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CMEIAS Publications

Below is a list of studies that include data acquired by CMEIAS. We will periodically update this list with references sent to us by CMEIAS users. Please send references to us in the format shown below using the Register and Contact Us webpage or directly to cmeiasfd@msu.edu. NOTE: * = comprehensive application of CMEIAS

  1. Tiedje, J. M., K. Nusslein, J. Zhou, B. Xia, C. Moyer and Frank B. Dazzo. 1997. The vast world of microbial diversity. 5th JST International Symposium on New Frontiers in Microbiology, Tokyo Japan.

  2. Tiedje, J., A. Fernandez, S. Hashsham, S. Dollhopf, F. Dazzo, R. Hickey and C. Criddle. 2000. Stability, persistence and resilience in anaerobic reactors: a community unveiled. Int'l. Symp. on Establishment and Evaluations of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community. 6-8 March, 2000 Univ. of Tokyo, Japan.

  3. Fernandez, A., S. Hashsham, S. Dollhopf, L. Raskin, O. Glagoleva, F. B. Dazzo, R. Hickey, C. Criddle and J. M. Tiedje. 2000. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4058-4067. [abstract]

  4. Hashsham, S., A. Fernandez, S. Dollhopf, F. B. Dazzo, J. M. Tiedje, R. Hickey and C. S. Criddle. 2000. Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4050-4057. [abstract]

  5. Hashsham, S., T. Marsh, S. Dollhopf, A. Fernandez, F. Dazzo, R. Hickey, C. Criddle and J. Tiedje. 2000. Relating function and community structure of complex microbial systems using neural networks. Int'l. Symp. on Establishment and Evaluations of Advanced Water Treatment Technology Systems Using Functions of Complex Microbial Community. 6-8 March, 2000 Univ. of Tokyo, Japan.

  6. Dazzo, F., and J. Wopereis. 2000. Unraveling the infection process in the Rhizobium-legume symbiosis by microscopy. In: E. Triplett (ed.), Prokaryotic nitrogen fixation: a model system for the analysis of a biological process; Chap. 19; pp. 295-347. Horizon Scientific Press, UK.

  7. Dazzo, F. B., Y. G. Yanni, R. Rizk, F. De Bruijn, J. Rademaker, A. Squartini, V. Corich, P. Mateos, E. Martinez-Molina, E. Velazquez, J. Biswas, R. Hernandez, J. K. Ladha, J. Hill, J. Weinman, B. Rolfe, M. Vega-Hernandez, J. J. Bradford, R. I. Hollingsworth, P. Ostrom, E. Marshall, T. Jain, G. Orgambide, S. Philip-Hollingsworth, E. Triplett, K. Malik, J. Maya-Flores, A. Hartmann, M. Umali-Garcia and M.L. Izaguirre-Mayoral. 2000. Progress in multi-national collaborative studies on the beneficial association between Rhizobium leguminosarum bv. trifolii and rice. In: J.K. Ladha and P.M. Reddy (eds.), The Quest for Nitrogen Fixation in Rice. International Rice Research Institute, Manila, The Philippines, pp. 167-189.

  8. *Liu, J., F. B. Dazzo, O. Glagoleva, B. Yu and A. Jain. 2001. CMEIAS: a computer-aided system for the image analysis of bacterial morphotypes in microbial communities. Microbial Ecology 41: 173-194 and 42:215. [abstract] DOI: 10.1007/s002480000004

  9. Tiedje J., A. Fernandez, S. Hashsham, S. Dollhopf, F. Dazzo, R. Hickey and C. Criddle. 2001. Stability, persistence and resilience in anaerobic reactors: a community unveiled. Advances in Water and Wastewater Treatment Technology (Matsuo, Hanaki, Takizawa, Setoh, eds.), pp. 13-20. Elsevier, Amsterdam.

  10. Dollhopf, S., S. A. Hashsham, F. B. Dazzo, C. Criddle and J. M. Tiedje. 2001. The impact of fermentative organisms on carbon flow in methanogenic systems under constant low substrate conditions. Appl. Microbiol. Biotechnol. 56: 531-538. [abstract] DOI: 10.1007/s002530100612

  11. Dazzo, F. B., J. Liu, F-I. Liu, and G. P. Robertson. 2001. In situ analysis of microbial communities on the 2 day-old white clover rhizoplane and the mature BT-corn phylloplane using CMEIAS innovative software for computer-assisted microscopy. Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  12. Liu, J., F-I. Liu, E. Marshall and F. B. Dazzo. 2000. CMEIAS© Software for Computer-Assisted Microscopy of Microbial Communities. 2000 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  13. Wopereis, J., E. Pajuelo, F. B. Dazzo, Q. Jiang, P. M. Gresshoff, F. J. De Bruijn, J. Stouggard, and K. Szczyglowski. 2000. Short root mutant of Lotus japonicus with a dramatically altered symbiotic phenotype. Plant J. 23: 97-114.

