Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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FICUS EMSL-JGI Publication List

Updated August 1, 2020

Below are the 41 publications resulting from research conducted at DOE JGI and EMSL under the FICUS initiative and their associated project abstracts.

FY2020  |  5 publications

Nelson W.C., E.B. Graham, A.R. Crump, S.J. Fansler, E.V. Arntzen, D.W. Kennedy, and J.C. Stegen. 2020. "Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome." PLoS One 15, no. 1:Article No. e0228165. doi:10.1371/journal.pone.0228165
[EMSL Project # 48473]

Velickovic D., V.S. Lin, A. Rivas-Ubach, C.R. Anderton, and J.J. Moran. 2020. "An approach for broad molecular imaging of the root-soil interface via indirect matrix-assisted laser desorption/ionization mass spectrometry." Soil Biology and Biochemistry 146. doi:10.1016/j.soilbio.2020.107804
[EMSL Project # 50395]

Wilken S., S. Seppala, T.S. Lankiewicz, M. Saxena, J.K. Henske, A. Salamov, I.V. Grigoriev, and M.A. O'Malley. 2020. "Genomic and Proteomic Biases Inform Metabolic Engineering Strategies for Anaerobic Fungi." Metabolic Engineering Communications Published online. doi:10.1016/j.mec.2019.e00107
[EMSL Project # 48080]

Zayas-Santiago C., A. Rivas-Ubach, L. Kuo, N.D. Ward, and R.C. Zimmerman. 2020. "Metabolic profiling reveals biochemical pathways responsible for eelgrass response to elevated CO2 and temperature." Scientific Reports 10, no. 1:Article No. 4693. doi:10.1038/s41598-020-61684-x
[EMSL Project # 50358]

Waldo N.B., B. Hunt, E. Fadely, J.J. Moran, and R.B. Neumann. 2019. "Plant Root Exudates Increase Methane Emissions through Direct and Indirect Pathways." Biogeochemistry 145, no. 1-2:213–234. doi:10.1007/s10533-019-00600-6
[EMSL Project # 49017]

FY2019  |  10 publications

Bohutskyi P., R.S. McClure, E.A. Hill, W.C. Nelson, W.B. Chrisler, J. Nunez, R.S. Renslow, M. Charania, S. Lindemann, and A.S. Beliaev. 2019. "Metabolic effects of vitamin B12 on physiology, stress resistance, growth rate and biomass productivity of Cyanobacterium stanieri planktonic and biofilm cultures." Algal Research 42. doi:10.1016/j.algal.2019.101580
[EMSL Project # 50944]

Evans M.V., G. Getzinger, J.L. Luck, A.J. Hanson, M.C. McLaughlin, J. Blotevogel, S. Welch, C.D Nicora, S.O Purvine, C. Xu, D.R. Cole, T.H. Darrah, D.W. Hoyt, T.O. Metz, P.L. Ferguson, M.S. Lipton, M.J. Wilkins, and P.J. Mouser. 2019. "In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing." The ISME Journal. Published online. doi:10.1038/s41396-019-0466-0
[EMSL Project # 48483]

Velickovic D., H. Liao, R. Vilgalys, R.K. Chu, and C.R. Anderton. 2019. "Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization." Journal of Natural Products 82, no. 5:1382-1386. doi:10.1021/acs.jnatprod.8b01050
[EMSL Project # 49514]

Ward N.D., E. Morrison, Y. Liu, A. Rivas-Ubach, T. Osborne, A. Ogram, and T.S. Bianchi. 2019. "Marine microbial community responses related to wetland carbon mobilization in the coastal zone." Limnology and Oceanography: Letters 4, no. 1:25-33. doi:10.1002/lol2.10101
[EMSL Project # 49505]

Daly R., S. Roux, M. Borton, D.M. Morgan, M.D. Johnston, A.E. Booker, D.W. Hoyt, T. Meulia, R. Wolfe, A.J. Hanson, P.J. Mouser, J.D. Moore, K. Wunch, M.B. Sullivan, K.C. Wrighton, and M.J. Wilkins. 2018. "Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing." Nature Microbiology  4:352–361. doi: 10.1038/s41564-018-0312-6
[EMSL Project # 48483]

