Abstract
A novel Gram-stain negative, aerobic and ovoid to short rod shaped bacterium with a single polar flagellum, named strain B57T, was isolated from sediment of Clam Island, Liaoning Province, China. The optimal growth of this strain was found to occur at 37 °C, pH 6–6.5, and in the presence of 2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B57T forms a distinct lineage within the family Rhodobacteraceae, sharing high 16S rRNA gene sequence similarity with Sinirhodobacter populi sk2b1T (97.4%). The average amino acid identity of B57T and the closely related species were lower than the threshold level for genus delineation. The dominant respiratory quinone of strain B57T was identified as Q-10. The major fatty acids were found to be Summed Feature 8 (C18:1ω7c and/or C18:1ω6c), Summed Feature 3 (C16:1ω7c and/or C16:1ω6c) and C16: 0. The polar lipids were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, two unidentified phospholipids, one unidentified glycolipid, and one unidentified lipid. The DNA G + C content of strain B57T was determined to be 64.1 mol%. Based on the biochemical, phylogenetic and chemotaxonomic analysis, strain B57T is concluded to represent a novel species of a novel genus, for which the name Sedimentimonas flavescens gen. nov., sp. nov.is proposed. The type strain is B57T (= CGMCC1.19488T = KCTC 92053T).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The GenBank accession numbers of the 16S rRNA gene and the draft genome sequences of strain B57T are MZ433255 and JAHVAI000000000, respectively. All other data generated or analysed during this study are included in this published article and its supplementary information files.
References
Adlan NA, Sabri S, Masomian M et al (2020) Microbial biodegradation of paraffin wax in malaysian crude oil mediated by degradative enzymes. Front Microbiol 11:565608. https://doi.org/10.3389/fmicb.2020.565608
Auch AF, Klenk HP, Göker M (2010) Standard operating procedure for calculating genome–to–genome distances based on high–scoring segment pairs. Stand Genomic Sci 2:142–148. https://doi.org/10.4056/sigs.541628
Aziz RK, Bartels D, Best AA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. https://doi.org/10.1093/nar/29.12.2607
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. https://doi.org/10.1038/nmeth.3176
Chhetri G, Kang M, Kim J et al (2021) Fuscibacter oryzae gen. nov., sp. nov., a phosphate-solubilizing bacterium isolated from the rhizosphere of rice plant. Antonie Van Leeuwenhoek 114:1453–1463. https://doi.org/10.1007/s10482-021-01619-2
Chu C, Liu B, Lian Z et al (2020) Solirhodobacter olei gen. nov., sp. nov., a nonphotosynthetic bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 70:582–588. https://doi.org/10.1099/ijsem.0.003795
Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. https://doi.org/10.1093/bioinformatics/btu661
Contreras-Moreira B, Vinuesa P (2013) GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 79:7696–7701. https://doi.org/10.1128/AEM.02411-13
Ding W, Liu P, Xu Y et al (2019) Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench. FEMS Microbiol Lett 366:fnaa004. doi: https://doi.org/10.1093/femsle/fnaa004
Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology (English translation). Scientific Press, Beijing
Felföldi T, Somogyi B, Marialigeti K, Vörös L (2009) Characterization of photoautotrophic picoplankton assemblages in turbid, alkalinelakes of the Carpathian Basin (Central Europe). J Limnol 68:385–395. https://doi.org/10.3274/JL09-68-2-21
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.1093/sysbio/20.4.406
Garrity GM, Bell JA, Lilburn T (2005) Family I. Rhodobacteraceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn, The Proteobacteria, Part C. The Alpha-, Beta-, Delta-, and Epsilonproteobacteria. Springer, New York, pp 161–228
Girija KR, Sasikala C, Ramana CV et al (2010) Rhodobacter johrii sp. nov., an endospore-producing cryptic species isolated from semi-arid tropical soils. Int J Syst Evol Microbiol 60:2099–2107. https://doi.org/10.1099/ijs.0.011718-0
