*postdoc, **PhD student, ^undergrad in our group, #equal contributions


**ter Horst, A.M., ^Adebiyi, T.V., Hernandez, D.A., **Fudyma, J.D., Emerson, J.B. (2023). Almond rhizosphere viral, prokaryotic, and fungal communities differed significantly among four California orchards and in comparison to bulk soil communities. bioRxiv. 2023.06.03.543555. link

*Sorensen, J.W., **ter Horst, A.M., *Zinke, L.A., Emerson, J.B. (2023). Soil viral communities differed by management and over time in organic and conventional tomato fields. bioRxiv. 2023.05.03.539301. link

Published or in press

55. **ter Horst, A.M., **Fudyma, J.D., Sones, J.L., Emerson, J.B. (2023). Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography. The ISME Journal, in press. preprint link

54. *Santos-Medellín, C., Blazewicz, S.J., Pett-Ridge, J., Firestone, M.K., Emerson, J.B. (2023). Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nature Ecology & Evolution, in press. preprint link

53. ^#Matsumoto, B.L., ,*#Sieradzki, E.T., Greenlon, A., Perilla-Henao, L.M., **ter Horst, A.M., **Geonczy, S.E., Cook, D.R., Emerson, J.B. (2023). Viruses of nitrogen-fixing Mesorhizobium bacteria in globally distributed chickpea root nodules. Phytobiomes, in press. preprint link

52. Emerson, J.B. (2023). Introducing our 15th Anniversary article collection. The ISME Journal. 10.1038/s41396-023-01418-9. link

51. Buivydaite, Z., Aryal, L., Correa, F.B., Chen, T., Langlois, V., Elberg, C.L., Netherway, T., Wang, R., Zhao, T., Acharya, B., Emerson, J.B., Hillary, L., Khadka, R.B., Mason-Jones, K., Sapkota, R., Sutela, S., Trubl, G., White III, R.A., Winding, A., Carreira, C. (2023). Meeting report: the first soil viral workshop (2022).  Virus Research. 331(2023):199121. link

50. *Santos-Medellín, C., Estera-Molina, K., Yuan, M., Pett-Ridge, J., Firestone, M.K., Emerson, J.B. (2022). Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands. Proceedings of the National Academy of Sciences. 119(45)e2209132119. link

49. #^Durham, D.M., #*Sieradzki, E.T., **ter Horst, A.M., *Santos-Medellín, C., ^Bess, C.W.A., **Geonczy, S.E., Emerson, J.B. (2022). Substantial differences in soil viral community composition within and among four Northern California habitats. ISME Communications. 2:100. link

48. #Roux, S. & #Emerson, J.B. (2022). Diversity in the soil virosphere: to infinity and beyond? Trends in Microbiology. 30(11):1025-1035. link

47. Martins, S.J., Taerum, S.J., Triplett, L., Emerson, J.B., Zasada, I., de Toledo, B.F., Kovac, J., Martin, K., Bull, C.T. (2022). Predators of soil bacteria in plant and human health. Phytobiomes Journal. 6:3. link

46. **ter Horst, A.M., **Fudyma, J.D., *Bak, A., Hwang, M.S., *Santos-Medellín, C., Stevens, K.A., Rizzo, D.M., Al Rwahnih, M., Emerson, J.B. (2022). RNA viral communities are structured by host plant phylogeny in oak and conifer leaves. Phytobiomes Journal, in press. link

45. Albright, M.B.N., Gallegos-Graves, L., Feeser, K.L., Montoya, K., Emerson, J.B., Shakya, M., Dunbar, J. (2022). Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition. ISME Communications. 2:24link

44. Lee, S., *Sorensen, J.W., Walker, R.L., Emerson, J.B., Nicol, G.W., Hazard, C. (2022). Soil pH influences the structure of virus communities at local and global scales. Soil Biology and Biochemistry. 166:108569. link

43. **ter Horst, A.M., *Santos-Medellín, C., *Sorensen, J.W., *Zinke, L.A., Wilson, R.M., Johnston, E.R., Trubl, G., Pett-Ridge, J., Blazewicz, S.J., Hanson, P.J., Chanton, J.P., Schadt, C.W., Kostka, J.E., Emerson, J.B. (2021). Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations. Microbiome. 9:233. link

42. *Sorensen, J.W., *Zinke, L.A., **ter Horst, A.M., *Santos-Medellín, C., ^Schroeder, A., Emerson, J.B. (2021). DNase treatment improves viral enrichment in agricultural soil viromes. mSystems. 6(5):e00614-21. link

