Partial Formalization: An Approach for Critical Analysis of Definitions and Methods Used in Bulk Extraction-Based Molecular Microbial Ecology

DOI: 10.4236/oje.2015.58033   PDF   HTML   XML   4,016 Downloads   4,475 Views   Citations


Partial formalization, which involves the development of deductive connections among statements, can be used to examine assumptions, definitions and related methodologies that are used in science. This approach has been applied to the study of nucleic acids recovered from natural microbial assemblages (NMA) by the use of bulk extraction. Six pools of bulk-extractable nucleic acids (BENA) are suggested to be present in a NMA: (pool 1) inactive microbes (abiotic-limited); (pool 2) inactive microbes (abiotic permissive, biotic-limited); (pool 3) dormant microbes (abiotic permissive, biotic-limited, but can become biotic permissive); (pool 4) in situ active microbes (the microbial community); (pool 5) viruses (virocells/virions/cryptic viral genomes); and (pool 6) extracellular nucleic acids including extracellular DNA (eDNA). Definitions for cells, the microbial community (in situ active cells), the rare biosphere, dormant cells (the microbial seed bank), viruses (virocells/virions/cryptic viral genomic), and diversity are presented, together with methodology suggested to allow their study. The word diversity will require at least 4 definitions, each involving a different methodology. These suggested definitions and methodologies should make it possible to make further advances in bulk extraction-based molecular microbial ecology.

Share and Cite:

