Skip to main content
SpringerLink
Log in

Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number SOKV00000000.2, BioProject number PRJNA528176 and BioSample number SAMN11175380. The genomic raw sequencing reads are available in the Sequence Read Archive (SRA) database under accession number SRR21863679. The bacterial strain is deposited in MTCC (CSIR-IMTECH) Chandigarh, India, and has an accession number 11829.

References

  • Agashe D, Shankar N (2014) The evolution of bacterial DNA base composition. J Exp Zool B Mol Dev Evol 322:517–528

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–408

    Article  CAS  PubMed  Google Scholar 

  • Andrews S, Krueger F, Seconds-Pichon A, Biggins F, Wingett S (2015) FastQC A quality control tool for high throughput sequence data. Babraham Bioinform Babraham Instit 1:1

    CAS  Google Scholar 

  • Anthony C (1982) The biochemistry of methylotrophs

  • Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R (2020) A 2-Tyr-1-carboxylate mononuclear iron center forms the active site of a paracoccus dimethylformamidase. Angew Chem Int Ed 59:16961–16966

    Article  CAS  Google Scholar 

  • Aziz RK et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75

    Article  Google Scholar 

  • Baker SC, Ferguson SJ, Ludwig B, Page MD, Richter OM, van Spanning RJ (1998) Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiol Mol Biol Rev 62:1046–1078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bankevich A et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Basak S, Mandal S, Ghosh TC (2005) Correlations between genomic GC levels and optimal growth temperatures: some comments. Biochem Biophys Res Commun 327:969–970

    Article  CAS  PubMed  Google Scholar 

  • Bentley SD, Parkhill J (2004) Comparative genomic structure of prokaryotes. Annu Rev Genet 38:771–792

    Article  CAS  PubMed  Google Scholar 

  • Bernal P, Llamas MA, Filloux A (2018) Type VI secretion systems in plant-associated bacteria. Environ Microbiol 20:1–15

    Article  PubMed  Google Scholar 

  • Bingle LEH, Bailey CM, Pallen MJ (2008) Type VI secretion: a beginner’s guide. Curr Opin Microbiol 11:3–8

    Article  CAS  PubMed  Google Scholar 

  • Bipp H, Kieczka H (2000) Formamides. In: Ullmann’s Encyclopedia of Industrial Chemistry. John Wiley & Sons, Ltd, Weinheim, Germany

  • Bockwoldt JA, Zimmermann M, Tiso T, Blank LM (2020) Complete genome sequence and annotation of the Paracoccus pantotrophus. type strain DSM 2944. Microbiol Resour Announc. https://doi.org/10.1128/MRA.01290-19

    Article  PubMed  PubMed Central  Google Scholar 

  • Bohlin J, Eldholm V, Pettersson JHO, Brynildsrud O, Snipen L (2017) The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes. BMC Genom 18:151

    Article  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bosi E, Donati B, Galardini M, Brunetti S, Sagot M-F, Lió P, Crescenzi P, Fani R, Fondi M (2015) MeDuSa: a multi-draft based scaffolder. Bioinformatics 31:2443–2451

    Article  CAS  PubMed  Google Scholar 

  • Boyd JM, Ellsworth H, Ensign SA (2004) Bacterial acetone carboxylase is a manganese-dependent metalloenzyme. J Biol Chem 279:46644–46651

    Article  CAS  PubMed  Google Scholar 

  • Braun A, Spona-Friedl M, Avramov M, Elsner M, Baltar F, Reinthaler T, Herndl GJ, Griebler C (2021) Reviews and syntheses: Heterotrophic fixation of inorganic carbon–significant but invisible flux in environmental carbon cycling. Biogeosciences 18:3689–3700

    Article  CAS  Google Scholar 

  • Bustillos-Cristales MDR, Corona-Gutierrez I, Castañeda-Lucio M, Águila-Zempoaltécatl C, Seynos-García E, Hernández-Lucas I, Muñoz-Rojas J, Medina-Aparicio L, Fuentes-Ramírez LE (2017) Culturable facultative methylotrophic bacteria from the cactus Neobuxbaumia macrocephala possess the locus xoxF and consume methanol in the presence of Ce3+ and Ca2+. Microbes Environ 32:244–251

    Article  Google Scholar 

  • Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH (2022) GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 39:105

