Publications

Google Scholar Profile

ResearchGate

BOOKS

Jones, J.B., and E.H. Stanley, editors.  2016. Stream Ecosystems in a Changing Environment. Elsevier. London, United Kingdom.

Jones, J.B., and P.J. Mulholland, editors. 2000. Streams and Ground Waters. Academic Press, San Diego.

PUBLICATIONS (PEER-REVIEWED) AND BOOK CHAPTERS

Iannucci, F.M., J.B. Jones, K.L. Olson, M.E. Muscarella, E.R. Hotchkiss. 2024. Temperature and flow control organic carbon metabolism in a boreal headwater stream. Journal of Geophysical Research Biogeosciences 129:e2024JG008281. doi.org/10.1029/2024JG008281 

Allen, D. C., J. Larson, C. A. Murphy, E. A. Garcia, K. E. Anderson, M. H. Busch, A. Argerich, A. M. Belskis, K. T. Higgins, B. E. Penaluna, V. Saenz, J. Jones, and M. R. Whiles. 2024. Global patterns of allochthony in stream–riparian meta-ecosystems. Ecology Letters 27:e14401. doi.org/10.1111/ele.14401 

Johnson, K., K. J. Jankowski, J. Carey, N. J. Lyon, W. H. McDowell, A. Shogren, A. Wymore, L. Sethna, W. M. Wollheim, A. E. Poste, P. Kortelainen, R. Heindel, H. Laudon, A. Räike, J. B. Jones, D. McKnight, P. Julian, S. Bush, and P. L. Sullivan. 2024. Establishing fluvial silicon regimes and their stability across the Northern Hemisphere. Limnology and Oceanography Letters. doi.org/10.1002/lol2.10372 

Jankowski, K.J., K. Johnson, L. Sethna, P. Julian, A.S. Wymore, A.J. Shogren, P.K. Thomas, P.L. Sullivan, D.M. McKnight, W.H. McDowell, R. Heindel, J.B. Jones, W. Wollheim, B. Abbott, L. Deegan, and J.C. Carey. 2023. Long-Term Changes in Concentration and Yield of Riverine Dissolved Silica from the Poles to the Tropics. Global Biogeochemical Cycles. 37. E2022GB007678. doi.org/10.1029/2022GB007678.

Kermorvant C, Liquet B, Litt G, Mengersen K, Peterson EE, Hyndman RJ, J.B. Jones, and C. Leigh. 2023. Understanding links between water-quality variables and nitrate concentration in freshwater streams using high frequency sensor data. PLoS ONE 18(6): e0287640. doi: 10.1371/journal.pone.0287640. 

Conroy, H. D., E. R. Hotchkiss, K. M. Cawley, K. Goodman, R. O. Hall Jr., J. B. Jones, W. M. Wollheim, and D. Butman. 2023. Seasonality Drives Carbon Emissions Along a Stream Network. Journal of Geophysical Research: Biogeosciences 128:e2023JG007439. doi:10.1029/2023JG007439.

Brown, B. C., A. H. Fullerton, D. Kopp, F. Tromboni, A. J. Shogren, J. A. Webb, C. Ruffing, M. Heaton, L. Kuglerová, D. C. Allen, L. McGill, J. P. Zarnetske, M. R. Whiles, J. B. Jones Jr., and B. W. Abbott. 2023. The Music of Rivers: The Mathematics of Waves Reveals Global Structure and Drivers of Streamflow Regime. Water Resources Research 59:e2023WR034484. doi:10.1029/2023WR034484.

Weaver, S.A., and J.B. Jones. 2022. Resource limitation of autotrophs and heterotrophs in boreal forest headwater streams. Freshwater Science. doi:10.1086/722256.

Campbell, J.L., C.T. Driscoll, J.A. Jones, E. Boose, H.A. Dugan, P.M. Groffman, C.R. Jackson, J.B. Jones, G.P. Juday, N.R. Lottig, B.E. Penaluna, R.W. Ruess, K. Suding, J.R. Thompson, J.K. Zimmerman. 2022. Forest and Freshwater Ecosystem Responses to Climate Change and Variability at US LTER Sites. BioScience. doi.org/10.1093/biosci/biab124.

