From January 7 to April 6, Dr. Skaidrė Supronienė, head of the Microbiology Laboratory, head researcher of Institute of Agriculture, Lithuanian Research Centre and Forestry (LAMMC) undertook a research internship at the University of Florence (Italy).
The aim of the internship was to establish closer contacts with the scientists of the University of Florence working in the field of agricultural microorganisms, to adopt their experience in commercialization of scientific production and services, and to gain knowledge about the application of the Phenotype MicroArray (PM) method in microorganism research.
Professors and researchers of the Department of Microbiology carry out research and training activities in the field of agricultural and environmental microbiology. Scientists from this department have been among the first (since 2005) to introduce PM technology for microorganism analysis using Biolog system. During the period of application of the PM method, they improved a number of PM technologies, published high-level publications and held three conferences on PM application (Florence Conference Phenotype MicroArray, 2008, 2010 and 2015). In September this year, it is planned to organize the PM summer courses.
In PM studies, different phenotypes of microorganisms are determined by differences in their ability to absorb various sources of carbon, nitrogen, phosphorus and sulphur, their sensitivity to the medium pH and chemicals of different classes (heavy metals, disinfectants, antibiotics, etc., estimated at around 2000 different sources). Incubation of microplates inoculated with the microorganisms, reading and collection of data are performed automatically by the OmniLog instrument. OmniLog is both a temperature-controlled incubator and an automated microplate reader that contains up to fifty 96-well microplates accommodated on 25 trays. Plates reading is performed by a CCD camera housed inside the rear of the instrument that captures the image of each plate every fifteen minutes throughout the user-defined incubation period.
OmniLog PM software includes: 1) data collection program; 2) kinetic module of data processing; 3) parametric module for data analysis, including comparison functions, calculation of specific kinetic curve parameters (height, area, slope, delay time, etc.) and data export functions.
Technological principles of PM analysis are described in detail in the standardized Biolog methodology, but they cover only a small number of specific microorganisms, thus in many cases the success of the study depends on the operator’s experience and ability to improve the underlying technology.
The open access Biolog system, available at the Microbiology Laboratory of the Institute of Agriculture, LAMMC has so far been used only for physiological profiling of soil microorganism communities. The knowledge and experience gained during the internship on the application of PM technologies will contribute to increasing the scientific, practical and commercial competence of the laboratory staff. The acquired experience will be shared with laboratory-trained and doctoral students.
This internship has helped to identify the research interests linking both institutions, to project potential prospects for future collaboration, and to exchange doctoral students for further training. Practical sessions provided valuable PM research data on the different strains of Rhizobium leguminosarum that are planned to be used for the preparation of a joint scientific publication. The research findings are also expected to be presented in the Congress “Microbiology 2019” organised by the University of Florence on June19–22.