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Lathuilliere, M.J., M.S. Johnson, G.L. Galford and E.G. Couto (2014). Environmental footprints show China and Europe’s evolving resource appropriation for soybean production in Mato Grosso, Brazil. Environmental Research Letters 9:074001. doi:10.1088/1748-9326/9/7/074001 pdf

Eykelbosh A.J., M.S. Johnson, E. Santos de Queiroz, H.J. Dalmagro, E.G. Couto (2014). Biochar from sugarcane filtercake reduces soil CO2 emissions relative to raw residue and improves water retention and nutrient availability in a highly-weathered tropical soil. PLoS ONE 9(6): e98523. doi: 10.1371/journal.pone.0098523 pdf

Schwerdtfeger, J., M.S. Johnson, R.S.S. Amorim, L. Sanches, J.H. Campelo Júnior, and M. Weiler (2014). Inundation and groundwater dynamics for quantification of evaporative water loss in tropical wetlands. In Discussion at Hydrol. Earth Syst. Sci. Discuss., 11, 4017-4062, 2014, doi: 10.5194/hessd-11-4017-2014 pdf

Schwerdtfeger, J., M. Weiler, M.S. Johnson, and E.G. Couto (2014). Estimating water balance components of tropical wetland lakes in the Pantanal dry season, Brazil. Hydrological Sciences Journal (in press). doi: 10.1080/02626667.2013.870665

Johnson, M.S., E.G. Couto, I. Messias, R. Amorim; J. Milesi, O.B. Pinto Jr, and M. Biudes (2013).  Soil CO2 dynamics in a tree island soil of the Pantanal: the role of soil water potential. PLoS ONE 8:e64874. doi:10.1371/journal.pone.0064874 pdf

Dinsmore, K.J., M.B. Wallin, M.S. Johnson, M.F. Billett, K. Bishop, J. Pumpanen and A. Ojala (2013). Contrasting CO2 concentration discharge dynamics in headwater streams: a multi-catchment comparison. Journal of Geophysical Research: Biogeosciences 118:445-461. doi:10.1002/jgrg.20047 pdf; AGU Research Highlight

Recha, J.W., J. Lehmann, M.T. Walter, A. Pell, L. Verchot, and M.S. Johnson (2013). Stream water nutrient and organic carbon exports from tropical headwater catchments at a soil degradation gradient. Nutrient Cycling in Agroecosystems 95:145-158. doi:10.1007/s10705-013-9554-0 pdf

I. Messias, E.G. Couto, O.B. Pinto Jr, and Johnson, M.S. (2013). Monitoramento contínuo do potencial redox e de variáveis complementares em ambiente hipersazonal no Pantanal Norte (Monitoring soil redox potential and its interactions with associated variables in the northern Pantanal). Revista Brasileira de Ciência do Solo (Brazilian Journal of Soil Science) 37:632-639. pdf

Lathuilliere, M.J., M.S. Johnson and S.D. Donner (2012). Water use by terrestrial ecosystems: temporal variability in rainforest and agricultural contributions to evapotranspiration in Mato Grosso, Brazil. Environmental Research Letters 7:024024. doi:10.1088/1748-9326/7/2/024024 pdf

Jollymore, A., M.S. Johnson and I. Hawthorne (2012). Submersible UV-Vis spectroscopy for quantifying streamwater organic carbon dynamics: implementation and challenges before and after forest harvest in a headwater stream. Sensors 12(4):3798-3813. doi:10.3390/s120403798 (Special issue: Underwater Sensor Nodes and Networks) pdf

Harma, K.J., M.S. Johnson, and S.J. Cohen (2012). Future water supply and demand in the Okanagan Basin, British Columbia: a scenario-based analysis of multiple, interacting stressors. Water Resources Management 26:667-689. doi:10.1007/s11269-011-9938-3 pdf

Novães Filho, J.P., E.G. Couto, L.C. Mattos Rodrigues, L.A. Chig, and M.S. Johnson (2012). Indicativos de descontinuidade litológica em perfis de solos de uma microbacia sob floresta amazônica (Indicators of lithological discontinuity in soil profiles of a forested catchment). Revista Brasileira de Ciência do Solo (Brazilian Journal of Soil Science) 36:317-324. doi:10.1590/S0100-06832012000200001 pdf

Molodovskaya, M., O. Singurindy, B.K. Richards, J. Warland, M.S. Johnson, and T. S. Steenhuis (2012). Temporal variability of nitrous oxide from fertilized croplands: hot moment analysis. Soil Science Society of America Journal 76:1728-1740. doi:10.2136/sssaj2012.0039 pdf

Recha, J.W., J. Lehmann, M.T. Walter, A. Pell, L. Verchot, and M.S. Johnson (2012). Stream discharge in tropical headwater catchments as a result of forest clearing and soil degradation. Earth Interactions 16, paper 13:1-18. doi:10.1175/2012EI000439.1 pdf

Johnson M.S., G. Jost (2011) Ecohydrology and Biogeochemistry of the Rhizosphere in Forested Ecosystems. In: Levia DFF, Carlyle-Moses D & Tanaka T (eds) Forest Hydrology and Biogeochemistry. Ecological Studies, vol 216. Springer Netherlands. p 483-498. doi:10.1007/978-94-007-1363-5_24 pdf

