An integrated method for taxonomic identification of microorganisms.

Yu E Uvarova,E A Demidov,S V Shekhovtsov,N M Slynko,T N Goryachkovskaya,A S Rozanov,S E Peltek,A V Bryanskaya,K V Starostin,V N Shlyakhtun

doi:10.18699/vj20.630

Abstract

For accurate species-level identification of microorganisms, researchers today increasingly use a combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e.g., the relationship with oxygen, type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms analyzed were combined into separate groups based on the similarities of their phenotypic characteristics. This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps, may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other collections

Highlights

Identification of prokaryotes, which are morphologically less diverse than eukaryotes, is based on a wide variety of phenotypic – and in many cases genotypic – characteris tics
During the description and identification of bacteria, researchers study their cultivation properties, morphology, cell organization, physiological and biochemical features, chemical composition of cells, GC content of DNA, nucleotide sequence of the gene coding for 16S ribosomal RNA, and other phenotypic and genotypic characteristics
The optimal temperature and pH for growth, NaCl tole rance, catalase and urease oxidase activities, anaerobic growth, amylolytic and caseinase activities, and other activities as well as the ability to utilize various substrates were determined according to Netrusov et al (2005) and Logan & De Vos (2009)

Summary

Introduction

Identification of prokaryotes, which are morphologically less diverse than eukaryotes, is based on a wide variety of phenotypic – and in many cases genotypic – characteris tics. During the description and identification of bacteria, researchers study their cultivation properties, morphology, cell organization, physiological and biochemical features, chemical composition of cells, GC content of DNA, nucleotide sequence of the gene coding for 16S ribosomal RNA (rRNA), and other phenotypic and genotypic characteristics

Objectives

Methods

Results

Discussion

Conclusion