  14. Karcher, D. E. 2000. Investigating causes and cures for localized dry spots on creeping bentgrass putting greens. In Investigations on Statistical Analysis of Turfgrass Rating Data, Localized Dry Spots of Greens, and Nitrogen Application Techniques for Turf. Ph.D. Dissertation, Dept. of Crop & Soil Sciences, Michigan State University, East Lansing, Michigan.

  15. Hashsham, S. A., T. L. Marsh, S. L. Dollhopf, A. S. Fernandez, F. B. Dazzo, R. F. Hickey, C. S. Criddle and J. M. Tiedje. 2001. Relating function and community structure of complex microbial systems using neural networks. Advances in Water and Wastewater Treatment Technology, (Matsuo, Hanaki, Takizawa, and Satoh, eds.), pp. 67-77, Elsevier, Amsterdam.

  16. Yanni, Y. G., R. Y. Rizk, F. K. Abd El-Fattah, A. Squartini, V. Corich, A. Giacomini, F. De Bruijn, J. Rademaker, J. Maya-Flores, P. Ostrom, M. Vega-Hernandez, R. I. Hollingsworth, E. Martinez-Molina, P. Mateos, E. Velazquez, J. Wopereis, E. Triplett, M. Umali-Garcia, J. A. Anarna, B. G. Rolfe, J. K. Ladha, J. Hill, R. Mujoo, P. K. Ng and F. B. Dazzo. 2001. The beneficial plant growth-promoting association of Rhizobium leguminosarum bv. trifolii with rice roots. Austr. J. Plant Physiol. (now Functional Plant Biology) 28: 845-870. DOI: 10.1071/PP01069

  17. Tübler, T., M. Schlüter, O. Dirsch, H. Sievert, I. Bösenberg, E. Grube, J. Waigand, J. Schofer. 2001. Balloon-protected carotid artery stenting: Relationship of periprocedural neurological complications with thparticulate debrise size of . Circulation 104: 2791-2796. DOI: 10.1161/hc4801.100353

  18. McDermott, T. R., and F. B. Dazzo. 2002. Use of fluorescent antibodies for studying the ecology of soil- and plant-associated microbes. In: C. Hurst, R.C. Crawford, G.R. Knudsen, M.J. McInerney, and L.D. Stetzenbach (eds.), Manual of Environmental Microbiology 2nd ed., Chapter 28, p. 615-626, American Society for Microbiology Press, Washington, DC.

  19. Reddy, C., J. Liu, M. Wadekar, A. Prabhu, D. Trione, E. Marshall, J. Zurdo, F-I. Liu, J. Urbance and F. B. Dazzo. 2002. New features of CMEIAS: innovative software for computer-assisted microscopy of microorganisms and their ecology. 2002 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  20. M. Forero-Vargas, F. Sroubek, J. Alvarez- Borrego, N. Malpica, G. Cristobal, A. Santos, L. Alcala, M. Desco and L. Cohen. 2002. Segmentation, autofocusing, and signature extraction of tuberculosis sputum images. Photonic Devices and Algoithms for Computing IV, Vol. 4788, SPIE Proc., Seattle WA.

  21. Dazzo, F. B., J. Liu, A. Prabhu, C. Reddy, M. Wadekar, R. Peretz, R. Bollempalli, D. Trione, E. Marshall, J. Zurdo, H. Hammoud, J. Wang, M. Li, D. McGarrell, A. Gore, J. Maya-Flores, S. Gantner and N. Hollingsworth. 2003. CMEIAS v. 3.0: Integrative software package to strengthen microscopy-based approaches for understanding microbial ecology. 2003 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  22. Dazzo, F. B., A.R. Joseph, A.B. Gomaa, Y.G. Yanni and G.P. Robertson. 2003. Quantitative indices for the autecological biogeography of a Rhizobium endophyte of rice at macro and micro spatial scales. Symbiosis 34: 147-158.

  23. Reddy, C. K., Feng-I Liu and Frank B. Dazzo. 2003. Semi-automated segmentation of microbes in color images. In: Color Imaging VIII: Processing, Hardcopy, and Applications. Proc. International Society for Electronic Imaging (SPIE)-2003, R. Eschbach & G. Marcu (eds.), 5008: 548-559. DOI:10.1117/12.472024

  24. Matsuyama, J., M. Fukuda, S. Nakano and F. B. Dazzo. 2003. Abundance, composition and bacterivory of protists on the pebbles in a stream environment. 8 th Intn'l. Congress of Ecology, Seoul, Korea.

  25. Dopp, H., F. Dazzo, E. J. Park and A. J. Smucker. 2003. Diversity of bacterial communities in concentric layers of soil aggregates from conventional till and natural forest ecosystems. Ann. Mtg., Amer. Assoc. Agronomy, Soil Sci. Soc. Amer., Denver, CO.

