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Description of Fuscovulum ytuae sp. nov, a facultative autotroph isolated from the intertidalite of Yangma island, China

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Abstract

In this study, we reported a Gram-stain-negative, ovoid to rod-shaped, atrichous, and facultative anaerobe bacteria strain named YMD61T, which was isolated from the intertidal sediment of Yangma island, China. Growth of strain YMD61T occurred at 10.0–45.0 °C (optimum, 30.0 °C), pH 7.0–10.0 (optimum, 8.0) and with 0–3.0% (w/v) NaCl (optimum, 2.0%). Phylogenetic tree analysis based on 16 S rRNA gene or genomic sequence indicated that strain YMD61T belonged to the genus Fuscovulum and was closely related to Fuscovulum blasticum ATCC 33,485T (96.6% sequence similarity). Genomic analysis indicated that strain YMD61T contains a circular chromosome of 3,895,730 bp with DNA G + C content of 63.3%. The genomic functional analysis indicated that strain YMD61T is a novel sulfur-metabolizing bacteria, which is capable of fixing carbon through an autotrophic pathway by integrating the processes of photosynthesis and sulfur oxidation. The predominant respiratory quinone of YMD61T was ubiquinone-10 (Q-10). The polar lipids of YMD61T contained phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unidentified lipids, unidentified aminolipid and unidentified aminophospholipid. The major fatty acids of strain YMD61T contained C18:1ω7c 11-methyl and summed feature 8 (C18:1 ω 7c or/and C18:1 ω 6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD61T represents a novel species of the genus Fuscovulum, and the name Fuscovulum ytuae sp. nov. is proposed. The type strain is YMD61T (= MCCC 1K08483T = KCTC 43,537T).

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Data availability

No datasets were generated or analysed during the current study.

Code availability

The GenBank accession number of the 16S rRNA gene sequence of strain YMD61T is OP740932. The GenBank accession number of complete genome sequence of strain YMD61T is CP124535.

Abbreviations

FAME:

Fatty acid methyl esters

ANI:

Average nucleotide identity

GGDC:

Genome-to-genome distance calculator

DSMZ:

Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

DDH:

DNA–DNA hybridizations.

References

  • Brinkhoff T, Giebel HA, Simon M (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 189:531–539

    Article  CAS  PubMed  Google Scholar 

  • Buchan A, González JM, Moran MA (2005) Overview of the marine Roseobacter lineage. Appl Environ Microb 71:5665–5677

    Article  CAS  ADS  Google Scholar 

  • Buchan A, Gonzalez JM, Moran MA (2005a) Overview of the marine Roseobacter lineage. Appl Environ Microbiol 71:5665–5677

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  • Cao W, Wong MH (2007) Current status of coastal zone issues and management in China: a review. Environ Int 33:985–992

    Article  PubMed  Google Scholar 

  • Chen L, Xiong Z, Sun L et al (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40(D1):D641–D645

    Article  CAS  PubMed  Google Scholar 

  • Collins M (1985) Isoprenoid quinone analysis in bacterial classification and identification. Chemical methods in Bacterial Systematics. Academic, London, pp 267–287

    Google Scholar 

  • Eckersley K, Dow CS (1980) Rhodopseudomonas blastica sp. nov., a member of the Rhodospirillaceae. J Gen Microbiol 119:465–473

    Google Scholar 

  • Gilman IS, Edwards EJ (2020) Crassulacean acid metabolism. Curr Biol 20(2):R57–R62

    Article  Google Scholar 

  • Grabarczyk DB, Berks BC (2017) Intermediates in the Sox sulfur oxidation pathway are bound to a sulfane conjugate of the carrier protein SoxYZ. PLoS ONE 12(3):e0173395

    Article  PubMed  PubMed Central  Google Scholar 

  • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  • Hiraishi A, Ueda Y (1994) Intrageneric structure of the genus Rhodobacter:transfer of Rhodobacter sulfidophilus and related marine species to the genus Rhodovulum gen. Nov. Int J Syst Bacteriol 44:15–23

    Article  Google Scholar 

  • Hugler M, Sievert SM (2011) Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. Ann Rev Mar Scie 3:261–289

    Article  Google Scholar 

  • Jia B, Raphenya AR, Alcock B et al (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45(Database issue):D566–D573

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62(3):716–721

    Article  CAS  PubMed  Google Scholar 

  • Kim M, Oh HS, Park SC et al (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee I, Ouk Kim Y, Park SC et al (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Pop M (2009) ARDB-antibiotic resistance genes database. Nucleic Acids Res 37(suppl 1):D443–D447