    Google Scholar 

  • Cherrak Y, Flaugnatti N, Durand E, Journet L, Cascales E (2019) Structure and activity of the type VI secretion system. Microbiol Spectr 7:7411

    Article  Google Scholar 

  • Chistoserdov AY, Tsygankov YD, Lidstrom ME (1991) Genetic Organization of Methylamine Utilization Genes from Methylobacterium extorquens AMI

  • Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2620

    Article  CAS  PubMed  Google Scholar 

  • Chistoserdova L (2016) Wide distribution of genes for Tetrahydromethanopterin/Methanofuran-linked C1 transfer reactions argues for their presence in the common ancestor of Bacteria and Archaea. Front Microbiol 7:1–5

    Article  Google Scholar 

  • Chistoserdova L, Lidstrom ME (2013a) Aerobic methylotrophic prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes, 4th edn. Springer, Berlin Heidelberg, Berlin, Heidelberg, pp 267–285

    Chapter  Google Scholar 

  • Chistoserdova L, Lidstrom ME (2013b) The prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) Prokaryotic physiology and biochemistry. Springer, Berlin Heidelberg, Berlin, Heidelberg, pp 267–285

    Google Scholar 

  • Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Claassens NJ, Sousa DZ, dos Santos VAPM, de Vos WM, van der Oost J (2016) Harnessing the power of microbial autotrophy. Nat Rev Microbiol 14:692–706

    Article  CAS  PubMed  Google Scholar 

  • Clément Y, Fustier M-A, Nabholz B, Glémin S (2015) The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biol Evol 7:336–348

    Article  Google Scholar 

  • Colby J, Zatman LJ (1973) Trimethylamine metabolism in obligate and facultative methylotrophs. Biochem J 132:101–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Consortium (2022) UniProt the universal protein knowledgebase in 2023. Nucleic Acids Res 51:D523–D531

    Article  Google Scholar 

  • Costa TRD, Felisberto-Rodrigues C, Meir A, Prevost MS, Redzej A, Trokter M, Waksman G (2015) Secretion systems in gram-negative bacteria: Structural and mechanistic insights. Nat Rev Microbiol 13:343–359

    Article  CAS  PubMed  Google Scholar 

  • Czarnecki J, Bartosik D (2019) Diversity of methylotrophy pathways in the genus paracoccus (Alphaproteobacteria). Curr Issues Mol Biol 33:117–131

    Article  PubMed  Google Scholar 

  • Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schlüter A, Pühler A, Bartosik D (2017) Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685. Environ Microbiol 19:4536–4550

    Article  CAS  PubMed  Google Scholar 

  • Daneshvar MI et al (2003) Paracoccus yeeii sp. nov. (Formerly CDC group EO-2), a novel bacterial species associated with human infection. J Clin Microbiol 41:1289–1294

    Article  PubMed  PubMed Central  Google Scholar 

  • Decewicz P, Dziewit L, Golec P, Kozlowska P, Bartosik D, Radlinska M (2019) Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches. Sci Rep 9:7899

    Article  PubMed  PubMed Central  Google Scholar 

  • DeRosier DJ (1998) The turn of the screw: the bacterial flagellar motor. Cell 93:17–20

    Article  CAS  PubMed  Google Scholar 

  • Ding S, Jiao N (2012) N, N-dimethylformamide: a multipurpose building block. Angew Chem Int Ed Engl 51:9226–9237

    Article  CAS  PubMed  Google Scholar 

  • Dziewit L, Dmowski M, Baj J, Bartosik D (2010) Plasmid pAMI2 of Paracoccus aminophilus JCM 7686 carries N, N-dimethylformamide degradation-related genes whose expression is activated by a LuxR family regulator. Appl Environ Microbiol 76:1861–1869

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schlüter A, Pühler A, Bartosik D (2014) Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids. BMC Genom 15:1–16

    Article  Google Scholar 

  • Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schüter A, Pühler A, Bartosik D (2015) Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686. Front Microbiol 6:1–13

    Article  Google Scholar 

  • Environmental Protection Agency (1975) Standard Methods for the Examination of Water and Wastewater, 14th Edition, p 496, Method 427C

  • Friedrich CG (1997) Physiology and genetics of sulfur-oxidizing bacteria. In: Poole RK (ed) Advances in microbial physiology. Elsevier, Academic Press, pp 235–289