  26. Gantner, S., R. Schuhegger, A. Steidle, C. Dürr, M. Schmid, C. Langebartels, L. Eberl, F. B. Dazzo and A. Hartmann. 2003. In situ production of N-acylhomoserine lactones by rhizosphere bacteria and their impact on the bacterial rhizoplane community in tomato roots. Structure and Function of Soil Microbiota.

  27. Gantner, S. 2003. Microbial ecology of N-acylhomoserine lactone producing bacteria in the rhizosphere of tomato plants. Ph. D. thesis, Ludwigs Maximilian Universitat Munchen, Germany, 135 pp. [abstract]

  28. Dethlefsen, L. 2004.   Translational power differs between bacteria pursuing different ecological strategies. Ph. D. Doctoral dissertation, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan.

  29. Reddy, C. K., and F. B. Dazzo. 2004. Computer-assisted segmentation of bacteria in color micrographs. Microscopy and Analysis 18(5): 5-7. (September, 2004 issue). [pdf will download in a new window]

  30. Dazzo, F.B. 2004. Applications of quantitative microscopy in studies of plant surface microbiology. In: A. Varma, L. Abbott, D. Werner, and R. Hampp (eds.), Plant Surface Microbiology, pp. 503-550. Springer-Verlag, Germany.

  31. Dazzo, F. B. 2004. Production of anti-microbial antibodies and their utilization in studies of microbial autecology by immunofluorescence microscopy and in situ CMEIAS image analysis. In: G. Kowalchuk, F. deBruijn, I. Head, A. Akkermans, J. Elsas (eds.), Molecular Microbial Ecology Manual, 2nd Ed., Chapter 4.04, pp. 911-932. Kluwer Publishers, Dordrecht, Netherlands.

  32. Dazzo, F. B. 2004. New CMEIAS image analysis software for computer-assisted microscopy of microorganisms and their ecology. Microscopy Today 12(3): 18-23. [NOTE: must scroll down to the volume 12 link, click on issue #3 for pdf, then scroll to p. 18]

  33. Dazzo, F. B., J. Liu, A. Jain, A. Prabhu, C. Reddy, M. Wadekar, R. Peretz, R. Bollempalli, D. Trione, E. Marshall, J. Zurdo, H. Hammoud, J. Wang, M. Li, D. McGarrell, J. Maya-Flores, S. Gantner, C. Dowling, A. B. Gomaa and Y. Yann. 2004. CMEIAS V3.0 upgrade: Advanced image analysis software to strengthen microscopy-based approaches for understanding microbial ecology. 2004 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  34. Dazzo, F. B. 2004. CMEIAS: advanced image analysis software to strengthen microscopy-based approaches for understanding microbial ecology. (poster) 10th Int. Symp. Microbial Ecology, Cancun, Mexico.

  35. Matsuyama, J., M. Fukuda, F. Dazzo, and S. Nakano. 2004. Changes in bacterial cell volume and morphological diversity analyzed with an image analysis system in a streambed environment. (poster). 10th Int. Symp. Microbial Ecology, Cancun, Mexico.

  36. Hartmann, A., S. Gantner, R. Schuhegger, A. Steidle, C. Dürr, M. Schmid, C. Langebartels, F. B. Dazzo and L. Eberl. 2004. N-Acyl homoserine lactones of rhizosphere bacteria trigger systemic resistance in tomato plants. In: Biology of Molecular Plant-Microbe Interaction, Vol. 4 , pp. 554-556. Eds: B Lugtenberg, I Tikhonovich, N Provorov, IS-MPMI, St. Paul, Minnesota, USA.

  37. Janssens, F., and F. B. Dazzo. 2004. Image Analysis, Morphometry and Classification of Scanned Collembola Samples Applied to Specimen Identification. [website]

  38. Dazzo, F. B. 2004. CMEIAS: advanced image analysis software to strengthen microscopy-based approaches for understanding rhizoplane microbial ecology. Rhizosphere - 2004: Perspectives & Challenges (abstract). Munich, Germany.

  39. Gantner, S., M. Schmid, C. Dürr, R. Schuhegger, A. Steidle, P. Hutzler, C. Langebartels, L. Eberl, A. Hartmann and F. B. Dazzo. 2004. In situ calling distances and high population-independent rhizobacterial cell-to-cell communication. (poster) International Congress- Rhizosphere 2004. Munich, Germany.

