{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T18:37:09Z","timestamp":1790361429304,"version":"4.1.0"},"reference-count":115,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Hydrocarbon pollution is a widespread issue in both groundwater and surface-water systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic\u2013anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbon-exposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (<jats:italic>Azospira, Paracoccus<\/jats:italic>, and <jats:italic>Thermomonas<\/jats:italic>). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land\u2013water interface.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1388973","type":"journal-article","created":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T04:40:26Z","timestamp":1715316026000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Microbial community response to hydrocarbon exposure in iron oxide mats: an environmental study"],"prefix":"10.3389","volume":"15","author":[{"given":"Chequita N.","family":"Brooks","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin K.","family":"Field","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,5,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2016\/5654129","article-title":"Benzene removal by Iron oxide nanoparticles decorated carbon nanotubes","volume":"2016","author":"Abbas","year":"2016","journal-title":"J. Nanomater."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e114570","DOI":"10.1371\/journal.pone.0114570","article-title":"Diversity, distribution and hydrocarbon biodegradation capabilities of microbial communities in oil-contaminated cyanobacterial Mats from a constructed wetland","volume":"9","author":"Abed","year":"2014","journal-title":"PLoS One"},{"key":"ref3","author":"Alneberg","year":"2013"},{"key":"ref4","volume-title":"FastQC: A quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1038\/nbt.4163","article-title":"KBase: the United States Department of Energy Systems Biology Knowledgebase","volume":"36","author":"Arkin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"ref6","author":"Arnold","year":"2019"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"4490","DOI":"10.1038\/s41598-018-22617-x","article-title":"A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways","volume":"8","author":"Atashgahi","year":"2018","journal-title":"Sci. Rep."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.marpolbul.2016.07.023","article-title":"The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats","volume":"111","author":"Aub\u00e9","year":"2016","journal-title":"Mar. Pollut. Bull."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.tox.2006.10.021","article-title":"Investigating the role of the aryl hydrocarbon receptor in benzene-initiated toxicity in vitro","volume":"229","author":"Badham","year":"2007","journal-title":"Toxicology"},{"key":"ref11","doi-asserted-by":"publisher","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":"ref12","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1089\/ast.2011.0672","article-title":"Microbially induced iron precipitation associated with a neutrophilic spring at Borra caves, Vishakhapatnam, India","volume":"12","author":"Baskar","year":"2012","journal-title":"Astrobiology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-59745-535-0_4","article-title":"UniProtKB\/Swiss-Prot: the manually annotated section of the UniProt KnowledgeBase","volume-title":"Plant bioinformatics","author":"Boutet","year":"2007"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1002\/rem.21317","article-title":"Perils of categorical thinking: \u201cOxic\/anoxic\u201d conceptual model in environmental remediation","volume":"22","author":"Bradley","year":"2012","journal-title":"Remediat. J."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"8365","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":"ref16","author":"Brooks","year":"2021"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e02720","DOI":"10.1128\/mbio.02720-20","article-title":"Iron flocs and the three domains: microbial interactions in freshwater Iron Mats","volume":"11","author":"Brooks","year":"2020","journal-title":"MBio"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1111\/1758-2229.12932","article-title":"Orange leads to black: evaluating the efficacy of co-culturing iron-oxidizing and sulfate-reducing bacteria to discern ecological relationships","volume":"13","author":"Brooks","year":"2021","journal-title":"Environ. Microbiol. Rep."