41. Albright, M.B.N., Louca, S., Winkler, D.E., Feeser, K.L., Haig, S.-J., Whiteson, K.L., Emerson, J.B., Dunbar, J. (2021). Solutions in microbiome engineering: prioritizing barriers to organism establishment. The ISME Journal. 16:331-338. link

40. Emerson, J.B., Varner, R.K., Wik, M., Parks, D.H., Neumann, R.B., Johnson, J.E., Singleton, C.M., Woodcroft, B.J., Tollerson II, R., Owusu-Dommey, A., Binder, M., Freitas, N.L., Crill, P.M., Saleska, S.R., Tyson, G.W., Rich, V.I. (2021). Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications. 12:5815. link

39. Wilson, R.M., Zayed, A., Crossen, K., Woodcroft, B.J., Tfaily, M., Emerson, J.B., Raab, N., Hodgkins, S.B., Verbeke, B., Tyson, G.W., Crill, P.M., Saleska, S.R., Chanton, J.P., Rich, V.I. (2021). Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PLoS ONE. 16(2):e0245857. link

38. *Santos-Medellín, C., *Zinke, L.A., **ter Horst, A.M., Gelardi, D.L., Parikh, S.J., Emerson, J.B. (2021). Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities. The ISME Journal. 15:1956-1970. link

37. Trubl, G., Stedman, K., Bywaters, K., Boston, P.J., Kaelber, J.T., Roux, S., Emerson, J.B., Breitbart, M., Yin, J., Janjic, A., Sommers, P., Rodriguez-Roman, E. (2021). Astrovirology: Expanding the Search for Life. Bulletin of the American Astronomical Society. 53(4):516. link

36. *Zinke, L.A., Evans, P.N., *Santos-Medellín, C., ^Schroeder, A.L., Parks, D.H., Varner, R.K., Rich, V.I., Tyson, G.W., Emerson, J.B. (2021). Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environmental Microbiology. 23(1):340-357. link

35. Bolduc, B., Hodgkins, S.B., Varner, R.K., Crill, P.M., McCalley, C.K., Chanton, J.P., Tyson, G.W., Riley, W.J., Palace, M., Duhaime, M.B, Hough, M.A., IsoGenie Project Coordinators, IsoGenie Project Team (including Emerson, J.B.), A2A Project Team, Saleska, S.R, Sullivan, M.B., Rich, V.I. (2020). The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ. 8:e9467. link

34. *Bak, A. & Emerson, J.B. (2020). Cauliflower mosaic virus (CaMV) biology, management, and relevance to GM plant detection for sustainable organic agriculture. Frontiers in Sustainable Food Systems. 4:21. link

33. Dundore-Arias, J.P., Eloe-Fadrosh, E., Schriml, L.M., Beattie, G.A., Brennan, F.P., Busby, P.E., Calderon, R.B., Castle, S.C., Emerson, J.B., Everhart, S.E., Eversole, K., Frost, K.E., Herr, J.R., Huerta, A.I., Iyer-Pascuzzi, A.S., Kalil, A.K., Leach, J.E., Leonard, J., Maul, J.E., Prithiviraj, B., Potrykus, M., Redekar, N.R., Rojas, J.A., Silverstein, K.A.T., Tomso, D.J., Tringe, S.G., Vinatzer ,B.A., Kinkel, L.L. (2020). Community-driven Metadata Standards for Agricultural Microbiome Research. Phytobiomes Journal. 4(2):115-121. link

32. *Bak, A. & Emerson, J.B. (2019). Multiplex quantitative PCR for single-reaction genetically modified (GM) plant detection and identification of false-positive GM plants linked to Cauliflower mosaic virus (CaMV) infection. BMC Biotechnology. 19(1):73. link

31. Emerson, J.B. (2019). Soil Viruses: A New Hope. mSystems. 4(3):e00120-19. link

30. Roux S., Adriaenssens, E.M., Dutilh, B.E., Koonin, E.V., Kropinski, A.M., Krupovic, M., Kuhn, J.H., Lavigne, R., Brister, J.R., Varsani, A., Amid, C., Aziz, R.K., Bordenstein, S.R., Bork, P., Breitbart, M., Cochrane, G.R., Daly, R.A., Desnues, C., Duhaime, M.B., Emerson, J.B., Enault, F., Fuhrman, J.A., Hingamp, P., Hugenholtz, P., Hurwitz, B.L., Ivanova, N.N., Labonte, J.M., Lee, K.-B., Malmstrom, R.R., Martinez-Garcia, M., Mizrachi, I., Ogata, H., Paez-Espino, D., Petit, M.-A., Putonti, C., Rattei, T., Reyes, A., Rodriguez-Valera, F., Rosario, K., Schriml, L., Schulz, F., Steward, G.F., Sullivan, M.B., Sunagawa, S., Suttle, C.A., Temperton, B., Tringe, S.G., Thurber, R.V., Webster, N.S., Whiteson, K.L., Wilhelm, S.W., Wommack, K.E., Woyke, T., Wrighton, K.C., Yilmaz, P., Yoshida, T., Young, M.J., Yutin, N., Zeigler-Allen, L., Kyrpides, N.C., Eloe-Fadrosh, E.A. (2019). Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology. 37(1):29. link