  40. Forero, M. G., F. Sroubek, and G. Cristobal. 2004. Identification of tuberculosis bacteria based on shape and color. Real Time Imaging 10: 251-262. DOI:10.1016/j.rti.2004.05.007

  41. Howgrave-Graham, A., F. Wallis. 2004. Quantification of bacterial morphotypes within anaerobic digester granules from transmission electron microraphs using image analysis. J Biotechnol. Techniques 7:142-148. DOI: 10.1007/BF00157386

  42. Stelzer, M. and H. Reber. 2005. Combined methods of image and cluster analysis to estimate the structural diversity of fungal communities. Biol. Fertility Soils 42: 10-16. DOI: 10.1007/s00374-005-0868-1

  43. Chi, F., S. H. Shen, H. P. Cheng, Y. X. Jing, Y. G. Yanni and F. B. Dazzo. 2005. Ascending migration of endophytic rhizobia from roots to leaves inside rice plants and assessment of their benefits to the growth physiology of rice. Appl. Environ. Microbiol. 71:7271-7278. DOI: 10.1128/AEM.71.11.7271-7278.2005

  44. Ponder, M., S. Gilmour, P. Bergholz, C. Mindock, R. Hollingsworth, M. Thomashow and J. M. Tiedje. 2005. Characterization of potential stress responses in ancient Siberian permafrost psychroactive bacteria. FEMS Microbiology Ecology 53:103-115. DOI: 10.1016/j.femsec.2004.12.003

  45. *Gantner, S., M. Schmid, C. Durr, R. Schuhegger, A. Steidle, P. Hutzler, C. Langebartels, L. Eberl, A. Hartmann and F. B. Dazzo. 2006. In situ quantitation of the spatial scale of calling distances and population density-independent N-acylhomoserine lactone-mediated communication by rhizobacteria colonized on plant roots. FEMS Microbiology Ecology 56:188-194. DOI: 10.1111/j.1574-6941.2005.00037.x

  46. Dazzo, F. B. G. Tang, G. Zhu, C. Gross, D. Nasr, C. Passmore, K. Kulek, E. Polone, A. Squartini, A. Prabhu, C. Reddy, R. Peretz, L. Gao, R. Bollempalli, D. Trione, E. Marshall, J. Wang, M. Li, D. McGarrell, S. Gantner, J. Liu, and Y. Yanni. 2006. CMEIAS v3.0: Advanced image analysis software to strengthen microscopy-based approaches for understanding microbial ecology. 2006 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. East Lansing, MI. [link to most recent update]

  47. Fukuda, M., J. Matsuyama, T. Katano, S. Nakano and F. B. Dazzo. 2006. Assessing primary and bacterial production rates in epilithic biofilms on pebbles in Ishite Stream, Japan. Microbial Ecology 52:1-9. [abstract | full text] DOI: 10.1007/s00248-006-9114-0

  48. Dazzo, F. B. 2006. Spatial analysis of Microbial Colonization on Plant Roots Grown in Soil. In: R. Finlay and J. Luster (eds). COST 631 Handbook of Methods Used in Rhizosphere Research, Chapter 4.1 Microbial Growth and Visualization of Bacteria and Fungi.

  49. Dazzo, F. B., M. Schmid and A. Hartmann. 2006. Immunofluorescence microscopy and fluorescence in situ hybridization combined with CMEIAS and other image analysis tools for soil- and plant-associated microbial autecology. In: J. L. Garland, C. Hurst, D. Lipson, A. Mills, L. Stezenbach, and R. C. Crawford (eds.), Manual of Environmental Microbiology, 3rd ed., Chapter 59, pp. 712-733, American Society for Microbiology Press, Washington, DC.

  50. Dazzo, F. B., and Y. G. Yanni. 2006. The natural Rhizobium-cereal crop association as an example of plant-bacteria interaction. In: N. Uphoff et al. (eds.), Biological Approaches to Sustainable Soil Systems, pp. 109-127, CRC Press, Boca Raton FL.

  51. Kakizaki, T., N. Hamada, S. Wada, T. Funayama, T. Sakashita, T. Hohdatsu, T. Sano, M. Natsuhori, Y. Kobayashi, and N. Ito. 2006. Distinct modes of cell death by ionizing radiation observed in two lines of feline T-lymphocytes. J. Radiation Res. DOI: 10.1269/jrr.0618

  52. Parnell, J., J. Park, V. Denef, T. Tsoi, S. Hashsham, J. Quesen, and J. M. Tiedje. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl. Environ. Microbiol. 72: 6607-6614. DOI: 10.1128/AEM.01129-06

  53. Dethlefsen, L., and T. Schmidt. 2007. The performance of the translational apparatus varies with the ecological strategies of bacteria. J. Bacteriol. 189: 3237-3245. DOI: 10.1128/JB.01686-06

  54. Dazzo, F. B., D. Nasr, I. Leader, C. Monosmith, C. Gross, R. Verhelst, T. Marsh and C. Holzman. 2007. Perturbations in microbial community structure associated with bacterial vaginosis measured by CMEIAS computer-assisted microscopy and digital image analysis. Poster 1-9, 2nd Research Forum, MSU Center for Microbial Pathogenesis, March 29, 2007.

  55. Eichorst, S. A., J. Breznak and T. Schmidt. 2007. Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol. 73: 2708-2717. DOI: 10.1128/AEM.02140-06

  56. Eichorst, S. A. 2007. Isolation and characterization of members of the Phylum Acidobacteria from soils. Ph. D. Dissertation. Dept. of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan.

