Publications
EMERGE Team Members bolded
2024
26. Sun CL†, Pratama AA†, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B, IsoGenie Project Field Teams 2010-2017, the IsoGenie and EMERGE Projects Coordinators, Wrighton KC, Rich VI, Sullivan MB. 2024. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environmental Microbiology. 26:e16665. († denotes co-first authors)
25. Kuhn MA, Varner RK, McCalley C, Perryman CR, Aurela M, Burke SA, Chanton J, Crill P, DelGreco J, Deng J, Heffernan L, Herrick C, Hodgkins SB, Jones CP, Juutinen S, Kane E, Lamit LJ, Larmola T, Lilleskov E, Olefeldt D, Palace MW, Rich V, Schulze C, Shorter JH, Sullivan F, Sonnentag O, Turetsky MR, Waldrop MP. 2024. Controls on Stable Methane Isotope Values in Northern Peatlands and Potential Shifts in Values Under Permafrost Thaw Scenarios. Journal of Geophysical Research - Biogeosciences. 10.1029/2023JG007837.
24. Li Z, Grant R, Chang K-Y, Hodgkins S, Tang J, Cory A, Mekonnen ZA, Saleska SR, Brodie E, Varner RK, Rich V, Wilson RM, Chanton J, Crill P and Riley WJ. Soil incubation methods lead to large differences in inferred methane production temperature sensitivity. Environmental Research Letters. 19:044069.
23. Ellenbogen JB, Borton MA, McGivern BB, Cronin DR, Hoyt DW, Freire-Zapata V, McCalley CK, Varner RK, Crill PM, Wehr RA, Chanton JP, Woodcroft BJ, Tfaily MM, Tyson GW, Rich VI, and Wrighton KC. 2024. Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems. 9:e00698-23.
22. McGivern BB, Cronin DR, Ellenbogen JB, Borton MA, Knutson EL, Freire-Zapata V, Bouranis JA, Bernhardt L, Hernandez AI, Flynn RM, Woyda R, Cory AB, Wilson RM, Chanton JP, Woodcroft BJ, Ernakovich JG, Tfaily MM, Sullivan MB, Tyson GW, Rich VI, Hagerman AE, Wrighton KC. 2024. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology. 9: 1454–1466.
2023
21. Chklovski A, Parks DH, Woodcroft BJ, Tyson G. 2023. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods. 20:1203–1212.
20. McDonald MD, Owusu-Ansah C, Ellenbogen JB, Malone ZD, Ricketts MP, Frolking SE, Ernakovich JG, Ibba M, Bagby SC, Weissman JL. 2023. What is microbial dormancy? Trends in Microbiology. 32:142-150. (Published as part of the 2022 Summer Program.)
2022
19. Fofana A, Anderson D, McCalley CK, Hodgkins S, Wilson RM, Cronin D, Raab N, Torabi M, Varner RK, Crill P, Saleska SR, Chanton JP, Tfaily MM, Rich VI. 2022. Mapping substrate use across a permafrost thaw gradient. Soil Biology and Biochemistry. 175:108809.
18. Dominguez-Huerta G†, Zayed AA†, Wainaina JM, Guo J, Tian F, Pratama AA, Bolduc B, Mohssen M, Zablocki O, Pelletier E, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J; Tara Oceans Coordinators§, Bowler C, Eveillard D, Guidi L, Karsenti E, Kuhn JH, Ogata H, Wincker P, Culley A, Chaffron S, Sullivan MB. 2022. Diversity and ecological footprint of Global Ocean RNA viruses. Science. 3769:1202. († denotes co-first authors)
17. Zayed AA†, Wainaina JM†, Dominguez-Huerta G†, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury J-M, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh H-J, Salazar G, Shatoff E, Tara Oceans Coordinators, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. 2022. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science. 376:156. († denotes co-first authors)
16. Ernakovich JG, Barbato RM†, Rich VI†, Schädel C†, Hewitt RE, Doherty SJ, Whalen ED, Abbott BW, Barta J, Biasi C, Chabot C, Hultman J, Knoblauch C, Lau Vetter CYM, Leewis MC, Liebner S, Mackelprang R, Onstott TC, Richter A, Schütte U, Siljanen H, Tas N, Timling I, Vishnivetskaya TA, P Waldrop MP, Winkel M. 2022. Microbiome assembly in thawing permafrost and its feedbacks to climate. Opinion. Global Change Biology. 17:5007. († denotes equal author contributions)
15. Verbeke BA, Lamit LJ, Lilleskov EA, Hodgkins SB, Basiliko N, Kane ES, Andersen R, Rebekka Artz RRE, Benavides JC, Benscoter BW, Borken W, Bragazza L, Brandt SM, Bräuer SL, Carson MA, Charman D, Chen X, Clarkson BR, Cobb AR, Convey P, del Águila Pasquel J, Enriquez AS, Griffiths H, Grover SP, Harvey CF, Harris LI, Hazard C, Hodgson D, Hoyt AM, Hribljan J, Jauhiainen J, Juutinen S, Knorr K-H, Kolka RK, Könönen M, Larmola T, McCalley CK, McLaughlin J, Moore TR, Mykytczuk N, Normand AE, Rich V, Roulet N, Royles J, Rutherford J, Smith DS, Svenning MM, Tedersoo L, Thu PQ, Trettin CC, Tuittila E-S, Urbanová Z, Varner RK, Wang M, Wang Z, Warren M, Wiedermann MM, Williams S, Yavitt JB, Yu Z-G, Yu Z, Chanton JP. 2022. Latitude, elevation, and mean annual temperature predict peat organic matter chemistry at a global scale. Global Biogeochemical Cycles. 36:e2021GB007057.
