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Soil management for orchard depends on the effects of soil microbial activities. The present study evaluated the soil microbial community of 25 orchard (5 sites for sandy loam, 7 sites for silt loam, and 13 sites for loam) in Gyeongnam Province by fatty acid methyl ester (FAME) method. The average values for 25 orchard soil samples were 270 nmol g -1 of total FAMEs, 72 nmol g -1 of total bacteria, 34 nmol g -1 of Gram-negative bacteria, 34 nmol g -1 of Gram-positive bacteria, 6 nmol g -1 of actinomycetes, 49 nmol g -1 of fungi, and 7 nmol g -1 of arbuscular mycorrhizal fungi. In addition, silt loam soils had significantly low ratio of cy17:0 to 16:1ω7c and cy19:0 to 18:1ω7c compared with those of loam soils (p < 0.05), indicating that microbial activity increased. The average soil microbial communities in the orchard soils were 26.7% of bacteria, 17.9% of fungi, 12.6% of Gram-negative bacteria, 12.5% of Gram-positive bacteria, 2.5% of arbuscular mycorrhizal fungi, and 2.2% of actinomycetes. The soil microbial community of Gram-negative bacteria in silt loam soils was significantly higher than those of sandy loam and loam soils (p < 0.05).

To estimate the effect of long-term fertilization on metabolically active bacterial communities in a rice field, RNA was extracted from endosphere (rice root), rhizosphere, and bulk soil that had been subjected to different fertilization regimes for 59 years, and the 16S rRNAs were analyzed using the pyrosequencing method. The richness and diversity of metabolically active bacteria were higher in bulk soil than in the endosphere and rhizosphere, and showed no significant difference between non-fertilized and fertilized plots. Weighted UniFrac analysis showed that each compartment had characteristic bacterial communities and that the effect of long-term fertilization on the structure of bacterial community was more pronounced in bulk soil than in the endosphere and rhizosphere. The 16S rRNAs affiliated with Alphaproteobacteria and Firmicutes were more abundant in the endosphere than in bulk soil while those affiliated with Chloroflexi and Acidobacteria were more abundant in bulk soil than in the endosphere. Several dominant operational taxonomic units (clustered at a 97% similarity cut-off) showed different frequencies between non-fertilized and fertilized plots, suggesting that the fertilization affected their activities in the rice field.

Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.

Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.

The soil chemical properties, microbial community structures and biochemical properties of lettuce or cucumber-cultivated greenhouse soil samples were analyzed to assess soil health and characterize microbial distribution in 8 locations in Korea. Although most of chemical properties were within the soil management guidelines, the available phosphate, and the contents of exchangeable potassium and calcium were higher than those of recommended levels. In the culture-dependent analysis, 841 bacterial strains were isolated from the greenhouse soils and were identified at the genus level by 16S rRNA gene sequences analysis. The dominant bacterial genera were Bacillus (35.7%), Microbacterium (9.3%), Arthrobacter (5.7%) and Lysobacter (5.1%). The abundance of pseudomonads was highly variable depending on the soil samples. In the culture-independent analysis, soil microbial community was investigated by using phospholipid fatty acid (PLFA) method. Principal component analysis (PCA) showed that a specific grouping for microbial community structure in the greenhouse soils was not observed based on cultivated crops and investigated sites. The results revealed that the greenhouses soils examined are relatively sound managed in terms of soil chemical contents and microbial properties.