Michael Doudoroff

The Aerobic Pseudomonads a Taxonomic Study

SUMMARY A collection of 267 strains, representing many of the principal biotypes among aerobic pseudomonads, has been subjected to detailed study, with particular emphasis on biochemical, physiological and nutritional characters. A total of 146 different organic compounds were tested for their ability to serve as sources of carbon and energy. Other characters that were studied included : production of extracellular hydrolases; nitrogen sources and growth factor requirements H-chemolithotrophy; denitrifying ability; pigment production; ability to accumulate poly-p-hydroxybutyrate as a cellular reserve material; biochemical mechanisms of aromatic ring cleavage; and nature of the aerobic electron transport system. The resultant data have revealed many hitherto unrecognized characters of taxonomic significance. As a consequence, it has become possible to recognize among the biotypes examined a limited number of species which can be readily and clearly distinguished from one another by multiple, unrelated phenotypic differences.

Nucleic Acid Homologies in the Genus Pseudomonas

On the basis of ribosomal ribonucleic acid homologies, the genus Pseudomonas can be divided into at least five distinct groups, some of which are as distantly related to each other as they are to Escherichia coli. One of these groups contains members of the genus Xanthomonas. The data presented support and extend the previous grouping based on deoxyribonucleic acid homologies and support the current view that the portion of the genome coding for ribosomal ribonucleic acid is more conserved in the course of evolution than the bulk of the genome.

Proposal to reject the genus Hydrogenomonas: Taxonomic implications

ABSTRACT Fifty-six strains of “hydrogen bacteria” and related nonautotrophic bacteria, including nearly all existing named Hydrogenomonas spp., have been compared. It is proposed that the genus Hydrogenomonas should be rejected, since its type species H. pantotropha, appears to be a nomen dubium; and that the various species of “hydrogen bacteria” should be assigned to other genera, not specifically characterized by the ability to grow autotrophically with H2. The two species of hydrogen bacteria most frequently isolated by enrichment show a peritrichous or degenerate peritrichous flagellar arrangement; one is nonpigmented, the other produces yellow (carotenoid) cellular pigments. Of the various possible generic assignments for these two species, assignment to the genus Alcaligenes is proposed. The nonpigmented species, previously named Hydrogenomonas eutropha, but never legitimately described, is here described as A. eutrophus. The yellow species which includes both facultatively autotrophic and nonautotrophic strains, is described as a new species, A. paradoxus. The Gram-negative, coccoid hydrogen bacterium, formerly known as Micrococcus denitrificans, is placed in a new genus, Paracoccus. The polarly flagellated species of hydrogen bacteria, including the previously named species Hydrogenomonas facilis, H. flava, H. ruhlandii and Pseudomonassa saccharophila, are all assigned to the genus Pseudomonas.

Taxonomy of the aerobic pseudomonads: the properties of the Pseudomonas stutzeri group.

SUMMARY: Strains of Pseudomonas stutzeri and related denitrifying bacteria were compared in their phenotypic properties and mean deoxyribonucleic acid (DNA) base composition. On the basis of this comparison and of in vitro DNA hybridization experiments, it was concluded that, using practical diagnostic tests, no more than two nomenspecies can be recognized within the group. One, P. stutzeri, was extremely variable in phenotypic characteristics and in DNA base composition; we included in it the strains previously assigned to P. stanieri. The other was a new species, P. mendocina Palleroni, which was more homogeneous in phenotypic characters, and in DNA base composition and homology. The comparative properties of known denitrifying pseudomonads are tabulated.

Taxonomy of the aerobic pseudomonads: Pseudomonas cepacia, P. marginata, P. alliicola and P. caryophylli

SUMMARY: On the basis of phenotypic characterization and DNA-DNA homology studies of strains of phytopathogenic Pseudomonas species, it is concluded that P. cepacia is so similar to P. multivorans that the latter name should be regarded as a synonym. On similar grounds, P. alliicola appears to be a synonym of P. marginata. P. caryophylli is a readily distinguishable species. From the DNA-DNA hybridization studies all of these species seem to be related to each other and to the animal pathogens P. pseudomallei and P. mallei.

Pseudomonas pickettii, a new species of clinical origin related to Pseudomonas solanacearum.