Klein, D. (2015) Partial Formalization: An Approach for Critical Analysis of Definitions and Methods Used in Bulk Extraction-Based Molecular Microbial Ecology. Open Journal of Ecology, 5, 400-407. doi: 10.4236/oje.2015.58033.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Fang, F.C. and Casadevall, A. (2012) Reforming Science. Microbe, 7, 254-255.
[2] Rudner, R.S. (1966) Philosophy of Social Science. Prentice Hall, Englewood Cliffs.
[3] Lewis, R.W. (1977) Biological Theories: Formalization and Teaching. A Selected List of References That Discuss and Illlustrate Partial Formalization of Theories. 28th Annual AIBS Meeting, Michigan State University, East Lansing.
[4] Lederberg, J. (1959) Genes and Antibodies. Science, 129, 1649-1653.
[5] Monod, J., Wyman, J. and Changeux, J.-P. (1965) On the Nature of Allosteric Transitions: A Plausible Model. Journal of Molecular Biology, 12, 88-118.
[6] Suppes, P. (1968) The Desirability of Formalization in Science. Journal of Philosophy, 65, 651-664.
[7] Forterre, P. (2013) The Virocell Concept and Environmental Microbiology. The ISME Journal, 7, 233-236.
[8] (1993) Merriam Webster’s Collegiate Dictionary. 10th Edition, Merriam-Webster Inc., Springfield.
[9] Klein, D.A. (2007) Seeking Microbial Communities in Nature: A Postgenomic Perspective. Microbe, 2, 591-595.
[10] Bjornsson, L., Hugenholtz, P., Tyson, G.W. and Blackall, L.L. (2002) Filamentous Chloroflexi (Green Non-Sulfur Bacteria) Are Abundant in Wastewater Treatment Processes with Biological Nutrient Removal. Microbiology, 148, 2309-2318.
[11] Froehlich, J. and Koenig, H. (2000) New Techniques for Isolation of Single Prokaryotic Cells. FEMS Microbiology Reviews, 24, 567-572.
[12] Swan, B.K., Tupper, B., Sczyrba, A., Lauro, F.M., Martinez-Garcia, M., González, J.M., et al. (2013) Prevalent Genome Streamlining and Latitudinal Divergence of Planktonic Bacteria in the Surface Ocean. Proceedings of the National Academy of Sciences of the United States of America, 110, 11463-11468.
[13] Czechowska, K., Johnson, D.R. and van der Meer, J.R. (2008) Use of Flow Cytometric Methods for Single-Cell Analysis in Environmental Microbiology. Current Opinion in Microbiology, 11, 205-212.
[14] Kalyuzhnaya, M.G., Zabinsky, R., Bowerman, S., Baker, D.R., Lidstrom, M.E. and Chistoserdova, L. (2006) Fluorescence in Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations. Applied and Environmental Microbiology, 72, 4293-4301.
[15] Harrison, B.K. and Orphan, V.J. (2012) Method for Assessing Mineral Composition Dependent Patterns in Microbial Diversity Using Magnetic and Density Separation. Geomicrobiology Journal, 29, 435-449.
[16] Martinez-Garcia, M., Swan, B.K., Poulton, N.J., Gomez, M.L., Masland, D., Sieracki, M.E. and Stepanauskas, R. (2012) High-Throughput Single-Cell Sequencing Identifies Photoheterotrophs and Chemoautotrophs in Freshwater Bacterioplankton. The ISME Journal, 6, 113-123.
[17] Stepanauskas, R. (2012) Single Cell Genomics: An Individual Look at Microbes. Current Opinion in Microbiology, 15, 1-8.
[18] Woyke, T., Xie, G., Copeland, A., González, J.M., Han, C., Kiss, H., et al. (2009) Assembling the Marine Metagenome, One Cell at a Time. PLoS ONE, 4, e5299.
[19] Swan, B.K., Martinez-Garcia, M., Preston, C.M., Sczyrba, A., Woyke, T., Lamy, D., et al. (2011) Potential for Chemolithoautotrophy among Ubiquitous Bacteria Lineages in the Dark Ocean. Science, 333, 1296-1300.
[20] Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.-F., et al. (2013) Insights into the Phylogeny and Coding Potential of Microbial Dark Matter. Nature, 499, 431-437.
[21] Hatzenpichler, R. (2012) Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea. Applied and Environmental Microbiology, 78, 7501-7510.
[22] Ghosh, D., Roy, K., Williamson, K.E., White, D.C., Wommack, K.E., Sublette, K.L. and Radosevich, M. (2008) Prevalence of Lysogeny among Soil Bacteria and Presence of 16S rRNA and trzN Genes in Viral-Community DNA. Applied and Environmental Microbiology, 74, 495-502.
[23] Forterre, P. and Prangishvili, D. (2009) The Great Billion-Year War between Ribosome- and Capsid-Encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties. Annals of the New York Academy of Sciences, 1178, 65-77.
[24] Feinstein, L.M., Sul, W.J. and Blackwood, C.B. (2009) Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil. Applied and Environmental Microbiology, 75, 5428-5433.
[25] Klein, D.A. and Paschke, M.W. (2004) Filamentous Fungi: The Indeterminate Lifestyle and Microbial Ecology. Microbial Ecology, 47, 224-235.
[26] del Giorgio, P.A. and Gasol, J.M. (2008) Physiological Structure and Single-Cell Activity in Marine Bacterioplankton. in Microbial Ecology of the Oceans. John Wiley & Sons, Inc., Hoboken, 243-298.
[27] Luna, G.M., Manini, E. and Danovaro, R. (2002) Large Fraction of Dead and Inactive Bacteria in Coastal Marine Sediments: Comparison of Protocols for Determination and Ecological Significance. Applied and Environmental Microbiology, 68, 3509-3513.
[28] Gobet, A., Boer, S.I., Huse, S.M., van Beusekom, J.E.E., Quince, C., Sogin, M.L., et al. (2012) Diversity and Dynamics of Rare and of Resident Bacterial Populations in Coastal Sands. The ISME Journal, 6, 542-553.
[29] Shade, A., Hogan, C.S., Klimowicz, A.K., Linske, M., McManus, P.S. and Handelsman, J. (2012) Culturing Captures Members of the Soil Rare Biosphere. Environmental Microbiology, 14, 2247-2252.
[30] Gilbert, F., Galgani, F. and Cadiou, Y. (1992) Rapid Assessment of Metabolic Activity in Marine Microalgae: Application in Ecotoxicological Tests and Evaluation of Water Quality. Marine Biology, 112, 199-205.
[31] James, M.R., Hall, J.A. and Barrett, D.P. (1996) Grazing by Protozoa in Marine Coastal and Oceanic Ecosystems off New Zealand. New Zealand Journal of Marine and Freshwater Research, 30, 313-324.
[32] Gest, H. (2003) Anaerobes in the Recycling of Elements in the Biosphere. In: Ljungdahl, L.G., Adams, M.W., Barton, L.L., Ferry, J.G. and Johnson, M.K., Eds., Biochemistry and Physiology of Anaerobic Bacteria, Springer-Verlag, New York, 1-10.
[33] Klein, D.A. (2015) QIIME Better Described as EMSAP? Microbe, 10, 90-91.
[34] Bockelmann, U., Janke, A., Kuhn, R., Neu, T.R., Wecke, J., Lawrence, J.R. and Szewzyk, U. (2006) Bacterial Extracellular DNA Forming a Defined Network-Like Structure. FEMS Microbiology Letters, 262, 31-38.
[35] Pietramellara, G., Ascher, J., Borgogni, F., Ceccherini, M.T., Guerri, G. and Nannipieri, P. (2009) Extracellular DNA in Soil and Sediment: Fate and Ecological Relevance. Biology and Fertility of Soils, 45, 219-235.
[36] Dell'Anno, A. and Danovaro, R. (2005) Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning. Science, 309, 2179.
[37] Bass, J.I.F., Russo, D.M., Gabelloni, M.L., Geffner, J.R., Giordano, M., Catalano, M., et al. (2010) Extracellular DNA: A Major Proinflammatory Component of Pseudomonas Aeruginosa Biofilms. The Journal of Immunology, 184, 6386-6395.
[38] Baas Becking, L.G.M. (1934) Geobiologie of Inleiding Tot De Milieukunde. W.P. Van Stockum & Zoon, The Hague.
[39] De Wit, R. and Bouvier, T. (2006) Everything Is Everywhere, but, the Environment Selects; What Did Baas Becking and Beijerinck Really Say? Environmental Microbiology, 8, 755-758.

comments powered by Disqus

Copyright © 2020 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.