Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

Goff, Jennifer L.; Szink, Elizabeth G.; Durrence, Konnor L.; Lui, Lauren M.; Nielsen, Torben N.; Kuehl, Jennifer V.; Hunt, Kristopher A.; Chandonia, John-Marc; Huang, Jiawen; Thorgersen, Michael P.; Poole, II, Farris L.; Stahl, David A.; Chakraborty, Romy; Deutschbauer, Adam M.; Arkin, Adam P.; Adams, Michael W. W.

doi:10.1186/s40793-024-00570-9

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

Journal Article · Thu Apr 25 20:00:00 EDT 2024 · Environmental Microbiome

DOI:https://doi.org/10.1186/s40793-024-00570-9· OSTI ID:2341350

Goff, Jennifer L.; Szink, Elizabeth G.; Durrence, Konnor L.; Lui, Lauren M.; Nielsen, Torben N.; Kuehl, Jennifer V.; Hunt, Kristopher A.; Chandonia, John-Marc; Huang, Jiawen; Thorgersen, Michael P.; Poole, II, Farris L.; Stahl, David A.; Chakraborty, Romy; Deutschbauer, Adam M.; Arkin, Adam P.;

Abstract

Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase ( nos ) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.

View Journal Article

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2341350

Alternate ID(s):: OSTI ID: 2570721
OSTI ID: 2470942

Journal Information:: Environmental Microbiome, Journal Name: Environmental Microbiome Journal Issue: 1 Vol. 19; ISSN 2524-6372

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (96)