Martinez M.A., B.J. Woodcroft, J.C. Ignacio-Espinozaa, A.A. Zayed, C.M. Singleton, J. Boyd, Y. Li, S.O. Purvine, H. Maughan, S. Hodgkins, D. Anderson, M. Soderholm, B. Temperton, B. Bolduc, S. Saleska, V. Rich, P.M. Crill, J. Chanton, G.W. Tyson, R. Varner, M.B. Sullivan, S. Frolking, and C. Li. 2019. "Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov." Systematic and Applied Microbiology 42, no. 1:54-66. doi:10.1016/j.syapm.2018.12.003
[EMSL Project # 48467]

Solomon KV, JK Henske, SP Gilmore, A Lipzen, IV Grigoriev, D Thompson, and MA O'Malley. 2018. "Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts." Fungal Genetics and Biology 121. doi:10.1016/j.fgb.2018.09.004
[EMSL Project # 48080]

Graham E.B., A.R. Crump, D.W. Kennedy, E.V. Arntzen, S.J. Fansler, S.O. Purvine, C.D. Nicora, W.C. Nelson, M.M. Tfaily, and J.C. Stegen. 2018. "Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone." Science of the Total Environment 642. doi:10.1016/j.scitotenv.2018.05.256
[EMSL Project # 48473]

Daly P., S.C. Lopez, M. Peng, C.S. Lancefield, S.O. Purvine, Y. Kim, E.M. Zink, A. Dohnalkova, V. Singan, A. Lipzen, D. Dilworth, M. Wang, V. Ng, E.W. Robinson, G. Orr, S.E. Baker, P. Bruijnincx, K.S. Kilden, I.V. Grigoriev, M. Makela, and R.P. de Vries. 2018. "Dichomitus squalens partially tailors its molecular responses to the composition of solid wood." Environmental Microbiology 20, no. 11:4141-4156. doi:10.1111/1462-2920.14416
[EMSL Project # 48459]

Solden L., A. Naas, S. Roux, R. Daly, W.B. Collins, C.D. Nicora, S.O. Purvine, D.W Hoyt, J. Schuckel, B. Jorgensen, W. Willats, D.E. Spalinger, J.L. Firkins, M.S. Lipton, M.B. Sullivan, P. Pope, and K.C. Wrighton. 2018. "Interspecies cross-feedings orchestrate carbon degradation in the rumen ecosystem." Nature Microbiology 3:1274-1284. doi:10.1038/s41564-018-0225-4
[EMSL Project # 49495]


FY2018  |  10 publications

Woodcroft BJ, CM Singleton, J Boyd, PN Evans, JB Emerson, AA Zayed, RD Hoelzle, TO Lamberton, CK McCalley, S Hodgkins, RM Wilson, SO Purvine, CD Nicora, C Li, S Frolking, J Chanton, PM Crill, S Saleska, V Rich, and GW Tyson. 2018. "Genome-centric view of carbon processing in thawing permafrost." Nature. 560:49-54. doi:10.1038/s41586-018-0338-1
[EMSL Project # 49521]

Borton M, DW Hoyt, S Roux, R Daly, S Welch, CD Nicora, SO Purvine, EK Eder, AJ Hanson, J Sheets, DM Morgan, R Wolfe, S Sharma, TR Carr, DR Cole, PJ Mouser, MS Lipton, MJ Wilkins, and KC Wrighton. 2018. "Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales." Proceedings of the National Academy of Sciences of the United States of America 115, no. 28:E6585-E6594. doi:10.1073/pnas.1800155115
[EMSL Project # 48483]

Warshan D., A. Liaimer, E. Pederson, S. Kim, N. Shapiro, T. Woyke, B. Altermark, K. Pawlowski, P.D. Weyman, C. Dupont, and U. Rasmussen. 2018. "Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont." Molecular Biology and Evolution 35, no. 5:1160–1175. doi:10.1093/molbev/msy029
[EMSL Project # 48081]

Zhu Y, R Zhao, PD Piehowski, RJ Moore, S Lim, VJ Orphan, L Pasa Tolic, WJ Qian, RD Smith, and RT Kelly. 2018. "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples." International Journal of Mass Spectrometry 427:4-10. doi:10.1016/j.ijms.2017.08.016
[EMSL Project # 49001]

