Abstract
The genus Gallaecimonas, proposed by Rodríguez-Blanco et al. (Int J Syst Evol Microbiol 60:504–509, 2010), is mainly isolated from marine environments. So far, only three species have been identified and characterized in this genus. In this study, a new Gallaecimonas strain named Q10T was isolated from the sediments of mangrove plant Kandelia obovate taken from Dapeng district, Shenzhen, China. Strain Q10T was a Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium, and grew with 0–8.0% (w/v) NaCl, at 10–45 °C and at pH 5.5–8.5. Phylogenetic analysis indicated that strain Q10T and the three Gallaecimonas species formed a clade in the tree, with 16S rRNA gene sequence similarities ranging from 96.0 to 97.0%. The major respiratory quinone is Q8. The polar lipids comprised aminolipid, aminophospholipid, diphosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylglycerol, glycophospholipid and phospholipid. The predominant fatty acids are C16:0, C17:1ω8c, summed feature 3 (C16:1ω7c/C16:1ω6c), and iso-C16:0. The complete genome of strain Q10T is 3,836,841 bp with a G+C content of 62.6 mol%. The orthologous proteins analysis revealed 55 unique proteins in strain Q10T related to important biological processes, especially three frataxins related to iron–sulfur cluster assembly, which may play a pivotal role in environmental adaptability of this species. Based on polyphasic taxonomic data, strain Q10T is considered to represent a novel species within the genus Gallaecimonas, for which the name Gallaecimonas kandelia sp. nov. is proposed. The type strain is Q10T (=KCTC 92860T=MCCC 1K08421T). These results contribute to a better understanding of general features and taxonomy of the genus Gallaecimonas.
Similar content being viewed by others
References
Adinolfi S, Iannuzzi C, Prischi F, Pastore C, Iametti S, Martin SR, Bonomi F, Pastore A (2009) Bacterial frataxin CyaY is the gatekeeper of iron–sulfur cluster formation catalyzed by IscS. Nat Struct Mol Biol 16:390–396. https://doi.org/10.1038/nsmb.1579
Alcock BP, Raphenya AR, Lau TT, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-LV, Cheng AA, Liu S (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:D517–D525. https://doi.org/10.1093/nar/gkz935
Almeida E, Dias TV, Ferraz G, Carvalho MF, Lage OM (2020) Culturable bacteria from two Portuguese salterns: diversity and bioactive potential. Antonie Van Leeuwenhoek 113:459–475. https://doi.org/10.1007/s10482-019-01356-7
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. https://doi.org/10.1038/75556
Barbier EB, Koch EW, Silliman BR, Hacker SD, Wolanski E, Primavera J, Granek EF, Polasky S, Aswani S, Cramer LA (2008) Coastal ecosystem-based management with nonlinear ecological functions and values. Science 319:321–323. https://doi.org/10.1126/science.1150349
Consortium U (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212. https://doi.org/10.1093/nar/gku989
Ding L, Xu P, Zhang W, Yuan Y, He X, Su D, Shi Y, Naman CB, Yan X, Wu B (2020) Three new diketopiperazines from the previously uncultivable marine bacterium Gallaecimonas mangrovi HK-28 cultivated by iChip. Chem Biodivers 17:e2000221. https://doi.org/10.1002/cbdv.202000221
Fei J, Wang Y-S, Cheng H, Su Y-B, Zhong Y-J, Zheng L (2022) The Kandelia obovata transcription factor KoWRKY40 enhances cold tolerance in transgenic Arabidopsis. BMC Plant Biol 22:1–15. https://doi.org/10.1186/s12870-022-03661-2
Gago JF, Viver T, Urdiain M, Pastor S, Kämpfer P, Robledo PA, Ferreira E, Rosselló-Móra R (2021) Comparative genome analysis of the genus Hydrotalea and proposal of the novel species Hydrotalea lipotrueae sp. nov., isolated from a groundwater aquifer in the south of Mallorca Island Spain. Syst Appl Microbiol 44:126277. https://doi.org/10.1016/j.syapm.2021.126277
Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:D261–D269. https://doi.org/10.1093/nar/gku1223
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Grant JR, Stothard P (2008) The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181–W184. https://doi.org/10.1093/nar/gkn179
Hassanshahian M (2014) Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance). Mar Pollut Bull 86:361–366. https://doi.org/10.1016/j.marpolbul.2014.06.043
