Proposal of the genus

No abstract

The 16S rRNA gene from various bacterial cultures was amplified by the polymerase chain reaction without DNA purification, and sequenced directly by using a laser fluorescent DNA sequencer and Tth polymerase with a cycle sequencing protocol. The described procedures provide almost complete 16S rDNA sequence data within a couple of days and facilitate systematic studies.

Mutations in the clk-1 gene of Caenorhabditis elegans result in an extended life span and an average slowing down of developmental and behavioral rates. However, it has not been possible to identify biochemical changes that might underlie the extension of life span observed in clk-1 mutants, and therefore the function of CLK-1 in C. elegans remains unknown. In this report, we analyzed the effect of clk-1 mutation on ubiquinone (UQ 9 ) biosynthesis and show that clk-1 mutants mitochondria do not contain detectable levels of UQ 9 . Instead, the UQ 9 biosynthesis intermediate, demethoxyubiquinone (DMQ 9 ), is present at high levels. This result demonstrates that CLK-1 is absolutely required for the biosynthesis of UQ 9 in C. elegans. Interestingly, the activity levels of NADH-cytochrome c reductase and succinate-cytochrome c reductase in mutant mitochondria are very similar to those in the wild-type, suggesting that DMQ 9 can function as an electron carrier in the respiratory chain. To test this possibility, the short side chain derivative DMQ 2 was chemically synthesized. We find that DMQ 2 can act as an electron acceptor for both complex I and complex II in clk-1 mutant mitochondria, while another ubiquinone biosynthesis precursor, 3-hydroxy-UQ 2 , cannot. The accumulation of DMQ 9 and its use in mutant mitochondria indicate, for the first time in any organism, a link between the alteration in the quinone species used in respiration and life span.The understanding of the biological pathways that control life span can be studied in Caenorhabditis elegans through the identification of genes that alter the length of life when mutated (1). For example, mutations in clk-1 are known to cause an extended life span, as well as the slowing of a variety of developmental and physiological events, including the cell cycle, embryogenesis, post-embryonic development, and rhythmic adult behaviors (2, 3). Thus, CLK-1 is expected to play a unique biological role that is necessary to determine the life span and to coordinate these various biological processes. However, the biochemical differences between clk-1 mutants and the wildtype strain, which might indicate the function of CLK-1, have yet to been identified (1, 4 -7).clk-1 encodes a 187-residue polypeptide that is homologous to yeast coq7/cat5 (8). COQ7/CAT5 is located in the inner membrane of yeast mitochondria and is necessary for the biosynthesis of ubiquinone (UQ) 1 in yeast (9, 10). Therefore, yeast coq7/cat5 mutants, which lack UQ 6 , are unable to grow on nonfermentable carbon sources (9). Orthologs of clk-1/coq7/ cat5 have also been reported from mammals, including human (11-13), and appear to be highly conserved among species.Recently, a green fluorescent protein fusion to C. elegans CLK-1 was shown to localize to the mitochondria of all the somatic cells of the worm (14). However, in contrast to the situation in yeast, which is defective in respiratory growth, C. elegans clk-1 mutants are able to respire almost normally. In fact, the metabolic capacities and the A...

The distribution and phylogenetic affiliations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)-degrading denitrifying bacteria in activated sludge were studied by a polyphasic approach including cultureindependent biomarker and molecular analyses as well as cultivation methods. A total of 23 strains of PHBV-degrading denitrifiers were isolated from activated sludges from different sewage treatment plants. 16S ribosomal DNA (rDNA) sequence comparisons showed that 20 of the isolates were identified as members of the family Comamonadaceae, a major group of ␤-Proteobacteria. When the sludges from different plants were acclimated with PHBV under denitrifying conditions in laboratory scale reactors, the nitrate removal rate increased linearly during the first 4 weeks and reached 20 mg NO 3 ؊ -N h ؊1 g of dry sludge ؊1 at the steady state. The bacterial-community change in the laboratory scale sludges during the acclimation was monitored by rRNA-targeted fluorescence in situ hybridization and quinone profiling. Both approaches showed that the population of ␤-Proteobacteria in the laboratory sludges increased sharply during acclimation regardless of their origins. 16S rDNA clone libraries were constructed from two different acclimated sludges, and a total of 37 clones from the libraries were phylogenetically analyzed. Most of the 16S rDNA clones were grouped with members of the family Comamonadaceae. The results of our polyphasic approach indicate that ␤-Proteobacteria, especially members of the family Comamonadaceae, are primary PHBV-degrading denitrifiers in activated sludge. Our data provide useful information for the development of a new nitrogen removal system with solid biopolymer as an electron donor.Biological denitrification is an important process for nitrogen removal in wastewater treatment. Published reports suggest that 10 to 90% of bacteria in the activated-sludge system are capable of denitrification (16,33,44). However, the system is often confronted with the problem that the efficiency of nitrogen removal decreases due to low availability of organic matter as the reducing power for denitrification. To overcome this problem, a simple organic compound, such as methanol or acetate, is added intentionally as an electron donor to the denitrification process (16). In recent years, a new biotechnology of nitrogen removal using solid biopolymer as the electron donor has been developed (7). This type of nitrogen removal process, called here the solid-phase denitrification process, may have some advantages, e.g., a constant supply of reducing power, no secondary organic pollution, and ease of operation. A promising solid substrate for denitrification is the bacterial polyester poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) (6, 30, 40, 52), which serves as the source of biodegradable plastic (4,17,34,50). The biodegradability of PHBV in natural environments has been extensively studied, and a number of PHBV-degrading bacteria have been isolated and characterized (1, 11, 38, 39, 41-43, 45, 55). The asso...