus Apolloniradiicaulis in Maricaulaceae with the name A. salifontis gen. nov., sp. nov.

1. Introduction

There is a diverse subset of bacteria that can perform anoxygenic photosynthesis, a process typically associated with anaerobes, in oxygenated environments. Aptly named aerobic anoxygenic phototrophs (AAP), they can use light as a supplemental energy source to aerobic respiration [1,2]. Unable to grow autotrophically due to the absence of RuBisCo [3], the capability to perform photosynthesis provides AAP an advantage over other heterotrophs in nutrient deficient or starvation situations [4,5,6,7]. They use the photosynthetic pigment bacteriochlorophyll a (BChl a), which is incorporated into reaction center (RC) and light-harvesting (LH) complex(es) to initiate a light-induced energy transfer that ultimately triggers ATP synthesis [1]. AAP have been found in every aerobic environment tested, including marine, terrestrial, polar and freshwater sites [8,9,10,11,12,13]. Their roles within communities include participation in organic carbon cycling as well as bioremediation, particularly involving reducing heavy metal oxides of tellurium, selenium and vanadium to less toxic forms [14,15,16,17]. They are primarily phylogenetically distributed among the Alpha-, Beta- and Gammaproteobacteria classes [8,18,19,20,21].
In the Caulobacterales order (Alphaproteobacteria), some key traits are the production of prosthecate and a dimorphic lifestyle containing motile swarmer and reproductive stalked phases [22]. A prostheca is an extension of the bacterial envelope which increases the surface area of the cell [22,23]. They aid in increasing nutrient uptake, with length enhanced in low phosphate habitats [22]. It also serves as a holdfast to fix cells to surfaces [22]. Interestingly, photosynthesis is emerging as a more recently discovered feature in the order [23]. There are currently two AAP genera, Brevundimonas [16,23] and Photocaulis [24], which have been confirmed to contain the photosynthetic apparatus through absorption spectral analysis. However, there are likely more, as additional isolated strains and uncultured members in Oceanicaulis, Alkalicaulis and Aquidulcibacter have been identified with genes responsible for anoxygenic photosynthesis [23,24]. Of these genera, Photocaulis, Oceanicaulis and Alkalicaulis, all belong to Maricaulaceae [25]. This family was recently separated from Hyphomonadaceae [26] and mainly comprises members isolated from sea water or organisms found in marine systems (dinoflagellates, red algae, reef- building corals) [26]. Notable exceptions include species from oil fields [27] and alpine meromictic lakes [24].
In West-Central Manitoba along the shores of one of the largest freshwater lakes in Canada, Lake Winnipegosis, lies a series of ancient saline springs [28]. First detailed by Tyrell in 1892 [29], written reports of the sites date much earlier in La Vérendrye’s journals from the early 1700s [30]. These areas have garnered interest in astrobiological research, being proposed as an analog for Mars’ spring brines [31] as some may still be active and, therefore, prime candidate sites for Martian life [31]. Such studies also included those exploring the organisms that exist around the springs. As in many other extremely saline habitats, it was predominantly microbial [32,33]. Interestingly, this inland habitat comprises microorganisms usually found in marine ecosystems [33,34]. The most well studied location is the East German Creek. It has been the subject of thorough examination regarding its geochemistry [28,35] and hydrochemistry [36]. More detailed investigations of specific subsets of microorganisms followed, including the anaerobic population [37] and our study on the AAP [38]. As a result, a diverse community was found, with new genera and species such as Charonomicrobium ambiphototrophicum [39] and gammaproteobacterial AAP Chromatocurvus halotolerans [18]. There was also the identification of ‘vanadiphillic’ AAP Roseovarius strain EG13, which is tolerant of sodium metavanadate at high concentrations (>5000 µg/mL) and when grown in these conditions it has enhanced pigment production [17].
With the previous success of discovering unknown taxa from saline springs [38], we pursued another round of sampling, this time not at East German Creek, but at less explored locations, with the goal of uncovering AAP. Here, we describe a prosthecae-producing species with high levels of the anoxygenic photosynthetic apparatus as the first saline spring representative of Maricaulaceae. Strain MS644T belongs to a new genus and species for which we propose the name Apolloniradiicaulis salifontis gen. nov., sp. nov.

2. Materials and Methods

2.1. Isolation and Cultivation

Strain MS644T was isolated from water (0.9% NaCl, 18.9 °C, pH 8.1) of a saline spring in the Lake Winnipegosis region (coordinates 51°36′39″ N 99°52′09″ W) in June 2024. The site had a light gray microbial mat that was located at the bottom of the spring. The sample was kept on ice until return to the laboratory and then subjected to a decimal serial dilution of 10−5 using the following media (pH 7.0, g/L): MgCl2, 0.5; KH2PO4, 0.3; NH4Cl, 0.3; CaCl2, 0.1, NaCl, 20.0. The dilutions were plated (50 µL) in triplicate on solid (2% agar) 2RO medium (pH 7, g/L): MgSO4, 0.5; KH2PO4, 0.3; NH4Cl, 0.3; KCl, 0.3; CaCl2, 0.05; NaCl, 20.0; Na-acetate, 1.0; yeast extract, 0.1; bactopeptone, 0.5; casamino acids, 0.5; trace element solution (TES) [40], 2 mL; and vitamin solution (VS) [40], 2 mL. Plates were incubated aerobically at 28 °C in the dark for a month and throughout that period they were screened for colored colonies with the first check after 3 days. Strain MS644T was isolated from a 10−3 plate after 31 days.
For subsequent characterization, MS644T was grown in liquid 2RO for 7 days in the dark at 28 °C on a shaking incubator, unless stated otherwise. For tests where the strain was incubated in light, an incandescent light bulb was used (2270 lx, measured with a 21800-014 light meter (VWR, Radnor, PA, USA)). For long-term storage, cells were cryopreserved at −80 °C in 2RO modified with 10% (w/v) of original organics and 30% (v/v) glycerol.