    Google Scholar 

  • Gallique M, Bouteiller M, Merieau A (2017) The type VI secretion system: a dynamic system for bacterial communication? Front Microbiol. https://doi.org/10.3389/fmicb.2017.01454

    Article  PubMed  PubMed Central  Google Scholar 

  • Ghosh W, Mandal S, Roy P (2006) Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant. Syst Appl Microbiol 29:396–403

    Article  CAS  PubMed  Google Scholar 

  • Gong F, Cai Z, Li Y (2016) Synthetic biology for CO2 fixation. Sci China Life Sci 59:1106–1114

    Article  CAS  PubMed  Google Scholar 

  • Green ER, Mecsas J (2016) Bacterial secretion systems: an overview. Microbiol Spectr. https://doi.org/10.1128/microbiolspec.VMBF-0012-2015

    Article  PubMed  Google Scholar 

  • Gupta RS, Mok A (2007) Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups. BMC Microbiol 7:106

    Article  PubMed  PubMed Central  Google Scholar 

  • Harms N, van Spanning RJM (1991) C1 metabolism in Paracoccus denitrificans: genetics of Paracoccus denitrificans. J Bioenerg Biomembr 23:187–210

    Article  CAS  PubMed  Google Scholar 

  • Harms N, Reijnders WN, Koning S, van Spanning RJ (2001) Two-component system that regulates methanol and formaldehyde oxidation in Paracoccus denitrificans. J Bacteriol 183:664–670

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hasegawa Y, Matsuo M, Yoshinori Sigemoto T, Etsuhiko S, Tokuyama T (1997) Purification and characterization of N, N-dimethylformamidase from Alcaligenes sp. KUFA-1. J Ferment Bioeng 84:543–547

    Article  CAS  Google Scholar 

  • Heravi MM, Ghavidel M, Mohammadkhani L (2018) Beyond a solvent: Triple roles of dimethylformamide in organic chemistry. RSC Adv 8:27832–27862

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hildebrand F, Meyer A, Eyre-Walker A (2010) Evidence of selection upon genomic GC-content in bacteria. PLoS Genet 6:e1001107

    Article  PubMed  PubMed Central  Google Scholar 

  • IARC MONOGRAPHS. 2018. Some Industrial Chemicals: IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, pp. 119–170. Iarc Monographs On The Evaluation Of Carcinogenic Risks To Humans.

  • Islam T, Hernández M, Gessesse A, Murrell JC, Øvreås L (2021) A novel moderately thermophilic facultative methylotroph within the class alphaproteobacteria. Microorganisms 9:477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jaworska K et al (2019) TMA, A forgotten uremic toxin, but Not TMAO is involved in cardiovascular pathology. Toxins (basel) 11:490

    Article  CAS  PubMed  Google Scholar 

  • Jordan SL, McDonald IR, Kraczkiewicz-Dowjat AJ, Kelly DP, Rainey FA, Murrell JC, Wood AP (1997) Autotrophic growth on carbon disulfide is a property of novel strains of Paracoccus denitrificans. Arch Microbiol 168:225–236

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katayama Y, Hiraishi A, Kuraishi H (1995) Paracoccus thiocyanatus sp. nov, a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus. Microbiology (reading) 141(6):1469–1477

    Article  CAS  PubMed  Google Scholar 

  • Kelly DP, Rainey FA, Wood AP (2006) The genus paracoccus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, New York, NY, pp 232–249

    Chapter  Google Scholar 

  • Koprivova A, Kopriva S (2014) Molecular mechanisms of regulation of sulfate assimilation: first steps on a long road. Front Plant Sci. https://doi.org/10.3389/fpls.2014.00589

    Article  PubMed  PubMed Central  Google Scholar 

  • Kushkevych I, Cejnar J, Treml J, Dordević D, Kollar P, Vítězová M (2020) Recent advances in metabolic pathways of sulfate reduction in intestinal bacteria. Cells 9:698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lasek R, Szuplewska M, Mitura M, Decewicz P, Chmielowska C, Pawłot A, Sentkowska D, Czarnecki J, Bartosik D (2018a) Genome structure of the opportunistic pathogen Paracoccus yeei (Alphaproteobacteria) and identification of putative virulence factors. Front Microbiol. https://doi.org/10.3389/fmicb.2018.02553