Kermorvant, C., B. Liquet, G. Litt, J.B. Jones, K. Mengersen, E.E. Peterson, R.J. Hyndman, and C. Leigh. 2021. Reconstructing Missing and Anomalous Data Collected from High-Frequency In-Situ Sensors in Fresh Waters. International Journal of Environmental Research and Public Health.  doi:10.3390/ijerph182312803.

Rodríguez-Cardona, B., A. Wymore, R. Barnes, S. Bernal, E. Brookshire, A. Coble, W. Dodds, H. Fezekas, A. Helton, P. Johnes, S. Jonson, J. Jones, S. Kaushal, P. Kortelainen, C. López-Lloreda, R. Spencer, and W. McDowell. 2021. Shifting Stoichiometry: Long‐term Trends in Stream Dissolved Organic Matter Reveal Altered C:N Ratios Due to History of Atmospheric Acid Deposition. Global Change Biology. doi:10.1111/gcb.15965

Wymore, A.S., P.J. Johnes, S.E. Bernal, N.J. Brookshire, H.M Fazekas, A.M Helton, A. Argerich, R.T. Barnes, A.A. Coble, W.K. Dodds, S. Haq, S.L. Johnson, J.B. Jones, S.S. Kaushal, P. Kortelainen, C. López-Lloreda, B.M. Rodríguez-Cardona, R.G.M. Spencer, P.L. Sullivan, C.A. Yates, and W.H. McDowell. 2021. Gradients of Anthropogenic Nutrient Enrichment Alter N Composition and DOM Stoichiometry in Freshwater Ecosystems. Global Biogeochemical Cycles. doi:10.1029/2021GB006953

Ardon, Marcelo, L. Zeglin, R. Utz, Ryan, S. Cooper, W. Dodds, R. Bixby, A. Burdett, J. Follstad Shah, N. Griffiths, T. Harms, S. Johnson, J. Jones, J. Kominoski, W. McDowll, A. Rosemond, M. Trentman, D. Van Horn, and A. Ward. 2020. Experimental nitrogen and phosphorus enrichment stimulates multiple trophic levels of algal and detrital-based food webs: A global meta-analysis from streams and rivers. Biological Reviews. doi:10.1111/brv.12673

Allen, D.C., T. Datry, K.S. Boersma, M.T Bogan, A.J. Boulton, D. Bruno, M.H. Busch, K.H. Costigan, W.K. Dodds, K.M. Fritz, S.E. Godsey, J.B. Jones, T. Kaletova, S.K. Kampf, M.C. Mims, T.M. Neeson, J.D Olden, A.V. Pastor, N.L. Poff, B.L. Ruddell, A. Ruhi, G. Singer, P. Vezza, A.S. Ward, and M. Zimmer. 2020. River ecosystem conceptual models and non-perennial rivers: A critical review. WIREs Water. doi:10.1002/wat2.1473

Patrick., C.J., D.J. McGarvey, J.H. Larson, W.F. Cross, D.C. Allen, A.C. Benke, T. Brey T., A.D. Huryn, J.B. Jones, C. Murphy, C. Ruffing, P. Saffarinia, M.R. Whiles, J.B. Wallace, and G. Woodward. 2019. Precipitation and temperature drive continental scale patterns in stream invertebrate production. Science Advances. doi:10.1126/sciadv.aav2348

Smits, A.P., C.M. Ruffing, T.V. Royer, A.P. Appling, N.A. Griffiths, R. Bellmore, M.D. Scheuerell, T.K. Harms, and J.B. Jones, J.B. 2019. Detecting Signals of Large-scale Climate Phenomena in Discharge and Nutrient Loads in the Mississippi-Atchafalaya River Basin. Geophysical Research Letters. doi:10.1029/2018GL081166 

Mutschlecner, A.E., J.J. Guerard, J.B. Jones, and T.K. Harms. 2018. Regional and intra-annual stability of dissolved organic matter composition and biolability in high-latitude Alaskan rivers. Limnology and Oceanography. doi:10.1002/lno.10795.

