University of California, Riverside

Center for Conservation Biology

AMARSS Publications

AMARSS Publications

Our current publications list from 2007.


  • Allen, M.F., E.B. Allen, J.L.Lansing, K.S. Pregitzer, R.L. Hendrick, R.W. Ruess and S.L. Collins. 2010. Responses to chronic N fertilization of ectomycorrhizal piñon but not arbuscular mycorrhizal juniper in a piñon-juniper woodland. Journal of Arid Environments 74: 1170-1176.
  • Estrada-Medina, H., W. Tuttle, R.C. Graham, M.F. Allen, and J.J. Jiménez-Osornio. 2010. Identification of underground karst features using ground-penetrating radar (GPR) in northern Yucatán, México Vadose Zone 9: 653-661.
  • Goode, L.K., E.B. Erhardt, L.S. Santiago, and M.F. Allen. 2010. Carbon stable isotopic composition of soluble sugars in Tillandsia epiphytes varies in response to shifts in habitat. Oecologica 163: 583-590.
  • Hasselquist N.J., R. Vargas, and M.F. Allen. 2010. Using soil sensing technology to examine interactions and controls between ectomycorrhizal growth and environmental factors on soil CO2 dynamics. Plant and Soil 331: 17-29.
  • Hasselquist, N., L.S. Santiago, and M.F. Allen. 2010. Belowground nitrogen dynamics in relation to hurricane damage along a tropical dry forest chronosequence. Biogeochemistry 98: 89 -100.
  • Hasselquist, N., M.F. Allen, and L.S. Santiago. In press. Water relations of evergreen and drought-deciduous trees along a seasonally dry tropical forest chronosequence. Oecologia. Accepted July 4, 2010. 31 manuscript pages.
  • Kitajima, K., K.E. Anderson, and M.F. Allen. 2010. Effect of soil temperature and soil water content on fine root turnover rate in a California mixed-conifer ecosystem. Journal of Geophysical Research- Biogeosciences. Accepted September 9, 2010. 42 manuscript pages.
  • Vargas, R., D.D Baldocchi, J.I. Wuerejeta, P.A. Curtis, N.J. Hasselquist, I.A. Janssens, M.F. Allen and L. Montagnani. 2010. Ecosystem CO2 fluxes of arbuscular and ectomycorrhizal dominated vegetation types are differentially influenced by precipitation and temperature. New Phytologist 185: 226-236.
  • Vargas, R., D.D. Baldocchi, M. F. Allen, M. Bahn, T. A. Black, S. L. Collins, J. Curiel Yuste, T. Hirano, R. S. Jassal, J. Pumpanen, J.Tang. 2010. Looking deeper into the soil: biophysical controls and seasonal lags of soil CO2 production and efflux. Ecological Applications 20: 1569-1582.
  • Vargas, R., M. Detto, D.D. Baldocchi, and M.F. Allen. 2010. Multiscape analysis of temporal variability of soil CO2 production as influenced by weather and vegetation. Global Change Biology. 16: 1589-1605.
  • Vargas, R., N. Hasselquist, E.B. Allen and M.F. Allen 2010. Effects of a hurricane disturbance on aboveground forest structure, arbuscular mycorrhizae and belowground carbon in a restored tropical forest. Ecosystems 13: 118-128.
  • Zhu, J., Q. Guo, D. Li, and T.C. Harmon. 2010. Reducing mis- registration and shadow effects on change detection in wetlands. Photogrammetric Engineering and Remote Sensing. Accepted September 24, 2010. 40 manuscript pages.


  • Goode, L.K. and M.F. Allen. 2009. Seed germination conditions and implications for establishment of an epiphyte, Aechmea bracteata (Bromeliaceae). Plant Ecology 204: 179-188
  • Hasselquist, N. and M.F. Allen. 2009. Increasing demands on limited water resources: consequences for two endangered species in Amargosa Valley, USA. American Journal of Botany 96: 1- 7.
  • Li, D., Q. Guo, P.J.A. Rahilly, G.M. Phelps, T.C. Harmon. In press. Correlation between soil apparent electroconductivity and moist soil plant hyperspectral reflectance in a managed wetland. International Journal of Remote Sensing. Accepted December 12, 2009. 36 manuscript pages.
  • Querejeta, J.I., L.M. Egerton-Warburton, and M.F. Allen. 2009. Topographic position modulates the mycorrhizal response of oak trees to inter-annual rainfall variability in a California woodland. Ecology. 90: 649.
  • Rundel, P., E. Graham, M.F. Allen, J.C. Fisher, and T.C. Harmon. 2009. Tansley Review. Environmental sensor networks in ecological research. New Phytologist 182:589-607.
  • Vargas, R., E.B. Allen, and M.F. Allen. 2009. Effects of vegetation thinning on above and belowground carbon in a seasonally dry tropical forest. Biotropica 41: 302-311.
  • Vargas, R., S.E. Trumbore, and M.F. Allen. 2009. Evidence of old carbon used to grow new fine roots in a tropical forest. New Phytologist 182: 710-718.


