Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baesa Y, et al. Balance trees reveal microbial niche differentiation. MSystems. 2017;2:e00162–16.Stegen JC, Lin X, Konopka AE, Fredrickson JK. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 2012;6:1653–64.CAS
PubMed
PubMed Central
Google Scholar
Salles JF, Poly F, Schmid B, Le Roux X. Community niche predicts the functioning of denitrifying bacterial assemblages. Ecology. 2009;90:3324–32.PubMed
Google Scholar
Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia J-M, Novichov PS, et al. Characterization of a metal-resistant bacillus strain with a high molybdate affinity ModA from contaminated sediments at the Oak Ridge Reservation. Front Microbiol. 2020;11:2543.
Google Scholar
Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.CAS
PubMed
Google Scholar
Moon J-W, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, et al. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere. 2020;255:126951.CAS
PubMed
Google Scholar
Berkowitz B, Silliman SE, Dunn AM. Impact of the capillary fringe on local flow, chemical migration, and microbiology. Vadose Zo J. 2004;3:534–48.CAS
Google Scholar
Winter J, Ippisch O, Vogel H-J. Dynamic processes in capillary fringes. Vadose Zo J. 2015;14:1–2.Silliman SE, Berkowitz B, Simunek J, van Genuchten MT. Fluid flow and solute migration within the capillary fringe. Ground Water. 2002;40:76–84.CAS
PubMed
Google Scholar
Haberer CM, Rolle M, Liu S, Cirpka OA, Prathwohl P. A high-resolution non-invasive approach to quantify oxygen transport across the capillary fringe and within the underlying groundwater. J Contam Hydrol. 2011;122:26–39.CAS
PubMed
Google Scholar
Bouskill NJ, Conrad ME, Bill M, Brodie EL, Cheng Y, Hobson C, et al. Evidence for microbial mediated NO3− cycling within floodplain sediments during groundwater fluctuations. Front Earth Sci. 2019;7:189.
Google Scholar
Rühle FA, von Netzer F, Lueders T, Stumpp C. Response of transport parameters and sediment microbiota to water table fluctuations in laboratory columns. Vadose Zo J. 2015;14:vzj2014.09.0116.Aigle A, Prosser JI, Gubry-Rangin C. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome. 2019;14:3.PubMed
PubMed Central
Google Scholar
Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW. Comparative genomics of marine sponge-derived Streptomyces spp. isolates SM17 and SM18 with their closest terrestrial relatives provides novel insights into environmental niche adaptations and secondary metabolite biosynthesis potential. Front Microbiol. 2019;10:1713.PubMed
PubMed Central
Google Scholar
Scheuerl T, Hopkins M, Nowell RW, Rivett DW, Barraclough TG, Bell T, et al. Bacterial adaptation is constrained in complex communities. Nat Commun. 2020;11:754.CAS
PubMed
PubMed Central
Google Scholar
Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev. 2014;38:720–60.CAS
PubMed
Google Scholar
Harrison E, Brockhurst MA. Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol. 2012;20:262–7.CAS
PubMed
Google Scholar
Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, et al. Genome sequence of Azospirillum brasilense CBG497 and comparative analyses of Azospirillum core and accessory genomes provide insight into niche adaptation. Genes. 2012;3:576–602.Conn HJ, Dimmick I. Soil bacteria similar in morphology to Mycobacterium and Corynebacterium. J Bacteriol. 1947;54:291–303.CAS
PubMed
PubMed Central
Google Scholar
Boivin-Jahns V, Bianchi A, Ruimy R, Garcin J, Daumas S, Cristen R, et al. Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl Environ Microbiol. 1995;61:3400–6.CAS
PubMed
PubMed Central
Google Scholar
Rusterholtz KJ, Mallory LM. Density, activity, and diversity of bacteria indigenous to a karstic aquifer. Microb Ecol. 1994;28:79–99.CAS
PubMed
Google Scholar
Eschbach M, Möbitz H, Rompf A, Jahn D. Members of the genus Arthrobacter grow anaerobically using nitrate ammonification and fermentative processes: anaerobic adaptation of aerobic bacteria abundant in soil. FEMS Microbiol Lett. 2003;223:227–30.CAS
PubMed
Google Scholar
Banerjee S, Palit R, Sengupta C, Standing D. Stress induced phosphate solubilization by ’Arthrobacter’ Sp. and ’Bacillus’ sp. isolated from tomato rhizosphere. Aust J Crop Sci. 2010;4:378–83.CAS
Google Scholar
Keddie RM, Collins D, Jones D. Genus Arthrobacter. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG, editors. Bergey’s manual of systematic bacteriology. Vol 2. Williams and Wilkins: New York, NY. 1986. p. 1288–301.Crocker FH, Fredrickson JK, White DC, Ringelberg DB, Balkwill DL. Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments. Microbiology. 2000;146:1295–310.CAS
PubMed
Google Scholar
Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, et al. Exometabolite niche partitioning among sympatric soil bacteria. Nat Commun. 2015;6:8289.CAS
PubMed
Google Scholar
Wu X, Spencer S, Gushgari-Doyle S, Yee MO, Voriskova J, Li Y, et al. Culturing of “unculturable” subsurface microbes: natural organic carbon source fuels the growth of diverse and distinct bacteria from groundwater. Front Microbiol. 2020;11:3171.