Song, C., W.K. Dodds, J. Rüegg, A. Argerich, C.L. Baker, W.B. Bowden, M.M. Douglas, K.J. Farrell, M.B. Flinn, E.A. Garcia, A.M. Helton, T.K. Harms, S. Jia, J.B. Jones, L.E. Koenig, J.S. Kominoski, W.H. McDowell, D. McMaster, S.P. Parker, A.D. Rosemond, C.M. Ruffing, K.R. Sheehan, M.T. Trentman, M.R. Whiles, W.M. Wollheim, and F. Ballantyne. 2018. Continental-scale decrease in net primary productivity in streams due to climate warming. Nature Geoscience11:415–420. doi:10.1038/s41561-018-0125-5.

Mutschlecner, A.E., J.J. Guerard, J.B. Jones, and T.K. Harms. 2017. Phosphorus Enhances Uptake of Dissolved Organic Matter in Boreal Streams. Ecosystems. doi:10.1007/s10021-017-0177-1 .

Abbott, B.W., J.B. Jones, E.A.G. Schuur, F.S. Chapin III, W.B. Bowden, H. Epstein, M. Flannigan, T.K. Harms, T.N. Hollingsworth, M.C. Mack, S.M. Natali, A.V. Rocha, S.E. Tank, M.R. Turetsky, J.E. Vonk, K.P. Wickland, and the Permafrost Carbon Balance Survey Group. 2016. Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire: an expert assessment.  Environmental Research Letters. doi:10.1088/1748-9326/11/3/034014 

Harms, T.K., J.W. Edmonds, H. Genet, I.F. Creed, D. Aldred, A. Balser, and J.B. Jones. 2016. Catchment influences on nitrate and dissolved organic matter in Alaska streams across a latitudinal gradient. Journal of Geophysical Research: Biogeosciences. doi:10.1002/2015JG003201.

Jones, J.B., and E.H. Stanley. 2016. Synthesis and conclusions.  In J.B. Jones and E.H. Stanley (editors). Stream Ecosystems in a Changing Environment. Elsevier.  London, United Kingdom.

Abbott, B.W., and J.B. Jones. 2015. Permafrost collapse alters soil carbon stocks, respiration, CH4, and N2O in upland tundra. Global Change Biology 21:4570-4587. doi:10.1111/gcb.13069.

Abbott, B.W., J.B. Jones, S.E. Godsey, J.R. Larouche, and W.B. Bowden. 2015. Patterns and persistence of hydrologic carbon and nutrient export from collapsing upland permafrost. Biogeosciences 12:3725-3740. doi:10.5194/bg-12-3725-2015.

Larouche, J.R., B.W. Abbott, W.B. Bowden, and J.B. Jones. 2015. The role of watershed characteristics, permafrost thaw, and wildfire on dissolved organic carbon biodegradability and water chemistry in Arctic headwater streams. Biogeosciences 12:4221–4233. doi:10.5194/bg-12-4221-2015.

Rinehart, A.J., J.B. Jones, and T.K. Harms. 2015. Hydrologic and biogeochemical influences on carbon processing in the riparian zone of a subarctic stream. Freshwater Science 34:222-232. doi:10.1086/679595.

Rüegg, J., W.K. Dodds, M.D. Daniels, C.L. Baker, W.B. Bowden, K.J. Farrell, M.B. Flinn, T.K. Harms, J.B. Jones, L.E. Koenig, J.S. Kominoski, W.H. McDowell, S.P. Parker, A.D. Rosemond, K.R. Sheehan, M.T. Trentman, M.R. Whiles, and W.M. Wollheim. 2015. Baseflow physical stream characteristics differ at multiple spatial scales in stream networks across diverse biomes. Landscape Ecology. doi:10.1007/s10980-015-0289-y.