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1080\/09593330.2018.1496147","article-title":"Biogenic iron oxides for phosphate removal","volume":"41","author":"Buliauskait\u0117","year":"2020","journal-title":"Environ. Technol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1007\/s00253-003-1526-x","article-title":"Anaerobic degradation of monoaromatic hydrocarbons","volume":"64","author":"Chakraborty","year":"2004","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref21","volume-title":"R graphics cookbook: Practical recipes for visualizing data","author":"Chang","year":"2013"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1038\/35082545","article-title":"Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas","volume":"411","author":"Coates","year":"2001","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2663","DOI":"10.1128\/aem.58.8.2663-2666.1992","article-title":"Complete mineralization of benzene by aquifer microorganisms under strictly anaerobic conditions","volume":"58","author":"Edwards","year":"1992","journal-title":"Appl. Environ. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"3085","DOI":"10.1128\/AEM.68.6.3085-3093.2002","article-title":"Neutrophilic Fe-oxidizing Bacteria are abundant at the Loihi seamount hydrothermal vents and play a major role in Fe oxide deposition","volume":"68","author":"Emerson","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"8066","DOI":"10.1128\/AEM.02832-15","article-title":"Microbial iron oxidation in the arctic tundra and its implications for biogeochemical cycling","volume":"81","author":"Emerson","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"98","DOI":"10.3390\/genes12010098","article-title":"Metagenome analysis of a hydrocarbon-degrading bacterial consortium reveals the specific roles of BTEX biodegraders","volume":"12","author":"Eze","year":"2021","journal-title":"Genes"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"390","DOI":"10.3389\/fmicb.2013.00390","article-title":"Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations","volume":"4","author":"Fabisch","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1111\/j.1472-765X.2008.02386.x","article-title":"Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer","volume":"47","author":"Fahy","year":"2008","journal-title":"Lett. Appl. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1111\/j.1574-6941.2006.00162.x","article-title":"Heterogeneous aerobic benzene-degrading communities in oxygen-depleted groundwaters","volume":"58","author":"Fahy","year":"2006","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"134111","DOI":"10.1016\/j.scitotenv.2019.134111","article-title":"Sorption of copper and phosphate to diverse biogenic iron (oxyhydr) oxide deposits","volume":"697","author":"Field","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/ismej.2013.197","article-title":"Ecological succession among iron-oxidizing bacteria","volume":"8","author":"Fleming","year":"2014","journal-title":"ISME J."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e02239","DOI":"10.1128\/AEM.02239-17","article-title":"Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea","volume":"84","author":"Fleming","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1264\/jsme2.ME18019","article-title":"Microbial diversity in actively forming iron oxides from weathered banded iron formation systems","volume":"33","author":"Gagen","year":"2018","journal-title":"Microbes Environ."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"2470","DOI":"10.1038\/s41396-018-0158-1","article-title":"A strong link between marine microbial community composition and function challenges the idea of functional redundancy","volume":"12","author":"Galand","year":"2018","journal-title":"ISME J."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3389\/fmicb.2020.00037","article-title":"FeGenie: a comprehensive tool for the identification of Iron genes and Iron gene neighborhoods in genome and metagenome assemblies","volume":"11","author":"Garber","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e00483-19","DOI":"10.1128\/AEM.00483-19","article-title":"Environmental evidence and genomic insight of Iron-oxidizing Bacteria preference towards more corrosion resistant stainless steel at higher salinities","volume":"85","author":"Garrison","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/s13059-019-1819-8","article-title":"SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines","volume":"20","author":"Gihawi","year":"2019","journal-title":"Genome Biol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1099\/mic.0.045344-0","article-title":"The iron-oxidizing proteobacteria","volume":"157","author":"Hedrich","year":"2011","journal-title":"Microbiology"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e0054323","DOI":"10.1128\/msystems.00543-23","article-title":"Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the F\u00e5vne deep-sea hydrothermal vent field","volume":"8","author":"Hribov\u0161ek","year":"2023","journal-title":"mSystems"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"52","DOI":"10.5539\/enrr.v8n1p52","article-title":"Environmental health threats associated with drainage from a coastal urban watershed","volume":"8","author":"Humphrey","year":"2018","journal-title":"Environ. Nat. Resour."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinform."