{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T15:41:37Z","timestamp":1793720497152,"version":"4.6.1"},"reference-count":93,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100006978","name":"University of California Berkeley","doi-asserted-by":"publisher","award":["51719"],"award-info":[{"award-number":["51719"]}],"id":[{"id":"10.13039\/100006978","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Environmental Management"],"published-print":{"date-parts":[[2022,11]]},"DOI":"10.1016\/j.jenvman.2022.116132","type":"journal-article","created":{"date-parts":[[2022,9,5]],"date-time":"2022-09-05T06:07:56Z","timestamp":1662358076000},"page":"116132","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":10,"special_numbering":"C","title":["Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment"],"prefix":"10.1016","volume":"322","author":[{"given":"Jos\u00e9 A.","family":"Siles","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5850-0281","authenticated-orcid":false,"given":"Andrew J.","family":"Hendrickson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norman","family":"Terry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jenvman.2022.116132_bib1","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1007\/s10482-015-0584-2","article-title":"A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater","volume":"108","author":"Abbas","year":"2015","journal-title":"Antonie Leeuwenhoek"},{"key":"10.1016\/j.jenvman.2022.116132_bib2","doi-asserted-by":"crossref","first-page":"3973","DOI":"10.1007\/s11033-020-05490-8","article-title":"Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium","volume":"47","author":"Abbaszade","year":"2020","journal-title":"Mol. Biol. Rep."},{"key":"10.1016\/j.jenvman.2022.116132_bib3","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1002\/jobm.202000695","article-title":"Complete genome sequence of plant growth-promoting and heavy metal-tolerant Enterobacter tabaci 4M9 (CCB-MBL 5004)","volume":"61","author":"Abdullahi","year":"2021","journal-title":"J. Basic Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib4","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2020.560768","article-title":"Mercury-tolerant Ensifer medicae strains display high mercuric reductase activity and a protective effect on nitrogen fixation in Medicago truncatula nodules under mercury stress","volume":"11","author":"Arregui","year":"2021","journal-title":"Front. Plant Sci."},{"key":"10.1016\/j.jenvman.2022.116132_bib5","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"10.1016\/j.jenvman.2022.116132_bib6","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.jes.2016.08.022","article-title":"High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism","volume":"56","author":"Bao","year":"2017","journal-title":"J. Environ. Sci."},{"key":"10.1016\/j.jenvman.2022.116132_bib7","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1080\/10643380600819625","article-title":"Weathered hydrocarbon wastes: a risk management primer","volume":"37","author":"Brassington","year":"2007","journal-title":"Crit. Rev. Environ. Sci. Technol."},{"key":"10.1016\/j.jenvman.2022.116132_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2019.135067","article-title":"Co-cropping with three phytoremediation crops influences rhizosphere microbiome community in contaminated soil","volume":"711","author":"Brereton","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.jenvman.2022.116132_bib9","doi-asserted-by":"crossref","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jenvman.2022.116132_bib10","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1094\/Phyto-78-1145","article-title":"The genetics of corky root resistance in lettuce","volume":"78","author":"Brown","year":"1988","journal-title":"Phytopathology"},{"key":"10.1016\/j.jenvman.2022.116132_bib11","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2019.7","article-title":"The effect of 16S rRNA region choice on bacterial community metabarcoding results","volume":"6","author":"Bukin","year":"2019","journal-title":"Sci. Data"},{"key":"10.1016\/j.jenvman.2022.116132_bib12","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00092-19","article-title":"A \u201ccultural\u201d renaissance: genomics breathes new life into an old craft","volume":"4","author":"Carini","year":"2019","journal-title":"mSystems"},{"key":"10.1016\/j.jenvman.2022.116132_bib13","series-title":"Summary of Findings Associated with Shell Pond Field Surveys","author":"Ch2M-Hill","year":"2010"},{"key":"10.1016\/j.jenvman.2022.116132_bib14","doi-asserted-by":"crossref","first-page":"1916","DOI":"10.3389\/fmicb.2019.01916","article-title":"Bacterial heavy-metal and antibiotic resistance genes in a copper tailing dam area in northern China","volume":"10","author":"Chen","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib15","doi-asserted-by":"crossref","first-page":"10337","DOI":"10.1021\/es502230b","article-title":"Volatilization of arsenic from polluted soil by Pseudomonas putida engineered for expression of the arsM Arsenic(III) S-adenosine methyltransferase gene","volume":"48","author":"Chen","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.jenvman.2022.116132_bib16","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.biotechadv.2015.05.003","article-title":"Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: applications, microbes and future research needs","volume":"33","author":"Chen","year":"2015","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.jenvman.2022.116132_bib17","first-page":"606","article-title":"The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities","volume":"48","author":"Davis","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jenvman.2022.116132_bib18","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1038\/s41396-019-0405-0","article-title":"Obscure soil microbes and where to find them","volume":"13","author":"Delgado-Baquerizo","year":"2019","journal-title":"ISME J."