Google Scholar
Watson DB, Kostka JE, Fields MW, Jardine PM. The Oak Ridge Field Research Center conceptual model. NABIR F. Res. Center: Oak Ridge, TN; 2004.Moon J, Roh Y, Phelps TJ, Phillips DH, Watson DB, Kim Y-J, et al. Physicochemical and mineralogical characterization of soil–saprolite cores from a field research site, Tennessee. J Environ Qual. 2006;35:1731–41.CAS
PubMed
Google Scholar
Wu X, Wu L, Liu Y, Zhang P, Li Q, Zhou J, et al. Microbial interactions with dissolved organic matter drive carbon dynamics and community succession. Front Microbiol. 2018;9:1234.PubMed
PubMed Central
Google Scholar
Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, et al. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci. 2017;12:23.PubMed
PubMed Central
Google Scholar
Guttenberger M, Hampp R. Ectomycorrhizins—symbiosis-specific or artifactual polypeptides from ectomycorrhizas? Planta. 1992;188:129–36.CAS
PubMed
Google Scholar
Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13:e1005595.PubMed
PubMed Central
Google Scholar
Hyatt D, Chen G, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.PubMed
PubMed Central
Google Scholar
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021;38:5825–9.Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013;14:60.PubMed
PubMed Central
Google Scholar
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2022;50:D801–D807.CAS
PubMed
Google Scholar
Price MN, Deutschbauer AM, Arkin AP. GapMind: automated annotation of amino acid biosynthesis. mSystems. 2020;5:e00291–20.CAS
PubMed
PubMed Central
Google Scholar
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–W101.CAS
PubMed
PubMed Central
Google Scholar
Bertelli C, Laird MR, Wiliams KP, Lau BY, Hoad G, Winsor GL, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45:W30–W35.CAS
PubMed
PubMed Central
Google Scholar
Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016;44:W232–W235.CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.CAS
PubMed
PubMed Central
Google Scholar
Procter JB, Carstairs GM, Soares B, Mourão K, Ofoegbu TC, Barton D, et al. Alignment of biological sequences with Jalview. In: Katoh K Editor. Multiple sequence alignment. Springer, Humana Press: New York, NY. 2021. p. 203–24.Letunic I, Bork P. Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–6. https://doi.org/10.1093/nar/gkab301.Eren AM, Esen O, Quince C, Vines JH, Horrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ’omics data. PeerJ. 2015;3:e1319.PubMed
PubMed Central
Google Scholar
Qiong W, Garrity GM, Tiedge JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Google Scholar
Liao J, Guo X, Weller DL, Pollak S, Buckley DH, Wiedmann M, et al. Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution. Nat Microbiol. 2021;6:1021–30.CAS
PubMed
Google Scholar
Schwyn B, Neilands JB. Universal chemical assay for detection and determination of siderophores. Anal Biochem. 1987;160:47–56.CAS
PubMed
Google Scholar
Pérez-Miranda S, Cabirol N, George-Téllez R, Zamudio-Rivera LS, Fernandez FJ. O-CAS, a fast and universal method for siderophore detection. J Microbiol Methods. 2007;70:127–31.PubMed
Google Scholar
Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JBH, et al. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front Microbiol. 2013;4:282PubMed