    Article  PubMed  PubMed Central  Google Scholar 

  • Leyton DL, Rossiter AE, Henderson IR (2012) From self sufficiency to dependence: Mechanisms and factors important for autotransporter biogenesis. Nat Rev Microbiol 10:213–225

    Article  CAS  PubMed  Google Scholar 

  • Li W et al (2021) RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 49:D1020–D1028

    Article  CAS  PubMed  Google Scholar 

  • Liang B, Zhao Y, Yang J (2020) Recent advances in developing artificial autotrophic microorganism for reinforcing CO2 fixation. Front Microbiol. https://doi.org/10.3389/fmicb.2020.592631

    Article  PubMed  PubMed Central  Google Scholar 

  • Lidbury I, Mausz MA, Scanlan DJ, Chen Y (2017) Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway. ISME J 11:1592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu R, Ochman H (2007a) Origins of flagellar gene: operons and secondary flagellar systems. J Bacteriol 189:7098–7104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu R, Ochman H (2007b) Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci U S A 104:7116–7121

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Z-P, Wang B-J, Liu X-Y, Dai X, Liu Y-H, Liu S-J (2008) Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 58:257–261

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Xie Q, Hong K, Li L, Zhao Y, Tang Y, An J, Zhu P, Xu C (2013) Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract. Antonie Van Leeuwenhoek 103:1133–1139

    Article  PubMed  Google Scholar 

  • Long G, Meek ME, Lewis M (2001) World Health Organization., International Labour Organisation., United Nations Environment Programme., Inter-Organization Programme for the Sound Management of Chemicals., and International Program on Chemical Safety.. N, N-dimethylformamide. World Health Organization

  • Lu X, Wang W, Zhang L, Hu H, Xu P, Wei T, Tang H (2019) Molecular mechanism of N, N-dimethylformamide degradation in methylobacterium sp. strain DM1. Appl Environ Microbiol 85:e00275-e319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luque-Almagro VM, Manso I, Sullivan MJ, Rowley G, Ferguson SJ, Moreno-Vivián C, Richardson DJ, Gates AJ, Roldán MD (2017) Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans. Biochem J 474:1769–1787

    Article  CAS  PubMed  Google Scholar 

  • Mann S, Chen YP (2010) Bacterial genomic G + C composition-eliciting environmental adaptation. Genomics 95:7–15

    Article  CAS  PubMed  Google Scholar 

  • Mausz MA, Chen Y (2019) Microbiology and ecology of methylated amine metabolism in marine ecosystems. Curr Issues Mol Biol 33:133–148

    Article  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182

    Article  PubMed  PubMed Central  Google Scholar 

  • Meijer EM, van Verseveld HW, van der Beek EG, Stouthamer AH (1977) Energy conservation during aerobic growth in Paracoccus denitrificans. Arch Microbiol 112:25–34

    Article  CAS  PubMed  Google Scholar 

  • Miyata ST, Kitaoka M, Brooks TM, McAuley SB, Pukatzki S (2011) Vibrio cholerae requires the type VI secretion system virulence factor VasX To Kill Dictyostelium discoideum. Infect Immun 79:2941–2949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ (2019) An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. Elife 8:e42535

    Article  PubMed  PubMed Central  Google Scholar 

  • Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F, Bernardi G (2004) Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 573:73–77

    Article  CAS  PubMed  Google Scholar 

  • Nakatani T, Ohtsu I, Nonaka G, Wiriyathanawudhiwong N, Morigasaki S, Takagi H (2012) Enhancement of thioredoxin/glutaredoxin-mediated L-cysteine synthesis from S-sulfocysteine increases L-cysteine production in Escherichia coli. Microb Cell Fact 11:62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Navarro-Garcia F, Ruiz-Perez F, Cataldi Á, Larzábal M (2019) Type VI secretion system in pathogenic Escherichia coli: Structure, role in virulence, and acquisition. Front Microbiol. https://doi.org/10.3389/fmicb.2019.01965

    Article  PubMed  PubMed Central  Google Scholar 

  • Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD (2018) Exploring the denitrification proteome of Paracoccus denitrificans PD1222. Front Microbiol. https://doi.org/10.3389/fmicb.2018.01137

