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New CMEIAS Image Analysis Software for Computer-Assisted Microscopy of Microorganisms and Their Ecology

Published online by Cambridge University Press:  14 March 2018

Frank B. Dazzo
Frank B. Dazzo*
Affiliation:
Michigan State University
*
dazzo@msu.edu

Extract

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Microscopy is one of the most important techniques in microbial ecology, since this is the most direct approach to examine the microbe's world from its own perspective and spatial scale. The value of quantitative microscopy in studies of microbial ecology can be increased even further when used in conjunction with computer assisted image analysis. There are two main advantages of using digital image processing and pattern recognition techniques in conjunction with microscopy for quantitative studies of microbial ecology. First, automatic image analysis reduces the amount of tedious work with microscopes needed to accurately quantify in situ morphological diversity, abundance and metabolic activity of microbes. Secondly, these techniques provide an important quantitative tool that can significantly enhance the polyphasic analysis of the structure, diversity, spatial features, and functions of complex microbial communities in situ without cultivation.

Type
Research Article
Information
Microscopy Today , Volume 12 , Issue 3 , May 2004 , pp. 18 - 23
Copyright
Copyright © Microscopy Society of America 2004

References

Citations:

1) Liu, J., Dazzo, F.B., Glagoleva, O., Yu, B., Jain, A.K.. 2001. CMEIAS: A computer-aided system for the image analysis of bacterial morphotypes in microbial communities, Microbial Ecology 41(3):173–194 and 42:215. http://cme.msu.edu/cmeias/ Google Scholar
2) Wilcox, C.D., Dove, S.B., Doss-McDavid, W., and Greer, D.B.. 1997. UTHSCSA ImageTool Ver. 1.27, http://www.ddsdx.uthscsa.edu/dig/itdesc.html.Univ. of Texas Health Science Center, San Antonio, TX, USA.Google Scholar
Below is a list of published studies thai include data acquired by CMEIAS. We will periodically update this list with references sent to us by CMEIAS users. Please send references in the format shown to or Google Scholar
Dazzo, F., and Wopereis, J.. 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.Google Scholar
Dazzo, F.B., Yanni, Y.G., Rizk, R., de Bruijn, F., Rademaker, J., Squartini, A., Corich, V., Mateos, P., Marti nez-Molina, E., Velazquez, E., Biswas, J., Hernandez, R., Ladha, J.K., Hill, J., Weinman, J., Rolfe, B., Vega-Hernandez, M., Bradford, J.J., Holling-sworth, R.I., Ostrom, P., Marshall, E., Jain, T., Orgambide, G., Philip-Hollingsworth, S., Triplett, E., Malik, K., Maya-Flores, J., Hartmann, A., Umali-Garcia, M., and Izaguirre-Mayoral, M.L.. 2000. Progress in multi-national collaborative studies on the beneficial association between Rhizobium leguminosarum bv, trifolii and rice. In Ladha, J.K. and Reddy, P.M. (eds.), The Quest for Nitrogen Fixation in Rice. International Rice Research Institute, Manila, The Philippines, pp. 167–189.Google Scholar
A., Fernandez, Hashsham, S., Dollhopf, S., Raskin, L., Glagoleva, O., Dazzo, F.B., Hickey, R., Criddle, C., and Tiedje, J.M.. 2000. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4058–4067.Google Scholar
Hashsham, S., Fernandez, A., Dollhopf, S., Dazzo, F.B., Tiedje, J.M., Hickey, R., and Criddle, C.S.. 2000. Parallel processing of substrate correlates with greater functional stability in melhanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66: 4050–4057.Google Scholar
Liu, J., Dazzo, F.B., Glagoleva, O., Yu, B., and Jain, A.. 2001. CMEIAS: a computer-aided system for the image analysis of bacterial morphotypes in microbial communities. Microbial Ecology 41: 173–194 and 42:215.Google Scholar
Dollhopf, S., Hashsham, S.A., Dazzo, F.B., Criddle, C., and Tiedje, J.M.. 2001. The impact of fermentative organisms on carbon flow in methanogenic systems under constant low substrate conditions. Appl. Microbiol. Biotechnol 56: 531–538.Google Scholar
Liu, J., Liu, F-I, Marshall, E., and Dazzo, F.B.. 2000, CMEIAS© Software for Computer-Assisted Microscopy of Microbial Communities. Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture, Michigan State Univ. East Lansing, MI.Google Scholar
Dazzo, F.B., Liu, J., Liu, F-I., and Robertson, G.P.. 2001. In situ analysis of microbial communities on the 2 day-old white clover rhizoplans and the mature BT-corn phylloplane using CMEIAS innovative software for cuinpliter-assisted microscopy. Annual Mtg. Long-Term Ecological Research in Row-Crop Agriculture, Michigan State Univ. East Lansing, MI.Google Scholar
Yanni, Y.G., Rizk, R.Y., Abd El-Fattah, F.K., Squartini, A., Corich, V., Giacomini, A., de Brnijn, F., Rademaker, J., Maya-Flores, J., Osrrom, P., Vega-Hernandea, M., Hollingsworth, R.L., Martinez-Molina, E., Mateos, P., Velazquez, E., Wopereis, J., Triplett, E., Umali-Garcia, M., Anarna, J.A., Rolfe, B.G., Ladha, J.K., Hill, J., Mujoo, R., Ng, P.K., and Dazzo, F.B.. 2001. The beneficial plant growth-promoting association of Rhizobiitm leguminosariim bv. trifolii with rice roots. Austr. J. Plant Physiol. (now Functional Plant Biology) 28: 845–870.Google Scholar
McDermott, T.R., and Dazzo, F.B.. 2002. Use of fluorescent antibodies for studying the ecology of soil- and plant-associated microbes. In Hurst, C., Crawford, R.C., Knudsen, G.R., Mclnerney, M.J., and Stetzenbach, L.D. (eds.), Manual of Environmental Microbiology 2nd ed., Chapter 28, p. 615–626, American Society for Microbiology Press, Washington, DC.Google Scholar
Reddy, C., Liu, J., Wadekar, M., Prabhu, A., Trione, D., Marshall, E., Zurdo, J., Liu, F-I., Urbance, J., and Dazzo, F.B.. 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 Stale Univ. East Lansing, ML. Google Scholar
Dazzo, F.B., Liu, J., Prabhu, A., Reddy, C., Wadekar, M., Peretz, R., Bollempalli, R., Trione, D., Marshall, E., Zurdo, J., Hammond, H., Wang, J., Li, M., McGarrell, D., Gore, A., Maya-Flores, J., Gantner, S., and Hollingsworth, N.. 2003 CMEIAS v. 3.0: Integrative software package Eo strengthen micros copy-based approaches tor understanding microbial ecology. 2003 Annual Mtg., Long-Term Ecological Research in Row-Crop Agriculture. Michigan State Univ. Easl Lansing, MI. (Summary of CMEIAS upgrade currently under development.) <http://lrer.kbs.msu.edu/Meetings/2003_All_Inv_.Meeting/Abstracts/dazzo.htm>>Google Scholar
Dazzo, F.B., Joseph, A.R., Gomaa, A.B., Yanni, Y.G., and Robertson, G.P.. 2003. Quantitative indices for the autecological biogeography of a Rhizobium endophyte of rice at macro and micro spatial scales. Symbiosis 34: 1 47–158.Google Scholar
Dazzo, F.B. 2004. Applications of quantitative microscopy in studies of plant surface microbiology. In: Varma, A., Abbott, L., Werner, D., and Hampp, R. (eds.), Plant surface microbiology. Springer-Verlag, Germany, pp. 503–550.Google Scholar