Johnson, M.S., J. Lehmann, M. Abdo and E.G. Couto (2011). Fluorescence index as an indicator of dissolved organic carbon quality in hydrologic flowpaths of forested tropical watersheds. Biogeochemistry 105:149-157. doi:10.1007/s10533-011-9595-x pdf

Richey, J.E., M.V. Ballester, E.A. Davidson, M.S. Johnson, and A.V. Krusche (2011). Land-Water interactions in the Amazon. Biogeochemistry 105: 1-5. doi:10.1007/s10533-011-9622-y pdf

Neill, C, J.E. Chaves, T. Biggs, L.A. Deegan, H. Elsenbeer, R.O. Figuereido, S. Germer, M.S. Johnson, A.V. Krusche, J. Lehmann, and D. Markewitz (2011). Runoff sources and land cover change in the Amazon: an end member mixing analysis from small watersheds. Biogeochemistry 105:7-18. doi:10.1007/s10533-011-9597-8 pdf

Markewitz, D., C. Lamon, M. Bustamante, J. Chavez, R. de O. Figueiredo, M.S. Johnson, A.V. Krusche, C. Neill, and J. Solimão (2011). Discharge–calcium concentration relationships in streams of the Amazon and Cerrado of Brazil: soil or land use controlled. Biogeochemistry 105:19-35. doi:10.1007/s10533-011-9574-2 pdf

Chen, B., N.C. Coops, T.A. Black, R. Jassal, J.M. Chen, and M.S. Johnson (2011). Modeling to discern nitrogen fertilization impacts on carbon sequestration in a Pacific Northwest Douglas-fir forest in the first-post fertilization year. Global Change Biology 17: 1442-1460. doi:10.1111/j.1365-2486.2010.02298.x pdf

Johnson, M.S., M.F. Billett, K.J. Dinsmore, M. Wallin, K.E. Dyson, and R.S. Jassal (2010). Direct and continuous measurement of dissolved carbon dioxide in freshwater aquatic systems – method and applications. Ecohydrology 3:68-78, doi:10.1002/eco.95. pdf

Johnson, M.S. (2010). Hydrology, greenhouse gases and forestry implications. Sustainable Forest Management Network, SFM Network Research Note Series No. 76. pdf

Feldpausch, T.R., E.G. Couto, L.C. Rodrigues, D. Pauletto, M.S. Johnson, T.J. Fahey, J. Lehmann, and S.J. Riha (2010). Nitrogen aboveground turnover and soil stocks to 8 m depth in primary and disturbed forest following selective logging in southern Amazonia. Global Change Biology 16: 1793-1805. doi: 10.1111/j.1365-2486.2009.02068.x. pdf

Johnson, M.S. (2009). Public participation and perceptions of watershed modeling. Society & Natural Resources 22:79-87. doi: 10.1080/08941920802220347. pdf

Richey, J.E., A.V. Krusche, M.S. Johnson, H.B. da Cunha, and M.V. Ballester (2009). The role of rivers in the regional carbon balance, in Amazonia and Global Change, Geophysical Monograph Series vol. 186, edited by M. Keller et al., pp. 489–504, AGU, Washington, D.C., doi:10.1029/2009GM000876

Moslemi, J.M., K.A. Capps, M.S. Johnson, J. Maul, P.B. Mcintyre, A.M. Melvin, T.M. Vadas, D.M. Vallano, J.M. Watkins and M. Weiss (2009). Training Tomorrow’s Environmental Problem Solvers: An Integrative Approach to Graduate Education (2009). BioScience 59:514-521. doi:10.1025/bio.2009.59.6.10. pdf

Johnson, M.S., J. Lehmann, S.J. Riha, A.V. Krusche, J.E. Richey, J.P.H.B. Ometto and E.G. Couto (2008). CO2 efflux from Amazonian headwater streams represents a significant fate for deep soil respiration. Geophysical Research Letters 35:L17401, doi:10.1029/2008GL034619. pdf

Johnson M.S., J. Lehmann and E.G. Couto (2008). A simple, direct method to measure dissolved CO2 using soda lime. Oecologia Brasiliensis 12:85-91. pdf

Johnson, M.S. and H.K. Wittman (2008). Carbon trading should not reduce social equity (contributed letter). Frontiers in Ecology and the Environment 6:10 doi: 10.1890/1540-9295(2008)6[10a:CT]2.0.CO;2 pdf

Wittman, H.K. and M.S. Johnson (2008). Fallow management practices in Guatemala’s Western Highlands: social drivers and biophysical impacts. Land Degradation and Development 19:178-189. doi: 10.1002/ldr.832 pdf

R.L. Victoria, M.V.R. Ballester, A.V. Krusche, H.B. da Cunha, M.E. Sales, B.M. Gomes, C. Salimon, K. Munhoz, L. Borma, R. Barbosa, J.E. Richey, C. Neill, L. Deegan, and M.S. Johnson (2008). O papel dos sistemas dos rios no balanço regional e global de carbono (The role of river systems in the regional and global carbon balance). Folha Amazônica 14:20-22. pdf

