New aerobic ammonium-dependent obligately oxalotrophic bacteria: description of Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov.

Abstract

The genus Ammoniphilus is proposed for aerobic endospore-forming Gramvariable rod-shaped bacteria, which are ammonium-dependent, obligately oxa lotrop h ic and haloa I ka I i to lerant, oxidase-and catal ase-pos i t ive, mesop h i I ic and motile b y peritrichous flagella. Cell wall contained two electron-dense layers. The external layer consists of a chain of electron-dense granules morphologically resembling the cellulosomes of CIostridium thermocellum. Two species are described, Ammoniphilus oxalaticus gen. nov., sp. nov. and Ammoniphilus oxalivorans gen. nov., sp. nov. The type strains of these species are strains RAOx-1 (= DSM 11538) and RAOx-FS (= DSM 11537), respectively. Ammoniphilus strains were isolated from the rhizosphere of sorrel (Rumex acetosa) and from decaying wood. The strains require a high concentration of ammonium ions and use oxalate as the sole organic source of carbon and energy for growth; no growth factors were required. Growth occurred a t pH 6-8-9-5. The optimum temperature and pH for growth were 28-30 "C and 80-8.5. All strains grew in a saturated solution of ammonium oxalate, and tolerated 3 O/ O NaCI. Whole-cell hydrolysates contain meso-diaminopimelic acid and glucose. The menaquinone of the strains was MK 7, and the major cellular fatty acids were 12-methyl tetradecanoic, cis-hexadec-9-enoic and hexadecanoic acids. The G+C content of the DNA was 4 5 4 6 mol O/ O for A. oxalaticus and 42 mol O/ O for A. oxalivorans. The almost complete 165 rDNA sequence of three strains of the two species of Ammoniphilus shows that the genus falls into the radiation of the Clostridium-Bacillus subphylum of Grampositive bacteria. The closest phylogenetic neighbour of Ammoniphilus is Oxalophagus oxalicus. The DNA-DNA hybridization value between strains RAOx-1 and RAOx-FS was 3997%.

Phylogenetic analysis of gram-positive bacteria based on grpE, encoded by the dnaK operon.

“…sakei formed another grouping within the low-GjC Gram-positive bacteria, whereas M. tuberculosis, M. avium and S. coelicolor (Gram-positive bacteria with high-GjC DNA content) formed the third cluster. These hierarchical arrangements are supported by the 5S rRNA-, 16S rRNA-and DnaK-based phylogenies (Gupta, 1998 ;de Vaux et al, 1998 ;Olsen et al, 1994 ;Tsakalidou et al, 1998 ;Zaitsev et al, 1998) but not by DnaJ-based phylogeny (Bustard & Gupta, 1997). The phylogenetic positioning of C. acetobutylicum and other Clostridium species is different in different trees.…”

“…This is also evidenced by the analyses of other highly conserved cistrons such as 5S rRNA and DnaK (Gupta, 1998 ;Olsen et al, 1994). However, in the phylogenetic tree derived from 16S rRNA sequences B. stearothermophilus branches from other Bacillus species earlier than does S. aureus and is in a separate cluster (Zaitsev et al, 1998). The tree topologies obtained with different markers should be interpreted with caution as some of these markers may contain very little sequence information (e.g.…”

“…Although exactly the same set of organisms is not shown, the discrepancies in the branching order among the trees are readily apparent. The tree based on 16S rRNA sequences depicts Bacillus stearothermophilus branching earlier than the branching of Lactococcus\Strepto-coccus species from other Bacillus\Staphylococcus species (Zaitsev et al, 1998). The tree based on DnaJ sequences places Mycobacterium tuberculosis closer to S. coelicolor than to Mycobacterium leprae, a result that is highly unlikely (Cole et al, 1998 (Olsen et al, 1994), (B) 16S rRNA sequencing (de Vaux et al, 1998 ;Macy et al, 1996 ;Morse et al, 1996 ;Stackebrandt et al, 1997 ;Tsakalidou et al, 1998 ;Wilde et al, 1997 ;Zaitsev et al, 1998), (C) the amino acid sequence identity of DnaK proteins (Gupta, 1998) and (D) DnaJ protein sequences (Bustard & Gupta, 1997).…”

“…A comparison of the phylogenetic trees derived by 5S rRNA sequencing (Olsen et al, 1994), 16S rRNA sequencing (de Vaux et al, 1998 ;Macy et al, 1996 ;Morse et al, 1996 ;Stackebrandt et al, 1997 ;Tsakalidou et al, 1998 ;Wilde et al, 1997 ;Zaitsev et al, 1998) and amino acid sequence comparisons for two of the HSPs encoded by the dnaK operon, DnaK (Gupta, 1998) and DnaJ (Bustard & Gupta, 1997) is shown in Fig. 1.…”

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

“…It is hoped that these methods may be replaced in future by use of various means of bacterial degradation involving either an alkalophilic Bacillus species (209) or Pseudomonas oxalaticus (11), an organism isolated from rhubarb patches (a rich source of oxalate). It is possible that the recently described new species of obligately oxalotrophic Ammonophilus oxalaticus and A. oxalivorans (319) isolated from the rhizosphere of sorrel (Rumex acetosa, another species with a high oxalate content) could be used for these purposes.…”