29. Trubl, G., Jang, H.B., Roux, S., Emerson, J.B., Solonenko, N., Vik, D.R., Solden, L.M., Ellenbogen, J., Runyon, A.T., Bolduc, B.J., Woodcroft, B.J., Saleska, S.R., Tyson, G.W., Wrighton, K.C., Sullivan, M.B., Rich, V.I. (2018) Soil viruses are underexplored players in ecosystem carbon cycling. mSystems. 3(5):e00076-18. link

28. Emerson, J.B., Roux, S., Brum, J.R., Bolduc, B., Woodcroft, B.J., Jang, H.B., Singleton, C.M., Solden, L.M., Naas, A.E., Boyd, J.A., Hodgkins, S.B., Wilson, R.M., Trubl, G., Li, C., Frolking, S., Pope, P.B., Wrighton, K.C., Crill, P.M., Chanton, J.P., Saleska, S.R., Tyson, G.W., Rich, V.I., Sullivan, M.B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology. 3(8):870. link

27. Woodcroft, B.J., Singleton, C.M., Boyd, J.A., Evans, P.N., Emerson, J.B., Zayed, A.A.F., Hoelzle, R.D., Lamberton, T.O., McCalley, C.K., Hodgkins, S.B., Wilson, R.M., Purvine, S.O., Nicora, C.D., Li, C., Frolking, S., Chanton, J.P., Crill, P.M., Saleska, S.R., Rich, V.I., Tyson, G.W. (2018). Genome-centric view of carbon processing in thawing permafrost. Nature. 560(7716):49link

26. Clements, N., Keady, P., Emerson, J.B., Fierer, N., Miller, S.L. (2018) Seasonal variability of airborne particulate matter and bacterial concentrations in Colorado homes. Atmosphere. 9(4):133link

25. Probst, A.J., Ladd, B., Jarett, J.K., Sieber, C.M.K., Emerson, J.B., Thomas, B.C., Stieglmeier, M., Klingl, A., Woyke, T., Ryan, C.M., Banfield, J.F. (2018) Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature Microbiology. 3:328-336link

24. Emerson, J.B., Adams, R.I., Betancourt Roman, C.M., Brooks, B.B., Coil, D.A., Dahlhausen, K., Ganz, H.H., Hartmann, E.M., Hsu, T., Justice, N.B., Paulino Lima, I.G., Luongo, J.C., Lymperopoulou, D., Gomez Silvan, C., Rothschild-Mancinelli, B., Balk, M., Huttenhower, C., Nocker, A., Vaishampayan, P., Rothschild, L.J. (2017) Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 5:86. link

23. Roux, S., Emerson, J.B., Eloe-Fadrosh, E.A., Sullivan, M.B. (2017) Benchmarking viromics: An in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 5:e3817. link

22. Emerson, J.B., Keady, P.B., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., Fierer, N. (2017) High temporal variability in airborne bacterial diversity and abundance inside single-family residences. Indoor Air. 27:576-586. link

21. Vik, D.R., Roux, S., Brum. J.R., Bolduc, B., Emerson, J.B., Padilla, C.C., Stewart, F.J., Sullivan, M.B. (2017) Putative archaeal viruses from the mesopelagic ocean. PeerJ. 5:e3428. link

20. Probst, A.J., Castelle, C.J., Singh, A., Brown, C.T., Anatharaman, K., Sharon, I., Hug, L.A., Burstein, D., Emerson, J.B., Thomas, B.C., Banfield, J.F. (2017) Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environmental Microbiology. 19(2):459-474. link

19. Emerson, J.B., Thomas, B.C., Alvarez, W., Banfield, J.F. (2016). Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environmental Microbiology. 18(6):1686-1703. link

18. Andrade, K., Logemann, J., Heidelberg, K.B., Emerson, J.B., Comolli, L.R., Hug, L.A., Probst, A.J., Keillar, A., Thomas, B.C., Miller, C.S., Allen, E.E., Moreau, J.W., Brocks, J.J., Banfield, J.F. (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. The ISME Journal. 9:2697-2711. link

17. Emerson, J.B., Keady, P.B., Brewer, T.E., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., Fierer, N. (2015). Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood. Environmental Science & Technology. 49(5):2675-2684. link