Uncoupling effect of nitrite during denitrification byPseudomonas fluorescens: An in vivo31P-NMR study Sijbesma, Wilbert F. H.; Almeida, Jonas S.; Reis, Maria A. M. Biotechnology and Bioengineering, Vol. 52, Issue 1 https://doi.org/10.1002/(SICI)1097-0290(19961005)52:1<176::AID-BIT18>3.0.CO;2-M	journal	October 1996
The relationships of Hg(II) volatilization from a freshwater pond to the abundance ofmer genes in the gene pool of the indigenous microbial community Barkay, T.; Turner, R. R.; VandenBrook, A. Microbial Ecology, Vol. 21, Issue 1 https://doi.org/10.1007/BF02539150	journal	December 1991
The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase Carreira, Cíntia; Nunes, Rute F.; Mestre, Olga JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 7 https://doi.org/10.1007/s00775-020-01812-0	journal	August 2020
Role of Streptococcus intermedius DnaK chaperone system in stress tolerance and pathogenicity Tomoyasu, Toshifumi; Tabata, Atsushi; Imaki, Hidenori Cell Stress and Chaperones, Vol. 17, Issue 1 https://doi.org/10.1007/s12192-011-0284-4	journal	January 2012
Nitrate and heavy metal pollution resulting from agricultural activity: a case study from Eskipazar (Karabuk, Turkey) Ekemen Keskin, Tülay Environmental Earth Sciences, Vol. 61, Issue 4 https://doi.org/10.1007/s12665-009-0385-x	journal	December 2009
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Biodegradability of some antibiotics, elimination of the genotoxicity and affection of wastewater bacteria in a simple test Kümmerer, K.; Al-Ahmad, A.; Mersch-Sundermann, V. Chemosphere, Vol. 40, Issue 7 https://doi.org/10.1016/S0045-6535(99)00439-7	journal	April 2000
Alcaligenes defragrans sp. nov., Description of Four Strains Isolated on Alkenoic Monoterpenes ((+)-menthene, α-pinene, 2-carene, and α-phellandrene) and Nitrate Foss, S.; Heyen, U.; Harder, J. Systematic and Applied Microbiology, Vol. 21, Issue 2 https://doi.org/10.1016/S0723-2020(98)80028-3	journal	June 1998
Polyphasic bacterial community analysis of an aerobic activated sludge removing phenols and thiocyanate from coke plant effluent Felföldi, Tamás; Székely, Anna J.; Gorál, Róbert Bioresource Technology, Vol. 101, Issue 10 https://doi.org/10.1016/j.biortech.2009.12.053	journal	May 2010
Mechanisms of acid tolerance in bacteria and prospects in biotechnology and bioremediation Liu, Yuping; Tang, Hongzhi; Lin, Zhanglin Biotechnology Advances, Vol. 33, Issue 7 https://doi.org/10.1016/j.biotechadv.2015.06.001	journal	November 2015
Recovery of heavy metals from industrial wastewater using bioelectrochemical system inoculated with novel Castellaniella species Amanze, Charles; Zheng, Xiaoya; Man, Meilian Environmental Research, Vol. 205 https://doi.org/10.1016/j.envres.2021.112467	journal	April 2022
Characterization of an aspartate‐dependent acid survival system in Yersinia pseudotuberculosis Hu, Yangbo; Lu, Pei; Zhang, Yong FEBS Letters, Vol. 584, Issue 11 https://doi.org/10.1016/j.febslet.2010.03.045	journal	April 2010
Persistence of endodontic infection and Enterococcus faecalis: Role of horizontal gene transfer Jain, Hansa; Mulay, Sanjyot; Mullany, Peter Gene Reports, Vol. 5 https://doi.org/10.1016/j.genrep.2016.09.010	journal	December 2016
Evaluating the occurrence frequency of horizontal gene transfer induced by different degrees of heavy metal stress Chen, Xiaomeng; Du, Zhuang; Song, Xiaoyang Journal of Cleaner Production, Vol. 382 https://doi.org/10.1016/j.jclepro.2022.135371	journal	January 2023
Treatment of nitrous oxide in a trickling bioreactor in the presence of glucose or phenol as the carbon source: Performance, kinetic study, and characterization of microbial community shift Ramezani, Mohammad; Zamir, Seyed Morteza Journal of Environmental Chemical Engineering, Vol. 10, Issue 6 https://doi.org/10.1016/j.jece.2022.108763	journal	December 2022
Deciphering the toxic effects of antibiotics on denitrification: Process performance, microbial community and antibiotic resistance genes Fan, Nian-Si; Bai, Yu-Hui; Chen, Qian-Qian Journal of Environmental Management, Vol. 262 https://doi.org/10.1016/j.jenvman.2020.110375	journal	May 2020
Flexible genomic islands as drivers of genome evolution Rodriguez-Valera, Francisco; Martin-Cuadrado, Ana-Belen; López-Pérez, Mario Current Opinion in Microbiology, Vol. 31 https://doi.org/10.1016/j.mib.2016.03.014	journal	June 2016
Careful use of 16S rRNA gene sequence similarity values for the identification of Mycobacterium species Beye, M.; Fahsi, N.; Raoult, D. New Microbes and New Infections, Vol. 22 https://doi.org/10.1016/j.nmni.2017.12.009	journal	March 2018
Multilocus sequence analysis (MLSA) in prokaryotic taxonomy Glaeser, Stefanie P.; Kämpfer, Peter Systematic and Applied Microbiology, Vol. 38, Issue 4 https://doi.org/10.1016/j.syapm.2015.03.007	journal	June 2015