},{"key":"10.1016\/j.jenvman.2022.116132_bib19","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1126\/science.aap9516","article-title":"A global atlas of the dominant bacteria found in soil","volume":"359","author":"Delgado-Baquerizo","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.jenvman.2022.116132_bib20","doi-asserted-by":"crossref","first-page":"358","DOI":"10.3389\/fmicb.2015.00358","article-title":"Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics","volume":"6","author":"Delmont","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib21","first-page":"763","article-title":"Kinetic and multidimensional profiling of accelerated degradation of oil sludge by biostimulation","volume":"17","author":"Dong","year":"2015","journal-title":"Environ. Sci.: Process. Impacts"},{"key":"10.1016\/j.jenvman.2022.116132_bib22","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2015.00152","article-title":"Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals","volume":"6","author":"Dziewit","year":"2015","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib23","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jenvman.2022.116132_bib24","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1007\/s12665-015-4805-9","article-title":"Blending Bacillus sp., Lysinibacillus sp. and Rhodococcus sp. for optimal reduction of heavy metals in leachate contaminated soil","volume":"75","author":"Emenike","year":"2015","journal-title":"Environ. Earth Sci."},{"key":"10.1016\/j.jenvman.2022.116132_bib25","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12866-018-1152-5","article-title":"Metagenomic analysis of microbial community and function involved in cd-contaminated soil","volume":"18","author":"Feng","year":"2018","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib26","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1099\/ijs.0.058909-0","volume":"64","author":"Francis","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib27","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/nature08058","article-title":"Microbial community structure and its functional implications","volume":"459","author":"Fuhrman","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jenvman.2022.116132_bib28","doi-asserted-by":"crossref","DOI":"10.1016\/j.ecoenv.2020.111267","article-title":"Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation","volume":"205","author":"Hamood Altowayti","year":"2020","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"10.1016\/j.jenvman.2022.116132_bib29","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/ilar\/ilv017","article-title":"Analyses of intestinal microbiota: culture versus sequencing","volume":"56","author":"Hiergeist","year":"2015","journal-title":"ILAR J."},{"key":"10.1016\/j.jenvman.2022.116132_bib30","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-2-reviews0003","article-title":"Exploring prokaryotic diversity in the genomic era","volume":"3","author":"Hugenholtz","year":"2002","journal-title":"Genome Biol."},{"key":"10.1016\/j.jenvman.2022.116132_bib31","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1126\/science.1070633","article-title":"Isolating \"uncultivable\" microorganisms in pure culture in a simulated natural environment","volume":"296","author":"Kaeberlein","year":"2002","journal-title":"Science"},{"key":"10.1016\/j.jenvman.2022.116132_bib32","doi-asserted-by":"crossref","first-page":"6317","DOI":"10.1128\/AEM.01237-07","article-title":"Bacteria metabolically engineered for enhanced phytochelatin production and cadmium accumulation","volume":"73","author":"Kang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib33","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0222901","article-title":"Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons","volume":"14","author":"Khan","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib34","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1099\/ijs.0.038075-0","article-title":"Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species","volume":"62","author":"Kim","year":"2012","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib35","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"Mega X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jenvman.2022.116132_bib36","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1099\/ijs.0.061721-0","article-title":"Hoppeia youngheungensis gen. nov., sp. nov., a member of the Flavobacteriaceae isolated from tidal flat sediment, and emended descriptions of the genus Sediminibacter and Sediminibacter furfurosus","volume":"64","author":"Kwon","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib37","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1038\/s41598-018-38123-z","article-title":"Metabarcoding reveals that rhizospheric microbiota of Quercus pyrenaica is composed by a relatively small number of bacterial taxa highly abundant","volume":"9","author":"Lasa","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jenvman.2022.116132_bib38","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1021\/acs.biochem.6b00175","article-title":"The Copc family: structural and bioinformatic insights into a diverse group of periplasmic copper binding proteins","volume":"55","author":"Lawton","year":"2016","journal-title":"Biochemistry"},{"key":"10.1016\/j.jenvman.2022.116132_bib39","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1007\/s12275-016-6410-3","article-title":"Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches","volume":"54","author":"Lee","year":"2016","journal-title":"J. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib40","article-title":"Innovations to culturing the uncultured microbial majority","author":"Lewis","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib41","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2021.117994","article-title":"Adaptation mechanisms of arsenic metabolism genes and their host microorganisms in soils with different arsenic contamination levels around abandoned gold tailings","volume":"291","author":"Li","year":"2021","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.jenvman.2022.116132_bib42","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.scitotenv.2018.03.161","article-title":"Remediation techniques for heavy metal-contaminated soils: principles and applicability","volume":"633","author":"Liu","year":"2018","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.jenvman.2022.116132_bib43","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1007\/s13762-021-03298-y","article-title":"Metagenomic insights into taxonomic diversity and metabolic potential of bacterial communities associated with tannery waste-contaminated soils","volume":"19","author":"Lukhele","year":"2021","journal-title":"Int. J. Environ. Sci. Technol."},{"key":"10.1016\/j.jenvman.2022.116132_bib44","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nrmicro3400","article-title":"Ecology and exploration of the rare biosphere","volume":"13","author":"Lynch","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib45","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1007\/s00248-016-0904-8","article-title":"Microbiology meets archaeology: soil microbial communities reveal different human activities at archaic Monte Iato (sixth century BC)","volume":"73","author":"Margesin","year":"2017","journal-title":"Microb. Ecol."},{"key":"10.1016\/j.jenvman.2022.116132_bib46","article-title":"The \u20181% culturability paradigm\u2019 needs to be carefully defined","author":"Martiny","year":"2019","journal-title":"ISME J."},{"key":"10.1016\/j.jenvman.2022.116132_bib47","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1111\/j.1574-6941.2010.00982.x","article-title":"Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil","volume":"74","author":"Militon","year":"2010","journal-title":"FEMS Microbiol. Ecol."},{"key":"10.1016\/j.jenvman.2022.116132_bib48","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2020.583120","article-title":"High culturable bacterial diversity from a European desert: the Tabernas desert","volume":"11","author":"Molina-Menor","year":"2021","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0198446","article-title":"Biodegradability of polyethylene by bacteria and fungi from Dandora dumpsite Nairobi-Kenya","volume":"13","author":"Muhonja","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib50","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.01145-18","article-title":"Effective soil extraction method for cultivating previously uncultured soil bacteria","volume":"84","author":"Nguyen","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib51","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1007\/s00239-018-9885-1","article-title":"An extension of the Kimura two-parameter model to the natural evolutionary process","volume":"87","author":"Nishimaki","year":"2019","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.jenvman.2022.116132_bib52","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.3390\/ijerph17072204","article-title":"Toxic metal implications on agricultural soils, plants, animals, aquatic life and human health","volume":"17","author":"Okereafor","year":"2020","journal-title":"Int. J. Environ. Res. Publ. Health"},{"key":"10.1016\/j.jenvman.2022.116132_bib94","unstructured":"Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P., O\u2019hara, R., Simpson, G., Solymos, P., Stevens, M.H.H., Wagner, H., 2013. vegan: Community Ecology Package. https:\/\/cran.r-project.org\/web\/packages\/vegan\/index.html."