Recent (since starting at UT in 2015)
- Rambo IM, Anda V, Langwig MV, Baker BJ. Unique viruses that infect Archaea related to eukaryotes. preprint.
- Langwig M, De Anda V, Dombrowski N, Seitz KW, Rambo I, Teske AP,
- Castelle CJ, Meheust R, Jaffe AL, Seitz KW, Gong X, Baker BJ, Banfield JF. (2021) Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea. Frontiers in Micro 12, 660052.
- Baker BJ, Appler KE, Gong X. (2021) New microbial biodiversity in marine sediments. Ann Rev Mar Sci. 13, 161-175.
- Murray AE, et al. (2020) Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiol. 5, 987-997.
- Baker BJ, de Anda V, Seitz KW, Dombrowski N, Santoro A, Lloyd KA. (2020) Diversity, ecology, and evolution of Archaea. Nature Micro. 5, 887-900.
- Rambo I, Dombrowski N, Erdner D, Baker BJ. (2019) Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ. Microbiol. 22, 1764-1783.
- Mullis MM, Rambo IM, Baker BJ, Reese BK. (2019) Diversity, ecology, and prevalence of antimicrobials in nature. Front. Microbiol. 10, 2518.
- Steen AD, Kevorkian RT, Bird JT, Dombrowski N, Baker BJ, Hagen SM, Mulligan SM, Schmidt JM, Webber AT, Royatly T, Alperin MJ. (2019) Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC. Appl Environ Microbiol In press.
- Huang J-M, Baker BJ, Li J-T, Wang Y. (2019) New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the Norther South China Sea. Appl Environ Microbiol In press.
- Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Seiber J, Teske AP, Ettema TJG, Baker BJ. (2019) New Asgard archaea capable of anaerobic hydrocarbon cycling. Nature Comm. 10, 1822.
- Spang A, Stairs C, Dombrowski N, Eme L, Lombard J, Caceres EF, Jorgensen SL, Baker BJ, Ettema TJG. (2019) A renewed syntrophy hypothesis for the origin of the eukaryotic cell based on comparative analysis of Asgard archaeal metabolism. Nature Micro. 4, 1138-1148.
- Dombrowski N, Teske AP, Baker BJ. (2018) Extensive metabolic versatility and redundancy in microbial diverse, dynamic Guaymas Basin hydrothermal sediments. Nature Comm. 9, 5999.
- Thrash JC, Seitz KW, Baker BJ,Temperton B, Gillies L, Rabalais NN, Henrissat B, Mason OU. (2018) Metagenomic assembly and prokaryotic MAGs from the northern Gulf of Mexico “Dead Zone”. Microbiol. Res. Announcements. 7, e01033-18.
- Narrowe AB, Spang A, Starirs C, Caceres EF, Baker BJ, Mills CS, Ettema TJG. (2018) Complex evolutionary history of translation elongation factor 2 and diphthamide biosynthesis in Archaea and parabasalids. Genome Biology and Evolution, evy154.
- Liu Y, Zhou Z, Pan J, Baker BJ, Gu J, Li M (2018) Comparative genomic inference reveals mixotrophic lifestyle of Thorarchaeota. ISME J. 12, 1021-1031.
- Bacosa HP, Erdner DL, Rosenheim BE, Shetty P, Seitz KW, Baker BJ, Lui Z. (2018) Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil. ISME J in press.
- Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalaies NN, Mason OU. (2017) Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone”. mBio. 8:e01017-17.
- Chen L, Mendez-Garcia C, Dombrowski N, Servin-Garciduenas LE, Eloe-Fadrosch EA, Fang Z-H, Zhi X-Y, Hua Z-S, Martinez-Romero E, Woyke T, Huang L-N, Sanchez J, Pelaez AI, Ferrer M, Baker BJ, Shu W-S (2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J. 12, 756-775.
- Dombrowski N, Seitz KW, Teske AP, Baker BJ. (2017) New insights into microbial hydrocarbon cycling and metabolic interdependencies in hydrothermal sediments. Microbiome. 5, 106.