Abbott, B.W., J.R. Larouche, J.B. Jones, W.B. Bowden, and A.W. Balser. 2014. Elevated dissolved organic carbon biodegradability from collapsing permafrost. Journal of Geophysical Research-Biogeosciences 2014JG002678. doi:10.1002/2014JG002678.  

Balser, A.W., J.B. Jones, and R. Gens. 2014. Timing of retrogressive thaw slump initiation in the Noatak Basin, Northwest Alaska, USA. Journal of Geophysical Research-Earth Surface 119, doi:10.1002/2013JF002889.

Ding, Y., Y. Yamashita, J.B. Jones, and R. Jaffé. 2014. Dissolved black carbon in boreal forest and glacial rivers of central Alaska: Assessment of biomass burning vs. anthropogenic sources. Biogeochemistry.  doi:10.1007/s10533-014-0050-7.

Harms, T.K., B.W. Abbott, and J.B. Jones. 2013.Thermo-erosion gullies increase nitrogen available for hydrologic export. Biogeochemistry. doi:10.1007/s10533-013-9862-0.

Schuur, E.A.G., B.W. Abbott, W.B. Bowden, V. Brovkin, P. Camill, J.G. Canadell, J.P. Chanton, F.S. Chapin III, T.R. Christensen, P. Ciais, B.T. Crosby, C.I. Czimczik, G. Grosse, J. Harden, D.J. Hayes, G. Hugelius, J.D. Jastrow, J.B. Jones, T. Kleinen, C.D. Koven, G. Krinner, P. Kuhry, D.M. Lawrence, A.D. McGuire, S.M. Natali, J.A. O’Donnell, C.L. Ping, W.J Riley, A. Rinke, V.E. Romanovsky, A.B.K. Sannel, C. Schädel, K. Schaefer, J. Sky, Z.M. Subin, C. Tarnocai, M. Turetsky, M. Waldrop, K. M. Walter-Anthony, K.P. Wickland, C.J. Wilson, and S.A. Zimov. 2013. Expert assessment of vulnerability of permafrost carbon to climate change. Climatic Change. doi:10.1007/s10584-013-0730-7.

Jaffé, R., Y. Yamashita, N. Maie, W.T. Cooper, T. Dittmar, W.K. Dodds, J.B. Jones, T. Myoshi, J.R. Ortiz-Zayas, D.C. Podgorski, and A. Watanabe. 2012. Dissolved organic matter in headwater streams: compositional variability across climatic regions of North America. Geochimica et Cosmochimica Acta 94:95-108. doi:10.1016/j.gca.2012.06.031.

Harms, T.K., and J.B. Jones. 2012. Thaw depth determines reaction and transport of inorganic nitrogen in valley bottom permafrost soils. Global Change Biology. doi:10.1111/j.1365-2486.2012.02731.x.

Bowden, W.B., J.R. Larouche, A.R. Pearce, B.T. Crosby, K. Krieger, M.B. Flinn, J. Kampman, M.N. Gooseff, S.E. Godsey, J.B. Jones, B.W. Abbott, M.T. Jorgenson, G.W. Kling, M. Mack, E.A.G. Schuur, A.F. Baron, and E.B. Rastetter. 2012. An integrated assessment of the influences of upland thermal-erosional features on landscape structure and function in the foothills of the Brooks Range, Alaska. Pages 61 – 66 inK.M. Hinkel, editor. Proceedings of the Tenth International Conference on Permafrost. Salekhard, Siberia.

Flinn, M.B., W.B. Bowden, A.W. Balser, J.B. Jones, and M.N. Gooseff. 2012. Soil and water chemistry characteristics of thermo-erosional features in the western Noatak River Basin, Alaska, USA. Pages 101 – 106 in K.M. Hinkel, editor. Proceedings of the Tenth International Conference on Permafrost. Salekhard, Siberia.

Roach, J., B. Griffith, D. Verbyla and J. Jones. 2011. Mechanisms influencing changes in lake area in the Alaskan boreal forest. Global Change Biology. doi:10.1111/j.1365-2486-2011.02446.x.