2.2. Morphology, Physiology and Chemotaxonomy

Cell shape, size and motility were determined after 1 day of growth with phase contrast microscopy (Zeiss Axioskop 2 (Zeiss, Oberkochen, Germany). The effect of phosphate on prosthecae production was assessed in 2RO modified to have glutamate (0.5%) as the sole carbon source and reduced phosphate concentration (0.15 g/L). Gram staining [41] was conducted alongside a KOH test [42] for confirmation. Colony morphology was observed throughout 3 weeks of growth.
Temperature optimum and range was evaluated by growing the cells at the following (°C): 4, 7, 16, 21, 25, 28, 32, 37 and 45; growth at pH 5.0 to 12.0 with 0.5 increments as well as NaCl from 0 to 20% (w/v) at 1% intervals. Utilization of complex (bactopeptone, casamino acids and yeast extract) and simple carbon sources ranging from organic Na salts (acetate, butyrate, citrate, formate, glutamate, lactate, malate, pyruvate, succinate), sugar alcohols (glycerol, sorbitol), simple alcohols (ethanol, methanol), sugars (arabinose, fructose, glucose, sucrose, trehalose, xylose), and amino acids (L-alanine, L-proline) were determined at 0.5% concentration in 2RO modified to exclude other organics. Use of nitrate, ammonium and N2 as a sole N source, aerobically, were tested in 2RO with no carbon sources except 0.5% Na-glutamate and adding 0.3 g/L of the respective N compound or none in the case for determining nitrogen fixation (atmospheric). Sulfur utilization was checked in a similar manner, except MgSO4 was substituted with Na2SO4, Na2S2O3, methionine or cysteine at 0.5 g/L. Requirement of vitamins was assessed by omitting all or one individual vitamin from vs. (nicotinic acid, thiamine, biotin and/or vitamin B12) in 2RO modified to include Na-succinate (0.5%) as the sole carbon source. Oxidase, catalase, nitrate reduction and indole tests as well as hydrolysis of tween 20, 40, 60 and 80, starch, gelatin and agar, were done as described [43]. Additional carbon sources and enzyme testing was performed using the API 20NE and API ZYM (bioMérieux, Lyon, France) following manufacturer’s instructions. Antibiotic susceptibility was observed with disk diffusion test for the following (μg): ampicillin (10), chloramphenicol (30), erythromycin (15), imipenem (10), kanamycin (30), penicillin G (10), polymyxin B (300), nalidixic acid (30), streptomycin (10), and tetracycline (30). In the case of no growth inhibition, strain MS644T was listed as resistant.
Photo- and chemo- heterotrophic anaerobic growth was investigated in screw-capped tubes incubated in light and dark using liquid 2RO and purple non-sulfur bacteria medium (PNSbM) supplemented with 2% NaCl [40]. Additional testing was done with different inorganic electron donors in PNSbM by substituting the amino acids (cysteine and methionine) with Na2S (1 mM) or Na2S2O3 (1 mM) [24]. Anaerobic fermentation of fructose, glucose, lactose, maltose and sucrose was determined in liquid minimal 2RO with screw-capped tubes incubated in the dark. Anaerobic denitrification was assessed similarly, except Na-Succinate was added as the carbon source/electron donor and NH4Cl was substituted with KNO3 (0.3 g/L). Microaerobic growth was determined in 2RO and Medium B [38] plates (g/L): MgCl2, 2.5; Na2SO4, 3.5; KH2PO4, 0.3; NH4Cl, 0.5; KCl, 0.7; CaCl2, 0.05; Na-acetate, 1.0; yeast extract, 0.5; NaHCO3, 1.5; FeCl3, 2.9 × 10−4; Na2S2O3, 0.3; NaCl, 20.0; TES, 10 mL and VS, 2 mL, and were put into an anaerobic jar with the GasPak EZ CampyPak (BD) sachets to create a microaerobic environment. Aerobic photoautotrophy in light was evaluated in liquid PNSbM without organics, supplemented with (g/L): NaHCO3, 1.5 and Na2S2O3, 0.5 as an inorganic carbon and sulfur source/electron donor, respectively [39]. Two subsequent cell transfers were done if growth was observed, to account for trace organics that remained in the initial inoculum.
For fatty acid analysis, cells were harvested in triplicate after being grown on 2RO plates for 3 days at 28 °C in the dark. Lipid extraction and purification were performed as in [44] and analyzed [45] using a Varian 450 GC gas chromatograph (Varian, Inc., Palo Alto, CA, USA) with standard GLC-461 (Nu-Chek Prep, Inc., Elysian, MN, USA).

2.3. Spectroscopy and Pigment Composition

Photosynthetic complex presence in MS644T was determined after cells were grown for 9 days on 2RO plates in constant darkness. Whole cells and pigment extracts (7:2 acetone:methanol) were prepared for absorption spectra reading, including correcting for light scattering and measured using equipment described [46].

2.4. Sequencing and Phylogenetic Analysis

The 16S rRNA gene fragment (1314 bp) covering V1-V8 region was obtained via Sanger sequencing using universal primers 27F (5`-AGAGTTTGATCCTGGCTCAG-3`) and 1492R (5`-GGTTACCTTGTTACGACTT-3`). Type species with the most similar sequences were identified through a standard nucleotide BLAST search [47]. A 16S rRNA-based phylogenetic tree was constructed with MEGA 12 software (Version 12.0.11) [48], using an alignment generated with ClustalW (default parameters), the Maximum Likelihood method and 1000 bootstrap replicates with the Kimura 2-parameter model [49] (chosen with the MEGA 12 ‘find best DNA model’ tool). To measure evolutionary rate differences among sites, a gamma distribution (+G, parameter = 0.6887) with five rate categories was applied and it was assumed that a certain fraction of sites are evolutionarily invariable ([+I], 68.96% sites). The final dataset had 24 nucleotide sequences and 1500 positions. The version with highest log likelihood (−5997.74) is presented.
To obtain the whole genome sequence, DNA was extracted, then sequenced with the Illumina MiniSeq system and the Oxford Nanopore MinION following manufacturer’s instructions [50]. The sequencing library was prepared using the Illumina DNA Library Prep kit and sequenced using paired-end (2 × 150 bp) sequencing by the Illumina MiniSeq. Oxford Nanopore DNA library prep was performed following the Ligation Sequencing Kit (SQK-LSK110) (Oxford Nanopore Technologies, Oxford, England) on a FLO-MIN106D flow cell with a MinION-Mk1B instrument (Oxford Nanopore Technologies, Oxford, England) [50]. No DNA shearing was performed. The MinION output was basecalled with ‘Superaccuracy Basecall’ using Guppy (Version 6.5.7) [51] and generated 361.40 Mb and the Illumina sequencing run produced 201.79 Mb. The long reads were assembled on BV-BRC [52] using flye (Version 2.9.1) [53], which generated a single contig assembly of 3,149,712 bp in size. The Illumina dataset was quality checked with FASTQC (Version 1.0.0) and cleaned with FASTQ Toolkit (Version 2.2.6) using a k-mer size of 5 and contamination filtering. Illumina reads were assembled on BV-BRC [52] using Unicycler [54] (Version 0.4.8). Resulting contigs were mapped to the MinION-generated long read assembly using Minimap 2 [55] on Geneious (Version 2025.1). The resulting circularized genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline [56]. G + C content (mol %) was estimated from the genome sequence. Digital DNA-DNA hybridization (dDDH) was calculated with formula d4 on the Genome-to-Genome Distance Calculator (Version 4.0) applying the recommended settings on the Type (Strain) Genome Server (TYGS) [57,58]. JSpeciesWS "https://jspecies.ribohost.com/jspeciesws/(accessed on 14 Septemeber 2025)" assessed average nucleotide identity (ANI) [59]. Two-way average amino acid identity (AAI) was compared among the available genomes of Maricaulaceae species and strain MS644T using the ezAAI calculator (Version 1.2.4) [60]. For phylogenomic tree inference, nucleotide sequences of 92 conserved marker genes were extracted from the genomes of 23 type strains of species including those within Maricaulaceae and Robiginitomaculum antarcticum as the outgroup using the UBCG v. 3 pipeline [61]. These aligned marker gene sequences were subjected to concatenation and partitioning with FASconCAT-G (version 1.06) [62]. A maximum-likelihood phylogeny was then inferred from the concatenated data matrix with edge-unlinked partitions, and branch support was inferred from 1000 replicates with non-parametric bootstrapping on IQ-TREE 3 (version 3.0.1) [63] with the model determined using ModelFinder [64]. Both 16S rRNA and genome-based trees were visualized with iTOL [65].