    Article  PubMed  PubMed Central  Google Scholar 

  • Ortmayer M et al (2016) An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme. Nature 539:593–597

    Article  CAS  PubMed  Google Scholar 

  • Pade N, Köcher S, Roeßler M, Hänelt I, Müller V (2013) Bioenergetics of the moderately halophilic bacterium Halobacillus halophilus: composition and regulation of the respiratory chain. Appl Environ Microbiol 79:3839–3846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pena RT et al (2019) Relationship between quorum sensing and secretion systems. Front Microbiol. https://doi.org/10.3389/fmicb.2019.01100

    Article  PubMed  PubMed Central  Google Scholar 

  • Qiu Z, Li G, An T (2021) In vitro toxic synergistic effects of exogenous pollutants-trimethylamine and its metabolites on human respiratory tract cells. Sci Total Environ 783:146915

    Article  CAS  PubMed  Google Scholar 

  • Rajta A, Bhatia R, Setia H, Pathania P (2020) Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater. J Appl Microbiol 128:1261–1278

    Article  CAS  PubMed  Google Scholar 

  • Ramos JL, Duque E, Gallegos M-T, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A (2002) Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 56:743–768

    Article  CAS  PubMed  Google Scholar 

  • Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931

    Article  CAS  PubMed  Google Scholar 

  • Rivers AR, Smith CB, Moran MA (2014) An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3. Stand Genom Sci 9:11

    Article  Google Scholar 

  • Saini R, Kapoor R, Kumar R, Siddiqi TO, Kumar A (2011) CO2 utilizing microbes — a comprehensive review. Biotechnol Adv 29:949–960

    Article  CAS  PubMed  Google Scholar 

  • Sanjeevkumar S, Nayak AS, Santoshkumar M, Siddavattam D, Karegoudar TB (2013) Paracoccus denitrificans SD1 mediated augmentation with indigenous mixed cultures for enhanced removal of N, N-dimethylformamidefrom industrial effluents. Biochem Eng J 79:1–6

    Article  CAS  Google Scholar 

  • Schaaper RM, Dunn RL (1991) Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129:317–326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scott M, Sandkvist M (2006) CHAPTER 5-toxin secretion systems. In: Alouf JE, Popoff MR (eds) The Comprehensive sourcebook of bacterial protein toxins (Third Edition), 3rd edn. Academic Press, London, pp 83–105

    Chapter  Google Scholar 

  • Shakya M, Soucy SM, Zhaxybayeva O (2017) Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 3:vex036

    Article  PubMed  PubMed Central  Google Scholar 

  • Shaw AJ, Gescher A, Mráz J (1988) Cytotoxicity and metabolism of the hepatotoxin N-methylformamide and related formamides in mouse hepatocytes. Toxicol Appl Pharmacol 95:162–170

    Article  CAS  PubMed  Google Scholar 

  • Shyntum DY, Venter SN, Moleleki LN, Toth I, Coutinho TA (2014) Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments. BMC Genomics 15:1–5

    Article  Google Scholar 

  • Simão FA, Waterhouse RM, Ioannidis P, Kriventseva E, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212

    Article  PubMed  Google Scholar 

  • Smith MO (1999) Multidrug-resistance efflux pumps — not just for resistance. Nat Rev Microbiol 4:15–17

    Google Scholar 

  • Spain AM, Krumholz LR, Elshahed MS (2009) Abundance, composition, diversity and novelty of soil Proteobacteria. ISME J 3:992–1000

    Article  CAS  PubMed  Google Scholar 

  • Spanning RJM, Stouthamer AH, Baker SC, Verseveld HW 2015. Paracoccus. Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley. pp. 1–14

  • Strong PJ, Xie S, Clarke WP (2015) Methane as a resource: can the methanotrophs add value? Environ Sci Technol 49:4001–4018

    Article  CAS  PubMed  Google Scholar 

  • Swaroop S, Sughosh P, Ramanathan G (2009) Biomineralization of N, N-dimethylformamide by Paracoccus sp. strain DMF. J Hazard Mater 171:268–272

    Article  CAS  PubMed  Google Scholar 

  • Tai Y, Zhang K (2015) C1 metabolism redesigned. Nat Publ Group 11:384–386

    CAS  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas S, Holland IB, Schmitt L (2014) The type 1 secretion pathway — the hemolysin system and beyond. Biochim Biophys Acta (BBA) Mol Cell Res 1843:1629–1641