},{"key":"ref46","doi-asserted-by":"crossref","DOI":"10.1117\/12.765420","article-title":"Color universal design: The selection of four easily distinguishable colors for all color vision types","author":"Ichihara","year":"2008"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"3355","DOI":"10.1128\/AEM.71.6.3355-3358.2005","article-title":"Anaerobic degradation of benzene, toluene, ethylbenzene, and o-xylene in sediment-free Iron-reducing enrichment cultures","volume":"71","author":"Jahn","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1007\/BF02817664","article-title":"Bacterial aerobic degradation of benzene, toluene, ethylbenzene and xylene","volume":"47","author":"Jindrov\u00e1","year":"2002","journal-title":"Folia Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1016\/S0013-7952(03)00102-9","article-title":"Contribution of anaerobic microbial activity to natural attenuation of benzene in groundwater","volume":"70","author":"Johnson","year":"2003","journal-title":"Eng. Geol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"10088","DOI":"10.1021\/acs.est.0c02834","article-title":"Integrated omics elucidate the mechanisms driving the rapid biodegradation of Deepwater horizon oil in intertidal sediments undergoing Oxic\u2013anoxic cycles","volume":"54","author":"Karthikeyan","year":"2020","journal-title":"Environ. Sci. Technol."},{"key":"ref52","author":"Kassambara","year":"2020"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1099\/ijs.0.058487-0","article-title":"Ferriphaselus amnicola gen. Nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep","volume":"64","author":"Kato","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1007\/s00248-017-1100-1","article-title":"Anaerobic benzene mineralization by nitrate-reducing and sulfate-reducing microbial consortia enriched from the same site: comparison of community composition and degradation characteristics","volume":"75","author":"Keller","year":"2018","journal-title":"Microb. Ecol."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1093\/bioinformatics\/btq166","article-title":"Picante: R tools for integrating phylogenies and ecology","volume":"26","author":"Kembel","year":"2010","journal-title":"Bioinformatics"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1111\/gbi.12293","article-title":"A case study for late Archean and Proterozoic biogeochemical iron-and Sulphur cycling in a modern habitat\u2014the Arvadi spring","volume":"16","author":"Koeksoy","year":"2018","journal-title":"Geobiology"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref37","article-title":"Trim Galore!: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data","author":"Krueger","year":"2015"},{"key":"ref58","author":"Lahti","year":"2017"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"116756","DOI":"10.1016\/j.seppur.2020.116756","article-title":"Efficiency and mechanisms of antimony removal from wastewater using mixed cultures of iron-oxidizing bacteria and sulfate-reducing bacteria based on scrap iron","volume":"246","author":"Li","year":"2020","journal-title":"Sep. Purif. Technol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.soilbio.2015.11.013","article-title":"Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil","volume":"94","author":"Li","year":"2016","journal-title":"Soil Biol. Biochem."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"138","DOI":"10.5006\/2162","article-title":"The relationship between Iron oxides\/Oxyhydroxides and toxic metal ions in drinking water distribution systems\u2014a review","volume":"73","author":"Little","year":"2016","journal-title":"Corrosion"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.marpolbul.2019.03.064","article-title":"Indigenous PAH degraders along the gradient of the Yangtze estuary of China: relationships with pollutants and their bioremediation implications","volume":"142","author":"Liu","year":"2019","journal-title":"Mar. Pollut. Bull."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"1536","DOI":"10.1128\/aem.53.7.1536-1540.1987","article-title":"Rapid assay for microbially reducible ferric iron in aquatic sediments","volume":"53","author":"Lovley","year":"1987","journal-title":"Appl. Environ. Microbiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1128\/aem.62.1.288-291.1996","article-title":"Rapid anaerobic benzene oxidation with a variety of chelated Fe(III) forms","volume":"62","author":"Lovley","year":"1996","journal-title":"Appl. Environ. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"fiaa132","DOI":"10.1093\/femsec\/fiaa132","article-title":"Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network","volume":"96","author":"Luo","year":"2020","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.ibiod.2004.06.012","article-title":"Evaluation of microbial diversity of different soil layers at a contaminated diesel site","volume":"55","author":"Maila","year":"2005","journal-title":"Int. Biodeterior. Biodegradation"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.ibiod.2012.05.018","article-title":"Diversity, activity, antibiotic and heavy metal resistance of bacteria from petroleum hydrocarbon contaminated soils located in Harghita County (Romania)","volume":"73","author":"M\u00e1th\u00e9","year":"2012","journal-title":"Int. Biodeterior. Biodegradation"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1016\/j.gca.2018.11.020","article-title":"Ferrous wheel hypothesis: abiotic nitrate incorporation into dissolved organic matter","volume":"245","author":"Matus","year":"2019","journal-title":"Geochim. Cosmochim. Acta"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.1038\/s41396-020-00849-y","article-title":"Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents","volume":"15","author":"McAllister","year":"2021","journal-title":"ISME J."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"3496","DOI":"10.3390\/ijerph8083496","article-title":"A review of centrifugal testing of gasoline contamination and remediation","volume":"8","author":"Meegoda","year":"2011","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1016\/j.jhazmat.2016.11.010","article-title":"In situ chemical oxidation of BTEX and MTBE by ferrate: pH dependence and stability","volume":"324","author":"Minetti","year":"2017","journal-title":"J. Hazard. Mater."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"101155","DOI":"10.1016\/j.rsma.2020.101155","article-title":"Coral reefs and watersheds of the Gulf of Mexico in Veracruz: hydrocarbon pollution data and bioremediation proposal","volume":"35","author":"Narciso-Ortiz","year":"2020","journal-title":"Reg. Stud. Mar. Sci."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"4341","DOI":"10.1093\/bioinformatics\/btaa512","article-title":"MetaSanity: an integrated microbial genome evaluation and annotation pipeline","volume":"36","author":"Neely","year":"2020","journal-title":"Bioinformatics"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"e10119","DOI":"10.7717\/peerj.10119","article-title":"Biases in genome reconstruction from metagenomic data","volume":"8","author":"Nelson","year":"2020","journal-title":"PeerJ"},{"key":"ref77","author":"Nowosad","year":"2018"},{"key":"ref78","volume-title":"Semiannual report of UST performance measures: End of fiscal year 2020 (October 1, 2019 \u2013 September 30, 2020)","year":"2020"},{"key":"ref79","author":"Oksanen","year":"2019"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"D206","DOI":"10.1093\/nar\/gkt1226","article-title":"The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST)","volume":"42","author":"Overbeek","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1111\/j.1574-6941.2008.00589.x","article-title":"Structure of bacterial communities along a hydrocarbon contamination gradient in a coastal sediment","volume":"66","author":"Paiss\u00e9","year":"2008","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1111\/1462-2920.13023","article-title":"Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples","volume":"18","author":"Parada","year":"2016","journal-title":"Environ. Microbiol."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"ref86","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1109\/TVCG.2016.2599030","article-title":"Vega-lite: a grammar of interactive graphics","volume":"23","author":"Satyanarayan","year":"2017","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.femsec.2004.11.007","article-title":"Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica","volume":"53","author":"Saul","year":"2005","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"e02013","DOI":"10.1128\/AEM.02013-17","article-title":"Microbially mediated coupling of Fe and N cycles by nitrate-reducing Fe (II)-oxidizing bacteria in littoral freshwater sediments","volume":"84","author":"Schaedler","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"e27310","DOI":"10.1371\/journal.pone.0027310","article-title":"Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies","volume":"6","author":"Schloss","year":"2011","journal-title":"PLoS One"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref91","doi-asserted-by":"publisher","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":"ref92","doi-asserted-by":"publisher","first-page":"8883","DOI":"10.1093\/nar\/gkaa621","article-title":"DRAM for distilling microbial metabolism to automate the curation of microbiome function","volume":"48","author":"Shaffer","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref93","volume-title":"Dereplication, aggregation and scoring tool (DAS tool) v1. 0","author":"Sieber","year":"2017"},{"key":"ref94","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal omega for making accurate alignments of many protein sequences","volume":"27","author":"Sievers","year":"2017","journal-title":"Protein Sci."