Sonia Estelle Tarnawski

Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity

Anaerobic oxidation of ammonium (anammox) is recognized as an important process in the marine nitrogen cycle yet nothing is known about the distribution, diversity and activity of anammox bacteria in the terrestrial realm. In this study, we report on the detection of anammox sequences of Candidatus ‘Brocadia’, ‘Kuenenia’, ‘Scalindua’ and ‘Jettenia’ in marshes, lakeshores, a contaminated porous aquifer, permafrost soil, agricultural soil and in samples associated with nitrophilic or nitrogen-fixing plants. This suggests a higher diversity of anammox bacteria in terrestrial than in marine ecosystems and could be a consequence of the larger variety of suitable niches in soils. Anammox bacteria were not ubiquitously present but were only detected in certain soil types and at particular depths, thus reflecting specific ecological requirements. As opposed to marine water column habitats where Candidatus ‘Scalindua’ dominates anammox guilds, ‘Kuenenia’ and ‘Brocadia’ appear to be the most common representatives in terrestrial environments.

Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil–associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatment.

Examination of Gould's modified S1 (mS1) selective medium and Angle's non-selective medium for describing the diversity of Pseudomonas spp. in soil and root environments

Abstract Studies on the diversity of environmental culturable Pseudomonas populations are dependent on the isolation procedure. This procedure includes the use of selective media which may influence the recovery of strains and thus the diversity described. In this study, we assessed the use of two agar isolation media for describing the diversity of soil- and root-inhabiting Pseudomonas associated with the perennial grass Molinia coerulea. A total of 382 Pseudomonas strains were recovered on either non-selective Angles medium, or on Goulds modified S1 (mS1) Pseudomonas-selective medium. Their diversity was assessed by restriction analysis of PCR (polymerase chain reaction)-amplified 16S-23S rDNA internal transcript spacer sequences. The comparison of mS1- and Angle-recovered populations showed that the use of mS1 selective medium led to an underestimation of both Pseudomonas counts and diversity, especially in the soil environment.