    Article  CAS  Google Scholar 

  • Thrash JC, Boyd A, Huggett MJ, Grote J, Carini P, Yoder RJ, Robbertse B, Spatafora JW, Rappé MS, Giovannoni SJ (2011) Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci Rep 1:13

    Article  PubMed  PubMed Central  Google Scholar 

  • Tsubokura A, Yoneda H, Mizuta H (1999) Paracoccus carotinifaciens sp. nov., a new aerobic Gram-negative astaxanthin-producing bacterium. Int J Syst Evol Microbiol 49:277–282

    Article  CAS  Google Scholar 

  • Urakami T, Tamaoka J, Suzuki K-I, Komagata K (1989) Paracoccus alcaliphilus sp. nov., an Alkaliphilic and Facultatively Methylotrophic Bacterium. Int J Syst Evol Microbiol 39:116–121

    Google Scholar 

  • Urakami T, Araki H, Oyanagi H, Suzuki KI, Komagata K (1990) Paracoccus aminophilus sp. nov. and Paracoccus aminovorans sp. nov., which utilize N N-Dimethylformamide. Int J Syst Bacteriol 40:287–291

    Article  CAS  PubMed  Google Scholar 

  • Verley A (1893) On the preparation of amides in general. Bull La Soc Chim De Paris 9:690–692

    Google Scholar 

  • Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22:2196–2203

    Article  CAS  PubMed  Google Scholar 

  • Wang H-C, Xia X, Hickey D (2006) Thermal adaptation of the small subunit ribosomal RNA gene: a comparative study. J Mol Evol 63:120–126

    Article  CAS  PubMed  Google Scholar 

  • William S, Feil H, Copeland A (2004) Bacterial DNA isolation CTAB protocol bacterial genomic DNA isolation using CTAB materials & reagents. Doe Joint Genom Instit. https://doi.org/10.3390/mps6020034

    Article  Google Scholar 

  • Wood IP, Elliston A, Ryden P, Bancroft I, Roberts IN, Waldron KW (2012) Rapid quantification of reducing sugars in biomass hydrolysates: improving the speed and precision of the dinitrosalicylic acid assay. Biomass Bioenergy 44:117–121. https://doi.org/10.1016/j.biombioe.2012.05.003

    Article  CAS  Google Scholar 

  • Wu H, Zhang Z, Hu S, Yu J (2012) On the molecular mechanism of GC content variation among eubacterial genomes. Biol Direct 7:2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Z-G, Zhang D-F, Liu Y-L, Wang F, Jiang X, Li C, Li S-P, Hong Q, Li W-J (2013) Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system. Antonie Van Leeuwenhoek 104:123–128

    Article  CAS  PubMed  Google Scholar 

  • Xu L et al (2019) OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 47:W52–W58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang X, Pan J, Wang Y, Shen X (2018) Type VI secretion systems present new insights on pathogenic yersinia. Front Cell Infect Microbiol 8:260

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank Dr. Aswin Sai Narain Seshasayee, NCBS, for the discussion, sequencing facility, and data acquisition.

Funding

University Grants Commission, F.16-6(DEC.2016)/2017(NET).

Author information

Authors and Affiliations

  1. Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India

    Shiwangi Maurya, Chetan Kumar Arya & Gurunath Ramanathan

  2. Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India

    Nidhi Parmar & Chaitanya G. Joshi

  3. Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India

    Nitish Sathyanarayanan

Authors
  1. Shiwangi Maurya
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chetan Kumar Arya
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nidhi Parmar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nitish Sathyanarayanan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chaitanya G. Joshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gurunath Ramanathan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SM, CA and RG analysed the data and wrote the manuscript. Data was collected in Gujarat (NP and CGJ) and NCBS (NS), wherein authors from those institutions helped.

Corresponding author

Correspondence to Gurunath Ramanathan.

Ethics declarations

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Ethical approval

NA.

Additional information

Communicated by Yusuf Akhter.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 4814 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Maurya, S., Arya, C.K., Parmar, N. et al. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 206, 6 (2024). https://doi.org/10.1007/s00203-023-03729-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00203-023-03729-z

Keywords

Search

Navigation