},{"key":"10.1016\/j.jenvman.2022.116132_bib53","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"Overbeek","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jenvman.2022.116132_bib54","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.136904","article-title":"Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities","volume":"715","author":"Pan","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.jenvman.2022.116132_bib55","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0146558","article-title":"Assessing bacterial diversity in the rhizosphere of Thymus zygis growing in the Sierra Nevada national park (Spain) through culture-dependent and independent approaches","volume":"11","author":"Pascual","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib56","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/j.tibtech.2012.05.007","article-title":"Cultivation of unculturable soil bacteria","volume":"30","author":"Pham","year":"2012","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.jenvman.2022.116132_bib57","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0059342","article-title":"Effect of sugarcane burning or green harvest methods on the Brazilian Cerrado soil bacterial community structure","volume":"8","author":"Rachid","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib58","first-page":"417","article-title":"The copper metallome in prokaryotic cells","volume":"12","author":"Rensing","year":"2013","journal-title":"Met. Ions Life Sci."},{"key":"10.1016\/j.jenvman.2022.116132_bib59","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1111\/j.1574-6941.2007.00331.x","article-title":"The plate debate: cultivable communities have no utility in contemporary environmental microbial ecology","volume":"60","author":"Ritz","year":"2007","journal-title":"FEMS Microbiol. Ecol."},{"key":"10.1016\/j.jenvman.2022.116132_bib60","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.jenvman.2022.116132_bib61","doi-asserted-by":"crossref","DOI":"10.1016\/j.micres.2021.126732","article-title":"Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation","volume":"247","author":"Romero","year":"2021","journal-title":"Microbiol. Res."},{"key":"10.1016\/j.jenvman.2022.116132_bib62","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jenvman.2022.116132_bib63","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00773-21","article-title":"Characterizing the uncultivated microbial minority: towards understanding the roles of the rare biosphere in microbial communities","volume":"6","author":"Saw","year":"2021","journal-title":"mSystems"},{"key":"10.1016\/j.jenvman.2022.116132_bib64","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jenvman.2022.116132_bib65","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1111\/j.1462-2920.2012.02817.x","article-title":"Culturing captures members of the soil rare biosphere","volume":"14","author":"Shade","year":"2012","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib66","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1016\/j.chemosphere.2012.09.044","article-title":"Transgenic poplar trees expressing yeast cadmium factor 1 exhibit the characteristics necessary for the phytoremediation of mine tailing soil","volume":"90","author":"Shim","year":"2013","journal-title":"Chemosphere"},{"key":"10.1016\/j.jenvman.2022.116132_bib67","doi-asserted-by":"crossref","first-page":"4409","DOI":"10.1007\/s00253-018-8932-6","article-title":"Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site","volume":"102","author":"Siles","year":"2018","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.1016\/j.jenvman.2022.116132_bib68","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0103035","article-title":"Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment","volume":"9","author":"Siles","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib69","doi-asserted-by":"crossref","first-page":"2248","DOI":"10.1099\/ijs.0.000241","article-title":"Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste","volume":"65","author":"Singh","year":"2015","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib70","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2018.02543","article-title":"Molecular and microbiological insights on the enrichment procedures for the isolation of petroleum degrading bacteria and fungi","volume":"9","author":"Spini","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib71","doi-asserted-by":"crossref","DOI":"10.1038\/s41396-019-0484-y","article-title":"High proportions of bacteria and archaea across most biomes remain uncultured","author":"Steen","year":"2019","journal-title":"ISME J."},{"key":"10.1016\/j.jenvman.2022.116132_bib72","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0128272","article-title":"Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils","volume":"10","author":"Stefani","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.jenvman.2022.116132_bib73","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jenvman.2022.116132_bib74","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1016\/j.scitotenv.2014.06.040","article-title":"Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium","volume":"493","author":"Teixeira","year":"2014","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.jenvman.2022.116132_bib75","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.jenvman.2011.12.030","article-title":"Microbial activity and diversity in long-term mixed contaminated soils with respect to polyaromatic hydrocarbons and heavy metals","volume":"99","author":"Thavamani","year":"2012","journal-title":"J. Environ. Manag."},{"key":"10.1016\/j.jenvman.2022.116132_bib76","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jenvman.2022.116132_bib77","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00130-19","article-title":"Culturing the uncultured: risk versus reward","volume":"4","author":"Thrash","year":"2019","journal-title":"mSystems"},{"key":"10.1016\/j.jenvman.2022.116132_bib78","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1111\/1758-2229.12898","article-title":"Towards culturing the microbe of your choice","volume":"13","author":"Thrash","year":"2021","journal-title":"Environ. Microbiol. Rep."