Jones, J.B., and A.J. Rinehart. 2010. The long term response of stream flow to climatic warming in headwater streams of interior Alaska. Canadian Journal of Forest Research 40:1210-1218. doi:10.1139/X10-047.

Chapin, F.S., III, A.D. McGuire, R.W. Ruess, T. N. Hollingsworth, E. S. Euskirchen, J. F. Johnstone, J. B. Jones, M. T. Jorgenson, E. S. Kasischke, K. Kielland, G. P. Kofinas, A. H. Lloyd, M. C. Mack, D. L. Taylor, M. R. Turetsky, and J. Yarie. 2010. Resilience and change in Alaska’s Boreal forest. Canadian Journal of Forest Research 40:1360-1370. doi:10.1139/X10-074. 

O’Donnell, J.A., G.R. Aiken, E.S. Kane, and J.B. Jones. 2010. Source water controls on DOC character and origin in streams of Yukon River basin, interior Alaska. Journal of Geophysical Research – Biogeosciences 115: G03025, https://doi.org/10.1029/2009JG001153.

Betts, E.F., and J.B. Jones. 2009. Impact of wildfire on stream nutrient chemistry and ecosystem metabolism in boreal forest catchments of interior Alaska. Arctic, Antarctic, and Alpine Research 41:407-417. doi:10.1657/1938-4246-41.4.407. 

Fellman, J.B., E. Hood, R.T. Edwards, and J.B. Jones. 2009. Uptake of allochthonuous dissolved organic matter from soil and salmon in coastal temperate rainforest streams. Ecosystems. doi:10.1009/s10021-009-9254-4.

Balcarczyk, K.L., J.B. Jones, R. Jaffé, and N. Maie. 2009. Stream dissolved organic matter bioavailability and composition in watersheds underlain with discontinuous permafrost. Biogeochemistry 94:255-270. doi:10.1007/s10533-009-9324-x.

Gooseff, M.N., A. Balser, W.B. Bowden, and J.B. Jones. 2009. Effects of hillslope thermokarst in northern Alaska. EOS, Transactions of the American Geophysical Union 90(4):29-30.

Clilverd, H.M., J.B. Jones, and K. Kielland. 2008. Nitrogen retention in the hyporheic zone of a glacial river in interior Alaska. Biogeochemistry 88:31-46. doi:10.1007/s10533-008-9192-9.

Kane, E.S., E.F. Betts, A.J. Burgin, H.M. Clilverd, C.L. Crenshaw, J.B. Fellman, I.H. Myers-Smith, J.A. O’Donnell, D.J. Sobota, W.J. Van Verseveld, and J.B. Jones. 2008. Precipitation control over nitrogen import-export budgets across watersheds: a synthesis of long-term ecological research. Ecohydrology doi:10.1002/eco.10.

Lisuzzo, N.J., K. Kielland, and J.B. Jones. 2008. Hydrologic controls of nitrogen availability to a high-latitude, semi-arid floodplain. Ecoscience 15:366-376, doi:10.2980/15-3-2998.

White, D., V. Autier, K. Yoshikawa, J. Jones, and S. Seelen. 2008. Using DOC to better understand local hydrology in a subarctic watershed. Cold Regions Science and Technology 51:68-75. doi:10.1016/j.coldregions.2007.08.005.

Petrone, K.C., L.D. Hinzman, H. Shibata, J.B. Jones, and R.D. Boone. 2007. The influence of fire and permafrost on sub-arctic stream chemistry during storms. Hydrologic Processes 21:423-434. doi:10.1002/hyp.6247. 

Jones, J.B., and D. Wagner. 2006. Microhabitat-specific controls on soil respiration and denitrification in the Mojave Desert: the role of harvester ant nests and vegetation. Western North American Naturalist 66:426-432.

Brenner, R.E., R.D. Boone, J.B. Jones, K. Lajtha, and R.W. Ruess. 2006. Successional and physical controls on the retention of nitrogen in an undisturbed boreal forest ecosystem. Oecologia doi:10.1007/s00442-006-0399-y.