Twenty strains of Pseudomonas isolated from clinical specimens were found to constitute a homogeneous group which we recognize as a species and name Pseudomonas pickettii. On the basis of deoxyribonucleic acid hybridization data, this species appears to be most closely related to the phytopathogenic species P. solanacearum. The type strain of P. pickettii is K-288 (ATCC 27511).

Taxonomic studies on some cram negative polarly flagellated “hydrogen bacteria” and related species

SummaryThe properties of several named and unnamed strains of polarly flagellated “hydrogen bacteria” are described and compared with those of related autotrophic and non-autotrophic species. Two new species ofPseudomonas are described: one, a yellow-pigmented hydrogen bacterium,P. palleronii Davis; the other, a non-autotrophic, non-pigmented species,P. delafieldii Davis.

Carbohydrate Metabolism in Rhodopseudomonas spheroides

SUMMARY: The wild-type strain of Rhodopseudomonas spheroides 2.4.1 does not utilize exogenously supplied gluconate and grows poorly with glucose, fructose or mannose as substrates, accumulating aldonic acids and 2-keto-3-deoxy gluconic acid in media containing these sugars. Mutants which are capable of growing well with glucose without the accumulation of acids acquire the enzyme ‘phosphogluconic acid dehydrase’ and oxidize hexoses mainly via the pathway described previously in Pseudomonas saccharophila. The Embden-Meyerhof pathway is constitutive in the wild-type and mutant strains of R. spheroides but appears to have a limited function as a result of very low aldolase activity. Phosphogluconic acid dehydrogenase is either absent or too low in activity to permit the utilization of the pentose-phosphate oxidative pathway. A new type of particulate ‘aldose dehydrogenase system’, constitutive in all strains is involved in the oxidation of glucose and mannose to the corresponding aldonic acid lactones. Gluconic and mannonic acids are both converted to 2-keto-3-deoxy acid through the action of two distinct dehydrating enzymes. A mutation leading to the utilization of gluconic acid is associated with the acquisition of a high level of ‘2-keto-3-deoxy gluconic acid kinase’, but not of phosphogluconic acid kinase. A permeability factor may also be involved in the adaptation of gluconate.

Evolution in Pseudomonas fluorescens.

The relationships among 93 strains of Pseudomonas fluorescens were investigated by (1) a numerical taxonomic analysis on the results of 150 phenotypic tests, (2) DNA hybridization studies using 16 reference strains, (3) quantitative microcomplement fixation studies using six reference strains with antibodies directed against the protein azurin. In general, the strains fell into distinct clusters. Assignment to these clusters on the basis of azurin immunological similarity showed 98% agreement with assignment based on DNA homology, suggesting that many genes will follow the same pattern. Of the strains that clustered on the basis of genotype (DNA, azurin) 88% also clustered on the basis of phenotype. The occasional noncongruency observed between the genotypic and phenotypic data may be due to the variable rates of phenotypic evolution. These results provide a perspective on the roles of horizontal and vertical transfer of genes in the evolution of this bacterial group.

Ammonia assimilation in blue-green algae

SummaryThe occurrence of alanine dehydrogenase (AlaDH), glutamate dehydrogenase (GDH), and 2-ketoglutarate: glutamine amidotransferase (GGAT), has been surveyed in a number of blue-green algae. Among nine unicellular strains grown with nitrate, and belonging to five of the major typological groups, AlaDH was present in seven, and GDH in all eight that were assayed. In ten filamentous strains grown with nitrate, and belonging to the three nonheterocyst-forming and four heterocyst-forming groups, AlaDH was present in six, but both AlaDH and GDH were present in only one strain. In those strains which could be grown with N2 as sole nitrogen source, levels of GDH were generally lower, and AlaDH higher in cells fixing N2 than in those growing with nitrate. GGAT was undetectable in N2-grown cells. Two unicellular and three filamentous strains were tested for their ability to use L-alanine, L-glutamate, L-glutamine, and L-asparagine as sole sources of nitrogen. Of these, L-asparagine was utilized most effectively. There was little difference in levels of GDH in cells grown with nitrate or with L-asparagine, while the levels of AlaDH were slightly lower in cells grown with L-asparagine.