3. Results and Discussion

3.1. Phenotypic Characteristics

When strain MS644T is grown on 2RO in the dark, isolated colonies appear 4–5 days after the initial streak as light pink (Figure 1A), then become darker (Figure 1B). As they continue to age, colonies turn lighter around the edges (Figure 1C). Most Maricaulaceae are non-pigmented or faint yellow, with the exception of Photocaulis spp. [24]. Strain MS644T is Gram-negative, rod-shaped, motile and readily produces prosthecae like all Maricaulaceae (Figure 1D,E). The size of the cells is approximately 1.1 ± 0.2 μm in length and 0.5 ± 0.1 μm in width when grown on 2RO for three days, with prosthecae approximately equal in length to the cell body (1.1 µm) (Figure 1D). In lower phosphate conditions, prosthecae were longer and more prominent and cells were pleomorphic, with vibroid, rod and spirillum morphologies (Figure 1E). The presence of elongated prosthecae when phosphate is limited matches previous observations in Caulobacter crescentus [66].
Strain MS644T is a moderate obligate halophile (Table 1) based on standard classification [67]. It could grow in up to 16% NaCl (Table 1), only comparable to Marinicauda salina in the family, but strain MS644T still has a higher optimum NaCl concentration (6% versus 5%) [68]. Therefore, it is the most halophilic of the currently described Maricaulaceae. Although salinity was diluted at the sampling period due to recent heavy rain fall (0.9% NaCl), typical habitat concentrations are higher and can increase significantly during hot, dry periods with limited precipitation, showing the strains adaptability to changing salt concentrations. The strain grows between pH 6.0 and 10.0, preferring environments closer to neutral (6.0) and is a mesophile, with an optimum of 25 °C (Table 1). It can utilize all complex carbon sources tested (casamino acids, bactopeptone and yeast extract), but only a select set of the single (Na-butyrate, Na-glutamate, L-proline and Na-succinate). This is very similar to other species in the family, which have limited single carbon sources that can support growth [24,27,69,70]. Strain MS644T was unable to grow with any of the tested N or S compounds as the sole sources. Vitamin B12, biotin and thiamine are required, but not nicotinic acid. It was negative for indole, amylase, tween 20, 40, 60 and 80 hydrolysis, arginine dihydrolase, urease, lipase (C14), valine arylamidase, cystine arylamidase, α-chymotrypsin, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase. It produces the following enzymes: gelatinase, oxidase, catalase, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, trypsin, acid phosphatase and naphthol-AS-BI-phosphorylase. MS644T is resistant to polymyxin B and susceptible to all other antibiotics tested: ampicillin, chloramphenicol, erythromycin, imipenem, kanamycin, penicillin G, nalidixic acid, streptomycin, and tetracycline. It did not grow in any of the anaerobic conditions, including chemoheterotrophically, photoheterotrophically, by fermentation or denitrification. Although there is preference for atmospheric oxygen levels, it can also grow microaerobically on MB medium. Aerobic photoautotrophic growth was not observed.
The fatty acid composition is as follows (%, values rounded to nearest decimal): C18:1 (72.9), C18:0 (23.7), C16:0 (1.2), C17:0 (0.8), C20:2 (0.5), C20:1 (0.5), C16:1 (0.2), C20:0 (0.1), C18:1 ω7c (<0.1), C14:0 (<0.1), C16:1 t (<0.1), C12:0 (<0.1) and C15:0 (<0.1).

3.2. Photosynthetic Pigment Analysis

Absorption spectrum of the acetone-methanol pigment extract confirmed production of BChl a with peak at 768 nm, while the in vivo whole cell reading of strain MS644T shows this pigment incorporated into the anoxygenic photosynthetic apparatus (590, 801, 872) (Figure 2). The RC is recognized by the 759 and 801 nm peaks. The RC’s third peak, which is usually around ~ 860 nm, is overlapped by the peak of LHI complex, detected at 872 nm. The major LHI peak is slightly shifted from what is commonly seen (870 nm) but is well within the known range found in AAP (854–879 nm) [3,21,73,74]. It is likely a result of changes to the amino acid sequence of LHI, which change the environment of the noncovalently bound BChl and therefore the wavelength of absorance [73]. The 484, 517, and 553 nm peaks in whole cells represent the absorption of carotenoids, the pigments primarily responsible for cell color. The 759 nm peak belongs to bacteriopheophytin incorporated to the RC. Often, it is not detectable in AAP due to poor presence of the photosynthetic apparatus. Notably in strain MS644T, LHI complex BChl expression is very high, with its absorbance being much greater than the carotenoid peaks (Figure 2). This is rare, because typically, it is the opposite in most AAP [73]. They produce many carotenoids to help combat photooxidative damage during BChl a synthesis and photosynthetic activity [73]. The estimated ratio of BChl:carotenoids in strain MS644T is 3.47:1 using the absorbance values at 768 and 529 nm peaks, respectively, from the pigment extract spectrum. In AAP, energy harnessed from light is supplemental to the yield gained from aerobic respiration [1]. Such enhanced synthesis of the photosynthetic apparatus has not been seen in Caulobacterales species. AAP Brevundimonas aurifodinae [16], Brevundimonas variabilis [23], Photocaulis sulfatitolerans [24] and Photocaulis rubescens [24] have typical, much lower height absorption peaks. Obviously, the regulation of photosynthesis expression in strain MS644T is less constrained and light energy may serve as a more valuable resource for the cell. Since strain MS644T neither produces RuBisCo, grows autotrophically, nor survives anaerobic conditions, but is still able to synthesize the anoxygenic photosynthetic apparatus, its designatation as an AAP is well supported.

3.3. Phylogeny

An almost complete 16S rRNA gene was obtained from Sanger sequencing (1314 bp, GenBank accession number PX499558), with the full gene (1474 bp) later identified in the chromosome. Based on the 16S gene sequence BLAST results, the most related species to strain MS644T were Glycocaulis albus (96.19%), Glycocaulis alkaliphilus (96.12%) and Glycocaulis abyssi (96.07%). While it had similarities to Glycocaulis in regard to pH, temperature tolerances and the production of prosthecae, there were also several important differences such as colony color, salinity growth range and photosynthetic capabilities (Table 1). Interestingly, despite the sequence similarity, on the 16S rRNA gene tree, strain MS644T was aligned more closely with Marinicauda (Figure 3). BLAST results in more detail showed that Marinicauda algicola (96.00%) and Marinicauda pacifica (95.65%) are almost as similar in sequence to strain MS644T as the Glycocaulis spp. This is evident from the fairly low bootstrap values on the branching of Glycocaulis away from strain MS644T, suggesting the tree is not well supported in the region.
Alongside the 16S rRNA gene tree, a genome-based phylogenomic tree was made (Figure 4). Here, strain MS644T aligns appropriately with Oceanicaulis, Alkalicaulis and Photocaulis, creating a different impression of relatedness. Notably, the lowest bootstrap value is from the node that groups those genera, MS644T and Marinicauda. The discrepancy between 16S rRNA gene sequence similarity and grouping of MS644T in each phylogenetic tree shows that strain MS644T cannot be placed in an existing genus within the family.

3.4. Genome Features

The complete genome of strain MS644T was sequenced and circularized (accession number JBSJZB000000000). It is 3.1 Mbp long, with a 179x average fold coverage from both the MinION and Illumina sequences. It contains a single chromosome and no plasmids. The G + C content is 66.03 mol %, falling within the family range (Table 2). It encodes 3018 genes for putative proteins and 43 tRNA. CheckM completeness was 100% and contamination was 0.4%, indicating sequence is of good quality. All genes for anoxygenic photosynthesis are contained within a photosynthetic gene cluster (PGC). It is 44 kbp, matching the PGC sizes found in Photocaulis rubescens and Alkalicaulis satelles [24]. It contains all the genes required for photosynthesis, including for bacteriochlorophyll and (bch) carotenoid synthesis (crt) as well as reaction center and light-harvesting complex proteins (puf and puh). The organization and composition of the PGC was almost identical to Alkalicaulis satelles [24], except MS644T had an additional gene located between bchG and bchP which was annotated as a membrane transporter protein. The quinone in cells is Q-10, determined based on the presence of decaprenyl diphosphate synthase, which creates the 10-unit isoprenoid side chain. No other quinone variations were detected among identified genes. The strain contains holdfast polysaccharide synthesis and anchoring genes. Polyhydroxyalkanoate polymerase (phaC) and depolymerase (phaZ) were found, suggesting strain MS644T accumulates polyhydroxyalkanoates for carbon and fuel storage.
The calculated ANI, AAI and dDDH of strain MS644T and close relatives fall well below the standard species cutoff values (<95%, <95–96% and <70%, respectively, Table 2, Figure 5) [75,76,77]. Current recommendations suggest that 60-65% AAI should be the cutoff for genus designation [75]. However, some publications have developed family-dependent values [78], as previously collected data show that the cutoff among families varies, with genera delineation thresholds between 60 and 85% [79,80]. Therefore, to clarify the taxonomic status of MS644T, the AAI between Maricaulaceae species were calculated (Figure 5). Alkalicaulis satelles has the highest similarity with MS644T (70.70%), falling right between the average for inter-genus (64.14%) and intra-genus (75.48%) AAI values. However, many inter-genus AAI values in Maricaulaceae are close to 70.70% (Figure 5), supporting the designation of strain MS644T as a new genus.