Chapin, F.S. III, A.D. McGuire, R.W. Ruess, M.W. Walker, R. Boone, M. Edwards, B. Finney, L.D. Hinzman, J.B. Jones, G.P. Juday, E.S. Kasischke, K. Kielland, A.H. Lloyd, M. Oswood, E. Rexstad, V. Romanovsky, J. Schimel, E. Sparrow, B. Sveinbjornsson, D.W. Valentine, K. Van Cleve, D.L. Verbyla, L.A. Viereck, R.A. Werner, T.L. Wurtz, and J. Yarie. 2006. Summary and Synthesis: Past and Future Changes. In F.S. Chapin, M.W. Oswood, K. van Cleve, L.A. Viereck, and D.L. Verbyla (editors). Alaska’s Changing Boreal Forest: a synthesis of the Bonanza Creek Long Term Ecological Research Program. Oxford University Press.

Hinzman, L.D., W.R. Bolton, K.C. Petrone, J.B. Jones, and P.C. Adams. 2006. Hydrologic processes in Alaska’s boreal forest. In F.S. Chapin et al. (editors). Alaska’s Changing Boreal Forest: a synthesis of the Bonanza Creek Long Term Ecological Research Program. Oxford University Press.

O’Donnell, J.A. and J.B. Jones. 2006. Nitrogen retention in the riparian zone of watersheds underlain by discontinuous permafrost. Freshwater Biology 51:854-864. doi:10.1111/j.1365-2427.2006.01535.x.

Petrone, K.C., J.B. Jones, L.D. Hinzman, and R.D. Boone. 2006. Seasonal export of carbon, nitrogen and major solutes from Alaskan catchments with discontinuous permafrost. Journal of Geophysical Research – Biogeosciences:G02020, doi:10.1029/2005JG000055.

Wagner, D., and J.B. Jones. 2006. The impact of harvester ants on decomposition, N mineralization, litter quality, and the availability of N to plants in the Mojave Desert. Soil Biology and Biochemistry 38:2593-2601. doi:10.1016/j.soilbio.2006.02.024. 

Jones, J.B., K.C. Petrone, J.C. Finlay, L.D. Hinzman, and W.R. Bolton. 2005. Nitrogen loss from watersheds of interior Alaska underlain with discontinuous permafrost. Geophysical Research Letters 32:L02401, doi:10.1029/2004GL021734.

Wagner, D., and J.B. Jones. 2004. Microsite variation in soil nutrient storage, microbial biomass, and soil erosion in the Mojave Desert: the contribution of harvester ants. Environmental Entomology 33:599-607. https://doi.org/10.1603/0046-225X-33.3.599.

Wagner, D., J.B. Jones, and D.W. Gordon. 2004. Development of harvester ant colonies alters soil chemistry. Soil Biology & Biochemistry 35:797-804. doi:10.1016/j.soilbio.2004.01.009. 

Stanley, E.H., S.G. Fisher, and J.B. Jones. 2004. Effects of water loss on primary producers: a landscape-scale model. Aquatic Sciences 66:130-138. doi:10.1007/s00027-003-0646-9. 

Jones, J.B., E.H. Stanley, and P.J. Mulholland. 2003. Long-term decline in carbon dioxide supersaturation in rivers across the contiguous United States. Geophysical Research Letters 30. doi:10.1029/2003GL017056.

Bertilsson, S., and J.B. Jones. 2003. Supply of dissolved organic matter to aquatic ecosystems: autochthonous sources.  Pages 3-24 inS. Findlay, and R.L. Sinsabaugh, editors. Aquatic Ecosystems: Interactivity of Dissolved Organic Matter. Academic Press. San Diego.

Jones, J.B. 2002. Groundwater controls onnutrient cycling in a Mojave Desert stream. Freshwater Biology 47:971-983. doi:10.1046/j.1365-2427.2002.00828.x.

Stanley, E.H., and J.B. Jones. 2000. Surface-subsurface interactions: past, present, and future. Pages 405-415 in J.B. Jones, and P.J. Mulholland, editors. Streams and Ground Waters. Academic Press. San Diego.

