Genus Devosia Research Articles

Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China.

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35°C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Devosia rhodophyticola sp. nov. and Devosia algicola sp. nov., isolated from a marine red alga.

Two Gram-stain-negative, obligately aerobic, motile rod bacteria, designated as G2-5T and G20-9T, exhibiting catalase- and oxidase-positive activities, were isolated from the phycosphere of a Chondrus species, a marine red alga. Strain G2-5T exhibited optimal growth at 30 °C and pH 5.0-6.0 and in the presence of 0.5-1.0% NaCl. In contrast, strain G20-9T demonstrated optimal growth at 25 °C and pH 6.0 and in the presence of 0.5-1.5% NaCl. Both strains contained ubiquinone-10, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C18 : 0 and 11-methyl-C18 : 1 ω7c, and diphosphatidylglycerol and phosphatidylglycerol as the major respiratory isoprenoid quinone, cellular fatty acids and polar lipids, respectively. The genomic DNA G+C contents were 57.2 mol% for strain G2-5T and 57.5 mol% for strain G20-9T. Strains G2-5T and G20-9T exhibited 98.2 % 16S rRNA gene sequence similarity, along with 82.3 % average nucleotide identity (ANI) and 25.0 % digital DNA-DNA hybridization (dDDH) values, indicating that they represent different species. Phylogenetic analyses based on both 16S rRNA gene and genome sequences revealed that strains G2-5T and G20-9T formed distinct phylogenic lineages within the genus Devosia. Strains G2-5T and G20-9T were most closely related to Devosia limi DSM 17137T and Devosia beringensis S02T with 97.7 and 96.9 % 16S rRNA gene sequence similarities, respectively. The ANI and dDDH values between strains G2-5T and G20-9T and other Devosia species were lower than 73.9 and 19.2 %, respectively, suggesting that they constitute novel species within the genus Devosia. Based on their distinct phenotypic, chemotaxonomic, and molecular characteristics, strains G2-5T and G20-9T represent two novel species of the genus Devosia, for which the names Devosia rhodophyticola sp. nov. (G2-5T=KACC 22601T=JCM 35404T) and Devosia algicola sp. nov. (G20-9T=KACC 22650T=JCM 35405T) are proposed, respectively.

Devosia lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic Microcystis.

A novel alphaproteobacterial strain JXJ CY 41T was isolated from a culture mass of Microcystis, collected from Lake Dianchi, south-west, China. Strain JXJ CY 41T was gram-strain-negative, aerobic, motile, with rod-shaped cells (0.4-1.0 × 1.7-3.5μm). It was positive for catalase and starch hydrolysis, negative for oxidase and hydrolysis of Tweens (20, 40, and 80). Growth occurred at 10-44°C, pH 5.0-10.0, and 0-5.0% (w/v) NaCl. Major fatty acids included C16:0 (28.1%), 11-methyl C18:1 ω7c (36.7%) and C18:1 ω7c (20.8%). Q10 was the sole ubiquinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, and an unidentified lipid. The DNA G + C content was 63.1%. Its 16S rRNA gene sequence showed high similarities with Devosia oryziradicis G19T (99.5%; not validly published), D. yakushimensis Yak96BT (98.3%) and D. ginsengisoli Gsoil 520T (98.1%), and less than 98.1% similarities with other members of the genus Devosia. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain JXJ CY 41T and its 5 closest similar strains were 19.9-24.1% and 75.7-80.5%, respectively. Based on the data above, strain JXJ CY 41T was identified as a novel species of the genus Devosia, for which the epithet Devosia lacusdianchii sp. nov. was proposed. The type strain is JXJ CY 41T (= KCTC 72812T = CGMCC 1.17502T). Strain JXJ CY 41T exhibited different interactions with Microcystis aeruginosa FACHB-905 (Maf) under different conditions, and Maf could control the bacterial cellular density by secreting unknown specific chemical compounds according to its nutritional requirements.

