Publications

  1. Bice, K., Myers, T., Waldbusser, G. and Meile, C. 2024. Countering the effect of ocean acidification in coastal sediments through carbonate mineral additions. Biogeosciences. accepted. 
  2. Weston, N.B., Troy, C., Kearns, P.J., Bowen, J.L., Porubsky, W., Hyacinthe, C., Meile, C., Van Cappellen, P., and Joye, S. 2024. Physicochemical perturbation increases nitrous oxide production from denitrification in soils and sediments. Biogeosciences 21, 4837-4851. https://bg.copernicus.org/articles/21/4837/2024/
  3. He, X., Bhandarkar, S.M. and Meile, C. 2024. Multimodal registration of FISH and nanoSIMS images using convolutional neural networks. Peer-reviewed Proceeding of the Colour & Visual Computing Symposium 12th Edition. 5-6 September 2024, Gjovik, Norway.
  4. Deng, L., Fiskal, A., Boelsterli, D., Meier, D., Meile, C. and Lever, M.A. 2023. Differential impact of two major polychaete guilds on microbial communities in marine sediments: a microcosm study. Frontiers in Marine Science, section Aquatic Microbiology 10. https://doi.org/10.3389/fmars.2023.1119331
  5. Bice, K., J. Schalles, M. Alber, J. Sheldon and Meile, C. 2023. Temporal patterns and causal drivers of aboveground plant biomass in a coastal wetland: insights from time-series analyses. Frontiers in Marine Science. Sec. Marine Ecosystem Ecology. Volume 10, https://doi.org/10.3389/fmars.2023.1130958
  6. Stadler, M., Barnard, M.A., Bice, K., de Melo, M., Dwivedi, D., Freeman, E.C., Garayburu-Caruso, V.A., Linkhorst, A., Mateus-Barros, E., Shi, C., Tanentzap, A.J. and Meile, C. 2023. Applying the core-satellite species concept: Characteristics of rare and common riverine dissolved organic matter. Frontiers in Water, section Environmental Water Quality. Volume 5, https://doi.org/10.3389/frwa.2023.1156042
  7. Jung, H., Song, H.-S. and Meile, C. 2023. CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics. Geoscientific Model Development 16, 1683–1696, 2023. https://doi.org/10.5194/gmd-16-1683-2023.
  8. Thullner, M., Brodie, E.L. Meile, C., Pagel, H. 2022. Editorial: Modeling the link between microbial ecology and biogeochemical process dynamics. Front. Ecol. Evol. – Models in Ecology and Evolution. doi.org/10.3389/fevo.2022.994090
  9. Deng, L., Meile, C., Fiskal, A., Boelsterli, D., Han, X., Gajendra, N., Dubois, N., Bernasconi, S. and Lever, M.A. 2022. Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing. PNAS Nexus 1(4), pgac146, doi.org/10.1093/pnasnexus/pgac146
  10. Santitissadeekorn, N., Bollt, E., Meile, C., and Waldbusser, G. 2022. Parametric approach to promote a divergence-free flow in the image-based motion estimation with application to bioirrigation. European Journal of Applied Mathematics. doi.org/10.1017/S095679252200016X
  11. Jung, H. and Meile, C. 2021. Pore scale numerical investigation of evolving porosity and permeability driven by biofilm growth. Transport in Porous Media 139: 203-221.
  12. Tansik, A., Hopkinson, B. and Meile, C. 2021. Inorganic carbon fluxes and perturbations by ocean acidification estimated using a data-constrained, process-based model of coral physiology. Marine Biology. 168:116 doi:10.1007/s00227-021-03926-8.