4. Conclusions

Based on both genetic and phenotypic features, strain MS644T is a member of the Maricaulaceae family. It produces prosthecae, cannot grow without NaCl and is phylogenetically situated well within the family based on generated phylogenetic trees. However, it cannot be grouped to any described genera as the highest AAI similarity (70.70%) with MS644T is within the typical inter-genus value. Furthermore, phylogenetic branching on 16S rRNA and genome-based trees as well as 16S rRNA gene homology are not consistent, with each identifying a different genus as the closest relative (Marinicauda, Oceanicaulis and Glycocaulis, respectively). It is also capable of performing anoxygenic photosynthesis, adding another significantly differentiating aspect to its lifestyle that is not found in the closest related genera. Its natural habitat, saline springs, is also distinctly different from other isolation sites of Maricaulacae species. Therefore, with all considered features of strain MS644T, we propose it be classified as a new genus and species with the name Apolloniradiicaulis salifontis.

4.1. Description of Apolloniradiicaulis gen. nov.

Apolloniradiicaulis (Apo.llo.ni’ra.dii.cau’lis. Gr. masc. n. Apollo, God of light; L. masc. n. radius, ray or beam, in context of light; L. masc. n. caulis, stalk; N.L. masc. n. Apolloniradiicaulis, stalk with a ray of light from Apollo, referring to extensive photopigment production).
Gram-negative, motile rod cells that contain a single prostheca. Strict aerobes capable of anoxygenic photosynthesis. Synthesize bacteriochlorophyll a incorporated into a typical RC-LHI complex. Can grow chemo- or photo-heterotrophically, but not photoautotrophically or via fermentation. Member of the family Maricaulaceae (order Maricaulales). The type species is Apolloniradiicaulis salifontis.

4.2. Description of Apolloniradiicaulis salifontis sp. nov.

Apolloniradiicaulis salifontis (sa.li.fon’tis. L. masc. n. sal, salt; L. masc. n. fons, spring; N.L. gen. n. salifontis, of a salt spring).
Cells are rod-shaped, motile and approximately 1.1 ± 0.2 μm in length and 0.5 ± 0.1 μm in width after a day of growth. Colonies are Gram-negative, oxidase- and catalase-positive. It grows in the following conditions (optimum): temperature range of 16 to 37 °C (25 °C); pH of 6.0 to 10.0 (6.0); and NaCl (% w/v) at 1 to 16% (6%). Colonies are light pink early in growth (5 days) becoming dark pink (9 days), then later becoming lighter at the edges (20 days). When grown on 2RO medium aerobically in the dark, colonies are of a deep pink-red color. Bacteriochlorophyll a, carotenoids, photosynthetic reaction center and light-harvesting I complex are produced, indicative of the aerobic anoxygenic photosynthesis. It can grow aerobically and in microaerobic conditions, but not anaerobically. It is incapable of photoautotrophic growth. Biotin, thiamine and vitamin B12 are required for growth, but it can synthesize nicotinic acid. It uses complex carbon sources (casamino acids, bactopeptone, yeast extract), some organic Na salts (butyrate, glutamate, succinate) and L-proline but none of the alcohols (ethanol, methanol, sorbitol, glycerol,), sugars (arabinose, fructose, glucose, sucrose, trehalose, xylose) remaining organic Na salts (acetate, citrate, formate, lactate, malate, pyruvate), carbon sources tested on API strips (adipic acid, capric acid, K-gluconate, mannitol, maltose, mannose, N-acetyl-glucosamine, phenylacetic acid) or L-alanine. Major fatty acids (%) are C18:1 (72.9) and C18:0 (23.7). The genome has a G+C content of 66.02 mol %. It comprises a single chromosome—3.1 Mbp in length.
The type strain is MS644T (=NCIMB 15625T = DSM 121292T), isolated from saline springs near Lake Winnipegosis, in West-Central Manitoba, Canada. The GenBank accession numbers for the 16S rRNA gene sequence and genome assembly are PX499558 and GCA_053756655.1, respectively.

Author Contributions

Conceptualization, K.M. and V.Y.; formal analysis, K.M., C.P., J.A.K., M.P. and V.Y.; funding acquisition, J.A.K., M.P. and V.Y.; investigation, C.P., K.M., J.A.K., M.P. and V.Y.; methodology, K.M., C.P., J.A.K., M.P. and V.Y.; project administration, V.Y.; resources, J.A.K., M.P. and V.Y.; supervision, V.Y.; writing—first draft, K.M.; writing—review and editing, K.M., C.P., J.A.K., M.P. and V.Y. All authors have read and agreed to the published version of the manuscript.

Funding

This study was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant 1501 awarded to V. Yurkov, and the Wilson Enhancement Fund for Applied Research in Science at Bellevue University, to J. Kyndt. Sampling for this work was supported by NSERC Discovery Grant 5462 and the University of Manitoba’s Faculty of Science Field Work Support Program 2024 awarded to M. Palmer.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Strain MS644T ribosomal 16S rRNA gene sequence is available under the GenBank accession number: PX499558. This Whole Genome Shotgun project has been deposited at the DDBJ/ENA/GenBank under the accession JBSJZB000000000, which was used in this study.

Acknowledgments

We would like to thank the following: Logan Lytwyn and the Lytwyn family for permission to sample and access to the spring on their lands; the undergraduate summer research students Aman Chauhan, Jacob Hruska, and Tiana Steeves in the Palmer lab at the University of Manitoba that performed the sampling; J. Kyndt’s visiting students, Alyssia Lespes and Solenn Bosmans from Erasmus University Brussels (Belgium), for their help with sequencing preparation; and Aharon Oren for his assistance with checking the Latin grammar and the spelling of the new name.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
AAPAerobic Anoxygenic Phototrophs
BChl aBacteriochlorophyll a
RCReaction Center
LHLight-Harvesting Complex
VSVitamin Solution
TESTrace element solution
PNSbMPurple Non-sulfur Bacteria Medium
dDDHDigital DNA-DNA Hybridization
ANIAverage Nucleotide Identity
AAIAverage Amino Acid Identity
MBMedium B

