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Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny)

¹ Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA
² Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195-2700, USA

Correspondence
David A. Stahl
dastahl{at}u.washington.edu

A Gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm Eisenia foetida. Comparisons of 16S rRNA gene sequences indicated its relatedness to the betaproteobacterial genus Acidovorax and the novel isolates shared 92–94 % sequence similarity with recognized species of this genus. Gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and independent clade. The DNA G+C content was 67.0±0.2 mol%. Major fatty acids were C_{16 : 0}, C_{16 : 1}7c and C_{17 : 0} cyclo. While capable of growing in fully aerated media, all isolates favoured low oxygen concentrations and all required biotin or a mix of amino acids in order to grow on defined mineral media. Based on phylogenies inferred from three housekeeping gene sequences (gap, recA and rpoC), DNA–DNA hybridization values, the unique ecology and the distinct physiology of the novel strains, the new genus Verminephrobacter gen. nov. is proposed for the earthworm nephridial symbionts. The name Verminephrobacter eiseniae sp. nov. is proposed for the type species with strain EF01-2^T (=ATCC BAA-1489^T=DSM 19286^T) as the type strain of the type species.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of Verminephrobacter eiseniae isolates EF01-1, EF01-2^T, EF02-2, EF03-1, EF03-2, EF04-1, EF05-1 and EF05-2 are DQ327662, DQ327663, DQ327664, DQ327665, DQ327666, DQ327667, DQ327668 and DQ327669, respectively. The GenBank accession numbers for the MLST sequences are EU165058–88 and EU350960.

Details of the methods used for soil DNA surveys and siderophore production and uptake are available as supplementary methods with the online version of this paper. Also available are supplementary tables giving the results of DNA-DNA hybridization studies and the pairwise sequence identities of 16S rRNA sequences. Supplementary figures show additional phylogenetic trees, the reactions in ‘deep phytagel’ tubes, vitamin requirements and siderophore production assays for the strains studied.