- Bowers RM, Kyrpides N, Stepanauskas R, Harmon-Smith M, Doud D, Jarett J, Schulz F, Reddy TBK, Rivers A, Eloe-Fadrosh E, Tringe S, Ivanova N, Copeland A, Clum A, Becraft E, Malmstrom R, Birren B, Schriml L, Podar M, Bork P, Weinstock G, Banfield JF, Garrity G, Hugenholtz P, Parks GH, Tyson GW, Rinke C, Dodsworth JA, Yooseph S, Sutton G, Yilmaz P, Glöckner FO, Meyer F, Gilbert J, Nelson WC, Hallam S, Jungbluth SP, Ettema T, Jetten M, Voordoeuw G, Tighe S, Konstantinidis K, Wen-Tso Liu, Baker BJ, Eren MA, Hedlund B, McMahon K, Fierer N, Eisen J, Knight R, Cochrane G, Finn R, Mizrachi I and Woyke T. (2017) Genome standards for single-cell genomes (MIxS-SCG) and genomes from metagenomes (MIxS-GFM) of bacteria and archaea. Nat Biotechnol. 35, 725-731.
- Zaremba-Niedzwiedzka, K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, and Ettema TJG. (2017) Asgard archaea illuminates the origin of eukaryotic cellular complexity. Nature 541, 353.
- Lazar CS, Baker BJ, Seitz KW, Hinrichs K-U, Teske AP. (2017) Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME J. 11, 1118-1129.
- Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd K (2016) Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Frontiers in Microbiol. 7, 1221.
- Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Schramm A, Stepanauskas R, Reinhardt R, Jørgensen BB, Loy A, Adrian L. (2016) Single cell genome sequencing and targets gene amplifications implicate members of the class Dehalococcoidia (phylum Chloroflexi) in sulfur cycling. mBio. 7, 0026-16.
- Dombrowski N, Donaho J, Teske AP, Gutierrez T, Baker BJ. (2016) Hydrocarbon degradation pathways in uncultured bacteria from the Deep Water Horizon Oil Spill. Nat Micro. 1, 16057.
- Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdort AW, Amano Y, Kotaro I, Suzuki Y, Dudek N, Reman DA, Finstad KM, Amundsen R, Thomas BC, Banfield JF. A new view of The Tree of life’s diversity. Nat Micro. 1, 16048.
- Hu P, Tom LM, Singh A, Thomas BC, Baker BJ, Piceno YM, Andersen GL, Banfield JF. (2016) Genome-resolved analysis reveals roles for candidate phyla bacteria in biogeochemical transformations in hydrocarbon reservoirs. mBio. 7, e01669-15.
- Baker BJ, Saw J, Lind A, Lazar CS, Hinrichs K-U, Teske AP, Ettema T. (2016) Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat Microbiol. 1, 16002.
- Seitz K, Lazar CS, Teske AP, Baker BJ. (2016) Genomic reconstruction of novel, deeply-branching sediment archaeal group capable of degradation of organic matter and sulfur cycling. ISME J. 10, 1696-1705.
- Lazar CS, Baker BJ, Seitz KW, Hyde A, Dick GJ, Hinrichs K-U, Teske AP. (2016) Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol. 18, 1200-1211.
- Li M, Baker BJ, Anantharaman K, Jain S, Dick GJ. (2015) Widespread uncultured deep-sea Archaea scavenge a variety of organic compounds. Nat Comm 6, 8933.
- Baker BJ, Lazar C, Teske A, Dick GJ. (2015) Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome, 3, 14.
Reviews
- Baker BJ, Dick GJ. (2013) Omic approaches in microbial ecology; charting the unknown. Microbe 8, 353-359.
- Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbial Ecol. 44, 1-14.
Bioinformatics
- Miller CS, Baker BJ, Thomas BC, Singer S, Banfield JF (2011) EMIRGE: Reconstruction of full length ribosomal genes from microbial community short read sequencing data. Genome Biology 12, R44.
- Dick GJ, Andersson, A, Baker BJ, Yelton P, Sheri SS, Thomas BC, Banfield JF. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85.
Deep-Sea
- Li M, Toner BM, Baker BJ, Myneni S, Dick GJ. (2014) Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Comm. 5, 3192.
- Li M, Jain S, Baker BJ, Taylor C, Dick GJ. (2014) Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ. Microbiol. 16, 60-71.
- BakerBJ, Taylor C, Jain S, Shiek CS, Bhasi A, Cavalcoli JD, Dick GJ (2013) Community transcriptomic assembly reveals microbes contribute to carbon and nitrogen cycling in the deep sea. ISME J. 7, 1962-1973.
- Dick GJ, Anantharaman K, Baker BJ, Li M, Reed DC, Sheik CS. (2013) The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology. 4, 1-16.
- Baker BJ, Lesniewski R, Dick GJ (2012) Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume. ISME J. 6, 2269-2279.