Hu M-J, Sun W-H, Tsai W-C, Xiang S, Lai X-K, Chen D-Q, Liu X-D, Wang Y-F, Le Y-X, Chen S-M (2020) Chromosome-scale assembly of the Kandelia obovata genome. Hortic Res. https://doi.org/10.1038/s41438-020-0300-x
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D462. https://doi.org/10.1093/nar/gkv1070
Kates M (1986) Radioisotopic techniques in lipidology, In: Techniques of lipidology. 2. rev. ed
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547. https://doi.org/10.1093/molbev/msy096
Lagesen K, Hallin P, Rødland EA, Stærfeldt H-H, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160
Lai Q, Wang L, Wang W, Shao Z (2012) Genome sequence of Gallaecimonas xiamenensis type strain 3-C-1. J Bacteriol 194:6937. https://doi.org/10.1128/JB.01854-12
Lin X, Hetharua B, Lin L, Xu H, Zheng T, He Z, Tian Y (2019) Mangrove sediment microbiome: adaptive microbial assemblages and their routed biogeochemical processes in Yunxiao mangrove national nature reserve, China. Microb Ecol 78:57–69. https://doi.org/10.1007/s00248-018-1261-6
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/nar/25.5.955
Medema MH, Blin K, Cimermancic P, De Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. https://doi.org/10.1093/nar/gkr466
Ramasubburayan R, Sumathi S, Bercy DM, Immanuel G, Palavesam A (2015) Antimicrobial, antioxidant and anticancer activities of mangrove associated bacterium Bacillus subtilis subsp. subtilis RG. Biocatal Agric Biotechnol 4:158–165. https://doi.org/10.1016/j.bcab.2015.01.004
Retnowati W (2010) Identification of streptomyces sp-MWS1 producing antibacterial compounds. Indones J Trop Infect Dis 1:82–85. https://doi.org/10.20473/ijtid.v1i2.2171
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Rodríguez-Blanco A, Vetion G, Escande M-L, Delille D, Ghiglione J-F (2010) Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 60:504–509. https://doi.org/10.1099/ijs.0.013532-0
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI inc, Newark
Wang W, Wang L, Shao Z (2010) Diversity and abundance of oil-degrading bacteria and alkane hydroxylase (alkB) genes in the subtropical seawater of Xiamen Island. Microb Ecol 60:429–439. https://doi.org/10.1007/s00248-010-9724-4
Wang J, Lai Q, Duan X, Fu Y, Wang L, Wang W, Shao Z (2013) Gallaecimonas xiamenensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63:930–933. https://doi.org/10.1099/ijs.0.042283-0
Wayne L, Brenner D, Colwell R, Grimont P, Kandler O, Krichevsky M, Moore L, Moore W, Murray R, Stackebrandt E (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464. https://doi.org/10.1099/00207713-37-4-463
Xie C-H, Yokota A (2003) Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349. https://doi.org/10.2323/jgam.49.345
Zhang W-Y, Yuan Y, Su D-Q, He X-P, Han S-B, Epstein SS, He S, Wu M (2018) Gallaecimonas mangrovi sp. nov., a novel bacterium isolated from mangrove sediment. Antonie Van Leeuwenhoek 111:1855–1862. https://doi.org/10.1007/s10482-018-1076-y
Acknowledgements
We thank all the laboratory members for their critical reviews and comments on this manuscript, and we thank Professor Aharon Oren (The Hebrew University of Jerusalem, Israel) for his kind help in naming the novel species.
Funding
This work was financially supported by the Sustainable Development Project of Shenzhen Science and Technology Program (KCXFZ20211020165547010), and the Shenzhen Science and Technology Program (JCYJ20220530140813030).
Author information
Authors and Affiliations
Contributions
M.L. wrote the main manuscript text, and S.S.T and H.M.F collected the sediments samples. All authors reviewed the manuscript.
Corresponding author
Ethics declarations
Conflicts of interest
The authors declare that there are no conflicts of interest.
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
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.
About this article
Cite this article
Long, M., Tang, S., Fan, H. et al. Description and genomic characterization of Gallaecimonas kandeliae sp. nov., isolated from the sediments of mangrove plant Kandelia obovate. Antonie van Leeuwenhoek 116, 893–905 (2023). https://doi.org/10.1007/s10482-023-01851-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-023-01851-y