Henske JK, SE Wilken, KV Solomon, CR Smallwood, V Shutthanandan, JE Evans, MK Theodorou, and MA O'Malley. 2018. "Metabolic characterization of anaerobic fungi provides a path forward for bioprocessing of crude lignocellulose." Biotechnology and Bioengineering 115(4):874-884. doi:10.1002/bit.26515
[EMSL Project # 48080]

Warshan D, JL Espinoza, R Stuart, AR Richter, SY Kim, N Shapiro, T Woyke, N Kyripides, KW Barry, V Singan, E Lindquist, CK Ansong, SO Purvine, HM Brewer, PD Weyman, C Dupont, and U Rasmussen. 2017. "Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant–cyanobacteria symbiosis." The ISME Journal 11:2821–2833. doi:10.1038/ismej.2017.134
[EMSL Project # 48081]

Graham E.B., M.M. Tfaily, A.R. Crump, A.E. Goldman, L.M. Bramer, E.V. Arntzen, E.B. Romero, C.T. Resch, D.W. Kennedy, and J.C. Stegen. 2017. "Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes." Journal of Geophysical Research. Biogeosciences 122, no. 12:3188-3205. doi:10.1002/2017JG003967
[EMSL Project # 48473]

Keiluweit M., T. Wanzek, M.W. Kleber, P.S. Nico, and S. Fendorf. 2017. "Anaerobic Microsites have an Unaccounted Role in Soil Carbon Stabilization." Nature Communications 8. doi:10.1038/s41467-017-01406-6
[EMSL Project #49518]

Ward CP, SG Nalven, B Crump, G Kling, and RM Cory. 2017. "Photochemical Alteration of Organic Carbon Draining Permafrost Soils Shifts Microbial Metabolic Pathways and Stimulates Respiration." Nature Communications 8:772. doi:10.1038/s41467-017-00759-2
[EMSL Project # 48484]

Wilson RM, MM Tfaily, V Rich, JK Keller, SD Bridgham, C Medvedeff Zalman, L Meredith, PJ Hanson, ME Hines, L Pfeifer-Meister, S Saleska, PM Crill, WT Cooper, J Chanton, and JE Kostka. 2017. "Hydrogenation of Organic Matter as a Terminal Electron Sink Sustains High CO2:CH4 Production Ratios During Anaerobic Decomposition." Organic Geochemistry 112:22-32. doi:10.1016/j.orggeochem.2017.06.011
[EMSL Project # 48467]  [EMSL Project # 49521]


FY2017  |  10 publications

Hou Z, WC Nelson, JC Stegen, CJ Murray, EV Arntzen, AR Crump, DW Kennedy, MC Perkins, TD Scheibe, JK Fredrickson, and JM Zachara. 2017. "Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies." Scientific Reports 7:Article No. 12006. doi:10.1038/s41598-017-12275-w
[EMSL Project # 48473]

Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Wu, CM Santelli, and CM Hansel. 2017. "Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi." Fungal Genetics and Biology: FG&B 106:61-75. doi:10.1016/j.fgb.2017.06.004
[EMSL Project # 48100]

Lin F, BJ Williams, PA Thangella, A Ladak, AA Schepmoes, HJ Olivos, K Zhao, SJ Callister, and LE Bartley. 2017. "Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode." Frontiers in Plant Science 8:1134. doi:10.3389/fpls.2017.01134
[EMSL Project # 49510]

Booker AE, M Borton, R Daly, S Welch, CD Nicora, DW Hoyt, T Wilson, SO Purvine, R Wolfe, S Sharma, PJ Mouser, DR Cole, MS Lipton, KC Wrighton, and MJ Wilkins. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2:Article No. e00257-17. doi:10.1128/mSphereDirect.00257-17
[EMSL Project # 48483]

Haitjema C, SP Gilmore, JK Henske, KV Solomon, RD Groot, A Kuo, SJ Mondo, A Salamov, KM LaButti, ZJ Zhao, J Chiniquy, KW Barry, HM Brewer, SO Purvine, AT Wright, M Hainaut, B Boxma, TA Van Alen, J Hackstein, B Henrissat, SE Baker, IV Grigoriev, and MA O'Malley. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2:Article No. 17087. doi:10.1038/nmicrobiol.2017.87
[EMSL Project # 48080]