Indoor air VOCs biofiltration by bioactive coating packed bed bioreactors

Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low concentrations, the wide range of compounds and the hydrophobicity of some indoor air VOCs, which are the most important bottlenecks regarding the implementation of conventional biotechnologies for indoor air treatment. A bioactive coating-based bioreactor was tested in this study for the abatement of different VOCs (n-hexane, toluene and α-pinene) at different empty bed residence times (EBRT) and inlet VOC concentrations. The performance of this reactor was compared with a conventional biofilm-based bioreactor operated with the same microbial inoculum. After an acclimation period, the bioactive coating-based bioreactor achieved abatements of over 50% for hexane, 80% for toluene and 70% for pinene at EBRTs of 112–56 s and inlet concentrations of 9–15 mg m−3. These results were about 25, 10 and 20% lower than the highest removals recorded in the biofilm-based bioreactor. Both bioreactors experienced a decrease in VOC abatement by ∼25% for hexane, 45% for toluene and 40% for pinene, after reducing the EBRT to 28 s. When inlet VOC concentrations were progressively reduced, VOC abatement efficiencies did not improve. This fact suggested that low EBRTs and low inlet VOCs concentration hindered indoor air pollutant abatement as a result of a limited mass transfer and bioavailability. Metagenomic analyses showed that process operation with toluene, hexane and pinene as the only carbon and energy sources favored an enriched bacterial community represented by the genera Devosia, Mesorhizobium, Sphingobacterium and Mycobacterium, regardless of the bioreactor configuration. Bioactive coatings were used in this work as packing material of a conventional bioreactor, achieving satisfactory VOC abatement similar to a conventional bioreactor.

Differences in clinical features and gut microbiota between individuals with methamphetamine casual use and methamphetamine use disorder.

The transition from methamphetamine (MA) casual use (MCU) to compulsive use is enigmatic as some MA users can remain in casual use, but some cannot. There is a knowledge gap if gut microbiota (GM) play a role in differing MCU from MA use disorder (MUD). We aimed to investigate the clinical features and GM differences between individuals with MCU and MUD. We recruited two groups of MA users -MCU and MUD - and matched them according to age and body mass index (n=21 in each group). Participants were accessed using the Semi-Structured Assessment for Drug Dependence and Alcoholism, and their fecal samples were undergone 16S ribosomal DNA sequencing. We compared the hosts' clinical features and GM diversity, composition, and structure (represented by enterotypes) between the two groups. We have identified differential microbes between the two groups and performed network analyses connecting GM and the clinical traits. Compared with the casual users, individuals with MUD had higher incidences of MA-induced neuropsychiatric symptoms (e.g., paranoia, depression) and withdrawal symptoms (e.g., fatigue, drowsiness, and increased appetite), as well as stronger cravings for and intentions to use MA, and increased MA tolerance. The GM diversity showed no significant differences between the two groups, but four genera (Halomonas, Clostridium, Devosia, and Dorea) were enriched in the individuals with MUD (p<0.05). Three distinct enterotypes were identified in all MA users, and Ruminococcus-driven enterotype 2 was dominant in individuals with MUD compared to the MCU (61.90% vs. 28.60%, p=0.03). Network analysis shows that Devosia is the hub genus (hub index = 0.75), which is not only related to the counts of the MUD diagnostic criteria (ρ=0.40; p=0.01) but also to the clinical features of MA users such as reduced social activities (ρ=0.54; p<0.01). Devosia is also associated with the increased intention to use MA (ρ=0.48; p<0.01), increased MA tolerance (ρ=0.38; p=0.01), craving for MA (ρ=0.37; p=0.01), and MA-induced withdrawal symptoms (p<0.05). Our findings suggest that Ruminococcus-driven enterotype 2 and the genera Devosia might be two influential factors that differentiate MA casual use from MUD, but further studies are warranted.

Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter.

A Gram-stain-negative, halotolerant bacterium designated as PTR5T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38°C (optimum 30°C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5T based on 16S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C16:0, C18:1 ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5T was 3,689,283bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5T (KCTC 82691T = TBRC 15163T) is proposed.

Effects of different rotation cropping systems on potato yield, rhizosphere microbial community and soil biochemical properties.

Continuous potato cropping systems cause yield reduction, soil-borne disease aggravation, and soil degradation, but crop rotation can alleviate these negative effects. However, there are limited studies on the relationships between microbial community and other soil biochemical properties of continuous potato cropping at both pre-planting and harvest in North China. A 4-year study was conducted to explore the effects of different rotation system on soil biochemical properties, microbial community at pre-planting and harvest, and potato yield, tuber number and black scurf incidence at harvest in 2020 and 2021, which included 4 treatments vis. potato-potato-potato-potato (PC), potato-oat-faba bean-potato (PR), oat-faba bean-potato-oat (O), and faba bean-potato-oat-faba bean (B). The results showed that soil biochemical properties and microbial community among all treatments showed no significant difference at pre-planting after a long cold winter generally. At harvest, PC reduced tuber yield and number and significantly increased black scurf incidence relative to potato rotation systems. PC also reduced soil enzyme activities, the content of soil nutrients, and fungal community diversity, and increased bacterial community diversity compared with the other treatments, insignificantly when compared with PR. Relative abundance of microorganisms related to the degradation of organic residues, soil nitrogen cycling, and disease suppression, such as the genera Devosia, Aeromicrobium, Paraphoma, and Papiliotrema, were significantly higher in O or B than in PC and PR, while microorganisms related to disease infection such as the genera Pseudomonas, Colletotrichum, Plectosphaerella, Fusarium, and Verticillium exhibited increased in PC and PR. Principal Coordinates Analysis (PCoA) showed that there were significant differences in the microbial community structure of PC and PR at harvest compared with that of O and B. Redundancy analysis (RDA) revealed that soil available potassium (AK), acid phosphatase (ACP), available phosphorus (AP), sucrase (SUC) and pH were the dominant factors that significantly affected bacterial and fungal community structure. Partial least squares structural equation model indicated rotation system had significant negative effect on fungal community. It was concluded that growing oat or faba bean after potato can increase soil beneficial microorganisms and maintain the ecosystem healthy, thus reducing the incidence of tuber black scurf and increasing potato yield.

