Closed genomes uncover a saltwater species of Candidatus … – Nature.com

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  • Pfeffer C, Larsen S, Music J, Dong M, Besenbacher F, Meyer RL, et al. Filamentous micro organism transport electrons over centimetre distances. Nature. 2012;491:218–21.

    Article 
    CAS 

    Google Scholar 

  • Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogeinternetically numerous electroactive microorganisms. Nat Rev Microbiol. 2022;20:5–19.

    Article 
    CAS 

    Google Scholar 

  • Bjerg JT, Boschker HTS, Larsen S, Berry D, Schmid M, Millo D, et al. Prolonged-distance electron transport in particular person, dwelling cable micro organism. Proc Natl Acad Sci USA. 2018;115:5786–91.

    Article 
    CAS 

    Google Scholar 

  • Trojan D, Schreiber L, Bjerg JT, Bøggild A, Yang T, Kjeldsen KU, et al. A taxonomic framework for cable micro organism and proposal of the candidate genperiod Electrothrix and Electronema. Syst Appl Microbiol. 2016;39:297–306.

    Article 

    Google Scholar 

  • Malkin SY, Rao AM, Seitaj D, Vasquez-Cardenas D, Zetsche EM, Hidalgo-Martinez S, et al. Pure prevalence of microbial sulphur oxidation by long-differ electron transport Inside the seafloor. ISME J. 2014;8:1843–54.

    Article 
    CAS 

    Google Scholar 

  • Risgaard-Petersen N, Kristiansen M, Frederiksen RB, Dittmer AL, Bjerg JT, Trojan D, et al. Cable micro organism in freshwater sediments. Appl Environ Microbiol. 2015;81:6003–11.

    Article 
    CAS 

    Google Scholar 

  • Burdorf LDW, Tramper A, Seitaj D, Meire L, Hidalgo-Martinez S, Zetsche EM, et al. Prolonged-distance electron transport occurs globally in marine sediments. Biogeosciences. 2017;14:683–701.

    Article 
    CAS 

    Google Scholar 

  • Scholz VV, Müller H, Koren K, Nielsen LP, Meckenstock RU. The rhizosphere of aquatic crops is a habitat for cable micro organism. FEMS Microbiol Ecol. 2019;95:fiz062.

    Article 
    CAS 

    Google Scholar 

  • Scholz VV, Martin BC, Meyer R, Schramm A, Fraser MW, Nielsen LP, et al. Cable micro organism at oxygen-releasing roots of aquatic crops: a widespstudy and numerous plant–microbe affiliation. N Phytol. 2021;232:2138–51.

    Article 
    CAS 

    Google Scholar 

  • Paver SF, Muratore D, Newton RJ, Coleman ML. Reevaluating the salty divide: phylogeinternetic particularity of transitions between marine and freshwater methods. mSystems. 2018;3:e00232–18.

    Article 
    CAS 

    Google Scholar 

  • Cabello-Yeves PJ, Rodriguez-Valperiod F. Marine-freshwater prokaryotic transitions require in depth modifications Inside The anticipated proteome. Microbiome. 2019;7:117.

    Article 

    Google Scholar 

  • Kjeldsen KU, Schreiber L, Thorup CA, Boesen T, Bjerg JT, Yang T, et al. On the evolution and physiology of cable micro organism. Proc Natl Acad Sci USA. 2019;116:19116–25.

    Article 
    CAS 

    Google Scholar 

  • Müller H, Marozava S, Probst AJ, Meckenstock RU. Groundwater cable micro organism protect power by sulfur disproportionation. ISME J. 2020;14:623–34.

    Article 

    Google Scholar 

  • Boschker HTS, Put together dinner PLM, Polerecky L, Eachambadi RT, Lozano H, Hidalgo-Martinez S, et al. Environment nice long-differ conduction in cable micro organism by way of nickel protein wires. Nat Commun. 2021;12:3996.

    Article 
    CAS 

    Google Scholar 

  • Thorup C, Petro C, Bøggild A, Ebsen TS, Brokjær S, Nielsen LP, et al. The biggest Method to develop your cable micro organism: institution of a safe single-strain tradition in sediment and proposal of Candidatus Electronema aureum GS. Syst Appl Microbiol. 2021;44:126236.

    Article 
    CAS 

    Google Scholar 

  • Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving micro organisml genome assemblies from brief and long sequencing studys. PLoS Comput Biol. 2017;13:e1005595.

    Article 

    Google Scholar 

  • Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nat Biotechnol. 2019;37:953–61.

    Article 
    CAS 

    Google Scholar 

  • Koren S, Phillippy AM. One chromosome, one contig: full microbial genomes from long-study sequencing and meeting. Curr Opin Microbiol. 2015;23:110–20.