References

  1. Yurkov, V.V.; Beatty, J.T. Aerobic Anoxygenic Phototrophic Bacteria. Microbiol. Mol. Biol. Rev. 1998, 62, 695–724. [Google Scholar] [CrossRef]
  2. Rathgeber, C.; Beatty, J.T.; Yurkov, V. Aerobic Phototrophic Bacteria: New Evidence for the Diversity, Ecological Importance and Applied Potential of This Previously Overlooked Group. Photosyn. Res. 2004, 81, 113–128. [Google Scholar] [CrossRef]
  3. Yurkov, V.; Hughes, E. Genes Associated with the Peculiar Phenotypes of the Aerobic Anoxygenic Phototrophs. In Advances in Botanical Research; Beatty, J.T., Ed.; Academic Press Inc.: Cambridge, MA, USA, 2013; Volume 66, pp. 327–358. [Google Scholar]
  4. Biebl, H.; Wagner-Döbler, I. Growth and Bacteriochlorophyll a Formation in Taxonomically Diverse Aerobic Anoxygenic Phototrophic Bacteria in Chemostat Culture: Influence of Light Regimen and Starvation. Process Biochem. 2006, 41, 2153–2159. [Google Scholar] [CrossRef]
  5. Kirchhoff, C.; Ebert, M.; Jahn, D.; Cypionka, H. Chemiosmotic Energy Conservation in Dinoroseobacter shibae: Proton Translocation Driven by Aerobic Respiration, Denitrification, and Photosynthetic Light Reaction. Front. Microbiol. 2018, 9, 903. [Google Scholar] [CrossRef] [PubMed]
  6. Soora, M.; Cypionka, H. Light Enhances Survival of Dinoroseobacter shibae during Long-Term Starvation. PLoS ONE 2013, 8, e83960. [Google Scholar] [CrossRef][Green Version]
  7. Zong, R.; Jiao, N. Proteomic Responses of Roseobacter litoralis OCh149 to Starvation and Light Regimen. Microbes Environ. 2012, 27, 430–442. [Google Scholar] [CrossRef] [PubMed]
  8. Spring, S.; Lünsdorf, H.; Fuchs, B.M.; Tindall, B.J. The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov. PLoS ONE 2009, 4, e4866. [Google Scholar] [CrossRef] [PubMed]
  9. Yurkov, V.V.; Gorlenko, V.M. Roseococcus gen. nov., a New Genus of Freshwater Aerobic, Bacteriochlorophyll a-Containing Bacteria. Mikrobiologiya 1991, 60, 902–907. [Google Scholar]
  10. Saitoh, S.; Suzuki, T.; Nishimura, Y. Proposal of Craurococcus roseus gen. nov., sp. nov and Paracraurococcus ruber gen. nov., sp. nov., Novel Aerobic Bacteriochlorophyll a-Containing Bacteria from Soil. Int. J. Syst. Bacteriol. 1998, 48, 1043–1047. [Google Scholar] [CrossRef][Green Version]
  11. Csotonyi, J.T.; Swiderski, J.; Stackebrandt, E.; Yurkov, V. A New Environment for Aerobic Anoxygenic Phototrophic Bacteria: Biological Soil Crusts. Environ. Microbiol. Rep. 2010, 2, 651–656. [Google Scholar] [CrossRef]
  12. Zeng, Y.; Chen, X.; Madsen, A.M.; Zervas, A.; Nielsen, T.K.; Andrei, A.S.; Lund-Hansen, L.C.; Liu, Y.; Hansen, L.H. Potential Rhodopsin-and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier. mBio 2020, 11, e02641-20. [Google Scholar] [CrossRef]
  13. Tahon, G.; Willems, A. Isolation and Characterization of Aerobic Anoxygenic Phototrophs from Exposed Soils from the Sør Rondane Mountains, East Antarctica. Syst. Appl. Microbiol. 2017, 40, 357–369. [Google Scholar] [CrossRef] [PubMed]
  14. Yurkov, V.; Jappé, J.; Vermeglio, A. Tellurite Resistance and Reduction by Obligately Aerobic Photosynthetic Bacteria. Appl. Environ. Microbiol. 1996, 62, 4195–4198. [Google Scholar] [CrossRef] [PubMed]
  15. Maltman, C.; Donald, L.J.; Yurkov, V. Tellurite and Tellurate Reduction by the Aerobic Anoxygenic Phototroph Erythromonas ursincola, Strain KR99 Is Carried out by a Novel Membrane Associated Enzyme. Microorganisms 2017, 5, 20. [Google Scholar] [CrossRef]
  16. Maltman, C.; Messner, K.; Kyndt, J.A.; Yurkov, V. Brevundimonas aurifodinae, sp. nov., an Aerobic Anoxygenic Phototroph Resistant to Metalloid Oxyanions Isolated from Gold Mine Tailings. Microorganisms 2024, 12, 2167, Erratum in: Microorganisms 2025, 14, 86. [Google Scholar] [CrossRef]
  17. Csotonyi, J.T.; Maltman, C.; Swiderski, J.; Stackebrandt, E.; Yurkov, V. Extremely ‘Vanadiphilic’ Multiply Metal-Resistant and Halophilic Aerobic Anoxygenic Phototrophs, Strains EG13 and EG8, from Hypersaline Springs in Canada. Extremophiles 2015, 19, 127–134. [Google Scholar] [CrossRef]
  18. Csotonyi, J.T.; Stackebrandt, E.; Swiderski, J.; Schumann, P.; Yurkov, V. Chromocurvus halotolerans gen. nov., sp. nov., a Gammaproteobacterial Obligately Aerobic Anoxygenic Phototroph, Isolated from a Canadian Hypersaline Spring. Arch. Microbiol. 2011, 193, 573–582. [Google Scholar] [CrossRef] [PubMed]
  19. Suyama, T.; Shigematsu, T.; Takaichi, S.; Nodasaka, Y.; Fujikawa, S.; Hosoya, H.; Tokiwa, Y.; Kanagawa, T.; Hanada, S. Roseateles depolymerans gen. nov., sp. nov., a New Bacteriochlorophyll a-Containing Obligate Aerobe Belonging to the β-Subclass of the Proteobacteria. Int. J. Syst. Bacteriol. 1999, 49, 449–457. [Google Scholar] [CrossRef]
  20. Imhoff, J.F.; Rahn, T.; Künzel, S.; Neulinger, S.C. Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of pufLM Reaction Center Proteins. Front. Microbiol. 2018, 8, 2679. [Google Scholar] [CrossRef]
  21. Yurkov, V.; Hughes, E. Aerobic Anoxygenic Phototrophs: Four Decades of Mystery. In Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects; Hallenbeck, P.C., Ed.; Springer: Cham, Switzerland, 2017; pp. 193–214. [Google Scholar]
  22. Hallgren, J.; Jonas, K. Diversity and Evolution of Alphaproteobacterial Dimorphism. Curr. Opin. Microbiol. 2025, 88, 102661. [Google Scholar] [CrossRef]
  23. Hallgren, J.; Dharamshi, J.E.; Rodríguez-Gijón, A.; Nuy, J.; Garcia, S.L.; Jonas, K. Widespread Potential for Phototrophy and Convergent Reduction of Lifecycle Complexity in the Dimorphic Order Caulobacterales. Nat. Commun. 2025, 16, 11003. [Google Scholar] [CrossRef] [PubMed]
  24. Kuzyk, S.B.; Jafri, M.; Humphrey, E.; Maltman, C.; Kyndt, J.A.; Yurkov, V. Prosthecate Aerobic Anoxygenic Phototrophs Photocaulis sulfatitolerans gen. nov. sp. nov. and Photocaulis rubescens sp. nov. Isolated from Alpine Meromictic Lakes in British Columbia, Canada. Arch. Microbiol. 2022, 204, 444, Erratum in: Arch Microbiol. 2022, 204, 646. [Google Scholar] [CrossRef]
  25. Parte, A.C.; Carbasse, J.S.; Meier-Kolthoff, J.P.; Reimer, L.C.; Göker, M. List of Prokaryotic Names with Standing in Nomenclature (LPSN) Moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 2020, 70, 5607–5612. [Google Scholar] [CrossRef]