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/S0883-2927(01)00014-2","article-title":"Conditions for biological precipitation of iron by Gallionella ferruginea in a slightly polluted ground water","volume":"16","author":"S\u00f8gaard","year":"2001","journal-title":"Appl. Geochem."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"2387","DOI":"10.3389\/fmicb.2019.02387","article-title":"Dispersant enhances hydrocarbon degradation and alters the structure of metabolically active microbial communities in shallow seawater from the northeastern Gulf of Mexico","volume":"10","author":"Sun","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"2517","DOI":"10.1111\/1462-2920.12133","article-title":"Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients","volume":"15","author":"Sun","year":"2013","journal-title":"Environ. Microbiol."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1016\/j.ecoleng.2010.04.019","article-title":"Recovery of phosphorus from natural water bodies using iron-oxidizing bacteria and woody biomass","volume":"36","author":"Takeda","year":"2010","journal-title":"Ecol. Eng."},{"key":"ref101","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-50391-2_13","article-title":"Functional genomics of metal-reducing microbes degrading hydrocarbons","volume-title":"Anaerobic utilization of hydrocarbons, oils, and lipids. Handbook of Hydrocarbon and Lipid Microbiology","author":"Tremblay","year":"2020"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"239","DOI":"10.2307\/1468254","article-title":"Hydrologic influences on groundwater-surface water ecotones: heterogeneity in nutrient composition and retention","volume":"16","author":"Valett","year":"1997","journal-title":"J. N. Am. Benthol. Soc."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"e00009","DOI":"10.1128\/msystems.00009-15","article-title":"Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys","volume":"1","author":"Walters","year":"2016","journal-title":"mSystems"},{"key":"ref104","volume-title":"EPA (Environmental Protection Agency) method study 25, method 602, purgeable aromatics. Report for Sep 79-Dec 82","author":"Warner","year":"1984"},{"key":"ref105","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1080\/01490450701670152","article-title":"Characterization of neutrophilic Fe (II)-oxidizing bacteria isolated from the rhizosphere of wetland plants and description of Ferritrophicum radicicola gen. Nov. sp. nov., and Sideroxydans paludicola sp. nov","volume":"24","author":"Weiss","year":"2007","journal-title":"Geomicrobiol J."},{"key":"ref106","author":"Wickham","year":"2007"},{"key":"ref107","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"ref108","author":"Wickham","year":"2020"},{"key":"ref109","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1038\/s41598-019-39576-6","article-title":"Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia","volume":"9","author":"Wilkins","year":"2019","journal-title":"Scientific Reports"},{"key":"ref110","doi-asserted-by":"publisher","first-page":"2702","DOI":"10.1093\/bioinformatics\/btw241","article-title":"OrfM: a fast open reading frame predictor for metagenomic data","volume":"32","author":"Woodcroft","year":"2016","journal-title":"Bioinformatics"},{"key":"ref111","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/2049-2618-2-26","article-title":"MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm","volume":"2","author":"Wu","year":"2014","journal-title":"Microbiome"},{"key":"ref112","doi-asserted-by":"publisher","first-page":"40093","DOI":"10.1038\/srep40093","article-title":"pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution","volume":"7","author":"Wu","year":"2017","journal-title":"Sci. Rep."},{"key":"ref113","doi-asserted-by":"publisher","first-page":"4721","DOI":"10.1016\/j.watres.2012.06.036","article-title":"Benzene removal by a novel modification of enhanced anaerobic biostimulation","volume":"46","author":"Xiong","year":"2012","journal-title":"Water Res."},{"key":"ref114","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1038\/s41396-018-0177-y","article-title":"A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria","volume":"12","author":"Yurchenko","year":"2018","journal-title":"ISME J."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"5772","DOI":"10.1038\/s41598-020-62840-z","article-title":"Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico","volume":"10","author":"Zhao","year":"2020","journal-title":"Sci. Rep."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1388973\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T04:40:33Z","timestamp":1715316033000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1388973\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,10]]},"references-count":115,"alternative-id":["10.3389\/fmicb.2024.1388973"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1388973","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,10]]},"article-number":"1388973"}}