Combined Analyses of Bacterial, Fungal and Nematode Communities in Andosolic Agricultural Soils in Japan

Abstract

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.

454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome

“…Arbuscular mycorrhizal fungal community composition in field soils was also shown to be the product of both dispersal and environmental variables [54]. In different studies, a range of physico-chemical parameters was found to structure the mycobiomes of soils sampled along a 2,370 km latitudinal gradient in the southern maritime Antarctic [55], in alpine soils [38], as well as field soils in Texas [56] and Japan [57]. By contrast, Hovatter et al [28] did not find evidence for either species sorting or dispersal limitation to be acting on a regional scale, on fungal community composition in the rhizosphere of Lobelia siphilitica plants or adjacent bulk soil.…”

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

“…The composition of soil invertebrates is commonly assessed by first extracting the organisms from the soil using a combination of approaches including pitfall traps (Drummond et al 2015) and modified Tullgren and Baermann funnels (Bao et al 2012), each of which rely on the capture of organisms during active movement. Similarly, aerial insects may be captured using malaise traps (Yu et al 2012).…”

Microbiological contamination sources of freshly cultivated vegetables

“…Also, the presence and absence of specific pathogens were similar in both the vegetable and the environmental samples. Agricultural importance of the current study Indeed, various earlier studies demonstrated the ability of water bodies to disseminate numerous microorganisms into the plantation soils, and to some extent unraveled the ability of organic fertilizers to propagate pathogenic bacteria into the vegetation objects (Munshi et al, 2012;Khan et al, 2014;Khairuzzaman et al, 2014;Ali, 2013;Chigor et al, 2013;Bao et al, 2012;FAO, 2012;Uddin et al, 2012;Faruque et al, 2003). These microorganisms, especially Bacillus spp., E. coli, Staphylococcus aureus, Pseudomonas spp.…”