Devosia litorisediminis sp. nov., isolated from a sand dune.

A Gram-negative, aerobic, non-motile, and rod-shaped bacterial strain, designated BSSL-BM10T, was isolated from sand of a dune that was collected from the Yellow Sea, Republic of Korea. It was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis showed that strain BSSL-BM10T fell phylogenetically within the radiation comprising type strains of Devosia species. The 16S rRNA gene sequence of strain BSSL-BM10T shared sequence similarities of 98.2% with the type strain of D. naphthalenivorans and 93.5-97.7% with type strains of other Devosia species. ANI and dDDH values between strain BSSL-BM10T and type strains of 18 Devosia species were 71.0-78.4% and 18.8-21.5%, respectively. The DNA G + C content of strain BSSL-BM10T was 60.9% based on its genomic sequence data. Strain BSSL-BM10T contained Q-10 as the predominant ubiquinone and 11-methyl C18:1 ω7c, C18:1 ω7c, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and C16:0 as its major fatty acids. Major polar lipids of strain BSSL-BM10T were phosphatidylglycerol and two unidentified glycolipids. Strain BSSL-BM10T showed distinguishable phenotypic properties with its phylogenetic and genetic distinctiveness separated from recognized Devosia species. Based on data presented in this study, strain BSSL-BM10T should be placed in the genus Devosia. The name Devosia litorisediminis sp. nov. is proposed for strain BSSL-BM10T (= KACC 21633T = NBRC 115152T).

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth.

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.

Complete genome sequence of Devosia beringensis S02T, a type strain with genes involved in deoxynivalenol degradation.

Members of the genus Devosia are known for their abilities to degrade deoxynivalenol (DON). The type strain Devosia beringensis S02T (= JCM 33772=CCTCC AB 2019343) was isolated from sediment of the Bering Sea and identified in 2021. However, the genome sequence of D. beringensis S02T remains unclear, which complicates the exploration into the function and ecological role of this strain in marine sediment. The genome of D. beringensis S02T contained a 4,048,765bp chromosome with a G+C content of 63.84mol%. Potential genes involved in DON degradation were found in the genome. In addition, multiple genes involved in polysaccharide degradation, including agarose, chitin, carrageen, pectate, starch, and xylan, were also annotated in the genome. These findings indicated the potential of strain S02T to be used for DON degradation and its ecological function in the carbon cycle in marine sediment.

Devosia salina sp. nov., isolated from South China Sea sediment.

An aerobic, Gram-stain-negative, rod-shaped and motile strain, designated SCS-3T, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA gene sequence similarities revealed that strain SCS-3T represented a novel species of the genus Devosia, with closely related strains 'Devosia sediminis' MSA67T (98.61 %), Devosia riboflavina IFO13584T (98.22 %) and Devosia indica IO390501T (97.72 %). The G+C content of the genomic DNA is 63.44 mol%. The digital DNA-DNA hybridization values with 'D. sediminis' MSA67T, D. riboflavina IFO13584T and D. indica IO390501T were 24.50, 21.8 and 24.80 %, respectively. The major polar lipids of strain SCS-3T were diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. Ubiquinone-10 was the sole isoprenoid quinone, and C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) were the major fatty acids. Based on polyphasic taxonomic data, strain SCS-3T represents a novel species of the genus Devosia, for which the name Devosia salina sp. nov. is proposed. The type strain is SCS-3T (=JCM 34403T=GDMCC 1.2221T).

Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Phylogenetic Analyses of Rhizobia Isolated from Nodules of Lupinus angustifolius in Northern Tunisia Reveal Devosia sp. as a New Microsymbiont of Lupin Species

Thirty-two bacterial isolates were obtained from root nodules of Lupinus angustifolius growing in Northern Tunisia. Phylogenetic analyses based on recA and gyrB partial gene sequences grouped the strains into six clusters: four clusters belonged to the genus Bradyrhizobium (22 isolates), one to Microvirga (8 isolates) and one to Devosia (2 isolates), a genus that has not been previously reported to nodulate lupin. Representative strains of each group were further characterized. Multi-Locus Sequence Analysis (MLSA) based on recA and glnII gene sequences separated the strains within the genus Bradyrhizobium into four divergent clusters related to B. canariense, B. liaoningense, B. lupini, and B. algeriense, respectively. The latter might constitute a new Bradyrhizobium species. The strains in the Microvirga cluster showed high identity with M. tunisiensis. The Devosia isolates might also represent a new species within this genus. An additional phylogenetic analysis based on the symbiotic gene nodC affiliated the strains to symbiovars genistearum, mediterranense, and to a possibly new symbiovar. These results altogether contributed to the existing knowledge on the genetic diversity of lupin-nodulating microsymbionts and revealed a likely new, fast-growing, salt-tolerant rhizobial species within the genus Devosia as a potentially useful inoculant in agricultural practices or landscape restoration.

Description of Devosia faecipullorum sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696T contained C16:0, C18:0, C18:1ω7c 11-methyl and C18:1ω6c/ C18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696T=BCRC 81284T=JCM 34167T) is proposed.

Devosia sediminis sp. nov., isolated from subterranean sediment.

A novel Gram-negative, cream-colored, rod-shaped, aerobic, non-motile bacterium, designated MSA67T, was isolated from a subterranean sediment sample of the Mohe Basin in Northeast China. Strain MSA67T was detected to grow at 4-40°C (optimum 28-30°C), pH 5.0-10.0 (optimum, pH 7.0) and in 0.0-8.0% (w/v) NaCl (optimum 2.0-3.0%). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MSA67T was a member of the genus Devosia, with the highest similarity with D. riboflavina IFO13584T (98.0%) and D. chinhatensis IPL18T (97.0%). The major cellular fatty acids are C16:0, C18:1ω7c 11-methyl and C18:1ω6c and/or C18:1ω7c. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, glycolipids and three unidentified phospholipids. The major respiratory quinone is ubiquinone 10 (Q-10). The genomic size of strain MSA67T is 4.1MB and DNA G + C content is 63.6%. Based on genotypic, phenotypic and phylogenetic results, strain MSA67T is concluded to represent a novel species of the genus Devosia, for which the name Devosia sediminis sp. nov. is proposed. The type strain is MSA67T (= CGMCC 1.18467T = KCTC 82192T).

Devosia aurantiaca sp. nov., Isolated from Mountain Soil and Proposal of Albitalea gen. nov. to Replace the Illegitimate Prokaryotic Genus Name Geomonas Khan et al. 2020.

Strain H239T, a gram-negative, strictly aerobic, and oxidase-positive, and catalase-negative bacterium, was isolated from mountain soil in Gangwon-do of South Korea. Colonies were orange colored, and cells were motile rods with a single polar flagellum. Growth was observed between 25 and 30°C (optimum, 30°C), between pH 7.0 and pH 9.0 (optimum, pH 7.5), and in the presence of 0-1.5% (w/v) NaCl (optimum 0.5-1%). Ubiquinone-10 was detected as the sole respiratory quinone. The major fatty acids (>10%) of strain H239T were C18:1 ω7c, C18:0, and C16:0. The polar lipids detected from strain H239T consisted of two unidentified glycolipids, two unidentified phospholipids, and three unidentified polar lipids. The G+C content of strain H239T based on its genome sequence was 62.0mol%. Comparative 16S rRNA gene sequence analysis indicated that strain H239T was most closely related to Devosia chinhatensis IPL18T (97.7%), Devosia submarina KMM 9415T (97.7%), and Devosia yakushimensis Yak96BT (97.3%). Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain H239T formed a distinct phyletic lineage as a new species within the genus Devosia. Based on its physiological, chemotaxonomic, and molecular properties, strain H239T represents a novel species of the genus Devosia, for which the name Devosia aurantiaca sp. nov. is proposed. The type strain is H239T (=KACC 21662T=JCM 33930T). In addition, because the prokaryotic genus name Geomonas Khan et al. 2020 is a later homonym of Geomonas Xu et al. 2020, the name is illegitimate (Principle 6 in the International Code of Nomenclature of Prokaryotes). Therefore, we propose to replace the problematic prokaryotic names Geomonas and Geomonas soli with Albitalea with Albitalea terrae, respectively.

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil.