Han H, Wang T, Chen Z et al (2020) Rhodobacter xinxiangensis sp. nov., isolated from pakchoi-cultivated soil contaminated with heavy metal and its potential to reduce Cd and Pb accumulation in pakchoi (Brassica campestris L.). Arch Microbiol 202:1741–1748. https://doi.org/10.1007/s00203-020-01885-0
Hansen TA, Imhoff J, F, (1985) Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int J Syst Bacteriol 35:115–116
Harwati TU, Kasai Y, Kodama Y et al (2009) Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia. Int J Syst Evol Microbiol 59:388–391. https://doi.org/10.1099/ijs.0.65822-0
Hernández-Romero D, Solano F, Sanchez-Amat A (2005) Polyphenol oxidase activity expression in Ralstonia solanacearum. Appl Environ Microbiol 71:6808–6815. https://doi.org/10.1128/AEM.71.11.6808-6815.2005
Hu Q, Zhang L, Hang P et al (2018) Xinfangfangia soli gen. nov., sp. nov., isolated from a diuron-polluted soil. Int J Syst Evol Microbiol 68:2622–2626. https://doi.org/10.1099/ijsem.0.002887
Kates M (1986) Lipid extraction procedures. Techniques of lipidology. Elsevier, Amsterdam, pp 100–111
Kinkar E, Kinkar A, Saleh M (2019) The multicopper oxidase of Mycobacterium tuberculosis (MmcO) exhibits ferroxidase activity and scavenges reactive oxygen species in activated THP-1 cells. Int J Med Microbiol 309:151324. https://doi.org/10.1016/j.ijmm.2019.06.004
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
Lee SD, Choe H, Kim JS, Kim IS (2020) Kangsaoukella pontilimi gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from a tidal mudflat. Int J Syst Evol Microbiol 70:5235–5242. https://doi.org/10.1099/ijsem.0.004401
Li AH, Zhou YG (2015) Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water. Int J Syst Evol Microbiol 65:1199–1206. https://doi.org/10.1099/ijs.0.000080
Li F, Huang Y, Hu W et al (2021) Mesobaculum littorinae gen. nov., sp. nov., a novel bacterium isolated from a sea snail Littorina scabra. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.004821
Liang KYH, Orata FD, Boucher YF, Case RJ (2021) Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the ``Roseobacter clade’’ into a novel family Roseobacteraceae fam nov. Front Microbiol 12:683109. https://doi.org/10.3389/fmicb.2021.683109
Liu Y, Lai Q, Shao Z (2017) Thioclava nitratireducens sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 67:2109–2113. https://doi.org/10.1099/ijsem.0.001844
Luo R, Liu B, Xie Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler [published correction appears in Gigascience. 2015;4:30]. Gigascience 1:18. https://doi.org/10.1186/2047-217X-1-18
Maidak BL, Cole JR, Lilburn TG et al (2000) The RDP (ribosomal database project) continues. Nucleic Acids Res 28:173–174. https://doi.org/10.1093/nar/28.1.173
Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418. https://doi.org/10.1007/s00203-013-0888-4
Moriya Y, Itoh M, Okuda S et al (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182-185. https://doi.org/10.1093/nar/gkm321
Na SI, Kim YO, Yoon SH et al (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:281–285. https://doi.org/10.1007/s12275-018-8014-6
Nguyen AD, Park JY, Hwang IY et al (2020) Genome-scale evaluation of core one-carbon metabolism in gammaproteobacterial methanotrophs grown on methane and methanol. Metab Eng 57:1–12. https://doi.org/10.1016/j.ymben.2019.10.004
Nicholson AC, Gulvik CA, Whitney AM et al (2020) Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 70:4432–4450. https://doi.org/10.1099/ijsem.0.003935
Pujalte MJ, Lucena T, Ruvira MA et al (2014) The family Rhodobacteraceae. In: The Prokaryotes. Springer Berlin Heidelberg, Berlin, pp 439–512.
Qin QL, Xie BB, Zhang XY et al (2014) A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196:2210–2215. https://doi.org/10.1128/JB.01688-14
Ren XB, Cha QQ, Guo XH et al (2020) Pelagovum pacificum gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from surface seawater of the Mariana Trench. Int J Syst Evol Microbiol 70:6155–6162. https://doi.org/10.1099/ijsem.0.004512
Reynolds J, Moyes R, Breakwell DP (2009) Differential staining of bacteria: endospore stain. CurrProtoc Microbiol Appendix 3: Appendix 3J. https://doi.org/10.1002/9780471729259.mca03js15
Saitou N, Nei M (1987) The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI.
