Changes in antibiotic resistance profile of soil bacterial community in association with land degradation

Abstract

When soil microbes function well, the soil may support plants and other lives in the ecosystem (Beare et al. 1995). Soil bacteria, as a part of the soil microbial community, may contribute to plant growth by mineral solubilization (Derylo and Skorupska 1992), nitrogen fixation (Albrecht et al. 1981), producing plant growth hormones (Neitko and Frankenberg 1989) and supressing plant pathogens (Handman et al. 1991). If an ecosystem is subjected to a degrading impact, the soil bacterial community may then change (Frostegård et al. 1993). Deforestation caused by logging and other human activities is a serious environmental issue in the tropics. The land deprived of the original tropical forest degrades rapidly under tropical climatic conditions (Eden and Parry 1996). The land degradation results in a hard to-rehabilitate soil conditions. In such a degraded soil, the soil bacterial community profile may differ from the original one (Doi and Sakurai 2003), often accompanied by crippled soil microbial functions (Doi 2004; Jha et al. 1992; Pérez-de-Mora et al. 2006). Thus, changes in soil bacterial community profile following the elimination of a tropical vegetative type warn us of ongoing degradation of the soil ecosystem. Methods for soil microbial community profiling have been developing (Kirk et al. 2004). Changes in soil quality can be detected by observing soil microbial aspects: fungal (Cuenca and Meneses 1996) and bacterial (Doi and Sakurai 2003) community structures, soil physiological functions (Biolog method, Garland and Mills 1991), and the distribution of biotic molecules such as respiratory quinines (Fujie et al. 1998), phospholipid fatty acids (Tunlid and White 1992), and nucleic acids (Yang et al. 2001). Profiling soil bacterial community may unveil a unique aspect of differences among soils, because the soil bacterial community profile may responds to a particular impact in a uniquely different way from the fungal community profile (Wu et al. 2008) or the physico-chemical profile (Doi and Sakurai 2003). Soil bacterial community profiles are available with the Biolog method (Garland and Mills 1991), amplified ribosomal DNA restriction analysis fingerprinting of 16S rDNA fragments (Wu et al. 2008) or counting bacterial cells that utilize single carbon sources (Doi and Sakurai 2003). We can obtain soil bacterial community profiles by testing soil bacterial isolates' resistance patterns to single antibiotics (Brönstad et al. 1996; Doyle and Stotzky 1993; Westover et al. 1997). The insight offered by these authors is that we would be able to obtain the soil bacterial community profile by counting the number of soil bacterial cells resistant to each of multiple antibiotics. Doi (2004) tested this possibility applying the antibiotic resistance most probable number (MPN) method to soils sampled at a forest and bare ground as a result of deforestation and subsequent human activities. Then, the MPN method could discriminate the soils. The discriminatory power was comparable (Doi 2004; Doi et al. 2004) to the Biolog method (Garland and Mills 1991). However, the soils profiled in their previous work were the extremes in the area, the most fertile forest soil and the most degraded bare ground soil (Doi and Sakurai 2004). Changes in soil microbial community profile responding any impacts are gradual, not abrupt (Frostegård et al. 1993). We were not sure how much the antibiotic resistance MPN method describes such gradual changes in soil bacterial community profile. Thus, in this research, we tried to describe a land degradation gradient with principal components derived from data sets on antibiotic resistance profiles of soil bacterial communities over a land degradation gradient as a result of deforestation in the Sakaerat Environmental Research Station, Thailand. The antibiotic MPN method was applied in finding the impacts of land degradation on soil bacterial community profile. We tried to describe the land degradation based on differences among the antibiotic resistance profiles. We also explored relationships between soil physico-chemical characteristics and the changes in antibiotic resistance profile. The most significant soil environmental changes related to changes in the antibiotic resistance profile of soil bacterial community were then specified.