  57. Dazzo, F. B., J. Liu, G. Tang, G. Zhu, C. Gross, C. Reddy, C. Monosmith, J. Wang, M. Li, A. Prabhu, D. Nasr, C. Passmore, L. Shan, K. Kulek, L. Gao, R. Bollempalli, D. McGarrell, Y. Yanni, A. Squartini, E. Polone, S. Gantner, A. Smucker, S. Nakano. 2007. CMEIAS 3.0: Advanced computational tools of image analysis software designed to strengthen microscopy-based approaches for understanding microbial ecology. 2007 Long-Term Ecological Research All Scientists Meeting, May 14, Kellogg Biological Station, Hickory Corners, Michigan. [link to most recent update]

  58. Gioacchini, P., L. Manici, W. Ramieri, C. Marzadori, and C. Ciavatta. 2007. Nitrogen dynamics and microbial response in soil amended with either olive pulp or its by-products after bio-gas production. Biology and Fertility of Soils 43: 621-630. DOI: 10.1007/s00374-006-0141-2

  59. Dazzo, F. 2007. Visualization of the rhizoplane microflora by computer-assisted microscopy and spatial analysis by CMEIAS image analysis. In P. Schwinger and R. Finlay (eds), Chapter 4.1. Microbial growth and visualization of bacteria and fungi. COST 631. Handbook of Methods Used in Rhizosphere Research. Section 41, Swiss Federal Research Institute, Birmensdorf, Switzlerland. pp. 382-383.

  60. Amalfitano, S. 2007. Structure and function of benthic microbial community in highly variable freshwater systems. Ph. D. Dissertation, Instituto Di Ricerca Suelle, Acque. University of Rome "Tor Vergata".

  61. Amalfitano, S., S. Fazi, A. Zoppini, A. Caracciolo, P. Gremni, and A. Puddu. 2008. Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers. Microbial Ecology 55:270-279. DOI: 10.1007/s00248-007-9274-6

  62. Mishra, R., R. Singh, J. Jaiswal, M. Singh, Y. G. Yanni and F. B. Dazzo. 2008. Rice-rhizobia association: Evolution of an alternate niche of beneficial plant-bacteria association. In I. Ahmad, J. Pitcel and S. Hayat. Plant-Bacteria Interactions: Strategies and Techniques to Promote Plant Growth, pp. 165-194. Wiley-VCH Verlag GmbH, Weinheim Germany.

  63. Polone, E. 2008. Intercellular communication in bacteria-nodulating plants of the family Leguminosae. Ph. D. Thesis, Dept. of Agricultural Biotechnology, University of Padu, Padua, Italy.

  64. Ruusuvuori, P., J. Seppala. T. Erkkila, A. Lehmussola, J. Puhakka, O. Yli-Harja. 2008. Efficient automated method for image-based classification of microbial cells. IEEE 978-1-4244-2175.

  65. Gomes de Costa, J. 2008. Supervision of transient anaerobic granular sludge process through quantitative image analysis and multivariate statistical techniques. Ph. D. Dissertation, University of Minho. p. 231. [pdf will download or open in a new window depending on your browser]

  66. Rodrigues, J. L., M. A. Duffy, A. J. Tessier, D. Ebert, L. Mouton, and T. M. Schmidt. 2008. Phylogenetic characterization and prevalence of Spirobacillus cienkowskii, a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species. Appl. Environ. Microbiol. 74: 1575-1582. DOI: 10.1128/AEM.02438-07

  67. Imai, H., K.H. Chang, M. Kusaba, and S. Nakano. 2008. Succession of harmful algae Microcystis (Cyanophyceae) species in a eutrophic pond. In: Y. Murakami, K. Nakayama, S.-I. Kitamura, H. Iwata and S. Tanab (eds.) Interdisciplinary Studies on Environmental Chemistry—Biological Responses to Chemical Pollutants, Terrapub, pp. 367-372.

  68. Dazzo, F. and S. Gantner. 2009. Rhizosphere. In M. Schaechter (ed.), Encyclopedia of Microbiology, pp. 335-349. Oxford: Elsevier.

  69. *Gross C.A., C.K. Reddy and F.B. Dazzo. 2009. CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution. Microbial Ecology (2010) 59: 400-414. [abstract] DOI: 10.1007/s00248-009-9616-7

  70. Imai, H., K.H. Chang, M. Kusaba and S. I. Nakano. 2009. Temperature-dependent dominance of Microcystis (Cyanophyceae) species: M. aeruginosa and M. wesenbergii. J. Plankton Research 31: 171-178. DOI: 10.1093/plankt/fbn110

  71. Kui-Xian, J., F. Chi, M-F Yang, S-H Shen, Y-X Jing, Frank B. Dazzo and H-P Cheng. 2009. Movement of rhizobia inside tobacco and lifestyle alternation from endophytes to free-living rhizobia on leaves. J. Microbiol. Biotech. 20 (2): 238-244.

