Rich Lab:Publications

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PUBLICATIONS

(bolded authors are Rich Lab members; † co-corresponding authors)

• Cavicchioli R, Ripple, W.J., Timmis, K.N., Azam, F., Bakken, L.R., Baylis, M., Behrenfeld, M.J., Boetius, A., Boyd, P.W., Classen, A.T., Crowther, T.W., Danovaro, R., Foreman, C.M., Huisman, J., Hutchins, D.A., Jansson, J.K., Karl, D.M., Koskella, B., Mark Welch, D.B., Martiny, J.B.H., Moran, M., Orphan, V., Reay, D., Remais, J.V., Rich, V., Singh, B.K., Stein, L.Y., Stewart, F.J., Sullivan, M.B., van Oppen, M.J.H., Weaver, S.C., Webb, E.A., Webster, N. 2019. Scientists’ Warning to Humanity: microorganisms and climate change. In press at Nature Reviews Microbiology.

• Trubl G, Roux S, Solonenko N, Li Y-F, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh E, Rich† VI, Sullivan† MB. 2019. Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils. In press at PeerJ. († co-corresponding authors).

• Rich VI. 2019. Viewpoint: Climate change microbiology - problems and perspectives. Fellow invited contributors: Hutchins DA, Jansson JK, Remais J, Singh BK, Trivedi P. Nature Reviews Microbiology. 17: 391-6.

• Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Marsan D, Chen F, Fuhrman JA, Northern TR, Coleman ML, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA. 2019. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ. 7:e6902

• Wilson RM, Neumann RB, Crossen K, Raab N, Hodgkins SB, Saleska SR, Bolduc B, Woodcroft B, Tyson G, J.P. Chanton JP, Rich VI. 2019. Community Analyses Inform Geochemical Reaction Network Models for Predicting Pathways of Greenhouse Gas Production. Frontiers in Earth Science. 7:59. DOI:10.3389/feart.2019.00059.

• Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li Y-F, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, IsoGenie Project Coordinators, Saleska SR, Tyson GW, Rich VI. 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, as part of the special issue “Classification of Uncultured Bacteria and Archaea”, Editors: Ramon Mosello-Mora and Konstantinos Konstantinidis. 42: 54-66.

• Chang K-Y, Riley W, Crill P, Grant R, Rich V, Saleska S. 2019. Large carbon cycle sensitivities to climate across a permafrost thaw gradient in subarctic Sweden. The Cryosphere. 13: 647-663.

• Hodgkins SB, Richardson C, Dommain R, Wang H, Glaser P, Verbeke B, Winkler B, Missilmani M, Flanagan N, Ho M, Hoyt A, Harvey C, Cobb A, Rich VI, Vining S, Hough M, De La Cruz F, Toufaily J, Hamdan R, Cooper WT, Chanton J. 2018. Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance. Nature Communications. 9: 3640. DOI: 10.1038/s41467-018-06050-2. Recipient of the 2018 "Nobel Peat Prize” https://twitter.com/MACecohydrology/status/1082767317900120064

• Woodcroft* BJ, Singleton* CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW. 2018. Genome-centric view of carbon processing in thawing permafrost. Nature. 560: 49–54. DOI 10.1038/s41586-018-0338-1. Nature microbiology blog https://naturemicrobiologycommunity.nature.com/channels/346-behind-the-paper/posts/36570-genomic-centric-view-of-carbon-processing-in-thawing-permafrost.

• Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB. 2018. Host-linked soil viral ecology along a permafrost thaw gradient Nature Microbiology. 3: 870–880. DOI 10.1038/s41564-018-0190-y, Open access. Nature microbiology blog https://naturemicrobiologycommunity.nature.com/channels/346-behind-the-paper/posts/36561-soil-viruses-unlocking-the-secret-garden.

• Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, Chanton JP, Frolking S, Crill PM, Saleska SR, Rich VI, Tyson GW. 2018. Methanotrophy across a natural permafrost thaw environment. ISMEJ. 12: 2544–2558. DOI 10.1038/s41396-018-0065-5, Open access.

• Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI. 2018. Soil viruses are underexplored players in ecosystem carbon processing mSystems, 3(5), e00076-18.

• Zhong Z-P, Solonenko NE, Gazitúa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG*, Sullivan MB. 2018. Clean low-biomass procedures and their application to ancient ice core microbes. Frontiers in Microbiology, section Extreme Microbiology. 9: 1094. DOI: 10.3389/fmicb.2018.01094

• Mondav R, McCalley CM, Hodgkins SB, Frolking S, Saleska SR, Rich VI, Chanton JP, Crill PM. 2017. Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient. Environmental Microbiology. 19: 3201–3218.

