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Evolutionary relationships among bifidobacteria and their hosts and environments.

Rodriguez CI, Martiny JBH.

BMC Genomics. 2020 Jan 8;21(1):26. doi: 10.1186/s12864-019-6435-1.


The emergence of microbiome centres.

Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL.

Nat Microbiol. 2020 Jan;5(1):2-3. doi: 10.1038/s41564-019-0644-x. No abstract available.


Quantum Phase Transition of Correlated Iron-Based Superconductivity in LiFe_{1-x}Co_{x}As.

Yin JX, Zhang SS, Dai G, Zhao Y, Kreisel A, Macam G, Wu X, Miao H, Huang ZQ, Martiny JHJ, Andersen BM, Shumiya N, Multer D, Litskevich M, Cheng Z, Yang X, Cochran TA, Chang G, Belopolski I, Xing L, Wang X, Gao Y, Chuang FC, Lin H, Wang Z, Jin C, Bang Y, Hasan MZ.

Phys Rev Lett. 2019 Nov 22;123(21):217004. doi: 10.1103/PhysRevLett.123.217004.


Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.

Chase AB, Arevalo P, Brodie EL, Polz MF, Karaoz U, Martiny JBH.

mBio. 2019 Oct 29;10(5). pii: e02361-19. doi: 10.1128/mBio.02361-19.


Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry.

Khalili B, Weihe C, Kimball S, Schmidt KT, Martiny JBH.

mSphere. 2019 Oct 9;4(5). pii: e00435-19. doi: 10.1128/mSphere.00435-19.


Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change.

Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, Allison SD.

ISME J. 2020 Jan;14(1):1-9. doi: 10.1038/s41396-019-0510-0. Epub 2019 Sep 25. Review. No abstract available.


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.


Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents.

Isobe K, Allison SD, Khalili B, Martiny AC, Martiny JBH.

Nat Commun. 2019 Jun 7;10(1):2499. doi: 10.1038/s41467-019-10390-y.


Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community.

Albright MBN, Chase AB, Martiny JBH.

mBio. 2019 Apr 16;10(2). pii: e00568-19. doi: 10.1128/mBio.00568-19.


Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1.

Wandro S, Oliver A, Gallagher T, Weihe C, England W, Martiny JBH, Whiteson K.

Front Microbiol. 2019 Jan 31;9:3192. doi: 10.3389/fmicb.2018.03192. eCollection 2018.


Decomposition responses to climate depend on microbial community composition.

Glassman SI, Weihe C, Li J, Albright MBN, Looby CI, Martiny AC, Treseder KK, Allison SD, Martiny JBH.

Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):11994-11999. doi: 10.1073/pnas.1811269115. Epub 2018 Nov 5.


Emergence of soil bacterial ecotypes along a climate gradient.

Chase AB, Gomez-Lunar Z, Lopez AE, Li J, Allison SD, Martiny AC, Martiny JBH.

Environ Microbiol. 2018 Nov;20(11):4112-4126. doi: 10.1111/1462-2920.14405. Epub 2018 Oct 5.


Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.

Albright MBN, Timalsina B, Martiny JBH, Dunbar J.

Microb Ecol. 2019 Apr;77(3):597-606. doi: 10.1007/s00248-018-1239-4. Epub 2018 Aug 13.


Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.

Glassman SI, Martiny JBH.

mSphere. 2018 Jul 18;3(4). pii: e00148-18. doi: 10.1128/mSphere.00148-18.


Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

Baker NR, Khalili B, Martiny JBH, Allison SD.

Ecology. 2018 Jun;99(6):1441-1452. doi: 10.1002/ecy.2345.


Towards a Natural History of Soil Bacterial Communities.

Martiny JBH, Walters KE.

Trends Microbiol. 2018 Apr;26(4):250-252. doi: 10.1016/j.tim.2018.02.010. Epub 2018 Mar 6.


Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits.

Chase AB, Karaoz U, Brodie EL, Gomez-Lunar Z, Martiny AC, Martiny JBH.

mBio. 2017 Nov 14;8(6). pii: e01809-17. doi: 10.1128/mBio.01809-17.


Dispersal alters bacterial diversity and composition in a natural community.

Albright MBN, Martiny JBH.

ISME J. 2018 Jan;12(1):296-299. doi: 10.1038/ismej.2017.161. Epub 2017 Oct 20.