    Article 
    CAS 

    Google Scholar 

  • Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, et al. Restoration of shut toly 8,000 metagenome-assembled genomes considerably expands the tree of life. Nat Microbiol. 2017;2:1533–42.

    Article 
    CAS 

    Google Scholar 

  • Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW. GroopM: An automated system for the recupperiodtey of inhabitants genomes from associated metagenomes. PeerJ. 2014;2:e603.

    Article 

    Google Scholar 

  • Vasudevan K, Devanga Ragupathi NK, Jacob JJ, Veperiodraghavan B. Extremely right-single chromosomal full genomes using IonTorrent and MinION sequencing of medical pathogens. Genomics. 2020;112:545–51.

    Article 
    CAS 

    Google Scholar 

  • Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, et al. ProDeGe: a computational protocol for absolutely automated decontamination of genomes. ISME J. 2016;10:269–72.

    Article 
    CAS 

    Google Scholar 

  • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing The regular of microbial genomes recupperiodteed from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    Article 
    CAS 

    Google Scholar 

  • Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. New insights from uncultivated genomes of The worldwide human gut microbiome. Nature. 2019;568:505–10.

    Article 
    CAS 

    Google Scholar 

  • Moss EL, Maghini DG, Bhatt AS. Complete, shutd micro organisml genomes from microbiomes using nanopore sequencing. Nat Biotechnol. 2020;38:1–7.

    Article 

    Google Scholar 

  • Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, et al. Producing lineage-resolved, full metagenome-assembled genomes from complicated microbial communities. Nat Biotechnol. 2022;40:711–9.

    Article 
    CAS 

    Google Scholar 

  • Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sørensen EA, Wollenberg RD, et al. Oxford Nanopore R10.4 long-study sequencing permits the period of shut to-fulld micro organisml genomes from pure traditions and metagenomes with out brief-study or reference sprucing. Nat Strategies. 2022;19:823–6.

    Article 
    CAS 

    Google Scholar 

  • Overholt WA, Hölzer M, Geesink P, Diezel C, Marz M, Küsel K. Inclusion of Oxford Nanopore long studys improves all microbial and viral metagenome-assembled genomes from A posh aquifer system. Environ Microbiol. 2020;22:4000–13.

    Article 
    CAS 

    Google Scholar 

  • De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, et al. Comparability of long-study sequencing utilized sciences Inside the hybrid meeting of complicated micro organisml genomes. Microb Genom. 2019;5:e000294.

  • Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. HASLR: quick hybrid meeting of long studys. iScience. 2020;23:101389.

    Article 
    CAS 

    Google Scholar 

  • Singleton CM, Petriglieri F, Kristensen JM, Kirkegaard RH, Michaelsen TY, Andersen MH, et al. Connecting construction to carry out with the recupperiodtey of over 1000 extreme-extreme quality metagenome-assembled genomes from activated sludge using long-study sequencing. Nat Commun. 2021;12:2009.

    Article 
    CAS 

    Google Scholar 

  • Cuscó A, Pérez D, Viñes J, Fàbregas N, Francino O. Prolonged-study metagenomics retrieves full single-contig micro organisml genomes from canine feces. BMC Genomics. 2021;22:330.

    Article 

    Google Scholar 

  • Liu L, Wang Y, Che Y, Chen Y, Xia Y, Luo R, et al. High-extreme quality micro organisml genomes of a partial-nitritation/anammox system by an itperiodtive hybrid meeting method. Microbiome. 2020;8:155.

    Article 
    CAS 

    Google Scholar 

  • Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Ochman H, Nielsen LP, et al. Pangenome evaluation of cable micro organism reveals the probably geinternetic basis Of huge sized micro organism in Candidatus Electrothrix gigas sp. nov [manuscript in preparation]. College of Antwerp and Aarhus College; 2022 [cited 2023 Jan 23].

  • Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, et al. Extensive unexplored human microbiome variety revealed by over 150,000 genomes from metagenomes spanning age, geography, and way of life. Cell 2019;176:649–662.e20.

    Article 
    CAS 

    Google Scholar 

  • Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. An complete area-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol. 2020;38:1079–86.

    Article 
    CAS 

    Google Scholar 

  • Dam AS, Marshall IPG, Risgaard-Petersen N, Burdorf LDW, Marzocchi U. Influence of salinity on cable micro organism species complace And selection. Environ Microbiol. 2021;23:2605–16.

    Article 
    CAS 

    Google Scholar 

  • Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, et al. A proposed genus boundary for the prokaryotes based mostly on genomic insights. J Bacteriol. 2014;196:2210–5.

    Article 

    Google Scholar 

  • Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D. A genus definition for micro organism and archaea based mostly on A conventional genome associatedness index. mBio 2020;11:e02475–19.

