Submitted to: Diversity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2011
Publication Date: 7/19/2011
Citation: Gardner, T., Acosta Martinez, V., Senwo, Z., Dowd, S. 2011. Soil Microbial Communities associated to Plant Rhizospheres in an Organic Farming System in Alabama. Diversity. 3(3):308-328. Interpretive Summary: Although it is assumed that organic farming is good for soils, little information is available on soil microbial communities and activities associated with organic crops. As more information becomes available about the relationship between organic farming and soil microbial functioning, adoption of this practice and best management decisions should increase. This study evaluated 5 different organic crops including: potato, lettuce, broccoli, onion and an undisturbed pasture site. Prior to this study, the farm was under organic potato production and pasture (2006 - 2008). During the first growing season of these crops, we found higher soil microbial biomass, fungal:bacterial ratios, and enzyme activities related to nutrient cycling associated with pasture and potato rhizospheres compared with onion, lettuce, and broccoli. Our results may suggest certain microbial suppression in soils where onion was produced. For instance, the lowest soil microbial biomass and enzyme activities were found under onion as compared to all the other crop rhizospheres. Interestingly, availability of a new powerful sequencing technique (pyrosequencing) showed higher Streptomycetaceae under onion compared to the other rhizospheres. This group of bacteria has shown potential antagonistic activities and biocontrol towards infection by pathogenic fungi populations of Fusarium oxysporum, the causal agent of onion wilt. This could explain the low presence of fungal FAME indicators in the soil rhizospheres under onion, which should be addressed with further studies to improve our understanding of plant/soil microbial interactions. These results are important for selection of crop rotations on organic farms because differences in microbial community structure and enzyme activities under different crop rhizospheres can affect soil functioning (i.e., processes), and the yield and nutritional value of each crop.
Technical Abstract: The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques. The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53, and total C of 2.25 g C kg-1 soil. Soil samples were taken under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, i10Me17:0, cy17:0, 16:1'5c and 18:1'9c) varied among the crop rhizospheres. Soil microbial community FAME profiles under pasture showed a significantly higher fungal: bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Fungal: bacterial ratios were higher under broccoli and potato compared to onion and lettuce. Furthermore, microbial biomass C and enzyme activities associated with pasture and potato rhizospheres were higher than the other crop rhizospheres. Another distinct trend found in this study was the lower soil microbial biomass C and enzyme activities under onion compared to all the other crop rhizospheres. Pyrosequencing revealed significant differences on maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0-10 cm (581.7- 770.0) compared to 10-20 cm (563.3 -727.7) soil depths, respectively. The lowest OTUs were detected at 0-10 cm under broccoli (581.7); whereas the lowest OTUs were found at 10-20 cm under potato (563.3). The predominant phyla (85%) in this soil at both depths were Flavobacteria, Sphingobacteria, Proteobacteria and Actinobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture (grass) compared to the broccoli, potato, onion and lettuce. This study demonstrated the significant differences in microbial communities influenced by each crop rhizosphere in an organic farming system. Differences in microbial community structure and enzyme activities can have implications in soil functioning, processes and soil health, and the yield and nutritional value of each crop.