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Items: 19

1.

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.

Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, RodrĂ­guez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB.

PeerJ. 2019 Jul 4;7:e7265. doi: 10.7717/peerj.7265. eCollection 2019.

2.

Scientists' warning to humanity: microorganisms and climate change.

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS.

Nat Rev Microbiol. 2019 Sep;17(9):569-586. doi: 10.1038/s41579-019-0222-5. Epub 2019 Jun 18. Review.

PMID:
31213707
3.

Optimizing de novo genome assembly from PCR-amplified metagenomes.

Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA.

PeerJ. 2019 May 9;7:e6902. doi: 10.7717/peerj.6902. eCollection 2019.

4.

Climate change microbiology - problems and perspectives.

Hutchins DA, Jansson JK, Remais JV, Rich VI, Singh BK, Trivedi P.

Nat Rev Microbiol. 2019 Jun;17(6):391-396. doi: 10.1038/s41579-019-0178-5. Review.

PMID:
31092905
5.

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.

Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, Saleska SR, Tyson GW, Rich VI; IsoGenie Project Coordinators, Saleska SR, Tyson GW, Rich VI.

Syst Appl Microbiol. 2019 Jan;42(1):54-66. doi: 10.1016/j.syapm.2018.12.003. Epub 2018 Dec 14.

6.

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

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.

mSystems. 2018 Oct 2;3(5). pii: e00076-18. doi: 10.1128/mSystems.00076-18. eCollection 2018 Sep-Oct.

7.

Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance.

Hodgkins SB, Richardson CJ, Dommain R, Wang H, Glaser PH, Verbeke B, Winkler BR, Cobb AR, Rich VI, Missilmani M, Flanagan N, Ho M, Hoyt AM, Harvey CF, Vining SR, Hough MA, Moore TR, Richard PJH, De La Cruz FB, Toufaily J, Hamdan R, Cooper WT, Chanton JP.

Nat Commun. 2018 Sep 7;9(1):3640. doi: 10.1038/s41467-018-06050-2.

8.

Host-linked soil viral ecology along a permafrost thaw gradient.

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.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.

9.

Genome-centric view of carbon processing in thawing permafrost.

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.

Nature. 2018 Aug;560(7716):49-54. doi: 10.1038/s41586-018-0338-1. Epub 2018 Jul 16.

PMID:
30013118
10.

Methanotrophy across a natural permafrost thaw environment.

Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, Chanton JP, Frolking S, Crill PM, Saleska SR, Rich VI, Tyson GW.

ISME J. 2018 Oct;12(10):2544-2558. doi: 10.1038/s41396-018-0065-5. Epub 2018 Jun 28.

11.

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.

Zhong ZP, Solonenko NE, GazitĂșa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG, Sullivan MB.

Front Microbiol. 2018 May 25;9:1094. doi: 10.3389/fmicb.2018.01094. eCollection 2018.

12.

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

Mondav R, McCalley CK, Hodgkins SB, Frolking S, Saleska SR, Rich VI, Chanton JP, Crill PM.

Environ Microbiol. 2017 Aug;19(8):3201-3218. doi: 10.1111/1462-2920.13809. Epub 2017 Jul 13.

PMID:
28574203
13.

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient.

Trubl G, Solonenko N, Chittick L, Solonenko SA, Rich VI, Sullivan MB.

PeerJ. 2016 May 17;4:e1999. doi: 10.7717/peerj.1999. eCollection 2016.

14.

Illuminating structural proteins in viral "dark matter" with metaproteomics.

Brum JR, Ignacio-Espinoza JC, Kim EH, Trubl G, Jones RM, Roux S, VerBerkmoes NC, Rich VI, Sullivan MB.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2436-41. doi: 10.1073/pnas.1525139113. Epub 2016 Feb 16.

15.

Methane dynamics regulated by microbial community response to permafrost thaw.

McCalley CK, Woodcroft BJ, Hodgkins SB, Wehr RA, Kim EH, Mondav R, Crill PM, Chanton JP, Rich VI, Tyson GW, Saleska SR.

Nature. 2014 Oct 23;514(7523):478-81. doi: 10.1038/nature13798.

PMID:
25341787
16.

Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production.

Hodgkins SB, Tfaily MM, McCalley CK, Logan TA, Crill PM, Saleska SR, Rich VI, Chanton JP.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5819-24. doi: 10.1073/pnas.1314641111. Epub 2014 Apr 7.

17.

Discovery of a novel methanogen prevalent in thawing permafrost.

Mondav R, Woodcroft BJ, Kim EH, McCalley CK, Hodgkins SB, Crill PM, Chanton J, Hurst GB, VerBerkmoes NC, Saleska SR, Hugenholtz P, Rich VI, Tyson GW.

Nat Commun. 2014;5:3212. doi: 10.1038/ncomms4212.

PMID:
24526077
18.

Time-series analyses of Monterey Bay coastal microbial picoplankton using a 'genome proxy' microarray.

Rich VI, Pham VD, Eppley J, Shi Y, DeLong EF.

Environ Microbiol. 2011 Jan;13(1):116-134. doi: 10.1111/j.1462-2920.2010.02314.x.

PMID:
20695878
19.

Design and testing of 'genome-proxy' microarrays to profile marine microbial communities.

Rich VI, Konstantinidis K, DeLong EF.

Environ Microbiol. 2008 Feb;10(2):506-21. Epub 2007 Nov 19.

PMID:
18028413

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