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| The effects of land use and management practices on soil microbial diversity as determined by PCR-DGGE and CLPP. | |
| Wallis;Patricia Dawn. | |
| 出版年 | 2011 |
| 英文摘要 | The environmental impact of anthropogenic disturbances such as agriculture, on the soil ecosystem, and particularly on soil microbial structural and functional diversity, is of great importance to soil health, conservation and remediation. Therefore, this study assessed the effects of various land use and management practices on both the structural (genetic) and functional (catabolic) diversity of the soil bacterial and fungal communities, at two long-term sites in KwaZulu-Natal. The first site is situated at Baynesfield Estate, and the second at Mount Edgecombe Sugarcane Research Institute. At site 1, the land uses investigated included soils under pre-harvest burnt sugarcane (Saccharum officinarum, Linn.) (SC); maize (Zea mays, Linn.) under conventional tillage (M); permanent kikuyu (Pennisetum clandestinum, Chiov) pasture (KIK); pine (Pinus patula, Schiede) plantation (PF); and wattle (Acacia mearnsii, De Wild) plantation (W), all fertilized; and undisturbed native grassland (NAT) that had never been cultivated or fertilized. At site 2, a sugarcane (Saccharum officinarum × S. spontaneum var. N27) pre-harvest burning and crop residue retention trial was investigated. The treatments studied included conventional pre-harvest burning of sugarcane with the tops removed (Bto), and green cane harvesting with retention of crop residues on the soil surface as a trash blanket (T). Each of these treatments was either fertilized (F) or unfertilized (Fo). The polymerase chain reaction (PCR), followed by denaturing gradient gel electrophoresis (DGGE) were used to determine the structural diversity, and community level physiological profiling (CLPP) using BIOLOG plates, the catabolic diversity. In addition, the soils were analysed with respect to selected physicochemical variables, and the effects of these on the soil microbial communities were determined. Replicate soil samples (0–5 cm) were randomly collected from three independent locations within each land use and management, at both sites. Soil suspensions for the CLPP analyses were prepared from fresh soil subsamples (within 24 h of collection) for the bacterial community analyses, and from 8-day-old soil subsamples (incubated at 4°C to allow for spore germination) for the fungal community analyses. BIOLOG EcoPlates™ were used for the bacterial CLPP study and SF-N2 MicroPlates™ for the fungal analysis, the protocols being adapted and optimized for local conditions. This data was log [X+1]-transformed and analysed by principal component analysis (PCA) and redundancy analysis (RDA). For PCRDGGE, total genomic DNA was isolated directly from each soil subsample, and purified using the MO BIO UltraClean™ soil DNA Isolation kit. Protocols were developed and optimized, and fragments of 16S rDNA from soil bacterial communities were PCR-amplified, using the universal bacterial primer pair 341fGC/534r. Different size 18S rDNA sequences were amplified from soil fungal communities, using the universal fungus-specific primer pairs NS1/FR1GC and FF390/FR1GC. Amplicons from both the bacterial and fungal communities were fingerprinted by DGGE, and bands in the fungal DGGE gels were excised and sequenced. The DGGE profiles were analysed by Bio-Rad Quantity One™ Image analysis software, with respect to band number, position, and relative intensity. Statistical analyses of this data then followed. Soil properties [organic C; pH (KCl); exchangeable acidity; total cations (ECEC); exchangeable K, Ca and Mg; and extractable P] were determined by PCA and were shown to have affected the structural and catabolic diversity of the resident microbial communities. At Baynesfield, canonical correspondence analysis (CCA) relating the selected soil variables to bacterial community structural diversity, indicated that ECEC, K, P and acidity were correlated with CCA1, accounting for 33.3% of the variance, whereas Mg and organic C were correlated with CCA2 and accounted for 22.9% of the variance. In the fungal structu |
| 英文关键词 | Soil microbiology. Soil microbial ecology. Crops and soil. Plant-soil relationships. Theses--Soil science. |
| 语种 | 英语 |
| URL | http://hdl.handle.net/10413/7974 |
| 资源类型 | 学位论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/245582 |
| 推荐引用方式 GB/T 7714 | Wallis;Patricia Dawn.. The effects of land use and management practices on soil microbial diversity as determined by PCR-DGGE and CLPP.[D],2011. |
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