A Gram-stain-negative, strictly aerobic, motile, ivory-coloured and rod-shaped bacterium (designated Gsoil 520T) isolated from ginseng cultivation soil was characterized by using a polyphasic approach to clarify its taxonomic position. Strain Gsoil 520T was observed to grow optimally at 30 °C and pH 7.0 on Reasoner's 2A agar medium. The results of phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that Gsoil 520T belongs to the genus Devosia of the family Hyphomicrobiaceae and was most closely related to Devosia epidermidihirudinis E84T (98.0 %), Devosia yakushimensis Yak96BT (97.7 %), Devosia neptuniae J1T (97.7 %) and Devosia chinhatensis IPL18T (96.8 %). The complete genome of strain Gsoil 520T is a presumptive circular chromosome of 4 480 314 base pairs having G+C content of 63.7 mol%. A total of 4 354 genes, 4 303 CDS and 43 rRNA genes were assigned a putative function. The major isoprenoid quinone was Q-10. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminolipids (AL1 and AL3). The predominant fatty acids of strain Gsoil 520T were C18 : 1ω7c 11-methyl, C16 : 0 and C18 : 1ω7c/C18 : 1ω6c (summed feature 8) supporting the affiliation of strain Gsoil 520T to the genus Devosia. The low values of DNA-DNA hybridization distinguished strain Gsoil 520T from the recognized species of the genus Devosia. Thus, the novel isolate represents a novel species of the genus Devosia, for which the name Devosia ginsengisoli sp. nov. is proposed, with the type strain Gsoil 520T (=KACC 19440T=LMG 30329T).

Devosia indica sp. nov., isolated from surface seawater in the Indian Ocean.

A Gram-stain-negative bacterium, designated IO390501T, was isolated from a sea water sample from the Indian Ocean and taxonomically characterized using a polyphasic approach. The strain is phylogenetically close to 'Devosia lucknowensis' L15 and Devosia chinhatensis IPL18T, with 16S rRNA gene sequence similarity of 97.7 and 97.4 %, respectively. The genome of IO390501T has a DNA G+C content of 61.9 mol% for the 3.9 Mb chromosome. Genome-based phylogenetic trees indicated that IO390501T clusters as an independent lineage with 'D. lucknowensis' L15. Genomic relatedness of in silico DNA-DNA hybridization between IO390501T and phylogenetic neighbours ranged from 18.8 to 21.5 %, below the cutoff of 70 %, and corresponding average nucleotide identity values were between 71.4 and 79.0 %, lower than the 95.0 % threshold. The predominant cellular fatty acids of IO390501T are summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C16 : 0. IO390501T contains ubiquinone-10 as the sole respiratory quinone, and phosphatidylglycerol and glycolipids as the major polar lipids. On the basis of the results of phenotypic, chemotaxonomic and genetic analyses, strain IO390501T represents a novel species of the genus Devosia for which the name Devosia indica sp. nov. is proposed. The type strain is IO390501T.

Devosia naphthalenivorans sp. nov., isolated from East Pacific Ocean sediment.

A Gram-stain-negative bacterium, designated CM5-1T, was isolated from a sediment sample collected from the East Pacific Ocean. 16S rRNA gene sequence analysis revealed that strain CM5-1T belongs to the genus Devosia, with closely related type strains Devosia submarina KMM 9415T (98.6 %), Devosia psychrophilaCr7-05T (98.6 %) and Devosia psychrophilaE84T (98.2 %). Up-to-date bacterial core gene set analysis revealed that strain CM5-1T represents one independent lineage with D. submarina KMM 9415T. The average nucleotide identity values of CM5-1T with D. submarina KMM 9415T and D. psychrophila Cr7-05T are 80.1 and 77.9 %, respectively. In silico DNA-DNA hybridization values between strain CM5-1T and D. submarina KMM 9415T and D. psychrophila Cr7-05T are 23.8 and 21.9 %, respectively. Strain CM5-1T contains diphosphatidylglycerol, phosphatidylglycerol and glycolipid as major polar lipids. The sole isoprenoid quinone is ubiquinone-10, and C18 : 1ω7c and 11-methyl C18 : 1ω7c are the dominant cellular fatty acids. The G+C content of the genomic DNA is 61.4 mol%. Differential phylogenetic distinctiveness and chemotaxonomic differences, together with the phenotypic properties observed in this study, revealed that strain CM5-1T could be differentiated from closely related species. Therefore, we propose strain CM5-1T as a novel species of the genus Devosia, for which the name Devosia naphthalenivorans sp. nov. is suggested. The type strain is CM5-1T (=JCM32509T=CGMCC 1.13553T).