Acid Mine Drainage
- Schönknecht G, Chen W-H, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Benning C, Carr K, Wilkerson C, Rensing SA, Gagneul D, Oesterhelt C, Lercher MJ, Weber APM. (2013) Gene Transfer from Bacteria and Archaea facilitated evolution of an extremophilic eukaryote. Science. 339, 1207-1210.
- Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. (2011) A unique tRNA splicing endonuclease found in ultrasmall archaeon is a chimeric protein consisting of three domains. Nucleic Acids Res.39, 9695-9704.
- Baker BJ, Comolli LR, Dick GJ, Hauser L., Land M, Hyatt, D, VerBerkmoes N, Hettich B, Banfield JF. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Natl. Acad. Sci. 107, 8806-8811.
- Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes, NC, Hettich RL, Banfield, JF. (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. 107, 2383-2390.
- Goltsman, DSA, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Muller R, Dick GJ, Sun C, Wheeler K, Zemla A, Baker BJ, Hauser L, Land M, Shah M, Thelen MP, Hettich RL, Banfield JF (2009) Community genomics and proteomics of chemoautotrophic, iron-oxidizing “Leptospirillum rubarum” and Leptospirillum ferrodiazotrophum populations in acid mine drainage. Appl. Environ. Microbiol. 75, 4599-4615.
- Baker BJ, Tyson GW, Goosherst L, Banfield JF (2009) Insights into the diversity eukaryotes in acid mine drainage biofilm communities. Appl. Environ. Microbiol. 75, 2192-2199.
- Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (2009) Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J. 3, 159-1671.
- Baker BJ, Tyson, GW, Webb RI, Flanagan J, Hugenholtz P, Banfield JF (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314, 1933-1935.
- Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, Banfield JF (2005) Genome-directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Appl. Environ. Microbiol. 71, 6319-6324.
- Ram RJ, VerBerkmoes N, Thelen MP, Tyson GW, Baker BJ, Shah M, RC Blake II, Hettich R, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308, 1915-1920.
- Baker BJ, Lutz MA, Dawson SC, Bond PL, Banfield JF (2004) Metabolically active eukaryotes in extremely acidic mine drainage. Appl. Environ. Microbiol. 70, 6264-6271.
- Druschel GK*, Baker BJ*, Gihring TH, Banfield JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem. Trans. 5, 13-32. *contributed equally
- Baker BJ, Hugenholtz, P, Dawson, SC, Banfield, JF (2003) Extremely acidophilic protists host Rickettsiales-lineage endosymbionts with an intervening sequence in their 16S rRNA genes. Appl Environ. Microbiol. 69, 5512-5518.
Deep Subsurface
- Moser DP, Gihring TM, Brockman FJ, Fredrickson JK, Balkwill DL, Dollhopf ME, Sherwood Lollar B, Pratt LM, Boice E, Southam G, Wanger G, Baker BJ, Pfiffner SM, L-H Lin, Onstott TC. (2005) Desulfotomaculum spp. and Methanobacterium spp. a dominate 4-5 km deep fault. Appl. Environ. Microbiol. 71, 8773-8783.
- Moser DP, Onstott TC, Fredrickson JK, Brockman FJ, Takai K, Balkwill DL, Drake, G, Pfiffner, S, White DC, Baker BJ, Pratt LM, Fong J, Lollar BS, Slater G, Phelps TJ, Spoelstra N, DeFlaun M, Southam G, Welty AT, Hoek J (2003) Evolution of microbial community structure and geochemistry in an ultradeep South African gold mine borehole. Geomicrobiology J. 20, 517-548.
- Baker BJ, Moser DP, MacGregor BJ, Fishbain S, Wagner M, Fry N, Jackson B, Speolstra N, Loos S, Takai K, Fredrickson J, Balkwill D, Onstott TC, Wimpee CF, Stahl DA (2003) Related assemblages of sulfate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environ. Microbiol. 5,267-277.
- Stahl DA, Fishbain S, Klein M, Baker BJ, Wagner M (2002) Origins and diversification of sulfate-respiring microorganisms. Antonie van Leeuwenhoek 81, 189-195.
Lake Michigan
- MacGregor BJ, Van Mooy B, Baker BJ, Mellon M, Moisander PH, Pearl HW, Zehr, J, Hollander, D, Stahl DA (2001) Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Environ. Microbiol. 3, 205-209.
- MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA (2001) Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Appl Environ. Microbiol. 67, 3908-3922.