Genomic islands are dynamic, ancient integrative elements in bacterial evolution Boyd, E. Fidelma; Almagro-Moreno, Salvador; Parent, Michelle A. Trends in Microbiology, Vol. 17, Issue 2 https://doi.org/10.1016/j.tim.2008.11.003	journal	February 2009
Genomics and Ecology of Novel N2O-Reducing Microorganisms Hallin, Sara; Philippot, Laurent; Löffler, Frank E. Trends in Microbiology, Vol. 26, Issue 1 https://doi.org/10.1016/j.tim.2017.07.003	journal	January 2018
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community Hemme, Christopher L.; Deng, Ye; Gentry, Terry J. The ISME Journal, Vol. 4, Issue 5 https://doi.org/10.1038/ismej.2009.154	journal	February 2010
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
DADA2: High-resolution sample inference from Illumina amplicon data Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J. Nature Methods, Vol. 13, Issue 7 https://doi.org/10.1038/nmeth.3869	journal	May 2016
Metal homeostasis and resistance in bacteria Chandrangsu, Pete; Rensing, Christopher; Helmann, John D. Nature Reviews Microbiology, Vol. 15, Issue 6 https://doi.org/10.1038/nrmicro.2017.15	journal	March 2017
The microbial nitrogen-cycling network Kuypers, Marcel M. M.; Marchant, Hannah K.; Kartal, Boran Nature Reviews Microbiology, Vol. 16, Issue 5 https://doi.org/10.1038/nrmicro.2018.9	journal	February 2018
Detecting genomic islands using bioinformatics approaches Langille, Morgan G. I.; Hsiao, William W. L.; Brinkman, Fiona S. L. Nature Reviews Microbiology, Vol. 8, Issue 5 https://doi.org/10.1038/nrmicro2350	journal	May 2010
Mixed heavy metal stress induces global iron starvation response Goff, Jennifer L.; Chen, Yan; Thorgersen, Michael P. The ISME Journal, Vol. 17, Issue 3 https://doi.org/10.1038/s41396-022-01351-3	journal	December 2022
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07641-9	journal	November 2018
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis Johnson, Jethro S.; Spakowicz, Daniel J.; Hong, Bo-Young Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13036-1	journal	November 2019
Environmental stress mediates groundwater microbial community assembly Ning, Daliang; Wang, Yajiao; Fan, Yupeng Nature Microbiology, Vol. 9, Issue 2 https://doi.org/10.1038/s41564-023-01573-x	journal	January 2024
Evolutionary causes and consequences of bacterial antibiotic persistence Bakkeren, Erik; Diard, Médéric; Hardt, Wolf-Dietrich Nature Reviews Microbiology, Vol. 18, Issue 9 https://doi.org/10.1038/s41579-020-0378-z	journal	May 2020
Horizontal gene transfer and adaptive evolution in bacteria Arnold, Brian J.; Huang, I-Ting; Hanage, William P. Nature Reviews Microbiology, Vol. 20, Issue 4 https://doi.org/10.1038/s41579-021-00650-4	journal	November 2021
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R. Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0209-9	journal	July 2019
Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222 Olaya-Abril, Alfonso; Hidalgo-Carrillo, Jesús; Luque-Almagro, Víctor M. Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-96559-2	journal	August 2021
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Brettin, Thomas; Davis, James J.; Disz, Terry Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08365	journal	February 2015
The diversity and biogeography of soil bacterial communities Fierer, N.; Jackson, R. B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 3 https://doi.org/10.1073/pnas.0507535103	journal	January 2006
Resistance, resilience, and redundancy in microbial communities Allison, S. D.; Martiny, J. B. H. Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1 https://doi.org/10.1073/pnas.0801925105	journal	August 2008
Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism Sullivan, M. J.; Gates, A. J.; Appia-Ayme, C. Proceedings of the National Academy of Sciences, Vol. 110, Issue 49 https://doi.org/10.1073/pnas.1314529110	journal	November 2013
Nitrate-Reducing Bacteria at the Nitrate and Radionuclide Contaminated Oak Ridge Integrated Field Research Challenge Site: A Review Spain, Anne M.; Krumholz, Lee R. Geomicrobiology Journal, Vol. 28, Issue 5-6 https://doi.org/10.1080/01490451.2010.507642	journal	June 2011
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
IslandPath: aiding detection of genomic islands in prokaryotes Hsiao, W.; Wan, I.; Jones, S. J. Bioinformatics, Vol. 19, Issue 3 https://doi.org/10.1093/bioinformatics/btg004	journal	February 2003
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
Genomes OnLine Database (GOLD) v.8: overview and updates Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa983	journal	November 2020
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 49, Issue W1 https://doi.org/10.1093/nar/gkab301	journal	April 2021
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR Olson, Robert D.; Assaf, Rida; Brettin, Thomas Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1003	journal	November 2022