PubMed Central
Google Scholar
Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Gregory Caporaso J, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010;4:1340–51.PubMed
Google Scholar
Oliveira PL, de, Duarte MCT, Ponezi AN, Durrant LR. Purification and partial characterization of manganese peroxidase from Bacillus pumilus and Paenibacillus sp. Braz J Microbiol. 2009;40:818–26.PubMed
PubMed Central
Google Scholar
Varrot A, Yip VLY, Li Y, Rajan SS, Yang X, Anderson WF, et al. NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-β-D-glucosides. J Mol Biol.2005;346:423–35.CAS
PubMed
Google Scholar
Lambers H. Introduction: dryland salinity: a key environmental issue in southern Australia. Plant Soil. 2003;257:v–vii.Galinski EA, Trüper HG. Microbial behaviour in salt-stressed ecosystems. FEMS Microbiol Rev. 1994;15:95–108.CAS
Google Scholar
Korom SF. Natural denitrification in the saturated zone: a review. Water Resour Res. 1992;28:1657–68.CAS
Google Scholar
Niewerth H, Schuldes J, Parschat K, Kiefer P, Vorholt JA, Daniel R, et al. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics. 2012;13:1–19.
Google Scholar
See-Too W-S, Ee R, Lim Y-L, Convey P, Pearce DA, Mohidin TBM, et al. Complete genome of Arthrobacter alpinus strain R3. 8, bioremediation potential unraveled with genomic analysis. Stand Genomic Sci. 2017;12:1–7.
Google Scholar
Bazhanov DP, Li C, Li H, Li J, Zhang X, Chen X, et al. Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, PR China. BMC Microbiol. 2016;16:1–21.
Google Scholar
Fan X, Nie MQ, Wang Y, Diwu ZJ, Liu L, Liu Y. Characteristics of the co-metabolism of 1-naphthol by Arthrobacter crystallopoietes NT16 and symbiotic Bacillus NG16. Acta Sci Circumstantiae. 2019;39:1482–8.CAS
Google Scholar
Nakatsu CH, Barabote R, Thompson S, Bruce D, Detter C, Brettin T, et al. Complete genome sequence of Arthrobacter sp. strain FB24. Stand Genomic Sci. 2013;9:106–16.PubMed
PubMed Central
Google Scholar
Shimasaki T, Masuda S, Garrido-Oter R, Kawasaki T, Aoki Y, Shibata A, et al. Tobacco root endophytic Arthrobacter harbors genomic features enabling the catabolism of host-specific plant specialized metabolites. MBio. 2021;12:e00846–21.CAS
PubMed Central
Google Scholar
Kumar R, Singh D, Swarnkar MK, Singh AK, Kumar S. Complete genome sequence of Arthrobacter alpinus ERGS4: 06, a yellow pigmented bacterium tolerant to cold and radiations isolated from Sikkim Himalaya. J Biotechnol. 2016;220:86–87.CAS
PubMed
Google Scholar
Russell DA, Hatfull GF. Complete genome sequence of Arthrobacter sp. ATCC 21022, a host for bacteriophage discovery. Genome Announc. 2016;4:e00168–16.PubMed
PubMed Central
Google Scholar
Fomenkov A, Akimov VN, Vasilyeva LV, Andersen DT, Vincze T, Roberts RJ, et al. Complete genome and methylome analysis of psychrotrophic bacterial isolates from Lake Untersee in Antarctica. Genome Announc. 2017;5:e01753–16.PubMed
PubMed Central
Google Scholar
Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, et al. Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami. BMC Genomics. 2016;17:1–13.
Google Scholar
Han S-R, Kim B, Jang JH, Park H, Oh T-J. Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. BMC Genomics. 2021;22:1–14.
