Range Of Soil Bacteria Research Articles

The Hydroxyquinol Degradation Pathway in Rhodococcus jostii RHA1 and Agrobacterium Species Is an Alternative Pathway for Degradation of Protocatechuic Acid and Lignin Fragments.

Deletion of the pcaHG genes, encoding protocatechuate 3,4-dioxygenase in Rhodococcus jostii RHA1, gives a gene deletion strain still able to grow on protocatechuic acid as the sole carbon source, indicating a second degradation pathway for protocatechuic acid. Metabolite analysis of wild-type R. jostii RHA1 grown on medium containing vanillin or protocatechuic acid indicated the formation of hydroxyquinol (benzene-1,2,4-triol) as a downstream product. Gene cluster ro01857-ro01860 in Rhodococcus jostii RHA1 contains genes encoding hydroxyquinol 1,2-dioxygenase and maleylacetate reductase for degradation of hydroxyquinol but also putative mono-oxygenase (ro01860) and putative decarboxylase (ro01859) genes, and a similar gene cluster is found in the genome of lignin-degrading Agrobacterium species. Recombinant R. jostii mono-oxygenase and decarboxylase enzymes in combination were found to convert protocatechuic acid to hydroxyquinol. Hence, an alternative pathway for degradation of protocatechuic acid via oxidative decarboxylation to hydroxyquinol is proposed.IMPORTANCE There is a well-established paradigm for degradation of protocatechuic acid via the β-ketoadipate pathway in a range of soil bacteria. In this study, we have found the existence of a second pathway for degradation of protocatechuic acid in Rhodococcus jostii RHA1, via hydroxyquinol (benzene-1,2,4-triol), which establishes a metabolic link between protocatechuic acid and hydroxyquinol. The presence of this pathway in a lignin-degrading Agrobacterium sp. strain suggests the involvement of the hydroxyquinol pathway in the metabolism of degraded lignin fragments.

Population energetics of bacterial-feeding nematodes: Carbon and nitrogen budgets

Bacterial-feeding nematodes participate in nitrogen mineralization in decomposition food webs to an extent determined by metabolic and behavioral attributes, by life history, and by the relative C-to-N ratios of the nematodes and their bacterial prey. The mean C-to-N ratio for eight nematode species cultured on Escherichia coli on agar was 5.89 (range 5.16–6.83). The mean C-to-N ratio was similar, although with greater variability among species, when nematodes were cultured in soil on a range of soil bacteria. The mean C-to-N ratio of five isolates of soil bacteria and E. coli was 4.12 (range 3.65–4.92). Where food was not limiting, production-to-assimilation ratios ranged from 0.58 to 0.86 and respiration-to-assimilation ratios from 0.14 to 0.42. The excess N assimilated during growth and egg production, and the excess N assimilated to meet the C needs of respiration, were similar across species at 20°C. The excess N from both sources provides an estimate of the amount of N excreted by each nematode during the life course. The weight of bacteria necessary to meet the growth and respiration costs at 20°C ranged from 0.87 μg μg-nematode −1 d −1 for Cephalobus persegnis to 1.99 μg μg-nematode −1 d −1 for Bursilla labiata, providing estimated consumption rates between 6.61 × 10 5 and 15.22 × 10 5 bacterial cells μg-nematode −1 d −1. At a field site, we estimate that the bacterial-feeding nematode community in the top 15 cm soil mineralized N at rates increasing to 1.01 μg-N g-soil −1 d −1 in rhizosphere soil. On a monthly basis, the community contributed 0.28 kg-N ha −1 in April, 0.98 kg-N ha −1 in May and 1.38 kg-N ha −1 in June in bulk soil. Contributions in the rhizosphere would be considerably greater depending on the ratio of rhizosphere to bulk soil. The contribution of individual species to N mineralization in the rhizosphere varied through the first 3 months of the summer growing season as a function of their abundance and their metabolic and development rates in relation to temperature. Rhabditis cucumeris was the predominant contributor in April; there were similar contributions by Acrobeloides bodenheimeri, B. labiata, Cruznema tripartitum, and R. cucumeris in May; A. bodenheimeri and B. labiata were the major contributors in June.

The nodDABC Genes of Rhizobium leguminosarum biovar trifolii Confer Root-Hair Curling Ability to a Diverse Range of Soil Bacteria and the Ability to Induce Novel Root Swellings on Beans

Cloned DNA fragments coding for the nodDABC genes of Rhizobium leguminosarum biovar trifolii strain ANU843 were introduced into Rhizobium strains possessing Sym plasmid deletions. These strains were able to: (a) synthesise four butanol-soluble Nod metabolites; (b) affect the normal growth pattern of plant root hairs of a wide range of host and non-host legumes; and (c) induce many root outgrowths on Phaseolus plants. The four Nod metabolites produced by these strains were labelled by supplying cultures with 14C-acetate in the presence of a flavonoid inducer of nod gene expression. In contrast, more than ten Nod metabolites were synthesised by wild-type strains or constructed strains containing the full complement of R. leguminosarum biovar. trifolii nodulation and host specific nodulation genes. Strain ANU845 containing nodDABC did not induce infection threads or nodule initiation sites but distorted and curled cells in plant root hairs. However strain ANU845 induced root outgrowths on beans (Phaseolus vulgaris) that appeared to result from a proliferation of the epidermal tissue. Transfer of plasmids bearing nodDABC to various Gram-negative bacteria, Agrobacterium tumefaciens, Pseudomonas aeruginosa, Lignobacter sp., Azospirillum brasilense and Escherichia coli, and different non-nodulating mutant rhizobia conferred on these strains the ability to cause root-hair curling and distortions. Several strains induced root-hair curling on clover and a range of other non-host legumes. We suggest that the expression of nodDABC in a range of soil bacteria may extend or alter the effects of these soil bacteria on the roots of host plants.