  • Allen, M.F. 2008. Water relations in the mycorrhizosphere. Progress in Botany 70 257-276. Allen, M.F. 2009. Commentary. Bidirectional water flows through the soil-fungal-plant mycorrhizal continuum. New Phytologist 182: 290-293.
  • Celis-Murillo, A., J. Deppe, and M.F. Allen. 2009. Using soundscape recordings to estimate species abundance, richness, and composition. Journal of Field Ornithology 80: 64-78.
  • Goode, L.K. and M.F. Allen. 2008. The impacts of Hurricane Wilma on the epiphytes of El Eden Ecological Reserve, Quintana Roo, Mexico. Journal of the Torrey Botanical Society 135: 377.
  • Vargas, R. and M.F. Allen. 2008. Diel patterns of soil respiration in a tropical forest after Hurricane Wilma. Journal of Geophysical Research 11 G03021. 10pgs.
  • Vargas, R. and M.F. Allen. 2008. Dynamics of fine root, fungal rhizomorphs and soil respiration in a mixed temperate forest: Integrating sensors and observations. Vadose Zone Journal 7: 1055- 1064.
  • Vargas, R. and M.F. Allen. 2008. Environmental controls and the influence of vegetation type, fine roots and rhizomorphs on diel and seasonal variation in soil respiration. New Phytologist 179: 460-471.
  • Vargas, R., M.F. Allen, and E.B. Allen. 2008. Biomass and carbon accumulation in a fire chronosequence of a seasonally dry tropical forest. Global Change Biology 14: 109-124.


  • Allen, M.F. 2007. Mycorrhizal fungi: highways for water and nutrients in arid soils. Vadose Zone Journal 6: 291-297.
  • Allen, M.F., R. Vargas, E. Graham, W Swenson, M. Hamilton, M. Taggart, T.C. Harmon, A Rat’ko, P Rundel, B. Fulkerson, and D. Estrin. 2007. Soil sensor technology: Life within a pixel. BioScience 57: 859-867.
  • Bendikov, T.A., S. Miserendino, Y-C. Tai and T.C. Harmon. 2007. A Parylene-Protected Nitrate Selective Microsensor on a Carbon Fiber Cross Section, Sensors and Actuators B: Chemical, 123(1),127-134.
  • Hamilton, M., E.A. Graham, P.W. Rundel, M.F. Allen, W. Kaiser, M.H. Hansen, and D.L. Estrin. 2007. New approaches in embedded networked sensing for terrestrial ecological observatories. Environmental Engineering Science 24: 192-204.


  • Allen, M.F. 2006. Water dynamics of mycorrhizas in arid soils. In: Fungi in biogeochemical cycles. G.M. Gadd, editor, pp 74-97. Cambridge University Press.


Current list of theses.


  • Ayesha T. Sirajuddin. Ph.D. 2009. Impact of Atmospheric Nitrogen Pollution on Belowground Mycorrhizal Fungal Community Structure and Composition in the San Bernardino Mountains
  • Dietrich, H (2009). Potential of Commercially Available In Situ Sensors as Systems for Monitoring and Managing Nitrogen in Soils Irrigated with Dairy Manure Water. M.S. Thesis Environmental Systems Program, University of California Merced.
  • Hector Estrada, Ph.D. 2009. Importance of the subsurface limestone and pockets of soil as sources of water for tree species in Yucatan, Mexico.
  • Laurel Salzman. Ph.D. 2009. Structure and functioning of epiphyte communities in a seasonal tropical forest.


  • Niles Hasselquist, Ph.D. 2009. Mycorrhizae, water and a changing climate: How do trees survive in a seasonally dry tropical forest.
  • Patrick Barnes, M.S. 2010. Measuring and Modeling Interannual Moisture and Salinity Time Series in Sandy and Clayey Soils.
  • Rodrigo Vargas, Ph.D. 2007. Carbon Dynamics in a Seasonally Dry Tropical Forest.
  • Sean Askay. MS. 2007. New visualization tools for environmental sensor networks: Using Google Earth as an interface to micro- climate and multimedia datasets.

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