Phylogenetic conservation of substrate use specialization in leaf litter bacteria.

Dolan KL, Peña J, Allison SD, Martiny JB.

PLoS One. 2017 Mar 30;12(3):e0174472. doi: 10.1371/journal.pone.0174472. eCollection 2017.


Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium.

Chase AB, Arevalo P, Polz MF, Berlemont R, Martiny JB.

Front Microbiol. 2016 Nov 22;7:1874. eCollection 2016.


Genomic diversification of marine cyanophages into stable ecotypes.

Marston MF, Martiny JB.

Environ Microbiol. 2016 Nov;18(11):4240-4253. doi: 10.1111/1462-2920.13556. Epub 2016 Oct 24.


The genomic content and context of auxiliary metabolic genes in marine cyanomyoviruses.

Crummett LT, Puxty RJ, Weihe C, Marston MF, Martiny JBH.

Virology. 2016 Dec;499:219-229. doi: 10.1016/j.virol.2016.09.016. Epub 2016 Sep 29.


Microbial legacies alter decomposition in response to simulated global change.

Martiny JB, Martiny AC, Weihe C, Lu Y, Berlemont R, Brodie EL, Goulden ML, Treseder KK, Allison SD.

ISME J. 2017 Feb;11(2):490-499. doi: 10.1038/ismej.2016.122. Epub 2016 Oct 14.


The Microbial Olympics 2016.

Nelson MB, Chase AB, Martiny JB, Stocker R, Nguyen J, Lloyd K, Oshiro RT, Kearns DB, Schneider JP, Ringel PD, Basler M, Olson CA, Vuong HE, Hsiao EY, Roller BR, Ackermann M, Smillie C, Chien D, Alm E, Jermy AJ.

Nat Microbiol. 2016 Jul 26;1(8):16122. doi: 10.1038/nmicrobiol.2016.122. No abstract available.


Effects of dispersal and selection on stochastic assembly in microbial communities.

Evans S, Martiny JB, Allison SD.

ISME J. 2017 Jan;11(1):176-185. doi: 10.1038/ismej.2016.96. Epub 2016 Aug 5.


Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates.

Hanson CA, Marston MF, Martiny JB.

Front Microbiol. 2016 Jun 24;7:983. doi: 10.3389/fmicb.2016.00983. eCollection 2016.


Global biogeography of microbial nitrogen-cycling traits in soil.

Nelson MB, Martiny AC, Martiny JB.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):8033-40. doi: 10.1073/pnas.1601070113.


History Leaves Its Mark on Soil Bacterial Diversity.

Martiny JB.

mBio. 2016 Jun 7;7(3). pii: e00784-16. doi: 10.1128/mBio.00784-16.


Microbiomes in light of traits: A phylogenetic perspective.

Martiny JB, Jones SE, Lennon JT, Martiny AC.

Science. 2015 Nov 6;350(6261):aac9323. doi: 10.1126/science.aac9323. Review.


Microbial composition alters the response of litter decomposition to environmental change.

Matulich KL, Martiny JB.

Ecology. 2015 Jan;96(1):154-63.


Nitrogen Cycling Potential of a Grassland Litter Microbial Community.

Nelson MB, Berlemont R, Martiny AC, Martiny JB.

Appl Environ Microbiol. 2015 Oct;81(20):7012-22. doi: 10.1128/AEM.02222-15. Epub 2015 Jul 31.


Nonlinear responses in salt marsh functioning to increased nitrogen addition.

Vivanco L, Irvine IC, Martiny JB.

Ecology. 2015 Apr;96(4):936-47.


Microbial response to simulated global change is phylogenetically conserved and linked with functional potential.

Amend AS, Martiny AC, Allison SD, Berlemont R, Goulden ML, Lu Y, Treseder KK, Weihe C, Martiny JB.

ISME J. 2016 Jan;10(1):109-18. doi: 10.1038/ismej.2015.96. Epub 2015 Jun 5.


Temporal variation overshadows the response of leaf litter microbial communities to simulated global change.

Matulich KL, Weihe C, Allison SD, Amend AS, Berlemont R, Goulden ML, Kimball S, Martiny AC, Martiny JB.