PHAST: A Fast Phage Search Tool Zhou, Y.; Liang, Y.; Lynch, K. H. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr485	journal	June 2011
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Overbeek, Ross; Olson, Robert; Pusch, Gordon D. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1226	journal	November 2013
BacMet: antibacterial biocide and metal resistance genes database Pal, Chandan; Bengtsson-Palme, Johan; Rensing, Christopher Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1252	journal	December 2013
PHASTER: a better, faster version of the PHAST phage search tool Arndt, David; Grant, Jason R.; Marcu, Ana Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw387	journal	May 2016
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets Bertelli, Claire; Laird, Matthew R.; Williams, Kelly P. Nucleic Acids Research, Vol. 45, Issue W1 https://doi.org/10.1093/nar/gkx343	journal	May 2017
UniProt: a worldwide hub of protein knowledge Consortium, The UniProt Nucleic Acids Research https://doi.org/10.1093/nar/gky1049		November 2018
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements Liu, Meng; Li, Xiaobin; Xie, Yingzhou Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1123	journal	November 2018
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent Systematic Biology, Vol. 59, Issue 3 https://doi.org/10.1093/sysbio/syq010	journal	March 2010
Anaerobic taurine oxidation: a novel reaction by a nitrate-reducing Alcaligenes sp. Denger, Karin; Laue, Heike; Cook, Alasdair M. Microbiology, Vol. 143, Issue 6 https://doi.org/10.1099/00221287-143-6-1919	journal	June 1997
Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species Rossi-Tamisier, Morgane; Benamar, Samia; Raoult, Didier International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_6 https://doi.org/10.1099/ijs.0.000161	journal	June 2015
Castellaniella ginsengisoli sp. nov., a -glucosidase-producing bacterium Kim, M. K.; Srinivasan, S.; Kim, Y. -J. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 9 https://doi.org/10.1099/ijs.0.008300-0	journal	July 2009
Castellaniella daejeonensis sp. nov., isolated from soil Lee, Myungjin; Jung, Hae-Min; Woo, Sung-Geun International Journal of Systematic and Evolutionary Microbiology, Vol. 60, Issue 9 https://doi.org/10.1099/ijs.0.018887-0	journal	September 2010
Castellaniella hirudinis sp. nov., isolated from the skin of Hirudo verbana Glaeser, Stefanie P.; Galatis, Harald; Martin, Karin International Journal of Systematic and Evolutionary Microbiology, Vol. 63, Issue Pt_2 https://doi.org/10.1099/ijs.0.041392-0	journal	February 2013
Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov. Kämpfer, P.; Denger, K.; Cook, A. M. International Journal of Systematic and Evolutionary Microbiology, Vol. 56, Issue 4 https://doi.org/10.1099/ijs.0.63989-0	journal	April 2006
DNA–DNA hybridization values and their relationship to whole-genome sequence similarities Klappenbach, Joel A.; Goris, Johan; Vandamme, Peter International Journal of Systematic and Evolutionary Microbiology, Vol. 57, Issue 1 https://doi.org/10.1099/ijs.0.64483-0	journal	January 2007
Castellaniella caeni sp. nov., a denitrifying bacterium isolated from sludge of a leachate treatment plant Liu, Q. -M.; Ten, L. N.; Im, W. -T. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 9 https://doi.org/10.1099/ijs.0.65314-0	journal	September 2008
Identification and taxonomic characterization of Bordetella pseudohinzii sp. nov. isolated from laboratory-raised mice Ivanov, Yury V.; Linz, Bodo; Register, Karen B. International Journal of Systematic and Evolutionary Microbiology, Vol. 66, Issue 12 https://doi.org/10.1099/ijsem.0.001540	journal	December 2016
Castellaniella fermenti sp. nov., isolated from a fermented meal Lin, Shih-Yao; Hameed, Asif; Hsieh, Yu-Ting International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 1 https://doi.org/10.1099/ijsem.0.002436	journal	January 2018
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain Jolley, K. A.; Bliss, C. M.; Bennett, J. S. Microbiology, Vol. 158, Issue Pt_4 https://doi.org/10.1099/mic.0.055459-0	journal	January 2012
gcplyr: an R package for microbial growth curve data analysis Blazanin, Michael https://doi.org/10.1101/2023.04.30.538883	preprint	March 2024
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments Goff, Jennifer L.; Szink, Elizabeth G.; Thorgersen, Michael P. Environmental Microbiology, Vol. 24, Issue 11 https://doi.org/10.1111/1462-2920.16173	journal	September 2022
Distribution, diversity and evolution of the bacterial mercury resistance ( mer ) operon Osborn, A. Mark; Bruce, Kenneth D.; Strike, Peter FEMS Microbiology Reviews, Vol. 19, Issue 4 https://doi.org/10.1111/j.1574-6976.1997.tb00300.x	journal	April 1997
Combinatorial events of insertion sequences and ICE in Gram-negative bacteria Toleman, Mark A.; Walsh, Timothy R. FEMS Microbiology Reviews, Vol. 35, Issue 5 https://doi.org/10.1111/j.1574-6976.2011.00294.x	journal	September 2011