16. Tully, B., Emerson, J.B., Andrade, K., Brocks, J.J., Allen, E.E., Banfield, J.F., Heidelberg, K.B. (2014). De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia reveal a variable genomic landscape. Archaea. 2014:875784. link

15. Probst, A.J., Weinmaier, T., Raymann, K., Perras, A., Emerson, J.B., Rattei, T., Wanner, G., Klingl, A., Berg, I., Yoshinaga, M., Viehweger, B., Hinrichs, K., Thomas, B.C., Meck, S., Auerbach, A.K., Heise, M., Schintlmeister, A., Schmid, M., Wagner, M., Gribaldo, S., Banfield, J.F., Moissl-Eichinger, C. (2014). Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nature Communications. 5:5497. link

14. Podell, S., Emerson, J.B., Jones, C.M., Ugalde, J.A., Welch, S., Heidelberg, K.B., Banfield, J.F., Allen, E.E. (2014). Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. The ISME Journal. 8(5):979-990. link

13. Bowers, R.M., Clements, N., Emerson, J.B., Wiedinmyer, C., Hannigan, M.P., Fierer, N. (2013). Seasonal variability in the bacterial and fungal diversity of the near-surface atmosphere. Environmental Science & Technology. 47(21):12097-12106. link

12. Doll, H.M., Armitage, D.W., Daly, R.A., Emerson, J.B., Goltsman, D.A., Yelton, A.P., Kerekes, J., Firestone, M.K., Potts, M.D. (2013). Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains. BMC Microbiology. 13:259. link

11. Emerson, J.B., Thomas, B.C., Andrade, K., Heidelberg, K.B., Banfield, J.F. (2013). New approaches indicate constant viral diversity despite shifts in assemblage structure in an Australian hypersaline lake. Applied and Environmental Microbiology. 79(21):6755-6764. link

10. Emerson, J.B., Andrade, K., Thomas, B.C., Norman, A., Allen, E.E., Heidelberg, K.B, Banfield, J.F. (2013). Virus-host and CRISPR dynamics in archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea. 2013:370871. link

9. Heidelberg, K.B., Nelson, W.C., Holm, J.B., Eisenkolb, N., Andrade, K., Emerson, J.B. (2013). Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia. Frontiers in Microbiology. 13(4):115. link

8. Emerson, J.B., Thomas, B.C., Andrade, K., Allen, E.E., Heidelberg, K.B, Banfield, J.F. (2012). Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Applied and Environmental Microbiology. 78(17):6309-6320. link

7. Narasingarao, P., Podell, S., Ugalde, J.A., Brochier-Armanet, C., Emerson, J.B., Brocks, J.J., Heidelberg, K.B., Banfield, J.F., Allen, E.E. (2012). De novo metagenomic assembly reveals abundant, novel major lineage of Archaea in hypersaline microbial communities. The ISME Journal. 6(1):81-93. link

6. Bik, E.M., Long, C.D., Armitage, G.C., Loomer, P., Emerson, J., Mongodin, E.F., Nelson, K.E., Gill, S.R., Fraser-Liggett, C.M., and Relman, D.A. (2010). Bacterial diversity in the oral cavity of 10 healthy individuals. The ISME Journal. 4(8):962-974. link

5. Brulc, J.M., Antonopoulos, D.A., Berg Miller, M.E., Wilson, M.K., Yannarell, A.C., Dinsdale, E.A., Edwards, R.E., Frank, E.D., Emerson, J.B., Wacklin, P., Coutinho, P.M., Henrissat, B., Nelson, K.E., White, B.A. (2009). Gene-centric metagenomics of the fiber adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences. 106(6):1948-1953. link

4. DeBoy, R.T., Mongodin, E.F., Fouts, D., Tailford, L., Khouri, H., Emerson, J.B., Mohamoud, Y., Watkins, K., Henrissat, B., Gilbert, H.J., Nelson, K.E. (2008). Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. Journal of Bacteriology. 190(15):5455-5463. link

3. Mongodin, E.F., Shapir, N., Daugherty, S.C., DeBoy, R.T., Emerson, J.B., Shvartzbeyn, A., Radune, D.,Vamathevan, J., Riggs, F., Grinberg, V., Khouri, H., Wackett, L.P., Nelson, K.E., Sadowsky, M.J. (2006). Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genetics. 2(12):e214. link

2. DeBoy, R.T., Mongodin, E.F., Emerson, J.B., Nelson, K.E. (2006). Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. Journal of Bacteriology. 188(7):2364-2374. link

1. Mongodin, E.F., Emerson, J.B., Nelson, K.E. (2005). Microbial metagenomics. Genome Biology. 6(10):347.1-347.3. link