  13. Zindorf, M.*, Rooze, J.*, Meile, C., Maerz, C., Jouet, G., Newton, R., Brandily, C. and Pastor, L. 2021. The evolution of early diagenetic processes and signatures during the last glacial-interglacial climate transition at the Mozambique margin. Geochimica et Cosmochimica Acta 300: 79-94. doi.org/10.1016/j.gca.2021.02.024. *co-first authors
  14. He, X., Chadwick, G.L., Kempes, C., Orphan, V. and Meile, C. 2021. Controls on interspecies electron transport and size limitation of anaerobically methane oxidizing microbial consortia. mBIO. 12 (3), Art. No. e03620-20
  15. He, X., Chadwick, G., Otero, F.J., Orphan, V. and Meile, C. 2021. Spatially resolved electron transport through anode-respiring Geobacter sulfurreducens biofilms: controls and constraints. Chem Electro Chem. 8(10): 1747-1758. doi.org/10.1002/celc.202100111
  16. Jung, H. and Meile, C. 2020. Numerical investigation of microbial quorum sensing under various flow conditions. PeerJ 8:e9942 https://doi.org/10.7717/peerj.9942.
  17. Deng, L., Boelsterli, D., Kristensen, E., Meile, C., Shu, C-C., Bernasconi, S.M., Seidenkrantz, M-S., Glombitz, C., Lagostina, L., Han, X., Jorgensen, B.B., Roy, H. and Lever, M.A. 2020. Macrofaunal control of microbial community structure in continental margin sediments. PNAS, doi.org/10.1073/pnas.1917494117
  18. Rooze, J., Peterson, L., Peterson, R.N. and Meile, C. 2020. Porewater flow patterns in surficial cold seep sediments inferred from conservative tracer profiles and early diagenetic modeling. Chemical Geology 536, doi.org/10.1016/j.chemgeo.2020.119468
  19. Meile, C. and Scheibe, T. 2019. Reactive transport modeling of microbial dynamics. Elements. 15, 111-116, doi: 10.2138/gselements.15.2.111
  20. Jung, H. and Meile, C. 2019. Upscaling of microbially driven first-order reactions in heterogeneous porous media. Journal of Contaminant Hydrology. doi.org/10.1016/j.jconhyd.2019.04.006
  21. Peterson, R.N., Meile, C. Peterson, L.E., Carter, M. and Miklesh, D. 2019. Groundwater discharge dynamics into a salt marsh tidal river. Estuarine, Coastal and Shelf Science 218, 324-333.
  22. He, X., Kempes, C., Chadwick, G., McGlynn, S. Shi, Y., Orphan, V. and Meile, C. 2018. Microbial interactions in the anaerobic oxidation of methane: Model simulations constrained by process rates and activity patterns. Environmental Microbiology; doi:10.1111/1462-2920.14507.
  23. Barcellos, D., O'Connell, C.S., Silver, W., Meile, C. and Thompson, A. 2018. Hot spots and hot moments of soil moisture explain fluctuations in iron and carbon cycling in a humid tropical forest soil. Soil Systems, 2(4), 59; doi.org/10.3390/soilsystems2040059.
  24. Miklesh, D. and Meile, C. 2018. Porewater salinity in a southeastern United States salt marsh: controls and interannual variation. PeerJ 6:e5911; doi.org/10.7717/peerj.5911.
  25. Chen, C., Meile, C., Wilmoth, J., Barcellos, D. and Thompson, A. 2018. Influence of pO2 on iron redox cycling and anaerobic organic carbon mineralization in a humid tropical forest soil. Environmental Science & Technology, doi:10.1021/acs.est.8b01368.
  26. Meile, C. and Scheibe, T.D. 2018. Reactive transport modeling and biogeochemical cycling. In: Reactive Transport Modeling (eds. Y. Xiao, F. Whitaker, T. Xu and C. Steefel). doi:10.1002/9781119060031.ch10
  27. Yuan, X., Cai, W.-J., Meile, C., Hopkinson, B.M., Ding, Q., Schoef, V., Warner, M.E., Hoadley, K.D., Chen, B., Liu, S., Huang, H., Ye, Y. and Grottoli, A.G. 2018. Quantitative interpretation of vertical profiles of calcium and pH in the coral coelentron. Marine Chemistry, doi:10.1016/j.marchem.2018.06.001. 
