Rhodospirillum oryzae sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy.

A reddish-brown bacterium, designated strain JA318(T), was purified from a photoheterotrophic enrichment culture obtained from the rhizosphere soil of paddy. Cells of strain JA318(T) are spiral shaped, Gram-stain-negative and motile by means of amphitrichous flagella. Strain JA318(T) has no NaCl requirement for growth but can tolerate up to 1.5 % (w/v) NaCl. Internal photosynthetic membranes are present as lamellar stacks. Photoorganoheterotrophy is the only growth mode observed. Strain JA318(T) contains bacteriochlorophyll a, lycopene and rhodopin as major carotenoids. Thiamine, niacin and para-aminobenzoic acid (PABA) are required as growth factors. Major fatty acids are C18 : 1ω7c and C16 : 0. Ubiquinone-8 and rhodoquinone-8 are the observed quinones. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid are the major polar lipids in strain JA318(T). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain JA318(T) clustered with species of the genus Rhodospirillum which belongs to the class Alphaproteobacteria. The highest sequence similarity of strain JA318(T) was found with Rhodospirillum sulfurexigens JA143(T) (99.9 %). The DNA-DNA reassociation values of strain JA318(T) with Rsp. sulfurexigens JA143(T) and Rhodospirillum photometricum DSM 122(T) were 52 ± 2 % and 45 ± 1 %, respectively. The genomic DNA G+C content of strain JA318(T) was 60.2 mol%. Based on the morphological, physiological, chemotaxonomical and molecular evidence, strain JA318(T) is significantly different from the type strains of species of the genus Rhodospirillum, of the family Rhodospirillaceae, and it is proposed that the strain be classified as a representative of a novel species for which the name Rhodospirillum oryzae sp. nov. is proposed. The type strain is JA318(T) (= KCTC 5960(T) = NBRC 107573(T)).

Detection of bacteria in environmental samples by direct PCR without DNA extraction.

Cultured cells and environmental samples were used directly in PCRs without the isolation of DNA. Serial dilution was used to eliminate the inhibitory effect of materials in natural samples. Primers specific for pmoA, which encodes a subunit of the particulate methane monooxygenase, were used to detect and quantify methanotrophic bacteria by direct most probable number PCR. Phototrophic bacteria were detected in environmental samples by direct PCR with primers specific for pufM, and members of the bacterial domain were detected with primers for 16S rDNA. Direct PCR provides a rapid, simple, and sensitive methodfor detecting and quantifying bacteria in environmental samples. Detection of methanotrophic bacteria can be applied to monitoring bioremediation.

Characterization of the dominant and rare members of a young Hawaiian soil bacterial community with small-subunit ribosomal DNA amplified from DNA fractionated on the basis of its guanine and cytosine composition.

The small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G + C) content by using bisbenzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63% G + C fraction) and a fraction with a low biomass (35% G + C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63% G + C fraction contained several dominant phylotypes, while the community members that were less successful (35% G + C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G + C contents used. The dominant phylotypes in the 63% G + C fraction were members of the Pseudomonas, Rhizobium-Agrobacterium, and Rhodospirillum assemblages, while all of the clones sequenced from the 35% G + C fraction were affiliated with several Clostridium assemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G + C separation step is also a way to detect some of the less dominant organisms in a community.

Rhodospirillum centenum, sp. nov., a thermotolerant cyst-forming anoxygenic photosynthetic bacterium.

A novel non-sulfur purple photosynthetic bacterium, designated Rhodospirillum centenum, was isolated from an enrichment culture designed to favor growth of anoxygenic photosynthetic N2-fixing bacteria. R. centenum grows optimally at 40-42 degrees C and has the capacity to produce cytoplasmic 'R bodies', refractile structures not observed hitherto in photosynthetic prokaryotes. The bacterium is also unusual among photosynthetic bacteria in that it forms desiccation-resistant cysts when grown aerobically in darkness with butyrate as the sole carbon source.

Distribution of purple photosynthetic bacteria in wetland and woodland habitats of central and northern Minnesota.

Enrichment cultures for purple nonsulfur and sulfur photosynthetic bacteria were prepared from soil samples collected in central and northern Minnesota. The purple nonsulfur bacteria were found in most wetland soils sampled but were uncommon in woodland and grassland soils. The pH range of the soils in which these bacteria occurred was 3.8 to 7.8, and the oxidation-reduction potential (E(h)) range was +510 to -65 mV. Soils with a pH below 5.0 or an E(h) above +370 mV had few purple nonsulfur bacteria (<10/g of soil). Rhodopseudomonas viridis, a photosynthetic bacterium containing bacteriochlorophyll b, and the purple sulfur bacteria were common only in low-acidity wetland soils that were usually being reduced.

Isolation and counting of Athiorhodaceae with membrane filters.

The number, type, and distribution of Athiorhodaceae in two Central Pennsylvania artificial lakes were investigated with an anaerobic modification of the membrane filter technique.

Rhodospirillum tenue sp. n., a new species of the purple nonsulfur bacteria.

Rhodospirillum tenue sp. n. differs from the rhodospirilla described so far by its small size, ultrastructure, and physiological and biochemical characteristics.