  72. Dazzo, Frank B. 2010.CMEIAS digital microscopy and quantitative image analysis of microorganisms. In A. Mendez-Vilas and J. Diaz (eds.) Microscopy: Science, Technology, Applications and Education. Microscopy Book Series No. 4, Vol. 2, pp. 1083-1090, Formatex Research Center, Badajoz, Spain. [Scroll contents list to chapter 36]

  73. Ng, Haig-They, David da Motta Marques, Erik Jeppese, Martin Sondergaard. 2010 Bacterioplankton in the littoral and pelagic zones of subtropical shallow lakes. Hydrobiologia 646: 311-326. DOI: 10.1007/S10750-010-0177-Z

  74. Dazzo, F.B., J. Liu, G. Tang, C. Gross, C. Reddy, C. Monosmith, G. Zhu, J. Wang, M. Li, N. Philips, A. Baruti, I. Leader, S. Zamani, R. Verhelst, C. Radek, K. Klemmer, K. Farrell, J. McCully, B. Krasnov, Zhou Ji, P. Smith, S. Kneeshaw, I. Ganesan, D. McGarrell, M. Leader-Wineland, R. Hollingsworth, A. Smucker, S. Nakano, A. Squartini, P. Mateos, S. Gantner, and Y. Yanni. 2011. CMEIAS v3.1: Advanced Computational Tools of Image Analysis Software Designed to Strengthen Microscopy-Based Approaches for Understanding Microbial Ecology at Multiple Spatial Scales. All Investigator Meeting, Long-Term Ecological Research program, April 15, 2011, Kellogg Biological Station, Hickory Corners, MI. [link to most recent update]

  75. Robledo, M., J. I. Jimenez-Zurdo, M. Jose Soto, E. Velazquez, F. B. Dazzo, E. Martinez-Molina, and P. F. Mateos. 2011. Development of functional symbiotic white clover root hairs and nodules requires tightly regulated production of Rhizobial cellulase CelC2. Molec. Plant-Microbe Interact. 24: 796-807. DOI: 10.1094/MPMI-10-10-0249

  76. Wu, L., L. Feinstein, O. Valverde-Barrantes, M. Kershner, L. Leff and C. Blackwood. 2011. Placing the effect of leaf litter diversity on saprophytic microorganisms in the context of leaf type and habitat. Microbial Ecology 61: 399-409. DOI: 10.1007/s00248-010-9760-0

  77. Hill, W., B. Roberts, S. Francoeur and S. Fanta. 2011. Resource synergy in stream periphyton communities. J. Ecology 99: 454-463. DOI: 10.1111/j.1365-2745.2010.01785.x

  78. Dazzo, Frank B., J. Liu, A. Jain, K. Klemmer, N. Philips, G. Tang, Z. Ji, C. Gross, C. Reddy, C. Monosmith, G. Zhu, J. Wang, M. Li, C. Radek, D. McGarrell, J. Tiedje, I. Leader, S. Zamani, A. Baruti, P. Smith, S. Gantner, Y. Yanni, I. Ganesan, S. Kneeshaw, C. Hagen, R. Chandler, M. Thanyakarn, A. Rosaen, S. Nakano. 2011. CMEIAS v. 3.1: advanced computational tools of image analysis software designed to strengthen microscopy-based approaches for understanding microbial ecology at single-cell resolution. Tiedje Symposium on Microbial Genomics & Ecology, 29 October 2011, Michigan State University. [link to most recent update]

  79. Dazzo, F.B., J. Liu, G. Tang, C. Gross, C. Reddy, C. Monosmith, G. Zhu, J. Wang, M. Li, N. Philips, K. Klemmer, Zhou Ji, C. Radek, D. McGarrell, I. Leader, S. Zamani, A. Baruti, P. Smith, S. Kneeshaw, I. Ganesan, M. Thanyakarn, R. Chandler, C. Hagen, I. Folland, S. Xia, M. Cavanaugh, A. Rosaen, K. Ogbenna, R. Hollingsworth, A. Smucker, S. Nakano, A. Squartini, P. Mateos, S. Gantner, Y. Yanni. 2012. CMEIAS v3.10: Advanced Computational Tools of Image Analysis Software Designed to Strengthen Microscopy-Based Approaches for Understanding Microbial Ecology. All Investigator Meeting, Long-Term Ecological Research program, March 15, 2012, Kellogg Biological Station, Hickory Corners, MI. [link to most recent update]

  80. *Dazzo, F. 2012. CMEIAS-aided microscopy of the spatial ecology of individual bacterial interactions involving cell-to-cell communication within biofilms. Sensors 12: 7047-7062. DOI: 10.3390/s120607047

  81. Trevisan, R., R. Pertile, V. Bronamonte, F. B. Dazzo and A. Squartini. 2012. Dinophyceae fluctuations in two alpine lakes of contrasting size during a 10-year fortnightly survey. J. Microbiology and Biotechnology. 22: 754-762. DOI: 10.4014/jmb.1110.10005

  82. Somvanshi, Vishal S., Rudolph E. Sloup, Jason M. Crawford, Alexander R. Martin, Anthony J. Heidt, Kwi-suk Kim, Jon Clardy, Todd A. Ciche. 2012. A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. Science 337: 88-93. DOI: 10.1126/science.1216641 (See Supplementary Information here.)