Schubert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes 9:88. https://doi.org/10.1186/s13104-016-1900-2
Smejkalová H, Erb TJ, Fuchs G (2010) Methanol assimilation in Methylobacterium extorquens AM1: demonstration of all enzymes and their regulation. PLoS ONE 5:e13001. https://doi.org/10.1371/journal.pone.0013001
Sorokin DY, Tourova TP, Spiridonova EM et al (2005) Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area. Int J Syst Evol Microbiol 55:1069–1075. https://doi.org/10.1099/ijs.0.63415-0
Srinivas TN, Anil Kumar P, Sasikala C et al (2007) Rhodobacter vinaykumarii sp. nov., a marine phototrophic alphaproteobacterium from tidal waters, and emended description of the genus Rhodobacter. Int J Syst Evol Microbiol 57:1984–1987. https://doi.org/10.1099/ijs.0.65077-0
Srinivas TN, Anil Kumar P, Sasikala C et al (2008) Rhodobacter ovatus sp. nov., a phototrophic alphaproteobacterium isolated from a polluted pond. Int J Syst Evol Microbiol 58:1379–1383. https://doi.org/10.1099/ijs.0.65619-0
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Subhash Y, Lee SS (2016) Rhodobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 66:2965–2970. https://doi.org/10.1099/ijsem.0.001130
Suman J, Zubrova A, Rojikova K et al (2019) Pseudogemmobacter bohemicus gen. nov., sp. nov., a novel taxon from the Rhodobacteraceae family isolated from heavy-metal-contaminated sludge. Int J Syst Evol Microbiol 69:2401–2407. https://doi.org/10.1099/ijsem.0.003493
Suresh G, Lodha TD, Indu B et al (2019) Taxogenomics resolves conflict in the genus Rhodobacter: A two and half decades pending thought to reclassify the genus Rhodobacter. Front Microbiol 10:2480. https://doi.org/10.3389/fmicb.2019.02480
Tamura K, Stecher G, Peterson D et al (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Thongphrom C, Kim JH, Bora N, Kim W (2017) Thioclava arenosa sp. nov., isolated from sea sand. Int J Syst Evol Microbiol 67:1735–1739. https://doi.org/10.1099/ijsem.0.001853
Tindall B (1990a) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1111/j.1574-6968.1990.tb03996.x
Tindall B (1990b) A Comparative Study of the Lipid Composition of Halobacterium saccharovorum from Various Sources. Syst Appl Microbiol 13:128–130. https://doi.org/10.1016/S0723-2020(11)80158-X
Wang Y, Liu L, Yu M et al (2020) Carideicomes alvinocaridis gen. nov., sp. nov., a marine bacterium isolated from shrimp gill in a hydrothermal field of Okinawa Trough. Int J Syst Evol Microbiol 70:1777–1784. https://doi.org/10.1099/ijsem.0.003971
Wirth JS, Whitman WB (2018) 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 68:2393–2411. https://doi.org/10.1099/ijsem.0.002833
Xi L, Qiao N, Zhang Z et al (2017) Sinorhodobacter hungdaonensis sp. nov. isolated from activated sludge collected from a municipal wastewater treatment plant. Antonie Van Leeuwenhoek 110:27–32. https://doi.org/10.1007/s10482-016-0770-x
Xu GT, Piao C, Chang JP et al (2019) Sinorhodobacter populi sp. nov., isolated from the symptomatic bark tissue of Populus × euramericana canker. Int J Syst Evol Microbiol 69:1220–1224. https://doi.org/10.1099/ijsem.0.003300
Xu L, Liu A, Zhang YJ (2021) Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov. Antonie Van Leeuwenhoek 114:137–149. https://doi.org/10.1007/s10482-020-01507-1
Yang G, Chen M, Zhou S et al (2013) Sinorhodobacter ferrireducens gen. nov., sp. nov., a non-phototrophic iron-reducing bacterium closely related to phototrophic Rhodobacter species. Antonie Van Leeuwenhoek 104:715–724. https://doi.org/10.1007/s10482-013-9979-0
Yoon SH, Ha SM, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole–genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Yuan XX, Wang N, Zhang MY et al (2019) Chachezhania antarctica gen. nov., sp. nov., a novel member of the family 'Rhodobacteraceae’ isolated from Antarctic seawater. Antonie Van Leeuwenhoek 112:1841–1848. https://doi.org/10.1007/s10482-019-01301-8
Zhang S, Sun C, Xie J et al (2018) Defluviimonas pyrenivorans sp. nov., a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 68:957–961. https://doi.org/10.1099/ijsem.0.002629
Zhu KL, Wang XQ, Zhang TS et al (2021) Salibaculum halophilum gen. nov., sp. nov. and Salibaculum griseiflavum sp. nov., in the family Rhodobacteraceae. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.004808
Acknowledgements
This work was supported by the Special Foundation for National Science and Technology Basic Research Program of China (NO. 2019FY100706), the Science Fund for Distinguished Young Scholars of Anhui Province (No. 2008085J12), and the Science and Technology Major Project of Anhui Province (No. 202103a06020006).
Funding
Funding was provided by Special Foundation for National Science and Technology Basic Research Program of China (NO. 2019FY100706), the Science Fund for Distinguished Young Scholars of Anhui Province (No. 2008085J12), and the Science and Technology Major Project of Anhui Province (No. 202103a06020006).
Author information
Authors and Affiliations
Contributions
Conceived and designed the experiments: FZ. Performed the experiments: ML, ZX, ZY. Analysed the data: ML, FZ, and XY. Wrote the paper: ML and FZ.
Corresponding author
Ethics declarations
Conflict of interests
The authors have no relevant financial or non-financial interests to disclose.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
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.
Rights and permissions
About this article
Cite this article
Mu, L., Zhang, X., Zhang, Y. et al. Sedimentimonas flavescens gen. nov., sp. nov., isolated from sediment of Clam Island, Liaoning Province. Antonie van Leeuwenhoek 115, 979–994 (2022). https://doi.org/10.1007/s10482-022-01754-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-022-01754-4