14. Wilson RM, Hough MA, Verbeke BA, Hodgkins SB, IsoGenie Coordinators, Chanton JP, Saleska SD, Rich VI, Tfaily MM. 2022. Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. Science of the Total Environment. 820:152757.
13. Cory AB, Chanton JP, Spencer RGM, Rich VI, McCalley CK, IsoGenie Project Coordinators, Wilson RM. 2022. Quantifying the Inhibitory Impact of Soluble Phenolics on Carbon Mineralization from Sphagnum-rich Peatlands. PLoS One. 17:e0252743.
12. Holmes ME, Crill PM, Burnett WC, McCalley CK, Wilson RM, Frolking S, Chang K-Y, Riley WJ, Varner RK, Hodgkins SB, IsoGenie Project Coordinators, IsoGenie Field Team, Rich VI, Saleska SR, Chanton JP. 2022. Carbon Accumulation, Flux, and Fate in Stordalen Mire, a Permafrost Peatland in Transition. Global Biogeochemical Cycles. 36:e2021GB007113.
11. Hough M, McCabe S, Vining SR, Pickering Pedersen E, Wilson RM, Lawrence R, Chang KY, Bohrer G, IsoGenie Coordinators, Riley WJ, Crill PM, Varner RK, Blazewicz SJ, Dorrepaal E, Tfaily MM, Saleska SR, Rich VI. 2022. Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland. Global Change Biology. 28:950.
2021
10. Emerson JB, Varner RK, Wik M, Parks DH, Neumann RB, Johnson JE, Singleton CM, Woodcroft BJ, Tollerson II R, Owusu-Dommey A, Binder M, Freitas NL, Crill PM, Saleska SR, Tyson GW, Rich VI. 2021. Sediment microbial community impacts on spatial differences in methane emission patterns from subarctic lakes. Nature Communications. 12:5815.
9. Affholder A, Guyot F, Sauterey B, Ferrière R, Mazevet S. 2021. Bayesian analysis of Enceladus’s plume data to assess methanogenesis. Nature Astronomy. 5:805.
8. Varner RK, Crill PM, Frolking S, McCalley CK, Burke SA, Chanton JP, Holmes ME, Saleska S, Isogenie Project Coordinators, Palace MW. 2021. Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970-2014. Philosophical Transactions of the Royal Society A. 380:20210022.
7. Roux S, Paul BG, Bagby SC, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Hallam SJ, Hernandez ME, Hess M, Liu W-T, O’Malley MA, Peng X, Rich VI, Saleska S, Eloe-Fadrosh E. 2021. Ecology and molecular targets of hypermutation in the global microbiome. Nature Communications. 12:3076.
6. Zinke LA, Evans PN, Santos-Medellín C, Schroeder AL, Parks DH, Varner RK, Rich VI, Tyson GW, Emerson JB. 2021. Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environmental Microbiology. 23:340.
5. Defrenne CE, Abs E, Cordeiro AL, Dietterich L, Hough M, Jones JM, Kivlin SN, Chen W, Cusak D, Franco ALC, Khasanova A, Stover D, Romero-Olivares AL. 2021. The Ecology Underground coalition: building a collaborative future of belowground ecology and ecologists. New Phytologist. 229:3058.
4. Bolduc B, Zablocki O, Guo J, Zayed AA, Vik D, Dehal P, Wood-Charlson EM, Arkin A, Merchant N, Pett-Ridge J, Roux S, Vaughn M, Sullivan MB. 2021. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology. ISME Communications. 1:77.
3. Pratama AA, Bolduc B, Zayed AA, Zhong Z, Guo J, Vik DR, Gazitúa MC, Wainaina JM, Roux S, Sullivan MB. 2021. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ. 9:e11447.
2. Zayed AA, Lücking D, Mohssen M, Cronin D, Bolduc B, Gregory AC, Hargreaves KR, Piehowski PD, White III RA, Huang EL, Adkins JN, Roux S, Moraru C, Sullivan MB. 2021. efam: an expanded, metaproteome-supported HMM profile database of viral protein families. Bioinformatics. btab451.
1. Wilson RM, Zayed AA, Crossen KB, Woodcroft B, Tfaily MM, Emerson J, Raab N, Hodgkins SB, Verbeke B, Tyson G, Crill P, Saleska S, Chanton JP, Rich VI, IsoGenie Project Coordinators, IsoGenie Project Field Team. 2021. Functional capabilities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PLoS ONE. 16:e0245857.