  28. Ginn, B., Meile, C., Wilmoth, J., Tang, Y. and Thompson, A. 2017. Rapid iron reduction rates are stimulated by high-amplitude redox fluctuations in a tropical forest soil. Environmental Science & Technology 51, 3250-3259.
  29. Li, L., Maher, K., Navarre-Sitchler, A., Druhan, J., Meile, C., 20 others. 2016. Expanding the Role of Reactive Transport Models in Earth Surface Processes. Earth-Science Reviews. doi:10.1016/j.earscirev.2016.09.001
  30. Meile, C. and Jones, C. 2016. A mathematical perspective on microbial processes in Earth’s biogeochemical cycles. In: Ancon, F., Cannarasa, C., Jones, C. and Portaluri, A. (eds.): “Mathematical paradigms of climate science”. Springer. 
  31. Rooze, J. and Meile, C. 2016. The effect of redox conditions and bioirrigation on nitrogen isotope fractionation in marine sediments. Geochimica et Cosmochimica Acta. doi:10.1016/j.gca.2016.04.040 
  32. Dornhoffer, T., Waldbusser, G.G. and Meile, C. 2015. A modeling study of lugworm irrigation behavior effects on sediment nitrogen cycling. Marine Ecology Progress Series, 534, 121-134.  doi:10.3354/meps11381 
  33. Lowell, R.P., Houghton, J., Farough, A., Craft, K., Larson, B., Meile, C. 2015. Mathematical modeling of diffuse flow in seafloor hydrothermal systems: The potential extent of the subsurface biosphere at mid-ocean ridges. Earth and Planetary Science Letters 425, 145-153.
  34. Larson, B.I., Houghton, J.L., Lowell, R.P., Farough, A., and Meile, C. 2015. Subsurface conditions in hydrothermal vents inferred from diffuse flow composition, and models of reaction and transport. Earth and Planetary Science Letters 424, 245-255. 
  35. Hoelker, F., Vanni, M.J., Kuiper, J.J., Meile, C., Grossart, H.-P., Stief, P., Adrian, R., Lorke, A., Dellwig, O., Brand, A., Hupfer, M., Mooij, W.M., Nuetzmann, G. and Lewandowski, J. 2015. Tube-dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems. Ecology Monographs 85, 333-351.
  36. Lai, M.J. and Meile, C. 2015. Scattered data interpolation with nonnegative preservation using bivariate splines and its application. Computer Aided Geometry Design 34, 37-48.
  37. Tishchenko, V., Meile, C., Scherer, M., Pasakarnis, T. and Thompson, A. 2015. Fe2+ catalyzed iron atom exchange and re-crystallization in a tropical soil. Geochimica et Cosmochimica Acta 148, 191-202. doi:10.1016/j.gca.2014.09.018
  38. Loftis, K. and Meile, C. 2014. Isotopes and elemental ratios in multi-parameter mixing models. Limnology and Oceanography Methods 12, 694-702.
