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Fincker, M., Huber, J.A., Orphan, V.J, Rappé, M.S., Teske, A., and A.M. Spormann. 2020. Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions. Environmental Microbiology.

Moulana, A., Anderson, R.*, Fortunato, C.F.* and J.A. Huber. 2020. Selection is a significant driver of gene gain and loss in the pangenome of the bacterial genus Sulfurovum in geographically distinct deep-sea hydrothermal vents. mSystems. 5:e00673-19.

Orcutt, B.N., Bradley, J., Brazelton, W.J., Estes, E.R., Goordial, J.M., Huber, J.A., Jones, R.M., Mahmoudi, N., Marlow, J.J., Murdock, S. and M. Pachiadaki. 2020. Impacts of deep-sea mining on microbial ecosystem services. Limnology and Oceanography. 65:1489-1510.


Galambos, D. Anderson, R.E.*, Reveillaud, J.*, and J.A. Huber. 2019. Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. Environmental Microbiology. 21:4395-4410.

Trembath-Reichert, E.*, Butterfield, D.A., and J.A. Huber. 2019. Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa. ISME Journal. 13:2264–2279.

Stewart, L.C., Algar, C.K.*, Fortunato, C.S.*, Larson, B.I., Vallino, J.J., Huber, J.A., Butterfield, D.A., and J.F. Holden. 2019. Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents. ISME Journal. 13:1711–1721.

Huber, J.A. and C. Preston. 2019. Take to the high seas: microbiology labs below the ocean surface. Crystal Ball Article. Environmental Microbiology Reports. 11:23–25. (Invited)


Vallino, J.J. and J.A. Huber. 2018. Using maximum entropy production to describe microbial biogeochemistry over time and space in a meromictic pond. Frontiers in Environmental Science. 6:100. doi: 10.3389/fenvs.2018.00100

Angermeyer, A., Crosby, S.C., & Huber, J.A. (2018). Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient. PeerJ, 6, 21 pages.

Walter, S R.S., Jaekel, U., Osterholz, H., Fisher, A.T., Huber, J.A., Pearson, A., Dittman, T., Girguis, P.R. (2018). Microbial decomposition of marine dissolved organic matter in cool oceanic crust. Nature Geoscience, 11(5), 334-339. doi:10.1038/s41561-018-0109-5.

Louca, S., Polz, M.F., Mazel, F., Albright, M.B.N., Huber, J.A., O'Connor, M.I., Ackermann, M., Hahn, A.S., Srivastava, D.S., Crowe, S.A., Doebeli, M., and Parfrey, L. W. (2018). Function and functional redundancy in microbial systems.. Nature ecology & evolution, 2(6), 936-943. doi:10.1038/s41559-018-0519-1.

Reveillaud, J., Anderson, R., Reves-Sohn, S., Cavanaugh, C., & Huber, J.A. (2018). Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into
metabolism and diversity. Microbiome, 6, 15 pages. doi:10.1186/s40168-018-0411-x.

Fortunato, C.S., Larson, B., Butterfield, D.A., & Huber, J.A. (2018). Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent
fluids. Environmental Microbiology, 20(2), 769-784. doi:10.1111/1462-2920.14011.

Tully, B.J., Wheat, C.G., Glazer, B.T., & Huber, J.A. (2018). A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME Journal, 12(1), 1-16.


Anderson, R.E., Reveillaud, J., Reddington, E., Delmont, T.O., Eren, A.M., Mcdermott, J.M., Seewald, J.S. and Huber, J.A., 2017. Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents. Nature Communications, 8(1): 1114, 10.1038/s41467-017-01228-6.

Mackey, K.R.M, Hunter-Cevera, K., Britten, G.L., Murphy, L.G., Sogin, M.L, and J.A. Huber. 2017. Seasonal succession and spatial patterns of Synechococcus microdiversity in estuarine waters of a salt marsh revealed through 16S rRNA gene oligotyping. Frontiers in Microbiology. 8:1496. doi: 10.3389/fmicb.2017.01496.

Sylvan, J., Wankel, S.D., LaRowe, D.E., Charoenpong, C.N., Huber, J.A., Moyer, C.L, and K.J. Edwards. 2017. Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii. Geochemical et Cosmochimica Acta. 198: 131–150. doi:


Fernandez-Gonzalez, N.*, Huber, J.A. and J.J. Vallino. 2016. Microbial communities are well adapted to disturbances in energy input. mSystems. 1(5) e00117-16; doi: 10.1128/mSystems.00117-16.