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Bao Y, Zhang X et al (2021) Rhodobacter kunshanensis sp. nov., a novel bacterium isolated from activated sludge. Curr Microbiol 78(10):3791–3797

    Article  CAS  PubMed  Google Scholar 

  • Martin MF (2020) Older than genes: the acetyl coa pathway and origins. Front Microbiol 4:11817

    Google Scholar 

  • Martin U, Rashmi P, Arathi R (2015) The Pathogen-host interactions database (PHI-base): additions and future developments. Nucleic Acids Res 43(Database issue):D645–D655

    Google Scholar 

  • Medema MH, Blin K, Cimermancic P et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39(suppl 2):W339–W346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP et al (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    Article  PubMed  PubMed Central  Google Scholar 

  • Minnikin DE, Odonnell AG, Goodfellow M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 2:233–241

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Pan K, Wang WX (2012) Trace metal contamination in estuarine and coastal environments in China. Sci Total Environ 421:3–16

    Article  PubMed  ADS  Google Scholar 

  • Pester M, Knorr KH, Friedrich MW et al (2012) Sulfate-reducing microorganisms in wetlands–fameless actors in carbon cycling and climate change. Front Microbiol 3:72–91

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petersen TN, Brunak S, von Heijne G et al (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785–786

    Article  CAS  PubMed  Google Scholar 

  • Rabus R, Venceslau SS, Woehlbrand L et al (2015) Pereira A post-genomic view of the ecophysiology, catabolism and biotechnological relevance of sulphate-reducing prokaryotes. Adv Microb Physiol 66:55–321

    Article  CAS  PubMed  Google Scholar 

  • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol 9:945–967

    CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 20:1–6

    Google Scholar 

  • Selje N, Simon M, Brinkhoff T (2004) A newly discovered Roseobacter Cluster in temperate and polar oceans. Nature 427:445–448

    Article  CAS  PubMed  ADS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suresh G, Lodha T, Indu B et al (2020) Taxogenomics resolves conflict in the genus Rhodobacter: a two and half decades pending thought to reclassify the genus Rhodobacter. Front Microbiol 11:1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tatusova T, Dicuccio M, Badretdin A et al (2016) NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wayne LG, Moore WEC, Stackebrandt E et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464

    Article  Google Scholar 

  • Wilms R, Sass H, Kopke B et al (2006) Specific bacterial, archaeal and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters. Appl Environ Microbiol 72:2756–2764

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  • Wu S, Li R, Xie S et al (2019) Shi depth-related change of sulfate-reducing bacteria community in mangrove sediments: the influence of heavy metal contamination. Mar Pollut Bull 140:443–450

    Article  CAS  PubMed  Google Scholar 

  • Xian WD, Liu ZT, Li MM (2020) Rhodobacter flagellatus sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 70(3):1541–1546

    Article  CAS  PubMed  Google Scholar 

  • Xu P, Li WJ, Tang SK et al (2005) Naxibacter alkalitolerans gen. nov., Sp nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  • Xu XD, Zhang J, Sun QL et al (2021) Description of Psychrosphaera ytuae sp. nov., isolated from the deep-sea cold seep sediment of South China Sea. Int J Syst Evol Microbiol 71(8):004983

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Natural Science Foundation of Shandong Province (ZR2020MC198), the Development Plan of Youth Innovation Team in Colleges and Universities of Shandong Province (2022KJ269) and Yantai University Doctoral Start-up Foundation (HX20B34).

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Authors and Affiliations

  1. School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China

    Bin-zhe Zhang, Xiu-dan Xu, Dan-dan Zhou, Xue-Peng Li & Jian Zhang

  2. Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 17 Chunhui Road, Yantai, 264003, China

    Xu-dong Jiao

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  1. Bin-zhe Zhang
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  2. Xiu-dan Xu
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  3. Dan-dan Zhou
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  6. Jian Zhang
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Contributions

BZZ: investigation, writing original draft. XDX: isolated the bacterium. DDZ: investigation. XPL: funding acquisition, phylogenetic and genomic characterisation. XDJ: supervision and writing-reviewing and editing. JZ: conceptualization, funding acquisition, funding acquisition.

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Correspondence to Xu-dong Jiao or Jian Zhang.

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Zhang, Bz., Xu, Xd., Zhou, Dd. et al. Description of Fuscovulum ytuae sp. nov, a facultative autotroph isolated from the intertidalite of Yangma island, China. Antonie van Leeuwenhoek 117, 52 (2024). https://doi.org/10.1007/s10482-024-01947-z

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