Chig, L.A., E.G. Couto, J.P. Novães Filho, L.C.M. Rodrigues, M.S. Johnson, and O.L. Weber (2008). Distribuição espacial da granulometria, cor e carbono orgânico do solo ao longo de um transecto em microbacias na Amazônia meridional (Spatial distribution of soil texture, color and soil organic carbon across a headwater transect in the southern Amazon). Acta Amazonica 38: 715-722. doi: 10.1590/S0044-59672008000400015 pdf

Johnson, M.S., P.B. Woodbury, A.N. Pell, and J. Lehmann (2007). Land use change and stream water fluxes: Decadal dynamics in watershed nitrate exports. Ecosystems 10:1182–1196. doi: 10.1007/s10021-007-9091-2 pdf

Johnson, M. S., M. Weiler, E. G. Couto, S. J. Riha, and J. Lehmann (2007). Storm pulses of dissolved CO2 in a forested headwater Amazonian stream explored using hydrograph separation. Water Resources Research 43, W11201, doi:10.1029/2007WR006359 pdf

Selva, E.C., E.G. Couto, M.S. Johnson and J. Lehmann (2007). Litterfall production and fluvial export in headwater catchments of the southern Amazon. Journal of Tropical Ecology 23:329-335. doi:10.1017/S0266467406003956 pdf

Jirka, S., A.J. McDonald, M.S. Johnson, T.R. Feldpausch, E.G. Couto and S.J. Riha (2007). Relationships between soil hydrology and forest structure and composition in the southern Brazilian Amazon. Journal of Vegetation Science 18: 183-194. doi: 10.1111/j.1654-1103.2007.tb02529.x pdf

Novães Filho, J.P., E.G. Couto, V.A. de Oliveira, M.S. Johnson, J. Lehmann and S.J. Riha (2007). Variabilidade espacial de atributos físicos de solo usada na identificação de classes pedológicas de microbacias na Amazônia meridional (Spatial variability of soil physical attributes used for soil mapping in small headwater catchments of the southern Amazon). Revista Brasileira de Ciência do Solo (Brazilian Journal of Soil Science) 31: 91-100. doi:10.1590/S0100-06832007000100010 pdf

Novães Filho, J.P., E.C. Selva, E.G. Couto, J. Lehmann, M.S. Johnson and S.J. Riha (2007). Distribuição espacial de carbono em solo sob floresta primária na Amazônia Meridional (Spatial distribution of soil carbon under primary forest cover in southern Amazônia). Revista Árvore (Tree Journal) 31: 83-92. doi:10.1590/S0100-67622007000100010 pdf

Johnson, M.S., J. Lehmann, S.J. Riha, J.P. Novães Filho and E.G. Couto (2006). DOC and DIC in flowpaths of Amazonian headwater catchments with hydrologically contrasting soils. Biogeochemistry 81: 45-57. doi: 10.1007/s10533-006-9029-3 pdf

Johnson, M.S. and J. Lehmann (2006). Double-funneling of trees: stemflow and root-induced preferential flow. Ecoscience 13: 324-333. doi: 10.2980/i1195-6860-13-3-324.1 pdf

Johnson, M.S., J. Lehmann, E.C. Selva, M. Abdo, S.J. Riha, and E.G. Couto (2006). Organic carbon fluxes within and streamwater exports from forested headwater catchments in the southern Amazon. Hydrological Processes 20: 2599-2614. doi: 10.1002/hyp.6218 pdf

Johnson, M.S. (2006). Invited book review of Forests, water and people in the humid tropics, M. Bonnel and L. A. Bruijnzeel (Eds.), Ecoscience 13(1):131. pdf

Johnson, M.S., J. Lehmann, T.S. Steenhuis, L. Vargem de Oliveira, and E.C.M. Fernandes (2005). Spatial and temporal variability of soil water repellency of Amazonian pastures. Australian Journal of Soil Research 43: 319-326. doi: 10.1071/SR04097 pdf

Coon W.F. and M.S. Johnson (2005). Effects of land-use changes and stormflow-detention basins on flooding and nonpoint-source pollution, in Irondequoit Creek basin, Monroe and Ontario Counties, New York--application of a precipitation-runoff model. U.S.G.S. Scientific Investigations Report 2005-5070, U.S. Geological Survey, Washington, DC. 67p. pdf

Mehta, V.K., M.T. Walter, E.S. Brooks, T.S. Steenhuis, M.S. Johnson, M.F. Walter, J. Boll, and D. Thongs (2004). Application of SMR for modeling watersheds in the Catskills Mountains. Environmental Modeling & Assessment 9: 77-89. doi: 10.1023/B:ENMO.0000032096.13649.92. pdf

Johnson, M.S., W.F. Coon, V.K. Mehta, T.S. Steenhuis, E.S. Brooks, and J. Boll (2003). Application of two hydrologic models with different runoff mechanisms to a hillslope dominated watershed in the Northeastern U.S.: A Comparison of HSPF and SMR. Journal of Hydrology 284: 57–76. doi:10.1016/j.jhydrol.2003.07.005. pdf