ISME J. 2015 Nov;9(11):2477-89. doi: 10.1038/ismej.2015.58. Epub 2015 May 15.


Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities.

Amend AS, Matulich KL, Martiny JB.

Front Microbiol. 2015 Feb 18;6:109. doi: 10.3389/fmicb.2015.00109. eCollection 2015.


Cellulolytic potential under environmental changes in microbial communities from grassland litter.

Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JB, Martiny AC.

Front Microbiol. 2014 Nov 25;5:639. doi: 10.3389/fmicb.2014.00639. eCollection 2014.


Abundance of broad bacterial taxa in the sargasso sea explained by environmental conditions but not water mass.

Sjöstedt J, Martiny JB, Munk P, Riemann L.

Appl Environ Microbiol. 2014 May;80(9):2786-95. doi: 10.1128/AEM.00099-14. Epub 2014 Feb 21.


Beta diversity of marine bacteria depends on temporal scale.

Hatosy SM, Martiny JB, Sachdeva R, Steele J, Fuhrman JA, Martiny AC.

Ecology. 2013 Sep;94(9):1898-904.


Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.

Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JB, Martiny AC, Brodie EL.

Front Microbiol. 2013 Sep 23;4:282. doi: 10.3389/fmicb.2013.00282. eCollection 2013.


Antagonistic coevolution of marine planktonic viruses and their hosts.

Martiny JB, Riemann L, Marston MF, Middelboe M.

Ann Rev Mar Sci. 2014;6:393-414. doi: 10.1146/annurev-marine-010213-135108. Epub 2013 Aug 28. Review.


Microbial abundance and composition influence litter decomposition response to environmental change.

Allison SD, Lu Y, Weihe C, Goulden ML, Martiny AC, Treseder KK, Martiny JB.

Ecology. 2013 Mar;94(3):714-25.


Marine cyanophages exhibit local and regional biogeography.

Marston MF, Taylor S, Sme N, Parsons RJ, Noyes TJ, Martiny JB.

Environ Microbiol. 2013 May;15(5):1452-63. doi: 10.1111/1462-2920.12062. Epub 2012 Dec 28.


Fundamentals of microbial community resistance and resilience.

Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JB, Matulich KL, Schmidt TM, Handelsman J.

Front Microbiol. 2012 Dec 19;3:417. doi: 10.3389/fmicb.2012.00417. eCollection 2012.


Microbial composition affects the functioning of estuarine sediments.

Reed HE, Martiny JB.

ISME J. 2013 Apr;7(4):868-79. doi: 10.1038/ismej.2012.154. Epub 2012 Dec 13.


Beyond biogeographic patterns: processes shaping the microbial landscape.

Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB.

Nat Rev Microbiol. 2012 May 14;10(7):497-506. doi: 10.1038/nrmicro2795. Review.


The effect of nitrogen enrichment on c(1)-cycling microorganisms and methane flux in salt marsh sediments.

Irvine IC, Vivanco L, Bentley PN, Martiny JB.

Front Microbiol. 2012 Mar 19;3:90. doi: 10.3389/fmicb.2012.00090. eCollection 2012.


An atomic force microscopy investigation of cyanophage structure.

Kuznetsov YG, Chang SC, Credaroli A, Martiny J, McPherson A.

Micron. 2012 Dec;43(12):1336-42. doi: 10.1016/j.micron.2012.02.013. Epub 2012 Feb 25.


Rapid diversification of coevolving marine Synechococcus and a virus.

Marston MF, Pierciey FJ Jr, Shepard A, Gearin G, Qi J, Yandava C, Schuster SC, Henn MR, Martiny JB.

Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4544-9. doi: 10.1073/pnas.1120310109. Epub 2012 Mar 2.


The abundance of pink-pigmented facultative methylotrophs in the root zone of plant species in invaded coastal sage scrub habitat.

Irvine IC, Brigham CA, Suding KN, Martiny JB.

PLoS One. 2012;7(2):e31026. doi: 10.1371/journal.pone.0031026. Epub 2012 Feb 24.


Functional metagenomics reveals previously unrecognized diversity of antibiotic resistance genes in gulls.

Martiny AC, Martiny JB, Weihe C, Field A, Ellis JC.

Front Microbiol. 2011 Nov 29;2:238. doi: 10.3389/fmicb.2011.00238. eCollection 2011.

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