Topçuoğlu, B.D., Stewart, L.C., Butterfield, D.A., Huber, J.A., and J.F. Holden. 2016.  Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents. Frontiers in Microbiology. 7:1240. doi: 10.3389/fmicb.2016.01240

*Meyer, J.L, Jaekel, U., *Tully, B. Glazer, B.T., Wheat, C.G., H-T, Lin., C-C, Hsieh, Cowen, J.P., Hulme, S.M., Girguis, P.R., and J.A. Huber. 2016. A distinct and active bacterial community in cold oxygenated fluids circulating beneath Mid-Atlantic seafloor. Scientific Reports. 6:22541. doi: 10.1038/srep22541

*Fortunato, C.F. and J.A. Huber. 2016. Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent. ISME Journal. 10:1925-1938. doi:10.1038/ismej.2015.258

*Reveillaud, J., *Reddington, E., McDermott, J., *Meyer, J.L., *Algar, C., Sylva, S., Seewald, J., German, C.G., and J.A. Huber. 2016. Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Environmental Microbiology. 8:1970–1987. doi: 10.1111/1462-2920.13173

*Angermeyer, A.A., Crosby, S.C. and J.A. Huber. 2016. Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria. Environmental Microbiology. 18:75-86.


*Meyer, J.L. and J.A. Huber. 2014. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME Journal. 8:867–880.

*Reveillaud, J., Maignien, L, Eren, M., Apprill, A., Huber, J.A., Sogin, M.L, and A. Vanreusel. 2014. Host-specificity among abundant and rare taxa in the sponge microbiome. ISME Journal. 8:1198-1209.

Vallino, J.J., *Algar, C.K., *Fernandez Gonzalez, N., and J.A. Huber. 2014. Use of receding horizon optimal control to solve MaxEP-based biogeochemistry problems. In Dewar, R.C., Lineweaver, C., Niven, R. and Regenauer-Lieb, K., (eds), 337-359. Beyond the Second Law: Entropy Production and Non-Equilibrium Systems. Springer, Berlin, Germany.

Reed, D.C., *Algar, C.K, Huber, J.A. and G.J. Dick. 2014. Gene-centric approach to integrating environmental genomics and biogeochemical models. Proceedings of the National Academy of Sciences USA. 111:1879-84.

Orcutt, B. N., LaRowe, D. E., Lloyd, K. G., Mills, H., Orsi, W., Reese, B. K., Sauvage, J., Huber, J. A., and Amend, J. 2014. IODP Deep Biosphere Research Workshop report – a synthesis of recent investigations, and discussion of new research questions and drilling targets. Scientific Drilling. 17:61–66.


*Merkel, A., Huber, J.A., Chernyh, N., Bonch-Osmolovskaya, E. and A. Lebedinsky. 2013. Detection of putatively thermophilic anaerobic methanotrophs (ANMEs) in diffuse hydrothermal vent fluids. Applied and Environmental Microbiology. 79:915-923.

Bennett, S.A., Coleman, M., Huber, J.A., *Reddington, E., Kinsley, J.C., McIntyre, C., Seewald, J.S., and C.R. German. 2013. Trophic regions of a hydrothermal plume dispersing away from an ultramafic-hosted vent-system: Von Damm vent-site, Mid-Cayman Rise. Geochemistry Geophysics Geosystems. 14:317-327.

Ver Eecke H.C., *Akerman, N.H., Huber, J.A., Butterfield, D.A., and J.F. Holden. 2013. Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions. Environmental Microbiology Reports. 5:665-671.

*Meyer, J.L., *Akerman, N.H., Proskurowski, G. and J.A. Huber. 2013. Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge. Frontiers in Microbiology. 4:153. doi: 10.3389/fmicb.2013.00153

*Akerman, N.H, Butterfield, D.A, and J.A. Huber. 2013. Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids. Frontiers in Microbiology. 4:185. doi: 10.3389/fmicb.2013.00185


Ver Eecke, H.C., Butterfield, D.A., Huber, J.A., Lilley, M.D., Olson, E.J., Roe, K.K., Evans, L.J., *Merkel, A.Y., *Cantin, H.V., and J.F. Holden. 2012. Hydrogen-limited growth of hyperthermophilic methanogens at deep-sea hydrothermal vents. Proceedings of the National Academy of Sciences USA. 109:13,674–13,679.

Breier, J.A., Gomez-Ibanez, D., *Reddington, E., Huber, J.A., and D. Emerson. 2012. A precision multi-sampler for deep-sea hydrothermal microbial mat studies. Deep-Sea Research Part I: Oceanographic Research Papers.70:83-90.


Resing, J.A, Rubin, K.H., Embley, R.W., Lupton, J.E., Baker, E.T. Dziak, R.P., Baumberger, T., Lilley, M.D., Huber, J.A., Shank, T.M., Butterfield, D.A., Clague, D.A., Keller, N.S., Merle, S.G., Buck, N.J., Michael, P.J., Soule, A. Caress, D.W., Walker, S.L. Davis, R., Cowen, J.P., Reysenbach, A-L., and H. Thomas. 2011. Active submarine eruption of boninite in the northeastern Lau Basin. Nature Geoscience. 4:799-806.


German, C.R., Bowen, A., Coleman, M.L., Honig, D.L., Huber, J.A., Jakuba, M.V., Kinsey, J.C., Kurz, M.D., Leroy, S., McDermott, J.M, Mercier de Lépinay, B., Nakamura, K., Seewald, J.S., *Smith, J.L., Sylva, S.P., Van Dover, C.L., Whitcomb, L.L., and D.R. Yoerger. 2010. Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise. Proceedings of the National Academy of Sciences USA. 107:14,020-14,025.

