Effects of Arbuscular Mycorrhizas on Ammonia Oxidizing Bacteria in an Organic Farm Soil
Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil.
KeywordsArbuscular Mycorrhizal Fungus Mycorrhizal Colonization Ammonia Oxidize Bacterium Much Probable Number amoA Gene
This work would not have been possible without the ongoing support of our farmer cooperators Jim and Deborah Durst. We wish to thank Professor Sally Smith (University of Adelaide) and Dr. Susan Barker (University of Western Australia), for allowing us to use the rmc tomato mutant/wild-type system. We thank Mr. Binyam Gebreyesus and Dr. Kevin Feris for valuable discussions and the four anonymous referees of this manuscript for their valuable comments. Our research is funded by the California Department of Food and Agriculture Specialty Crops Program (SA6674), the United States Department of Agriculture National Research Initiative Soils and Soil Biology Program (2004-03329), and grant number 5 P42 ES004699 from the National Institute of Environmental Health Sciences (NIEHS), NIH.
- 2.Arines, J, Vilarino, A, Sainz, M (1989) Effect of different inocula of vesicular–arbuscular mycorrhizal fungi on manganese content and concentration in red clover (Trifolium pretense L.) plants. New Phytol 37: 699–705Google Scholar
- 11.Cavagnaro, TR, Smith, FA, Hay, G, Carne-Cavagnaro, VL, Smith, SE (2004) Inoculum type does not affect overall resistance of an arbuscular mycorrhiza-defective tomato mutant to colonisation but inoculation does change competitive interactions with wild-type tomato. New Phytol 161: 485–494CrossRefGoogle Scholar
- 14.Forster, JC (1995) Soil nitrogen. In: Alef, K, Nannipiero, P (Eds.) Methods in Applied Soil Microbiology and Biochemistry, Academic Press, San Diego, pp 79–87Google Scholar
- 17.Gao, LL (2002) Control of arbuscular mycorrhizal colonisation. Studies of a mycorrhiza-defective tomato mutant. Ph.D. Thesis. The University of Adelaide, AdelaideGoogle Scholar
- 18.Hamel, C (2004) Impact of arbuscular mycorrhizal fungi on N and P cycling in the root zone. Can J Soil Sci 84: 383–395Google Scholar
- 19.Hashimoto, T, Hattori, T (1987) Length of incubation for the estimation of the most probable number of nitrifying bacteria in soil. Soil Sci Plant Nutr 33: 507–510Google Scholar
- 23.Hesselsoe, M, Brandt, KK, Sorensen, J (2001) Quantification of ammonia oxidizing bacteria in soil using microcolony technique combined with fluorescence in situ hybridization (MCFU-FISH). FEMS Microbiol Ecol 38: 87–95Google Scholar
- 30.Klopatek, CC, Klopatek, JM (1997) Nitrifiers and mycorrhizae in pristine and grazed Pinyon–Juniper ecosystems. Arid Soil Res and Rehabil 11: 331–342Google Scholar
- 41.Patra, AK, Abbadie, L, Clays-Josserand, A, Degrange, V, Grayston, SJ, Loiseau, P, Louault, F, Mahmood, S, Nazeret, S, Philippot, L, Poly, F, Prosser, JI, Richaume, A, LeRoux, X (2005) Effects of grazing on microbial functional groups involved in soil N dynamics. Ecol Monogr 75: 65–80CrossRefGoogle Scholar
- 46.Purkhold, U, Pommerening-Roser, A, Juretschko, S, Schmid, MC, Koops, H-P, Wagner, M (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66: 5368–5382PubMedCrossRefGoogle Scholar
- 49.Smith, SE, Read, DJ (1997) Mycorrhizal Symbiosis, 2nd ed. Academic Press Ltd., Cambridge, UKGoogle Scholar