  39. Crespo-Medina, M., Meile, C., Hunter, K.S., Diercks, A.-R., Asper, V.L., Orphan, V.J., Tavormina, R., Nigro, L, Battles, J., Chanton, J.P., Shiller, A.M., Joung, D.-J., Amon, R.M.W., Bracco, A., Montoya, J.P., Villareal, T.A., Wood, A.M., and Joye, S.B. 2014. The rise and fall of methanotrophy following a deepwater oil-well blowout. Nature Geoscience 7, 423-427. doi:10.1038/ngeo2156
  40. Ginn, B., Habteselassie, M.Y., Meile, C. and Thompson, A. 2014. Effects of sample storage on microbial Fe-reduction in tropical rainforest soils. Soil Biology and Biochemistry 68, 44-51. doi:10.1016/j.soilbio.2013.09.012
  41. Schutte, C.A., Hunter, K., McKay, P., Di Iorio, D., Joye, S. and Meile, C. 2013. Patterns and controls of nutrient concentrations in a southeastern United States tidal creek. Oceanography 26(3), 132-139. doi:10.5670/oceanog.2013.55
  42. Hopkinson, B.M., Meile, C., and Shen C. 2013. Quantification of extracellular carbonic anhydrase activity in two marine diatoms and investigation of its role. Plant Physiology 162(2), 1142-1152. doi:10.1104/pp.113.217737
  43. Volkenborn, N., Meile, C., Polerecky, L., Pilditch, C., Norkko, A., Norkko, J., Hewitt, J.E., Thrush, S.F., Wethey, D.S. and Woodin, S.A. 2013. Intermittent bioirrigation and oxygen dynamics in permeable sediments: An experimental and modeling study of three tellinid bivalves. Journal of Marine Research 70(6), 794-­823. doi:10.1357/002224012806770955
  44. Segarra, K.E.A., Samarkin, V., King, E., Meile, C. and Joye, S.B. 2013. Seasonal variations of methane fluxes from a tidal, freshwater wetland (Hammersmith Creek, GA). Biogeochemistry 115, 349-361. doi:10.1007/s10533-­013-­9840-­6
  45. Paloma, L., Meile, C. and Joye, S.B. 2012. Drought impacts on biogeochemistry and microbial processes in salt marsh sediments: a flow-through reactor approach. Biogeochemistry 112, 389-407. doi:10.1007/s10533-012-9734-z
  46. Chan, L.-K., Newton, R.J., Sharma, S., Smith, C.B., Rayapati, P., Limardo, A.J., Meile, C. and Moran, M.A. 2012. Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. Frontiers in Aquatic Microbiology Volume 3, Article 159, doi:10.3389/fmicb.2012.00159
  47. Dornhoffer, T., Waldbusser, G.G. and Meile, C. 2012. Burrow patchiness and oxygen fluxes in bioirrigated sediments. Journal of Experimental Marine Biology and Ecology 412: 81-86.
  48. Pennings, S., Alber, M., Alexander, C., Booth, M., Burd, A., Cai, W., Craft, C., DePratter, C., DiIorio, D., Hollibaugh, J., Hopkinson, C., Joye, S., Meile, C., Moore, B., Silliman, B., Thompson, V., Wares, J.P. 2011. South Atlantic tidal wetlands. In Batzer, D.P. and Baldwin, A.H. (eds.) Wetland Habitats of North America. Ecology and Conservation Concerns. University of California Press. 448p.
  49. Joye et al. 2011. Comment on “A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico”. Science 332(6033):1033, doi:10.1126/science.1203307
  50. Porubsky, W., Joye, S., Moore, W.S., Tuncay, K., Meile, C. 2010. Field measurements and modeling of groundwater flow and biogeochemistry at Moses Hammock, a backbarrier island on the Georgia coast. Biogeochemistry104, 69-90. doi:10.1007/s10533-010-9484-8
  51. Tilburg, C.E., Seay, J., Bishop, T.D., Miller III, H.L. and Meile, C. 2010. Distribution and retention of Petrolisthes armatus in a coastal plain estuary: the role of vertical movement in larval transport. Estuarine, Coastal and Shelf Science 88, 260-266.
  52. Jourabchi, P., L’Heureux, I., Meile, C. and Van Cappellen, P. 2010. Physical and chemical steady-state compaction in deep-sea sediments: role of mineral reactions. Geochimica et Cosmochimica Acta 74, 3493-3513.
  53. King, E.L., Tuncay, K., Ortoleva, P. and Meile, C. 2010. Modeling biogeochemical dynamics in porous media: practical considerations of pore scale variability, reaction networks, and microbial population dynamics in a sandy aquifer. Journal of Contaminant Hydrology 112, 130-140.