Jones, J.B., and P.J. Mulholland. 1998. Influence of drainage basin topography and elevation on carbon dioxide and methane supersaturation of stream water. Biogeochemistry 40:57-72. doi:10.1023/A:1005914121280. 

Jones, J.B., and P.J. Mulholland. 1998. Carbon dioxide variation in a hardwood forest stream: an integrative measure of whole catchment soil respiration. Ecosystems 1:183-196. doi:10.1007/s100219900014. 

Jones, J.B., and P.J. Mulholland. 1998. Methane input and evasion in a hardwood forest stream: effects of subsurface flow from shallow and deep pathways. Limnology and Oceanography 43:1243-1250. doi:10.4319/lo.1998.43.6.1243.

Fisher, S.G., N.B. Grimm, E. Marti, R.M. Holmes, and J.B. Jones. 1998. Material spiraling in stream corridors: a telescoping ecosystem model. Ecosystems 1:19-34. doi:10.1007/s100219900003. 

Jones, J.B. 1997. Benthic organic matter storage in streams: a synthesis of data from the Stream Organic Matter Workshop. Pages 109-119 in J.R. Webster and J.L. Meyer (editors). Stream organic matter budgets. Journal of the North American Benthological Society 16:3-161. doi:10.2307/1468243. 

Jones, J.B., J.D. Schade, S.G. Fisher, and N.B. Grimm. 1997. Organic matter dynamics in Sycamore Creek, a desert stream in Arizona, USA. Pages 78-82 in J.R. Webster and J.L. Meyer (editors). Stream organic matter budgets. Journal of the North American Benthological Society 16:3-161. doi:10.2307/1468238.

Jones, J.B., and R.M. Holmes. 1996. Surface-subsurface interactions in stream ecosystems. Trends in Ecology and Evolution 11:239-242. doi:10.1016/0169-5347(96)10013-6.

Jones, J.B., S.G. Fisher, and N.B. Grimm. 1996. A long-term perspective of dissolved organic carbon transport in Sycamore Creek, Arizona. Hydrobiologia 317:183-188. doi:10.1007/BF00036468. 

Holmes, R.M., J.B. Jones, S.G. Fisher, and N.B. Grimm. 1996. Denitrification in Sonoran Desert stream ecosystems. Biogeochemistry 33:125-146. doi:10.1007/BF02181035. 

Jones, J.B., S.G. Fisher, and N.B. Grimm. 1995. Vertical hydrologic exchange and ecosystem metabolism in a Sonoran Desert stream. Ecology 76:942-952. doi:10.2307/1939358. 

Jones, J.B., S.G. Fisher, and N.B. Grimm. 1995. Nitrification in the hyporheic zone of a desert stream ecosystem. Journal of the North American Benthological Society 14:249-258. doi:10.2307/1467777.

Jones, J.B. 1995. Factors controlling hyporheic respiration in a desert stream. Freshwater Biology 34:101-109. doi:10.1111/j.1365-2427.1995.tb00426.x. 

Jones, J.B., R.M. Holmes, S.G. Fisher, N.B. Grimm, and D.M. Greene. 1995. Methanogenesis in Arizona, USA dryland streams. Biogeochemistry 31:155-173. doi:10.1007/BF00004047. 

Jones, J.B., R.M. Holmes, S.G. Fisher, and N.B. Grimm. 1994. Chemoautotrophic production and respiration in the hyporheic zone of a Sonoran Desert stream. Pages 329 - 338 inJ.A. Stanford and H.M. Valett, editors. Proceeding of the Second International Conference on Ground Water Ecology. American Water Resources Association, Herndon, Virginia, USA.

Smock, L.A., L.C. Smith, J.B. Jones, and S.M. Hooper. 1994. Effects of drought and a hurricane on a coastal headwater stream. Archiv für Hydrobiologie 131:25-38.

Jones, J.B., and L.A. Smock. 1991. Transport and retention of particulate organic matter in two low-gradient headwater streams. Journal of the North American Benthological Society 10:115-126. doi:10.2307/1467572.