Building a genome-based understanding of bacterial pH preferences Ramoneda, Josep; Stallard-Olivera, Elias; Hoffert, Michael Science Advances, Vol. 9, Issue 17 https://doi.org/10.1126/sciadv.adf8998	journal	April 2023
Microbiomes in light of traits: A phylogenetic perspective Martiny, J. B. H.; Jones, S. E.; Lennon, J. T. Science, Vol. 350, Issue 6261 https://doi.org/10.1126/science.aac9323	journal	November 2015
Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer Spain, Anne M.; Peacock, Aaron D.; Istok, Jonathan D. Applied and Environmental Microbiology, Vol. 73, Issue 15 https://doi.org/10.1128/AEM.00331-07	journal	June 2007
Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation Thorgersen, Michael P.; Ge, Xiaoxuan; Poole, Farris L. Applied and Environmental Microbiology, Vol. 85, Issue 17 https://doi.org/10.1128/AEM.00896-19	journal	June 2019
Global Transcriptome and Mutagenic Analyses of the Acid Tolerance Response of Salmonella enterica Serovar Typhimurium Ryan, Daniel; Pati, Niladri Bhusan; Ojha, Urmesh K. Applied and Environmental Microbiology, Vol. 81, Issue 23 https://doi.org/10.1128/AEM.02172-15	journal	December 2015
Functional Analysis of Phenazine Biosynthesis Genes in Burkholderia spp. Hendry, Samuel; Steinke, Stephan; Wittstein, Kathrin Applied and Environmental Microbiology, Vol. 87, Issue 11 https://doi.org/10.1128/AEM.02348-20	journal	May 2021
Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination Green, S. J.; Prakash, O.; Gihring, T. M. Applied and Environmental Microbiology, Vol. 76, Issue 10 https://doi.org/10.1128/AEM.03069-09	journal	March 2010
Isolation of the Helicobacter pylori recA gene and involvement of the recA region in resistance to low pH Thompson, S. A.; Blaser, M. J. Infection and Immunity, Vol. 63, Issue 6 https://doi.org/10.1128/iai.63.6.2185-2193.1995	journal	June 1995
Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S. mBio, Vol. 6, Issue 3 https://doi.org/10.1128/mBio.00326-15	journal	May 2015
Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya mBio, Vol. 7, Issue 2 https://doi.org/10.1128/mBio.02234-15	journal	April 2016
Plasmid-Encoded Traits Vary across Environments Finks, Sarai S.; Martiny, Jennifer B. H. mBio, Vol. 14, Issue 1 https://doi.org/10.1128/mbio.03191-22	journal	February 2023
Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite against Pseudomonas aeruginosa Pormohammad, Ali; Firrincieli, Andrea; Salazar-Alemán, Daniel A. Microbiology Spectrum, Vol. 11, Issue 4 https://doi.org/10.1128/spectrum.00628-23	journal	August 2023
Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer Peng, Mu; Wang, Dongyu; Lui, Lauren M. Microbiology Spectrum, Vol. 10, Issue 1 https://doi.org/10.1128/spectrum.02591-21	journal	February 2022
What are Bacterial Species? Cohan, Frederick M. Annual Review of Microbiology, Vol. 56, Issue 1 https://doi.org/10.1146/annurev.micro.56.012302.160634	journal	October 2002
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models Waack, Stephan; Keller, Oliver; Asper, Roman BMC Bioinformatics, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2105-7-142	journal	March 2006
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen Petasch, Jan; Disch, Eva-Maria; Markert, Stephanie BMC Microbiology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2180-14-164	journal	June 2014
Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies Hassler, Hayley B.; Probert, Brett; Moore, Carson Microbiome, Vol. 10, Issue 1 https://doi.org/10.1186/s40168-022-01295-y	journal	July 2022
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Waste Characteristics of the Former S-3 Ponds and Outline of Uranium Chemistry Relevant to NABIR Field Research Center Studies Brooks, S. C. https://doi.org/10.2172/814525	report	June 2001
Microbially Mediated Immobilization of Contaminants Through In Situ Biostimulation: Scale up of EMSP project 55267 Jardine, Philip M.; Brooks, Scott C. https://doi.org/10.2172/838822	report	June 2004
Field-Scale Evaluation of Biological Uranium Reduction and Reoxidation in the Near-Source Zone at the NABIR Field Research Center in Oak Ridge, TN Criddle, Craig S. https://doi.org/10.2172/896791	report	June 2006
Oak Ridge Reservation Physical Characteristics and Natural Resources Parr, P. D.; Hughes, J. F. https://doi.org/10.2172/921773	report	September 2006
Effects of Cone Penetrometer Testing on Shallow Hydrogeology at a Contaminated Site Putt, Andrew D.; Kelly, Erin R.; Lowe, Kenneth A. Frontiers in Environmental Science, Vol. 9 https://doi.org/10.3389/fenvs.2021.821882	journal	January 2022
Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

References (96)

Similar Records

Related Subjects

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

Citation Formats

References (96)

Similar Records

Related Subjects