  83. Robeldo, M., L. Rivera, J., I.J. Jimenez-Zurdo, R. Rivas, F.B. Dazzo, E. Velazquez, E. Martinez-Molina, A. Hirsch, and P. F. Mateos. 2012. Role of Rhizobium endoglucanase CelC2 in cellulose biosynthesis and biofilm formation on plant roots and abiotic surfaces. Microbial Cell Factories 11: 125-132. DOI: 10.1186/1475-2859-11-125

  84. Ehrlich, K., B. Mack, Q. Wer, P. Li, L. Roze, F. Dazzo, J. Cary, D. Bhatnagar and J. Linz. 2012. Association with AflR in endosomes reveals new functions for AflJ in aflatoxin biosynthesis. Toxins 4: 1582-1600. DOI: 10.3390/toxins4121582

  85. Kist, D.L. 2012. Reguladores da variação temporal e espacial da comunidade bacteriana em lagoa rasa subtropical. Ph.D. Dissertation, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.

  86. Dazzo, Frank B. and Youssef G. Yanni. 2013. CMEIAS: an improved computing technology for quantitative image analysis of root colonization by rhizobacteria in situ at single-cell resolution. In: Frans DeBruijn (Ed.) Molecular Microbial Ecology of the Rhizosphere, Vol. 2, Chapter 69, pp. 733-742. J Wiley & Sons, NY. DOI: 10.1002/9781118297674.ch69

  87. Dazzo, Frank B. and Stephan Gantner. 2013. In situ calling distances and high population independent N-acylhomoserine lactone-mediated communication on plant root surfaces. In: Frans DeBruijn (Ed.) Molecular Microbial Ecology of the Rhizosphere, Vol. 2, Chapter 74, pp. 785-788. J Wiley & Sons, NY. DOI: 10.1002/9781118297674.ch74

  88. *Dazzo, F.B., J. Liu, C. Gross, C. Reddy, C. Monosmith, N. Philips, C. Radek, K. Klemmer, Zhou Ji, P. Smith, I. Ganesan, D. McGarrell, M. Thanyakarn, I. Folland, S. Xia, M. Cavanaugh, K. Ogbenna, A. Turmo, J. Ho, N. Duque-Feghali, K. Card, A. Baruti, N. Haque, U. Adia-Nimuwa, D. Colbry, T. McCann, C. Hagen, I. Leader, S. Zamani, R. Verhelst, S. Gantner and Y. Yanni. 2013. CMEIAS v3.10: Advanced computational tools of image analysis software designed to strengthen microscopy-based approaches for understanding microbial ecology. 2013 All-Scientist Long-Term Ecology Research meeting, April 4-5, 2013, Kellogg Center, MSU. [link to most recent update]

  89. *Dazzo, Frank B., Kevin J. Klemmer, Ryan Chandler and Youssef G. Yanni. 2013. In situ ecophysiology of microbial biofilm communities analyzed by CMEIAS computer-assisted microscopy at single-cell resolution. Diversity (Special issue on Microbial Ecology and Diversity) 5:426-460. DOI: 10.3390/d5030426.

  90. *Dazzo, F.B. and C.A. Gross. 2013. CMEIAS Quadrat Maker: a digital software tool to optimize grid dimensions and produce quadrat images for landscape ecology spatial analysis. J. Ecosystem & Ecography 3(4)(1000136):1-4. DOI: 10.4172/2157-7625.1000136.

  91. They, N.H., D.M. Marques, R.S. Souza and L.R. Rodrigues. 2013. Short-term photochemical and biological unreactivity of macrophyte-derived dissolved organic matter in a subtropical shallow lake. J. Ecosystems vol. 2013, Article ID 316709, 9 pages. DOI: 10.15/2013/15316709

  92. Gisela, C., H. Yarelis, P. Donald, P. Aleivi, P. Estefany, P. Josxy and R. Anthony. 2013. Length variation in cell and patterns formed in swarming Proteus strain sp. isolated from the Lake Maracaibo. Revista de la Sociedad Venezolana de Microbiologia 33: supplement, 10th Venezuelan Congress of Microbiology. [scroll down to view publication]

  93. A. Bohmer. 2013. Response of the cold-water coral Desmophyllum dianthus to future CO2 concentration. MS Biology Thesis, Carl von Ossietzy University, Oldenburg Germany.