    Article 
    CAS 

    Google Scholar 

  • Oren A. Microbial life at extreme salt concentrations: phylogeinternetic and metabolic variety. Saline Syst. 2008;4:2.

    Article 

    Google Scholar 

  • Stal LJ, Cretoiu MS (eds). The marine microbiome. 1st ed. Springer Cham, Yersseke, 2016.

  • Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three areas of life to extreme salt concentrations. FEMS Microbiol Rev. 2018;42:353–75.

    Article 
    CAS 

    Google Scholar 

  • Sannikov A. Marine sediments: intperiodction companions of cable micro organism revealed by way of metagenomics [grasp’s thesis On The internet]. College of Padua; 2021 [cited 2023 Jan 23]. Out there from: http://hdl.deal with.internet/20.500.12608/34057.

  • Fang Y, Liu J, Yang J, Wu G, Hua Z, Dong H, et al. Complaceal and metabolic responses of autotrophic microbial group to salinity in lacustrine environments. mSystems. 2022;7:e0033522.

    Article 

    Google Scholar 

  • Herz K, Vimont S, Padan E, Berche P. Roles of NhaA, NhaB, and NhaD Na+/H+ antiporters in survival of Vibrio cholperiode in a saline environment. J Bacteriol. 2003;185:1236–44.

    Article 
    CAS 

    Google Scholar 

  • Waditee R, Hibino T, Nakamura T, Incharoensakdi A, Takabe T. Overexpression of a Na+/H+ antiporter confers salt tolperiodnce on a freshwater cyanobacterium, making it In a place to progress in sea water. Proc Natl Acad Sci USA. 2002;99:4109–14.

    Article 
    CAS 

    Google Scholar 

  • Meng L, Meng F, Zhang R, Zhang Z, Dong P, Photo voltaic K, et al. Characterization of a novel two-factor Na + (Li + , K + )/H + antiporter from Halomonas zhaodongensis. Sci Rep. 2017;7:4221.

    Article 

    Google Scholar 

  • Wei Y, Liu J, Ma Y, Krulwich TA. Three putative cation/proton antiporters from the soda lake alkaliphile Alkalimonas amylolytica N10 complement an alkali-delicate Escherichia coli mutant. Microbiology. 2007;153:2168–79.

    Article 
    CAS 

    Google Scholar 

  • Marzocchi U, Thorup C, Dam AS, Schramm A, Risgaard-Petersen N. Dissimilatory nitrate discount by a freshwater cable bacterium. ISME J. 2022;16:50–7.

    Article 
    CAS 

    Google Scholar 

  • Gao H, Yang ZK, Barua S, Reed SB, Romine MF, Nealson KH, et al. Reduction of nitrate in Shewanella oneidensis Relies upon upon atypical NAP and NRF methods with NapB as a most properly-appreciated electron transport protein from CymA to NapA. ISME J. 2009;3:966–76.

    Article 
    CAS 

    Google Scholar 

  • Chen S, Zhou Y, Chen Y, Gu J. quickp: an extremely-quick all-in-one FASTQ preprocessor. Bioinformatics 2018;34:i884–90.

    Article 

    Google Scholar 

  • Wick RR, Judd LM, Gorrie CL, Holt KEY. 2017. Ending micro organisml genome assemblies with a quantity ofx MinION sequencing. Micro Genom. 2017;3:e000132.

    Google Scholar 

  • De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-study sequencing knowledge. Bioinformatics. 2018;34:2666–9.

    Article 

    Google Scholar 

  • Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, et al. metaFlye: scalable long-study metagenome meeting using repeat graphs. Nat Strategies. 2020;17:1103–10.

    Article 
    CAS 

    Google Scholar 

  • Vaser R, Sović I, Nagarajan N, Šikić M. Fast and right de novo genome meeting from long unrighted studys. Genome Res. 2017;27:737–46.

    Article 
    CAS 

    Google Scholar 

  • Li H. Minimap and miniasm: quick mapping and de novo meeting for noisy long sequences. Bioinformatics. 2016;32:2103–10.

    Article 
    CAS 

    Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMmodels. Bioinformatics. 2009;25:2078–9.

    Article 

    Google Scholar 

  • Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for strong and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.

    Article 

    Google Scholar 

  • Nissen JN, Johansen J, Allesøe RL, Sønderby CK, Armenteros JJA, Grønbech CH, et al. Improved metagenome binning and meeting using deep variational autoencoders. Nat Biotechnol. 2021;39:555–60.

    Article 
    CAS 

    Google Scholar 

  • Wu YW, Simmons BA, Singer SW. MaxBin 2.0: An automated binning algorithm to recupperiodte genomes from a quantity of metagenomic knowledgemodels. Bioinformatics. 2016;32:605–7.