},{"key":"10.1016\/j.jenvman.2022.116132_bib79","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/S0168-6445(02)00114-6","article-title":"Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution","volume":"26","author":"Valls","year":"2002","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.jenvman.2022.116132_bib80","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1111\/ppa.12188","article-title":"Differential interactions between strains of Rhizorhapis, Sphingobium, Sphingopyxis or Rhizorhabdus and accessions of Lactuca spp. with respect to severity of corky root disease","volume":"63","author":"van Bruggen","year":"2014","journal-title":"Plant Pathol."},{"key":"10.1016\/j.jenvman.2022.116132_bib81","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1111\/ppa.12212","article-title":"Non-pathogenic rhizosphere bacteria belonging to the genera Rhizorhapis and Sphingobium provide specific control of lettuce corky root disease caused by species of the same bacterial genera","volume":"63","author":"van Bruggen","year":"2014","journal-title":"Plant Pathol."},{"key":"10.1016\/j.jenvman.2022.116132_bib82","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/s11104-014-2312-5","article-title":"The vicious cycle of lettuce corky root disease: effects of farming system, nitrogen fertilizer and herbicide","volume":"388","author":"van Bruggen","year":"2015","journal-title":"Plant Soil"},{"key":"10.1016\/j.jenvman.2022.116132_bib83","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1128\/AEM.03112-12","article-title":"Isolation of a substantial proportion of forest soil bacterial communities detected via pyrotag sequencing","volume":"79","author":"VanInsberghe","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib84","first-page":"1","article-title":"Strategies for culture of \u2018unculturable\u2019 bacteria","volume":"309","author":"Vartoukian","year":"2010","journal-title":"FEMS (Fed. Eur. Microbiol. Soc.) Microbiol. Lett."},{"key":"10.1016\/j.jenvman.2022.116132_bib85","doi-asserted-by":"crossref","DOI":"10.1128\/MRA.00779-21","article-title":"Complete genome sequence of a Mucilaginibacter sp. strain isolated from estuarine soil contaminated with mine tailings from the samarco disaster at Fund\u00e3o Dam","volume":"10","author":"Vasconcelos","year":"2021","journal-title":"Microbiol. Resour. Announc."},{"key":"10.1016\/j.jenvman.2022.116132_bib86","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib87","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/jb.173.2.697-703.1991","article-title":"16S ribosomal DNA amplification for phylogenetic study","volume":"173","author":"Weisburg","year":"1991","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.jenvman.2022.116132_bib88","series-title":"ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics","author":"Wickham","year":"2016"},{"key":"10.1016\/j.jenvman.2022.116132_bib89","doi-asserted-by":"crossref","DOI":"10.1038\/s41564-019-0588-1","article-title":"Cultivation and functional characterization of 79 planctomycetes uncovers their unique biology","author":"Wiegand","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.jenvman.2022.116132_bib90","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.ibiod.2017.06.003","article-title":"Crude oil depletion by bacterial strains isolated from a petroleum hydrocarbon impacted solid waste management site in California","volume":"123","author":"Xia","year":"2017","journal-title":"Int. Biodeterior. Biodegrad."},{"key":"10.1016\/j.jenvman.2022.116132_bib91","doi-asserted-by":"crossref","first-page":"1062","DOI":"10.1080\/07388551.2017.1304357","article-title":"Biological technologies for the remediation of co-contaminated soil","volume":"37","author":"Ye","year":"2017","journal-title":"Crit. Rev. Biotechnol."},{"key":"10.1016\/j.jenvman.2022.116132_bib92","doi-asserted-by":"crossref","DOI":"10.1128\/Spectrum.00678-21","article-title":"Comparative analysis of the cultured and total bacterial community in the wheat rhizosphere microbiome using culture-dependent and culture-independent approaches","volume":"9","author":"Youseif","year":"2021","journal-title":"Microbiol. Spectr."}],"container-title":["Journal of Environmental Management"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0301479722017054?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0301479722017054?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,4]],"date-time":"2025-10-04T10:25:54Z","timestamp":1759573554000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0301479722017054"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11]]},"references-count":93,"alternative-id":["S0301479722017054"],"URL":"https:\/\/doi.org\/10.1016\/j.jenvman.2022.116132","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.02.20.481181","asserted-by":"object"}]},"ISSN":["0301-4797"],"issn-type":[{"value":"0301-4797","type":"print"}],"subject":[],"published":{"date-parts":[[2022,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment","name":"articletitle","label":"Article Title"},{"value":"Journal of Environmental Management","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jenvman.2022.116132","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"116132"}}