Differentiation of Micromonospora Isolates from a Coastal Sediment in Wales on the Basis of Fourier Transform Infrared Spectroscopy, 16S rRNA Sequence Analysis, and the Amplified Fragment Length Polymorphism Technique

Abstract

A number of actinomycetes isolates were recovered from coastal sediments in Aberystwyth (Wales, United Kingdom) with standard isolation techniques. Most of them were putatively assigned to the genera Streptomyces and Micromonospora on the basis of their morphological characteristics, and there appeared to be no difference whether the isolation media contained distilled water or seawater. A group of 20 Micromonospora isolates was selected to undergo further polyphasic taxonomic investigation. Three approaches were used to analyze the diversity of these isolates, 16S rDNA sequencing, fluorescent amplified fragment length polymorphism (AFLP), and Fourier transform infrared spectroscopy (FT-IR). The 16S rDNA sequence analysis confirmed that all of these isolates should be classified to the genus Micromonospora, and they were analyzed with a group of other Micromonospora 16S rDNA sequences available from the Ribosomal Database Project. The relationships of the 20 isolates were observed after hierarchical clustering, and almost identical clusters were obtained with these three techniques. This has obvious implications for high-throughput screening for novel actinomycetes because FT-IR spectroscopy, which is a rapid and reliable whole-organism fingerprinting method, can be applied as a very useful dereplication tool to indicate which environmental isolates have been cultured previously.

The genus Micromonospora is widespread in legume root nodules: the example of Lupinus angustifolius

“…Micromonospora is the type genus of the family Micromonosporaceae and contains microorganisms with potential biotechnological applications (Ismet et al, 2004;Thawai et al, 2004). Micromonosporae have been isolated from diverse habitats including soil, water and marine sediments (Kawamoto, 1989;Zhao et al, 2004;Maldonado et al, 2005;de Menezes et al, 2008). Recently, strains of this genus have also been recovered from diverse plant tissues, especially nitrogen-fixing nodules (Valdés et al, 2005;Trujillo et al, 2006Trujillo et al, , 2007Garcia et al, 2010).…”

Discrimination of Enterobacterial Repetitive Intergenic Consensus PCR Types of Campylobacter coli and Campylobacter jejuni by Fourier Transform Infrared Spectroscopy

“…The reference work of Helm and colleagues (14) prompted a large amount of research, reviewed by Mariey and colleagues (26). Since 2001, more groups and genera have been studied: Lactobacillus (3,36,37), Carnobacterium (21), Bacillus (1), Brucella (27), Acinetobacter (52), yeasts (20,41), enterococci (7,10,19), coryneforms (24,34), and actinomycetes (54). In all of them, the technique has shown qualities, such as high discriminatory power and reproducibility, allowing the differentiation of taxonomic entities at the species or subspecies level on the basis of changes in the IR absorption patterns of the microbial cell.…”

Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius

“…Members of Micromonospora are widely distributed in aquatic, marine and terrestrial environments (Kawamoto, 1989;Zhao et al, 2004;Maldonado et al, 2005) but, recently, members of this genus have also been recovered from diverse plant tissues, especially nitrogen-fixing root nodules (Valdés et al, 2005;Trujillo et al, 2006b;M. E. Trujillo, unpublished observations).…”