  26. Kevbrin, V.; Boltyanskaya, Y.; Koziaeva, V.; Uzun, M.; Grouzdev, D. Alkalicaulis satelles gen. nov., sp. nov., a Novel Haloalkaliphile Isolated from a Laboratory Culture Cyanobacterium Geitlerinema Species and Proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov. Int. J. Syst. Evol. Microbiol. 2021, 71, 004614. [Google Scholar] [CrossRef] [PubMed]
  27. Geng, S.; Pan, X.C.; Mei, R.; Wang, Y.N.; Liu, X.Y.; Wang, X.B.; Tang, Y.Q.; Wu, X.L. Glycocaulis alkaliphilus sp. nov., a Dimorphic Prosthecate Bacterium Isolated from Crude Oil. Int. J Syst. Evol. Microbiol. 2015, 65, 838–844. [Google Scholar] [CrossRef]
  28. Grasby, S.E. Saline Spring Geochemistry, West-Central Manitoba. In Report of Activities 2000; Manitoba Geological Survey: Winnipeg, MB, Canada, 2000. [Google Scholar]
  29. Tyrell, J.B. Report on Northwestern Manitoba with Portions of the Adjacent Districts of Assiniboia and Saskatchewan; Geological Survey of Canada: Dartmouth, NS, Canada, 1892. [Google Scholar]
  30. Petch, V.P. The Salt-Makers of Manitoba: A Study of the Use of Natural Saline Deposits. Master’s Thesis, University of Manitoba, Winnipeg, MB, Canada, 1990. [Google Scholar]
  31. Berard, G.; Applin, D.; Cloutis, E.; Stromberg, J.; Sharma, R.; Mann, P.; Grasby, S.; Bezys, R.; Horgan, B.; Londry, K.; et al. A Hypersaline Spring Analogue in Manitoba, Canada for Potential Ancient Spring Deposits on Mars. Icarus 2013, 224, 399–412. [Google Scholar] [CrossRef]
  32. Grasby, S.E.; Osadetz, K.; Betcher, R.; Render, F. Reversal of the Regional-Scale Flow System of the Williston Basin in response to Pleistocene Glaciation. Geology 2000, 28, 635–638. [Google Scholar] [CrossRef]
  33. Oren, A. Diversity of Halophilic Microorganisms: Environments, Phylogeny, Physiology, and Applications. J. Ind. Microbiol. Biotechnol. 2002, 28, 56–63. [Google Scholar] [CrossRef]
  34. Patterson, R.T.; McKillop, W.B.; Kroker, S.; Nielsen, E.; Reinhardt, E.G. Evidence for Rapid Avian-Mediated Foraminiferal Colonization of Lake Winnipegosis, Manitoba, during the Holocene Hypsithermal. J. Paleolimnol. 1997, 18, 131–143. [Google Scholar] [CrossRef]
  35. Bezys, R.K.; Ducharme, E.B.; Bamburak, J.D.; Fedikow, M.A.F. A Geochemical Study of Saline Brine Sediments as a Guide to Prairie-Type Microdisseminated Mineralization and Other Precious Metals in West-Central Manitoba. In Report of Activities 1997; Manitoba Geological Survey: Winnipeg, MB, Canada, 1997. [Google Scholar]
  36. Grasby, S.E.; Chen, Z. Subglacial Recharge into the Western Canada Sedimentary Basin—Impact of Pleistocene Glaciation on Basin Hydrodynamics. GSA Bull. 2005, 117, 500–514. [Google Scholar] [CrossRef]
  37. Grover, H.D. Carbon Isotopic Fractionation in Methanosarcina barkeri and the Study of Anaerobic Microbial Communities of Saline Springs in West Central Manitoba. Master’s Thesis, University of Manitoba, Winnipeg, MB, Canada, 2004. [Google Scholar]
  38. Csotonyi, J.T.; Swiderski, J.; Stackebrandt, E.; Yurkov, V.V. Novel Halophilic Aerobic Anoxygenic Phototrophs from a Canadian Hypersaline Spring System. Extremophiles 2008, 12, 529–539. [Google Scholar] [CrossRef]
  39. Csotonyi, J.T.; Stackebrandt, E.; Swiderski, J.; Schumann, P.; Yurkov, V. An Alphaproteobacterium Capable of Both Aerobic and Anaerobic Anoxygenic Photosynthesis but Incapable of Photoautotrophy: Charonomicrobium ambiphototrophicum, gen. nov., sp. nov. Photosynth. Res. 2011, 107, 257–268. [Google Scholar] [CrossRef] [PubMed]
  40. Bilyj, M.; Lepitzki, D.; Hughes, E.; Swiderski, J.; Stackebrandt, E.; Pacas, C.; Yurkov, V.V. Abundance and Diversity of the Phototrophic Microbial Mat Communities of Sulphur Mountain Banff Springs and Their Significance to the Endangered Snail, Physella johnsoni. Open J. Ecol. 2014, 4, 488–516. [Google Scholar] [CrossRef]
  41. Beveridge, T.J. Use of the Gram Stain in Microbiology. Biotech. Histochem. 2001, 76, 111–118. [Google Scholar] [CrossRef] [PubMed]
  42. Gregersen, T. Rapid Method for Distinction of Gram-Negative from Gram-Positive Bacteria. Eur. J. Appl. Microbiol. Biotech. 1978, 5, 123–127. [Google Scholar] [CrossRef]
  43. Yurkov, V.V.; Krieger, S.; Stackebrandt, E.; Beatty, J.T. Citromicrobium bathyomarinum, a Novel Aerobic Bacterium Isolated from Deep-Sea Hydrothermal Vent Plume Waters That Contains Photosynthetic Pigment- Protein Complexes. J. Bacteriol. 1999, 181, 4517–4525. [Google Scholar] [CrossRef]
  44. Folch, J.; Lees, M.; Sloane Stanley, G.H. A Simple Method for the Isolation and Purification of Total Lipides from Animal Tissues. J. Biol. Chem. 1957, 226, 497–509. [Google Scholar] [CrossRef]
  45. Politz, M.; Lennen, R.; Pfleger, B. Quantification of Bacterial Fatty Acids by Extraction and Methylation. Bio. Protoc. 2013, 3, 950. [Google Scholar] [CrossRef]
  46. Rathgeber, C.; Yurkova, N.; Stackebrandt, E.; Schumann, P.; Beatty, J.T.; Yurkov, V. Roseicyclus mahoneyensis gen. nov., sp. nov., an Aerobic Phototrophic Bacterium Isolated from a Meromictic Lake. Int. J. Syst. Evol. Microbiol. 2005, 55, 1597–1603. [Google Scholar] [CrossRef] [PubMed]
  47. Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol. 1990, 215, 403–410. [Google Scholar] [CrossRef]
  48. Kumar, S.; Stecher, G.; Suleski, M.; Sanderford, M.; Sharma, S.; Tamura, K. MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing. Mol. Biol. Evol. 2024, 41, msae263. [Google Scholar] [CrossRef] [PubMed]
  49. Kimura, M. A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences. J. Mol. Evol. 1980, 16, 111–120. [Google Scholar] [CrossRef] [PubMed]
  50. Jain, M.; Olsen, H.E.; Paten, B.; Akeson, M. The Oxford Nanopore MinION: Delivery of Nanopore Sequencing to the Genomics Community. Genome Biol. 2016, 17, 239, Erratum in: Genome Biol. 2016, 17, 256. [Google Scholar] [CrossRef]
  51. Wick, R.R.; Judd, L.M.; Holt, K.E. Performance of Neural Network Basecalling Tools for Oxford Nanopore Sequencing. Genome Biol. 2019, 20, 129. [Google Scholar] [CrossRef] [PubMed]
  52. Wattam, A.R.; Davis, J.J.; Assaf, R.; Boisvert, S.; Brettin, T.; Bun, C.; Conrad, N.; Dietrich, E.M.; Disz, T.; Gabbard, J.L.; et al. Improvements to PATRIC, the All-Bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2017, 45, D535–D542. [Google Scholar] [CrossRef]
  53. Kolmogorov, M.; Yuan, J.; Lin, Y.; Pevzner, P.A. Assembly of Long, Error-Prone Reads Using Repeat Graphs. Nat. Biotechnol. 2019, 37, 540–546. [Google Scholar] [CrossRef]
  54. 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]