Thor S, J Peterson, and ZA Luthey-Schulten. 2017. "Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function." Archaea 2017:9763848. doi:10.1155/2017/9763848
[EMSL Project # 48452]

Mondo SJ, RO Dannebaum, RC Kuo, KB Louie, AJ Bewick, KM LaButti, S Haridas, A Kuo, A Salamov, S Ahrendt, R Lau, BP Bowen, A Lipzen, W Sullivan, WB Andreopoulos, A Clum, E Lindquist, C Daum, TR Northen, GK Ramamoorthy, RJ Schmitz, A Gryganskyi, DE Culley, JK Magnuson, T James, MA O'Malley, JE Stajich, J Spatafora, A Visel, and IV Grigoriev. 2017. "Widespread Adenine N6-methylation of Active Genes in Fungi." Nature Genetics 49(6):964-968. doi:10.1038/ng.3859
[EMSL Project # 48080]

Boenisch MJ, KL Broz, SO Purvine, WB Chrisler, CD Nicora, L Connolly, M Freitag, SE Baker, and HC Kistler. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7:Article No. 44296. doi:10.1038/srep44296
[EMSL Project # 48096]

Seppälä S, KV Solomon, SP Gilmore, JK Henske, and MA O'Malley. 2016. "Mapping the Membrane Proteome of Anaerobic Gut Fungi Identifies a Wealth of Carbohydrate Binding Proteins and Transporters." Microbial Cell Factories 15:212. doi:10.1186/s12934-016-0611-7
[EMSL Project # 48080]

Peterson J, S Thor, L Kohler, PR Kohler, W Metcalf, and ZA Luthey-Schulten. 2016. "Genome-Wide Gene Expression and RNA Half-Life Measurements Allow Predictions of Regulation and Metabolic Behavior in Methanosarcina Acetivorans." BMC Genomics 17:924. doi:10.1186/s12864-016-3219-8
[EMSL Project # 48452]


FY2016  |  6 publications

Daly R, MA Borton, MJ Wilkins, DW Hoyt, DJ Kountz, R Wolfe, S Welch, DN Marcus, R Trexler, JD MacRae, JA Krzycki, DR Cole, PJ Mouser, and KC Wrighton. 2016. "Microbial metabolisms in a new 2.5 km deep ecosystem created by hydraulic fracturing in shales." Nature Microbiology 1(10):Article No. 16146. doi:10.1038/nmicrobiol.2016.146
[EMSL Project # 48483]

Hodgkins S, MM Tfaily, DC Podgorski, C McCalley, S Saleska, PM Crill, V Rich, J Chanton, and WT Cooper. 2016. "Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland." Geochimica et Cosmochimica Acta 187:123-140. doi:10.1016/j.gca.2016.05.015
[EMSL Project # 48467]

Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Haridas, S Wu, KM LaButti, IV Grigoriev, B Henrissat, CM Santelli, and CM Hansel. 2016. "Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi." PLoS One 11(7):Article No. e0157844. doi:10.1371/journal.pone.0157844
[EMSL Project # 48100]

Li GJ, et al (+134 additional authors, including KV Solomon, JK Henske, CH Haitjema, SP Gilmore, MK Theodorou, and MA.O'Malley). "Fungal diversity notes 253-366: taxonomic and phylogenetic contributions to fungal taxa." Fungal Diversity, 78(1): 1-237 (2016). doi:10.1007/s13225-016-0366-9
[EMSL Project # 48080]

Solomon KV, JK Henske, MK Theodorou, and MA O'Malley. 2016. "Robust and Effective Methodologies for Cryopreservation and DNA Extraction from Anaerobic Gut Fungi." Anaerobe 38:39-46. doi:10.1016/j.anaerobe.2015.11.008
[EMSL Project # 48080]

Solomon KV, C Haitjema, JK Henske, SP Gilmore, D Borges-Rivera, A Lipzen, HM Brewer, SO Purvine, AT Wright, MK Theodorou, IV Grigoriev, A Regev, D Thompson, and MA O'Malley. 2016. "Early-branching Gut Fungi Possess a Large, And Comprehensive Array Of Biomass-Degrading Enzymes." Science 351(6278):1192-1195. doi:10.1126/science.aad1431
[EMSL Project # 48080]