Schrenk M,O., Huber, J.A., and K.J. Edwards. 2010. Microbial Provinces in the Subseafloor. Annual Review of Marine Science. 2:279-304.

Huber, J.A., *Cantin, H.V., Huse, S.M., Mark Welch, D.B., Sogin, M.L., and D.A. Butterfield. 2010. Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiology Ecology. 73:538-549.


Huber, J.A., Morrison, H.G., Huse, S.M., Neal, P.R, Sogin, M.L., and D.B. Mark Welch. 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology. 11:1292-1302.


Huber, J.A. and J.F. Holden. 2008. Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks. In Lowell, R.P., J. S. Seewald, A. Metaxas, and M.R. Perfit (eds.), 215-231. Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges. American Geophysical Union Press, Washington, D.C.

Huse, S.M., Dethlefsen, L., Huber, J.A., Mark Welch, D.B., Relman, D.A., and M.L. Sogin. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 4:e1000255.


Huber, J.A., Mark Welch, D.B., Morrison, H.G., Huse, S.M., Neal, P.R., Butterfield, D.A., and M.L. Sogin. 2007. Microbial population structures in the deep marine biosphere. Science. 318:97-100.

Wells, L.E, Armstrong, J.C. and J.A. Huber. 2007. Disciplinary aspirations and educational opportunities. In W.T. Sullivan III and J.A. Baross (eds.), 547-557. Planets and Life:The Emerging Science of Astrobiology. Cambridge University Press, Cambridge, UK.

Baross, J.A., Schrenk, M.O, and J.A. Huber. 2007. Limits of Carbon Life on Earth and Elsewhere. In W.T. Sullivan III and J.A. Baross (eds.), 275-291. Planets and Life: The Emerging Science of Astrobiology, Cambridge University Press, Cambridge, UK.

Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L., and D.B. Mark Welch. 2007. Accuracy and quality of massively-parallel DNA pyrosequencing. Genome Biology. 8: R143.


Huber, J.A., Butterfield, D.A, and J.A. Baross. 2006. Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean. Journal of Geophysical Research, Biogeosciences. 111:G04016.

Huber, J.A., Butterfield, D.A., Johnson, H.P., and J.A. Baross. 2006. Microbial life in ridge flank crustal fluids. Environmental Microbiology. 88:88-99.

Sogin, M.L., Morrison, H.G., Huber, J.A., Mark Welch, D.B., Huse, S.M., Neal, P.R., Arrieta, J.M., and G.J. Herndl. 2006. Microbial diversity in the deep sea and the under-explored “rare biosphere.” Proceedings of the National Academy of Sciences USA. 103:12,115-12,120.


Mehta, M.P., Huber, J.A., and J.A. Baross. 2005. Incidence of novel and potentially archaeal nitrogenase genes in the deep NE Pacific Ocean. Environmental Microbiology. 7:1525-1534.


Butterfield, D.A., Lilley, M.D., Huber, J.A., Roe, K.K., Embley, R.W., Baross, J.A., and G.J. Massoth. 2004. Mixing, reaction, and microbial activity in sub-seafloor hydrothermal upflow zones: Evidence from diffuse flow outcrops across the 1998 Axial Volcano Sea-floor eruption area through time. In W.S.D. Wilcock, E.F. DeLong, D.S. Kelley, J.A.Baross, and S.C. Cary (eds.), 269-289. The Subseafloor Biosphere at Mid-Ocean Ridges. American Geophysical Union Press, Washington, D.C.


Huber, J.A., Butterfield, D.A., and J.A. Baross. 2003. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiolology Ecology. 43:393-409.


Huber, J.A., Butterfield, D.A., and J.A. Baross. 2002. Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Applied and Environmental Microbiology. 68:1585-1594.


Non-refereed publications

  • Huber, J.A. 2015. Making methane down deep. Science. 349:376-377.
  • C.R.German, Tyler, P.A., McIntyre, C., Amon, D., Cheadle, M., Clarke, J., John, B., McDermott, J., Bennett, S., Huber, J.A., Kinsey, J., Seewald, J. Van Dover, C., and K. Elliott. 2014. Exploration of the Mid-Cayman Rise.  Oceanography. 25:52-53.
  • Huber, J.A. 2012. Microbial Oceanography. iBio Magazine.
  • Chadwick, W.W., Butterfield, D.A., Embley, R.W., Tunnicliffe, V., Huber, J.A., Nooner, S., and D. Clague. 2010. Spotlight: Axial Seamount. Oceanography. 23:38-39.
  • Bach, W., Edward, K.J, Hayes, J.M., Huber, J.A., Sievert, S.M., and M.L. Sogin. 2006. Energy in the dark: Fuel for life in the deep ocean and beyond. Eos, Transactions AGU. 87:73-78.
  • Johnson, H.P. and LEXEN Scientific Party. 2003. Probing for life in the ocean crust with the LEXEN program. Eos, Transactions AGU. 84:109-112.