Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. ISME J. 2017;11:1949–63.
Google Scholar
Hall EK, Bernhardt ES, Bier RL, Bradford MA, Boot CM, Cotner JB, et al. Understanding how microbiomes influence the systems they inhabit. Nat Microbiol. 2018;3:977–82.
Google Scholar
Lloyd KG, Steen AD, Ladau J, Yin J, Crosby L. Phylogenetically novel uncultured microbial cells dominate earth microbiomes. mSystems 2018;3:e00055–18.
Google Scholar
Lewis WH, Tahon G, Geesink P, Sousa DZ, Ettema TJG. Innovations to culturing the uncultured microbial majority. Nat Rev Microbiol. 2021;19:225–40.
Google Scholar
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048.
Google Scholar
Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science. 2017;357:eaaf3883.
Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42.
Google Scholar
Chen S-C, Musat N, Lechtenfeld OJ, Paschke H, Schmidt M, Said N, et al. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 2019;568:108–11.
Google Scholar
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol. 2021;39:499–509.
Google Scholar
Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbiome function at single cell level. Nat Rev Microbiol. 2020;18:241–56.
Google Scholar
Baker BJ, De Anda V, Seitz KW, Dombrowski N, Santoro AE, Lloyd KG. Diversity, ecology and evolution of Archaea. Nat Microbiol. 2020;5:887–900.
Google Scholar
Abraham WR, Nogales B, Golyshin PN, Pieper DH, Timmis KN. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol. 2002;5:246–53.
Google Scholar
Galbán-Malagón C, Berrojalbiz N, Ojeda M-J, Dachs J. The oceanic biological pump modulates the atmospheric transport of persistent organic pollutants to the Arctic. Nat Commun 2012;3:862.
Google Scholar
Pieper DH. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol. 2005;67:170–91.
Google Scholar
Chain PSG, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA. 2006;103:15280.
Google Scholar
Furukawa K, Suenaga H, Goto M. Biphenyl dioxygenases: functional versatilities and directed evolution. J Bacteriol. 2004;186:5189–96.
Google Scholar
McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, Fernandes C, et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA. 2006;103:15582.
Google Scholar
Lee TK, Lee J, Sul WJ, Iwai S, Chai BC, Tiedje JM, et al. Novel biphenyl-oxidizing bacteria and dioxygenase genes from a Korean tidal mudflat. Appl Environ Microbiol. 2011;77:3888–91.
Google Scholar
Sul WJ, Park J, Quensen JF, Rodrigues JLM, Seliger L, Tsoi TV, et al. DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol. 2009;75:5501–6.
Google Scholar
Uhlik O, Jecna K, Mackova M, Vlcek C, Hroudova M, Demnerova K, et al. Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. Appl Environ Microbiol. 2009;75:6471.
Google Scholar
Jiang LF, Luo CL, Zhang DY, Song MK, Sun YT, Zhang G. Biphenyl-Metabolizing microbial community and a functional operon revealed in e-waste-contaminated soil. Environ Sci Technol. 2018;52:8558–67.
Google Scholar
Tillmann S, Strompl C, Timmis KN, Abraham WR. Stable isotope probing reveals the dominant role of Burkholderia species in aerobic degradation of PCBs. FEMS Microbiol Ecol. 2005;52:207–17.
Google Scholar
Leigh MB, Pellizari VH, Uhlik O, Sutka R, Rodrigues J, Ostrom NE, et al. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). ISME J. 2007;1:134–48.
Google Scholar
Chen S-C, Duan G-L, Ding K, Huang F-Y, Zhu Y-G. DNA stable-isotope probing identifies uncultivated members of Pseudonocardia associated with biodegradation of pyrene in agricultural soil. FEMS Microbiol Ecol. 2018;94:fiy026.
Neufeld JD, Dumont MG, Vohra J, Murrell JC. Methodological considerations for the use of stable isotope probing in microbial ecology. Micro Ecol. 2007;53:435–42.
Google Scholar
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6.
Google Scholar
Mohn WW, Westerberg K, Cullen WR, Reimer KJ. Aerobic biodegradation of biphenyl and polychlorinated biphenyls by Arctic soil microorganisms. Appl Environ Microbiol. 1997;63:3378–84.
Google Scholar
Wagner-Dobler I, Bennasar A, Vancanneyt M, Strompl C, Brummer I, Eichner C, et al. Microcosm enrichment of biphenyl-degrading microbial communities from soils and sediments. Appl Environ Microbiol. 1998;64:3014–22.
Google Scholar
Allen MB. Studies with cyanidium caldarium, an anomalously pigmented chlorophyte. Arch Mikrobiol. 1959;32:270–7.
Google Scholar
Rabus R, Widdel F. Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol. 1995;163:96–103.
Google Scholar
Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 1996;62:316.
Google Scholar
Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823–9.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013;41:D590–D6.
Google Scholar
Ouyang WY, Su JQ, Richnow HH, Adrian L. Identification of dominant sulfamethoxazole-degraders in pig farm-impacted soil by DNA and protein stable isotope probing. Environ Int. 2019;126:118–26.
Google Scholar
Tischer K, Zeder M, Klug R, Pernthaler J, Schattenhofer M, Harms H, et al. Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples. Syst Appl Microbiol. 2012;35:526–32.
Google Scholar
Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MMM. Look@NanoSIMS–a tool for the analysis of nanoSIMS data in environmental microbiology. Environ Microbiol. 2012;14:1009–23.
