Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae

Abstract

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).

Identification of Bacterial Groups Preferentially Associated with Mycorrhizal Roots of Medicago truncatula

“…The 16S rRNA gene fragment of the corresponding OTUs presented 99 and 97% similarity with that of C. fungivorans and M. petroleiphilum. C. fungivorans was previously described as a chitinolytic bacterium and to grow at the expense of different soil fungi in soil (9). These species differ from those described by Artursson and Jansson (4) as being preferentially associated with AM fungi, but their study was made directly in a fallow soil and not on roots.…”

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils

“…Colony PCR was performed using fresh colonies that were taken from 10-fold-diluted TSB agar after 24 h of incubation (Rademaker et al, 1997). Visual comparison of the banding profiles and UPGMA clustering of strains using Pearson's product-moment correlation coefficients in the Bionumerics version 3.5 software package revealed that the majority (n518) of the new isolates fell within clusters B and D described previously (De Boer et al, 2004). Only one of the new isolates fell in cluster A.…”

“…Collimonas strains have the interesting ability to grow at the expense of living fungal hyphae (mycophagy), albeit under laboratory conditions (De Boer et al, 2001. The taxonomy of these bacteria was examined using genomic fingerprinting (BOX-PCR), sequencing of 16S rRNA genes and physiological characterization, which revealed four clusters of strains (De Boer et al, 2004). So far, only cluster C strains have been formally classified, as the novel species Collimonas fungivorans.…”

“…After 2 days of incubation at 20 u C on 10-fold-diluted TSB agar, colonies are flat, translucent and whitish with a yellowish central part and 3-7 mm in diameter with a granular-structured periphery (colony type II) (De Boer et al, 2004). Cells exhibit oxidase and weak catalase activity.…”

“…After 2 days of incubation at 20 u C on 10-fold-diluted TSB agar, colonies are small, glossy and whitish, 1-3 mm in diameter (colony type III) (De Boer et al, 2004). One isolate (R-35518) produces a purple pigment, which deviates from the general genus description (De Boer et al, 2004). Cells exhibit oxidase but no or weak catalase activity.…”