  55. Li, H. Minimap2: Pairwise Alignment for Nucleotide Sequences. Bioinformatics 2018, 34, 3094–3100. [Google Scholar] [CrossRef]
  56. 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]
  57. 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]
  58. 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. 2022, 50, D801–D807. [Google Scholar] [CrossRef]
  59. Richter, M.; Rosselló-Móra, R.; Oliver Glöckner, F.; Peplies, J. JSpeciesWS: A Web Server for Prokaryotic Species Circumscription Based on Pairwise Genome Comparison. Bioinformatics 2016, 32, 929–931. [Google Scholar] [CrossRef]
  60. 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] [PubMed]
  61. Na, S.I.; Kim, Y.O.; Yoon, S.H.; Ha, S.M.; Baek, I.; Chun, J. UBCG: Up-to-date Bacterial Core Gene Set and Pipeline for Phylogenomic Tree Reconstruction. J. Microbiol. 2018, 56, 280–285. [Google Scholar] [CrossRef] [PubMed]
  62. Kück, P.; Longo, G.C. FASconCAT-G: Extensive Functions for Multiple Sequence Alignment Preparations Concerning Phylogenetic Studies. Front. Zool. 2014, 11, 81. [Google Scholar] [CrossRef]
  63. Wong, T.K.F.; Ly-Trong, N.; Ren, H.; Baños, H.; Roger, A.J.; Susko, E.; Bielow, C.; De Maio, N.; Goldman, N.; Hahn, M.W.; et al. IQ-TREE 3: Phylogenomic Inference Software Using Complex Evolutionary Models. EcoEvoRxiv 2025. [Google Scholar]
  64. Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef]
  65. Letunic, I.; Bork, P. Interactive Tree of Life (ITOL) v6: Recent Updates to the Phylogenetic Tree Display and Annotation Tool. Nucleic Acids Res. 2024, 52, W78. [Google Scholar] [CrossRef]
  66. Wagner, J.K.; Setayeshgar, S.; Sharon, L.A.; Reilly, J.P.; Brun, Y.V. A Nutrient Uptake Role for Bacterial Cell Envelope Extensions. Proc. Natl. Acad. Sci. USA 2006, 103, 11772–11777. [Google Scholar] [CrossRef] [PubMed]
  67. Larsen, H. Halophilism. In The Bacteria; Gunsalus, I.C., Stanier, R.Y., Eds.; Academic Press: New York, NY, USA, 1962; Volume 4, pp. 297–342. [Google Scholar]
  68. Zhai, T.J.; Liu, B.T.; Zhu, R.Q.; Chen, G.J.; Du, Z.J. Marinicauda salina sp. nov., Isolated from a Marine Solar Saltern. Int. J. Syst. Evol. Microbiol. 2019, 69, 2233–2238. [Google Scholar] [CrossRef]
  69. Lv, X.L.; Xie, B.S.; Cai, M.; Geng, S.; Tang, Y.Q.; Wang, Y.N.; Cui, H.L.; Liu, X.Y.; Ye, S.Y.; Wu, X.L. Glycocaulis albus sp. nov., A Moderately Halophilic Dimorphic Prosthecate Bacterium Isolated from Petroleum-Contaminated Saline Soil. Int. J. Syst. Evol. Microbiol. 2014, 64, 3181–3187. [Google Scholar] [CrossRef]
  70. Abraham, W.R.; Lünsdorf, H.; Vancanney, M.; Smit, J. Cauliform Bacteria Lacking Phospholipids from an Abyssal Hydrothermal Vent: Proposal of Glycocaulis abyssi gen. nov., sp. nov., Belonging to the Family Hyphomonadaceae. Int. J. Syst. Evol. Microbiol. 2013, 63, 2207–2215. [Google Scholar] [CrossRef]
  71. Zhang, X.Y.; Li, G.W.; Wang, C.S.; Zhang, Y.J.; Xu, X.W.; Li, H.; Liu, A.; Liu, C.; Xie, B.-B.; Qin, Q.L.; et al. Marinicauda pacifica gen. nov., sp. nov., a Prosthecate Alphaproteobacterium of the Family Hyphomonadaceae Isolated from Deep Seawater. Int. J. Syst. Evol. Microbiol. 2013, 63, 2248–2253. [Google Scholar] [CrossRef]
  72. Strömpl, C.; Hold, G.L.; Lünsdorf, H.; Graham, J.; Gallacher, S.; Abraham, W.R.; Moore, E.R.B.; Timmis, K.N. Oceanicaulis alexandrii gen. nov., sp. nov., a Novel Stalked Bacterium Isolated from a Culture of the Dinoflagellate Alexandrium tamarense (Lebour) Balech. Int. J. Syst. Evol. Microbiol. 2003, 53, 1901–1906. [Google Scholar] [CrossRef] [PubMed]
  73. Yurkov, V.; Messner, K. Phenomenal Diversity of the Photosynthetic Apparatus Evolved in Aerobic Anoxygenic Phototrophs. Microorganisms 2025, 13, 2446. [Google Scholar] [CrossRef]
  74. Yurkov, V.; Csotonyi, J.T. New Light on Aerobic Anoxygenic Phototrophs. In The Purple Phototrophic Bacteria; Hunter, C.N., Daldal, F., Thurnauer, M.C., Beatty, J.T., Eds.; Springer: Dordrecht, The Netherlands, 2009; pp. 31–55. [Google Scholar]
  75. Konstantinidis, K.T.; Tiedje, J.M. Towards a Genome-Based Taxonomy for Prokaryotes. J. Bacteriol. 2005, 187, 6258–6264. [Google Scholar] [CrossRef] [PubMed]
  76. Kim, M.; Oh, H.S.; Park, S.C.; Chun, J. Towards a Taxonomic Coherence between Average Nucleotide Identity and 16S RRNA Gene Sequence Similarity for Species Demarcation of Prokaryotes. Int. J. Syst. Evol. Microbiol. 2014, 64, 346–351. [Google Scholar] [CrossRef] [PubMed]
  77. Goris, J.; Konstantinidis, K.T.; Klappenbach, J.A.; Coenye, T.; Vandamme, P.; Tiedje, J.M. DNA-DNA Hybridization Values and Their Relationship to Whole-Genome Sequence Similarities. Int. J. Syst. Evol. Microbiol. 2007, 57, 81–91. [Google Scholar] [CrossRef] [PubMed]
  78. Park, M.J.; Kim, Y.J.; Park, M.; Yu, J.; Namirimu, T.; Roh, Y.R.; Kwon, K.K. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front. Microbiol. 2022, 13, 738205. [Google Scholar] [CrossRef]
  79. 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]
  80. Wirth, J.S.; Whitman, W.B. Phylogenomic Analyses of a Clade within the Roseobacter Group Suggest Taxonomic Reassignments of Species of the Genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the Proposal of Six Novel Genera. Int. J. Syst. Evol. Microbiol. 2018, 68, 2393–2411. [Google Scholar] [CrossRef] [PubMed]
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Figure 1. Colony and cellular morphology of strain MS644T. Colonies after 5 (A), 9 (B) and 20 (C) days of growth. Cells after 3 days in 2RO (D) and 6 days in minimal 2RO modified to include Na-glutamate as the sole carbon source and half the original phosphate levels (0.15 g/L) (E). Bar: 5.0 µm.
Figure 1. Colony and cellular morphology of strain MS644T. Colonies after 5 (A), 9 (B) and 20 (C) days of growth. Cells after 3 days in 2RO (D) and 6 days in minimal 2RO modified to include Na-glutamate as the sole carbon source and half the original phosphate levels (0.15 g/L) (E). Bar: 5.0 µm.
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Figure 2. Whole cell (black) and pigment extract (blue) absorption spectra of strain MS644T. Peaks and shoulders are indicated for each spectrum with the respective color.
Figure 2. Whole cell (black) and pigment extract (blue) absorption spectra of strain MS644T. Peaks and shoulders are indicated for each spectrum with the respective color.