  54. Newton, R., Griffin, L., Bowles, K., Meile, C., Gifford, S., Givens, C., Howard, E., King, E., Oakley, C., Reisch, C., Rinta-Kanto, J., Sharma, S., Sun, S., Varaljay, V., Vila-Costa, M., Westrich, J. and Moran, M.A. 2010. Genome characteristics of a generalist marine bacterial lineage. ISME Journal, doi:10.1038/ismej.2009.150
  55. Pallud, C., Kausch, M., Fendorf, S. and Meile, C. 2010. Spatial patterns and modeling of reductive ferrihydrite transformation observed in artifical soil aggregates. Environmental Science and Technology 44, 74-79.
  56. Joye, S.B., Samarkin, V.A., Orcutt, B.N., MacDonald, I., Hinrichs, K.-U., Elvert, M., Teske, A., Lloyd, K., Montoya, J.P. and Meile, C. 2009. Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics. Nature Geoscience, doi:10.1038/NGEO475.
  57. Meile, C., Porubsky, W.P., Walker, R.L., Payne, K. 2009. Natural attenuation of nitrogen loading from septic effluents: Spatial and environmental controls. Water Research 44(5), 1399-1408.
  58. King, E.L., Tuncay, K., Ortoleva, P. and Meile, C. 2009. In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models. Applied and Environmental Microbiology 75(1), 29-38.
  59. Orcutt, B. and Meile, C. 2008. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: Process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions. Biogeosciences 5, 1587-1599.
  60. Spiteri, C., Slomp, C., Charette, M.A., Tuncay, K. and Meile, C. 2008. Flow and nutrient dynamics in a subterranean estuary (Waquoit Bay, MA, USA): field data and reactive transport modeling. Geochimica et Cosmochimica Acta 72, 3398-3412.
  61. Donahue, M.A., Werne, J.P., Meile, C. and Lyons, T.W. 2008. Modeling sulfur isotope fractionation and differential diffusion during sulfate reduction in sediments of the Cariaco Basin. Geochimica et Cosmochimica Acta 72, 2287-2297.
  62. Jourabchi, P., Meile, C., Pasion L.R. and Van Cappellen P. 2008. Quantitative interpretation of pore water O2 and pH distributions in deep-sea sediments. Geochimica et Cosmochimica Acta 72: 1350-1364.
  63. Spiteri, C., Van Cappellen, P., Regnier, P., Meile, C. and Slomp, C. 2008. Phosphate mobilization in coastal aquifers due to seawater intrusion: A model assessment. In Hill, M.C. (ed.) Groundwater Quality 2007 - Securing Groundwater Quality in Urban and Industrial Environments. International Association of Hydrological Science IAHS Redbook. IAHS Publ. 324.
  64. Spiteri, C., Slomp, C.P., Tuncay, K. and Meile, C. 2007. Modeling biogeochemical processes in subterranean estuaries: The effect of flow dynamics and redox conditions on submarine groundwater discharge of nutrients. Water Resources Research 44, W02430. doi:10.1029/2007WR006071.
  65. Moran M.A. et al. 2007. Ecological Genomics of Marine Roseobacters. Applied and Environmental Microbiology 73, 4559-4569.