Google Scholar
Stryhanyuk H, Calabrese F, Kümmel S, Musat F, Richnow HH, Musat N. Calculation of single cell assimilation rates from SIP-NanoSIMS-derived isotope ratios: a comprehensive approach. Front Microbiol. 2018;9:2342.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–20.
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 2019;7:e7359–e.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020;36:1925–7.
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–3.
Google Scholar
Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.
Google Scholar
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–D30.
Google Scholar
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–D14. (D1)
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Google Scholar
Budhraja R, Karande S, Ding C, Ullrich MK, Wagner S, Reemtsma T, et al. Characterization of membrane-bound metalloproteins in the anaerobic ammonium-oxidizing bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1. Talanta. 2021;223:121711.
Google Scholar
Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 2004;20:1466–7.
Google Scholar
Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016;13:741–8.
Google Scholar
Sachsenberg T, Herbst F-A, Taubert M, Kermer R, Jehmlich N, von Bergen M, et al. MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics. J Proteome Res. 2015;14:619–27.
Google Scholar
Liu J, He XX, Lin XR, Chen WC, Zhou QX, Shu WS, et al. Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities. Environ Sci Technol. 2015;49:6438–47.
Google Scholar
Kumamaru T, Suenaga H, Mitsuoka M, Watanabe T, Furukawa K. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat Biotechnol. 1998;16:663–6.
Google Scholar
Garrido-Sanz D, Manzano J, Martín M, Redondo-Nieto M, Rivilla R. Metagenomic analysis of a biphenyl-degrading soil bacterial consortium reveals the metabolic roles of specific populations. Front Microbiol. 2018;9:232.
Kikuchi Y, Nagata Y, Ohtsubo Y, Koana T, Takagi M. Pseudomonas fluorescens KKL101, a benzoic acid degrader in a mixed culture that degrades biphenyl and polychlorinated biphenyls. Biosci Biotechnol Biochem. 1995;59:2303–4.
Google Scholar
Musat N, Halm H, Winterholler B, Hoppe P, Peduzzi S, Hillion F, et al. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc Natl Acad Sci USA. 2008;105:17861.
Google Scholar
Calabrese F, Voloshynovska I, Musat F, Thullner M, Schlömann M, Richnow HH, et al. Quantitation and comparison of phenotypic heterogeneity among single cells of monoclonal microbial populations. Front Microbiol. 2019;10:2814.
Google Scholar
Robertson BR, Button DK, Koch AL. Determination of the biomasses of small bacteria at low concentrations in a mixture of species with forward light scatter measurements by flow cytometry. Appl Environ Microbiol. 1998;64:3900–9.
Google Scholar
Troussellier M, Bouvy M, Courties C, Dupuy C. Variation of carbon content among bacterial species under starvation condition. Aquat Micro Ecol. 1997;13:113–9.
Google Scholar
Furukawa K, Miyazaki T. Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes. J Bacteriol. 1986;166:392–8.
Google Scholar
Seeger M, Timmis KN, Hofer B. Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400. Appl Environ Microbiol. 1995;61:2654–8.
Google Scholar
Chadhain SM, Moritz EM, Kim E, Zylstra GJ. Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol. 2007;34:605–13.
Google Scholar
Hofer B, Backhaus S, Timmis KN. The biphenyl/polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes. Gene 1994;144:9–16.
Google Scholar
Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol. 1996;50:553–90.
Google Scholar
Rather LJ, Knapp B, Haehnel W, Fuchs G. Coenzyme A-dependent aerobic metabolism of benzoate via epoxide formation. J Biol Chem. 2010;285:20615–24.
Google Scholar
Stegen JC, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, et al. Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover. Nat Commun. 2016;7:1–12.
Corteselli EM, Aitken MD, Singleton DR. Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds. Int J Syst Evol Microbiol 2017;67:311–8.
Google Scholar
Fernandez H, Prandoni N, Fernandez-Pascual M, Fajardo S, Morcillo C, Diaz E, et al. Azoarcus sp. CIB, an anaerobic biodegrader of aromatic compounds shows an endophytic lifestyle. PLoS ONE. 2014;9:e110771.
Iwai S, Johnson TA, Chai BL, Hashsham SA, Tiedje JM. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Appl Environ Microbiol. 2011;77:3551–7.
Google Scholar
Top EM, Springael D. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol. 2003;14:262–9.
Google Scholar
Dombrowski N, Donaho JA, Gutierrez T, Seitz KW, Teske AP, Baker BJ. Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill. Nat Microbiol. 2016;1:1–7.
de Lorenzo V. Systems biology approaches to bioremediation. Curr Opin Biotechnol. 2008;19:579–89.
Google Scholar
Rabus R, Wöhlbrand L, Thies D, Meyer M, Reinhold-Hurek B, Kämpfer P. Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov. Int J Syst Evol Microbiol. 2019;69:982–97.
Google Scholar
Vogt C, Richnow HH. Bioremediation via in situ microbial degradation of organic pollutants. Adv Biochem Engin/Biotechnol. 2014;142:123–46.
Cunningham JA, Rahme H, Hopkins GD, Lebron C, Reinhard M. Enhanced in situ bioremediation of BTEX-contaminated groundwater by combined injection of nitrate and sulfate. Environ Sci Technol. 2001;35:1663–70.
Google Scholar
Mondello FJ, Turcich MP, Lobos JH, Erickson BD. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol. 1997;63:3096–103.
Google Scholar
Gomez-Gil L, Kumar P, Barriault D, Bolin JT, Sylvestre M, Eltis LD. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J Bacteriol. 2007;189:5705–15.
Google Scholar
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