• Wilson* RM, Tfaily MM*, Rich VI, Keller JK, Bridgham SD, Medvedeff C, Meredith L, Hanson PJ, Hines M, Pfeifer-Meister L, Saleska SR, Crill P, Cooper WT, Chanton JP, Kostka JE. 2017. Hydrogenation of Organic Matter as a Terminal Electron Sink Sustains High CO2:CH4 Production Ratios Regulating Climate Feedbacks in Boreal Peatlands and Thawing Permafrost. Organic Geochemistry. 112: 22–32.

• Deng J, McCalley C, Frolking S, Chanton J, Crill P, Varner R, Tyson G, Rich V, Saleska S, Hines M, Li C. 2017. Adding Stable Carbon Isotopes Improves Model Representation of the Role of Microbial Communities in Peatland Methane Cycling. Journal of Advances in Modeling Earth Systems. 9: 1412–1430. DOI: 10.1002/2016MS000817

• Diaz KS, Rich VI, McLain JE. 2017. Searching for antibiotic resistance genes in a pristine Arctic wetland. Journal of Contemporary Water Research & Education. 160 (1), 42-59.

• Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI†, Sullivan MB†. 2016. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient Peer J. 4:e1999. († co-corresponding authors)

• Hodgkins SB, Tfaily MM, McCalley CK, Rich VI, Saleska SR, Crill PM, Chanton JP, Cooper WT. 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.

• Brum JR* & Ignacio-Espinoza JC* & Kim E-H*, Trubl G, Jones R, Roux S, VerBerkmoes N, Rich VI† & Sullivan MB†. 2016. Illuminating structural proteins in viral ‘dark matter’ with metaproteomics Proceedings of the National Academy of Sciences, USA. 113: 2436-2441. (*co-first authors,† co-corresponding authors)

• Angly FE, Pantos O, Morgan TC, Rich VI, Bourne DG, Mercurio P, Negri AP, Tyson GW. 2016. Diuron tolerance and potential degradation in pelagic microbiomes from the Great Barrier Reef lagoon Peer J. 4:e1758.

• Angly FE, Heath C, Morgan TC, Hemerson T, Rich VI, Schaffelke B, Bourne DG, Mercurio P, Tyson GW. 2016. Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ. 4:e1511; DOI 10.7717/peerj.1511.

• Hodgkins SB, Chanton JP, Langford L, McCalley CK, Saleska SR, Rich VI, Crill PM, Cooper WT. 2015. Soil incubations reproduce field methane dynamics in a subarctic wetland. Biogeochemistry. 126:241–249.

• McCalley CK, Woodcroft BJ, Hodgkins SB, Wehr R, Kim E-H, Mondav R, Crill PM, Chanton JP, Rich VI, Tyson GW, Saleska SR. 2014. Methane dynamics regulated by microbial community response to permafrost thaw. Nature. 514: 478-481.

• Hodgkins SB, Tfaily MM, McCalley CK, Logan T, Crill PM, Saleska SR, Rich VI, Chanton JP. 2014. Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production. Proceedings of the National Academy of Sciences, USA. 111: 5819–5824.

• Mondav* R & Woodcroft* BJ, Kim E-H, McCalley MK, Hodgkins SB, Crill PM, Chanton JP, Hurst GB, VerBerkmoes N, Saleska SR, Hugenholtz P, Rich VI, Tyson GW. 2014. Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications. 5: 3212. doi:10.1038/ncomms4212. (*co-first authors)

• Woodcroft* BJ, Mondav* R, Kim E-H, Hodgkins SB, Crill PM, Chanton JP, VerBerkmoes N, Saleska SR, Hugenholtz P, Rich VI, Tyson GW. 2014. A novel archaeal lineage drives methane flux in thawing permafrost. Nature Communications. 5:3212.

• Rich, V, Pham V, Eppley J, Shi Y, DeLong EF. 2011. Time-series analyses of Monterey Bay coastal microbial picoplankton using a ‘genome proxy’ microarray. Environmental Microbiology. 13: 116-134.

• Rich, V, Konstantinidis K, DeLong EF. 2008. Design and testing of “genome proxy” microarrays to profile marine microbial communities Environmental Microbiology, 10: 506-521.
  • Faculty of 1000 “Must Read” paper, 4 Feb 2008.

• DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. 311:496-503.
  • Faculty of 1000 “Recommended” paper, 17 Feb 2006

• Horz, H-P, Rich V, Avrahami S, and Bohannan BJ. 2005. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Applied and Environmental Microbiology. 71(5): 2642-2652.