  94. *Folland, I., D. Trione and F.B. Dazzo. 2014. Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities. Microbial Ecology 68(3): 596-610. DOI: 10.1007/s00248-014-0410-9

  95. Dazzo, F.B., I. Ganesan and Y. Yanni 2014. Spatial ecology of rhizobacterial colonization on roots analyzed by CMEIAS computer-assisted microscopy at single-cell resolution. In: D. P. Singh and H. Singh (eds.) Trends in Soil Ecology, Chapter 4, pp. 67-92, Studium Press, Houston.

  96. Trevisan, R., M. Picarella, F.B. Dazzo, S. Bona, G. Morabito and A. Squartini. 2014. Using a morpho-functional approach to assess phytoplankton dynamics in two adjacent high-mountain lakes: a 10-year survey. Journal of Limnology 73(3): 409-420. DOI: 10.4081/jlimnol.2014.891

  97. Jeremic, M., R. Jeremic, and D. Jovanovic. 2014. A comprehensive morphometric analysis of the internal thoracic artery with emphasis on age and gender. 9th Int. Medical Students' Congress, Univ. Novi Sad, Serbia, p. 34.

  98. * Ji, Z., K. J. Card, F. B. Dazzo. 2015. CMEIAS JFrad: a digital computing tool to discriminate the fractal geometry of landscape architectures and spatial patterns of individual cells in microbial biofilms. Microbial Ecology 69: 710-720. DOI: 10.1007/s00248-014-0495-1.

  99. Chande, C. and R. Phadke. 2015. A pico-liter semi-automated screening method for morphological identification of microorganisms from environmental samples. Conference Paper: Microfluidics and Lab-on-a-Chip India, Mumbai, January 2015. DOI: 10.13140/2.1.3342.3688.

  100. Dazzo, F.B. and B. Niccum. 2015. Use of CMEIAS image analysis software to accurately compute attributes of cell size, morphology, spatial aggregation and color segmentation that signify in situ ecophysiological adaptations in microbial biofilm communities. Computation 3: 72-98. DOI: 10.3390/computation3010072

  101. Dazzo, F. B., J. Liu, K. Kwatra, C. Gross, N. Philips, C. Monosmith, K. Klemmer, Z. Ji, C. Gidcumb, R. Shah, D. McGarrell, I. Folland, I. Ganesan, P. Smith, Y. Yanni, S. Gantner, P. Jha, K. Card, S. Lundback, B. Niccum, S. Zamani, I. Leader, D. Stawkey, B Patel, A. Jones, and T. Abukar. 2015. CMEIAS v3.10: Advanced computational tools of image analysis software designed to strengthen microscopy-based approaches for understanding microbial ecology. 2015 All-Scientist Meeting Kellogg Biological Station Long-Term Ecological Research, April 15-16, 2015, Kellogg Center, MSU. [link to most recent update]

  102. Figueiro, R., A. Calvet, L. H. Gil-Azevedo, T. Nascimento-Docile, R. F. Monteiro and M. Maia-Herzog. 2015. Evidence of phenotypic plasticity of larvae of Simulium subpallidum Lutz in different streams from the Brazilian Cerrado. Rev. Braziliera Entomologia 59: 28-31. DOI: 10.1016/j.rbe.2015.02.003

  103. Sayinci, B. 2015. The influence of strainer types on the flow and droplet velocity characteristics of ceramic flat-fan nozzles. Turk. J. Agric. Forestry 39: 1-13. DOI: 10.3906/tar-1411-140

  104. Majdi, N., W. Traunspurger, J. Richardson and A. Lecerf. 2015. Small stonefly predators affect microbenthic and meiobenthic communities in stream leaf packs. Freshwater Biology 60(9): 1930-1943. DOI: 10.1111/fwb.12622

  105. Dazzo, F. B., Y. G Yanni, A. Jones, A. Y. Elsadany. 2015. CMEIAS bioimage informatics that define the landscape ecology of immature microbial biofilms developed on plant rhizoplane surfaces. AIMS Bioengineering 2(4): 469-486. DOI: 10.3934/bioeng.2015.4.469

  106. Dazzo, F. B., Y. Yanni, J. Liu, K. Kwatra, A. Jain, C. Gross, N. Philips, C. Monosmith, C. Klemmer, Z. Ji, B. Niccum, I. Ganesan, N. DeSilva, D. McGarrell, I. Folland, K. Card, P. Jha, S. Lundback, W. Tan, M. Upadhye, D. Stawkey, A. Jones, D. Gusfa, K. Prater, N. Bakir, R. Sexton, M. Shears, and A. Makhoul. 2016. CMEIAS v4.0: Advanced computational tools of bioimage informatics software designed to strengthen microscopy-based approaches for understanding microbial ecology. 2016 All-Scientist Meeting and Investigators Field Tour, Kellogg Biological Station Long-Term Ecological Research, Sept. 16-17, 2016. [most recent update text summary]