  66. Miller, H.L. III, Meile, C. and Burd, A.B. 2007. Process model of oxygen and hydrogen sulfide dynamics in Thalassia testudinum. Ecological Modeling 205, 365-380. doi:10.1016/j.ecolmodel.2007.03.004
  67. Nehrke, G., Reichart, G.J., Van Cappellen, P., Meile, C. and Bijma, J. 2007. Dependence of calcite growth rate and Sr partitioning on solution stoichiometry: Non-Kossel crystal growth. Geochimica et Cosmochimica Acta 71(9), 2240-2249. doi:10.1016/j.gca.2007.02.002
  68. Spiteri, C., Slomp, C.P., Regnier, P., Meile, C. and Van Cappellen, P. 2007. Modelling the geochemical fate and transport of wastewater-derived phosphorus in contrasting groundwater systems. Journal of Contaminant Hydrology. doi:10.1016/j.jconhyd.2007.01.002
  69. Pallud, C., Meile, C., Laverman, A.M., Abell, J. and Van Cappellen, P. 2007. The use of flow-through sediment reactors in biogeochemical kinetics: Methodology and examples of applications. Marine Chemistry. doi:10.1016/j.marchem.2006.12.011
  70. Laverman, A.M, Meile, C., Van Cappellen, P. and Wieringa, E.B.A. 2007. Vertical distribution of denitrification in an estuarine sediment: Integrating sediment flowthrough reactor experiments and microprofiling via reactive transport modeling. Applied and Environmental Microbiology 73, 40-47.
  71. Meile, C., and Tuncay, K. 2006. Scale dependence of reaction rates in porous media. Advances in Water Resources 29, 62-71, doi:10.1016/j.advwatres.2005.05.007.
  72. Meile, C. and Van Cappellen, P. 2005. Particle age distribution and O2 exposure time: Time scales in bioturbated sediments. Global Biogeochemical Cycles 19: GB3013, doi:10.1029/2004GB002371.
  73. Meile, C., Berg, P., Van Cappellen, P. and Tuncay, K. 2005. Solute-specific pore water irrigation: Implications for chemical cycling in early diagenesis. Journal of Marine Research 63(3), 601-621.
  74. Koretsky, C., Meile, C. and Van Cappellen, P. 2005. Incorporating Ecological and Biogeochemical Information into Irrigation Models. In: E. Kristensen, J. Kostka and R.R. Haese (eds): Interactions between macro- and microorganisms in aquatic sediments.
  75. Hollibaugh, J.T., Carini, S., Gürleyük, H., Jellison, R., Joye, S.B., LeCleir, G., Meile, C., Vasquez, L. and Wallschläger, D. 2005. Distribution of Arsenic Species in an Alkaline, Hypersaline, Meromictic Lake and Response to Seasonal Stratification and Anoxia. Geochimica et Cosmochimica Acta 69(8), 1925-1937.
  76. Peretyazhko, T., Van Cappellen, P., Meile, C., Coquery, M., Musso, M., Regnier, P. and Charlet, L. 2005. Biogeochemistry of major redox elements and mercury in a tropical reservoir lake (Petit Saut, French Guiana). Aquatic Geochemistry 11, 33-55.
  77. Haese, R.R., Meile, C., Van Cappellen, P., and De Lange, G.J. 2003. Carbon geochemistry of cold seeps: Methane fluxes and transformation in sediments from Kazan mud volcano, eastern Mediterranean Sea. Earth and Planetary Science Letters 212(3-4), 361-375.
  78. Meile, C., Tuncay, K., and Van Cappellen, P. 2003 Explicit representation of spatial heterogeneity in reactive transport models: Application to bioirrigated sediments. Journal of Geochemical Exploration 78-79, 231-234.
  79. Koretsky, C., Moore, C., Lowe, K.L., Meile, C., DiChristina, T.J. and Van Cappellen, P. 2003. Seasonal oscillations of microbial respiratory pathways in saltmarsh sediments (Sapelo Island, GA, USA). Biogeochemistry 64, 179-203.
  80. Meile, C. and Van Cappellen, P. 2003. Global estimates of enhanced solute transport in marine sediments. Limnology and Oceanography 48(2), 777-786.
  81. Koretsky, C., Meile, C. and Van Cappellen, P. 2002. Quantification of bioirrigation using ecological data: A stochastic approach. Geochemical Transactions 3, 17-30.
  82. Meile, C., Koretsky, C. and Van Cappellen P. 2001. Quantifying bioirrigation in aquatic sediments - An inverse approach. Limnology and Oceanography 46(1), 164-177.