    Article 
    CAS 

    Google Scholar 

  • Wang Z, Huang P, You R, Photo voltaic F, Zhu S. MetaBinner: a extreme-efficiency and stand-alone ensemble binning method to recupperiodte particular person genomes from complicated microbial communities. Genome Biol. 2023;24:1.

    Article 

    Google Scholar 

  • Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Restoration of genomes from metagenomes by way of a dereplication, aggregation and scoring technique. Nat Microbiol. 2018;3:836–43.

    Article 
    CAS 

    Google Scholar 

  • Chan PP, Lowe TM. tRNAscan-SE: Wanting for tRNA genes in genomic sequences. Strategies Mol Biol. 2019;1962:1–14.

    Article 
    CAS 

    Google Scholar 

  • Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimal Particulars A few single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of micro organism and archaea. Nat Biotechnol. 2017;35:725–31.

    Article 
    CAS 

    Google Scholar 

  • Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a systemkit To categorise genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.

    CAS 

    Google Scholar 

  • Steinegger M, Söding J. MMseqs2 permits delicate protein sequence Wanting for the evaluation of huge knowledge models. Nat Biotechnol. 2017;35:1026–8.

    Article 
    CAS 

    Google Scholar 

  • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence knowledgebase of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61–5.

    Article 
    CAS 

    Google Scholar 

  • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    Article 
    CAS 

    Google Scholar 

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene knowledgebase enterprise: improved knowledge processing and internet-based mostly models. Nucleic Acids Res. 2013;41:D590–596.

    Article 
    CAS 

    Google Scholar 

  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A quick and efficient stochastic algorithm for estimating most-probability phylogenies. Mol Biol Evol. 2015;32:268–74.

    Article 
    CAS 

    Google Scholar 

  • Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for meals safety: gentle-rotting enteromicro organisml plant pathogens. Anal Strategies. 2015;8:12–24.

    Article 

    Google Scholar 

  • Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: extreme quality evaluation system for genome assemblies. Bioinformatics. 2013;29:1072–5.

    Article 
    CAS 

    Google Scholar 

  • Xie Z, Tang H. ISEScan: automated identification of insertion sequence parts in prokaryotic genomes. Bioinformatics. 2017;33:3340–7.

    Article 
    CAS 

    Google Scholar 

  • Seemann T. Prokka: speedy prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    Article 
    CAS 

    Google Scholar 

  • Edgar RC. MUSCLE: a a quantity of sequence alignment method with lowered time and space complicatedity. BMC Bioinform. 2004;5:113.

    Article 

    Google Scholar 

  • Website AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: speedy huge-scale prokaryote pan genome evaluation. Bioinformatics. 2015;31:3691–3.

    Article 
    CAS 

    Google Scholar 

  • Valleinternet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, et al. MicroScope: an constructed-in platform for the annotation and exploration of microbial gene carry outs by way of genomic, pangenomic and metabolic comparative evaluation. Nucleic Acids Res. 2020;48:D579–89.

    CAS 

    Google Scholar 

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

    Article 
    CAS 

    Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar null, et al. ARB: a gentleware program environment for sequence knowledge. Nucleic Acids Res. 2004;32:1363–71.

    Article 
    CAS 

    Google Scholar 

  • Yilmaz LS, Parnerkar S, Noguperiod DR. mathFISH, An interinternet system that makes use of thermodynamics-based mostly mathematical fashions for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl Environ Microbiol. 2011;77:1118–22.

    Article 
    CAS 

    Google Scholar 

  • Daims, H, Stoecker, K, Wagner M. Fluorescence in situ hybridization for the detection of prokaryotes. In: Molecular Microbial Ecology. Taylor & Francis; 2005. p. 213–39.

  • Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-focused oligonucleotide probes with circulate cytometry for analyzing mixed microbial inhabitantss. Appl Environ Microbiol. 1990;56:1919–25.

    Article 
    CAS 

    Google Scholar 

  • Daims H, Brühl A, Amann R, Schleifer KH, Wagner M. The area-particular probe EUB338 is insufficient for the detection of all Bacteria: enchancment and evaluation of a extra full probe set. Syst Appl Microbiol. 1999;22:434–44.

    Article 
    CAS 

    Google Scholar 

  • Wallner G, Amann R, Beisker W. Optimizing fluorescent in situ hybridization with rRNA-focused oligonucleotide probes for circulate cytometric identification of microorganisms. Cytometry. 1993;14:136–43.

    Article 
    CAS 

    Google Scholar 

  • Fernando EY, McIlroy SJ, Nierychlo M, Herbst FA, Petriglieri F, Schmid MC, et al. Resolving The particular person contribution of key microbial inhabitantss to enhanced organic phosphorus perioddicating with Raman-FISH. ISME J. 2019;13:1933–46.

    Article 
    CAS 

    Google Scholar 

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