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Figure 3. Phylogenetic tree of 16S rRNA gene sequences from strain MS644T and species in Maricaulaceae. Branch lengths are measured in the number of substitutions per site. The percentage of trees where associated taxa cluster together is represented next to the branch. Associated accession numbers for sequences are included within parentheses. Strain MS644T is in red. Robiginitomaculum antarcticum is used as the outgroup.
Figure 3. Phylogenetic tree of 16S rRNA gene sequences from strain MS644T and species in Maricaulaceae. Branch lengths are measured in the number of substitutions per site. The percentage of trees where associated taxa cluster together is represented next to the branch. Associated accession numbers for sequences are included within parentheses. Strain MS644T is in red. Robiginitomaculum antarcticum is used as the outgroup.
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Figure 4. Phylogenomic tree of MS644T and sequenced species in Maricaulaceae. Version with the highest log likelihood (−1241169.197) is shown and drawn to scale. The branch support values were generated from 1000 rounds of bootstrapping. Tree scale was defined as the mean number of nucleotide substitutions per site. GenBank assembly accession number for each genome is included in parentheses. Strain MS644T is in red. Robiginitomaculum antarcticum is used as the outgroup.
Figure 4. Phylogenomic tree of MS644T and sequenced species in Maricaulaceae. Version with the highest log likelihood (−1241169.197) is shown and drawn to scale. The branch support values were generated from 1000 rounds of bootstrapping. Tree scale was defined as the mean number of nucleotide substitutions per site. GenBank assembly accession number for each genome is included in parentheses. Strain MS644T is in red. Robiginitomaculum antarcticum is used as the outgroup.
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Figure 5. Heatmap of AAI calculated comparing strain MS644T to all Maricaulaceae with sequenced genomes. Robiginitomaculum antarcticum is used as an outgroup to compare AAI values within the family. Genomes are the same as in Figure 4. Created using R (Version 4.5.2) package pheatmap (Version 1.0.13), which implemented hierarchical clustering of genome AAI values.
Figure 5. Heatmap of AAI calculated comparing strain MS644T to all Maricaulaceae with sequenced genomes. Robiginitomaculum antarcticum is used as an outgroup to compare AAI values within the family. Genomes are the same as in Figure 4. Created using R (Version 4.5.2) package pheatmap (Version 1.0.13), which implemented hierarchical clustering of genome AAI values.
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Table 1. Features of strain MS644T compared to the phylogenetically related species in Maricaulaceae.
Table 1. Features of strain MS644T compared to the phylogenetically related species in Maricaulaceae.
SpeciesApolloniradiicaulis salifontisGlycocaulis
abyssi		Glycocaulis
albus		Glycocaulis  alkaliphilusMarinicauda pacificaPhotocaulis  sulfatitoleransAlkalicaulis  satellesOceanicaulis alexandrii
StrainMS644TMCS 33TSLG210-30A1T6B-8TP-1 km-3TBL14TG192TC116-18T
Colony ColorDark PinkColorlessFaint YellowWhiteWhitePinkWhiteColorless
Cell ShapeRodFusiform/Vibroid/RodRodsRodRodVibroidRodRod/Vibrioid
Prothecae++++++++
Bacteriochlorophyll a+− −−−+−−
Photosynthesis Genes+−−−−++−
Motility++++++++
Temperature range/optimum (°C)16–37/2520–40/3015–40/25–3720–37/30–376–40/304–41/325–46/35–404–37/30
pH range/optimum6–10/68–10/77–9/88–10/96–9.5/76.5–11/77.3–10.3/8–96–10/7–9
NaCl range/optimum (%)1–16/61–5/2–51–6/1–31–50.5–12/20.5–6.5/2.5–3.50–14/2–61–9/1–2
Oxygen requirementObligate AerobeObligate AerobeFacultative AnaerobeObligate AerobeObligate AerobeObligate AerobeObligate AerobeObligate Aerobe
Anaerobic growth−−+−−−−−
Reference data include type species G. abyssi [70], G. albus [69], G alkaliphilus [27], M. pacifica [71], P. sulfatitolerans [24], A. satelles [26], and O. alexandrii [72]. +, positive; − negative.
Table 2. Genome features of strain MS644T and other species in Maricaulaceae.
Table 2. Genome features of strain MS644T and other species in Maricaulaceae.
SpeciesApolloniradiicaulis salifontisGlycocaulis abyssiGlycocaulis albusGlycocaulis alkaliphilusMarinicauda pacificaPhotocaulis sulfatitoleransAlkalicaulis satellesOceanicaulis alexandrii
Strain 1MS644TMCS 33TSLG210-30A1T6B-8TP-1 km-3TBL14TG192TC116-18T
16S rRNA similarity (%) 210096.1996.1996.1295.7495.2195.4494.68
Genome Size (Mb)3.13.12.93.03.03.02.93.0
G + C Content66.0263.3563.4563.4164.865.966.862.5
Protein-coding genes30183009279829092850300527842854
No. of contigs1227112184
No. of tRNA genes4344444242424542
N503,149,8742,883,807203,7853,019,659782,3023,031,807903,5322,621,375
L5011512121
Check M Contamination (%)0.400.230.3800.681.100.342.57
Check M Completeness (%)10099.699.6298.9999.3210010098.13
AAI (%) 210066.8266.7066.6167.8270.5070.7070.69
ANI (%) 210071.4370.8971.0971.7273.3773.9173.08
dDDH (%) 210018.818.618.718.51919.119.1
1 GenBank Assembly Accession numbers of species from left to right: GCA_053756655.1, GCA_041429775.1, GCA_014639075.1, GCA_014637625.1, GCA_009806145.1, GCA_027627705.1, GCA_008630495.1 and GCA_000420265.1. 2 Values relative to strain MS644T.
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MDPI and ACS Style

Messner, K.; Pereira, C.; Kyndt, J.A.; Palmer, M.; Yurkov, V. Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs. Microorganisms 2026, 14, 525. https://doi.org/10.3390/microorganisms14030525

AMA Style

Messner K, Pereira C, Kyndt JA, Palmer M, Yurkov V. Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs. Microorganisms. 2026; 14(3):525. https://doi.org/10.3390/microorganisms14030525

Chicago/Turabian Style

Messner, Katia, Caleb Pereira, John A. Kyndt, Marike Palmer, and Vladimir Yurkov. 2026. "Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs" Microorganisms 14, no. 3: 525. https://doi.org/10.3390/microorganisms14030525

APA Style

Messner, K., Pereira, C., Kyndt, J. A., Palmer, M., & Yurkov, V. (2026). Apolloniradiicaulis salifontis gen. nov., sp. nov., a New Prosthecate Aerobic Anoxygenic Phototroph Isolated from Lake Winnipegosis Region Salt Springs. Microorganisms, 14(3), 525. https://doi.org/10.3390/microorganisms14030525

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