Google Scholar
Koh H-W, Kang M, Lee K, Lee E, Kim H, Park SJ. Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula. J Microbiol. 2019;57:732–7.CAS
PubMed
Google Scholar
Xu X, Xu M, Zhao Q, Xia Y, Chen C, Shen Z. Complete genome sequence of Cd (II)-resistant Arthrobacter sp. PGP41, a plant growth-promoting bacterium with potential in microbe-assisted phytoremediation. Curr Microbiol. 2018;75:1231–9.CAS
PubMed
Google Scholar
Lee GLY, Ahmad SA, Yasid NA, Zulkharnain A, Convey P, Johari WLW, et al. Biodegradation of phenol by cold-adapted bacteria from Antarctic soils. Polar Biol. 2018;41:553–62.
Google Scholar
Stockdale A, Davison W, Zhang H. Micro-scale biogeochemical heterogeneity in sediments: a review of available technology and observed evidence. Earth-Science Rev. 2009;92:81–97.CAS
Google Scholar
Whiting AK, Boldt YR, Hendrich MP, Wackett LP, Que L. Manganese (II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2. Biochemistry. 1996;35:160–70.CAS
PubMed
Google Scholar
Jeng W-Y, Wang M, Lin N, Lin C, Liaw Y, Cheng W, et al. Structural and functional analysis of three β-glucosidases from bacterium Clostridium cellulovorans, fungus Trichoderma reesei and termite Neotermes koshunensis. J Struct Biol. 2011;173:46–56.CAS
PubMed
Google Scholar
Stevenson IL. Utilization of aromatic hydrocarbons by Arthrobacter spp. Can J Microbiol. 1967;13:205–11.CAS
PubMed
Google Scholar
Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics. 2015;16:36.PubMed
PubMed Central
Google Scholar
Taylor R, Cronin A, Pedley S, Barker J, Atkinson T. The implications of groundwater velocity variations on microbial transport and wellhead protection–review of field evidence. FEMS Microbiol Ecol. 2004;49:17–26.CAS
PubMed
Google Scholar
Zhang X, Liu X, Yang F, Chen L. Pan-genome analysis links the hereditary variation of leptospirillum ferriphilum with its evolutionary adaptation. Front Microbiol. 2018;9:577.PubMed
PubMed Central
Google Scholar
Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, et al. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics. 2012;13:533.CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Sievert S. Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Front Microbiol. 2014;5:110.PubMed
PubMed Central
Google Scholar
Aminov R. Horizontal gene exchange in environmental microbiota. Front Microbiol. 2011;2:158.PubMed
PubMed Central
Google Scholar
Kothari A, Wu Y, Chandonia J-M, Charrier M, Rajiv L, Rocha AM, et al. Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes. MBio. 2019;10:e02899–18.CAS
PubMed
PubMed Central
Google Scholar
Penn K, Jenkins C, Nett M, Udwary DW, Gontang EA, McGlinchey RP, et al. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J. 2009;3:1193–203.CAS
PubMed
Google Scholar
Wu X, Kazakov AE, Gushgari-Doyle S, Yu X, Trotter V, Stuart RK, et al. Comparative genomics reveals insights into induction of violacein biosynthesis and adaptive evolution in Janthinobacterium. Microbiol Spectr. 2022;9:e01414–e01421.
Google Scholar
Jonkheer EM, Brankovics B, Houwers IM, van der Wolf JM, Bonants PJM, Vreeburg RAM, et al. The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool. BMC Genomics. 2021;22:265.CAS
PubMed
PubMed Central
Google Scholar
Abdel-Glil MY, Rischer U, Steinhagen D, McCarthy U, Neubauer H, Sprague LD. Phylogenetic relatedness and genome structure of Yersinia ruckeri revealed by whole genome sequencing and a comparative analysis. Front Microbiol. 2021;12:782415.González-Dominici LI, Saati-Santamaría Z, García-Fraile P. Genome analysis and genomic comparison of the novel species Arthrobacter ipsi reveal its potential protective role in its bark beetle host. Microb Ecol. 2021;81:471–82.PubMed
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–D596.CAS
PubMed
Google Scholar
Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol. 1997;63:2330–7.CAS
PubMed
PubMed Central
Google Scholar
Griebler C, Lueders T. Microbial biodiversity in groundwater ecosystems. Freshw Biol. 2009;54:649–77.
Google Scholar More