Effect of Soil Type and Fertilizer Management on Archaeal Community in Upland Field Soils

Abstract

The effects of soil and fertilizer types on archaeal communities were evaluated by real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S rRNA gene of total DNA directly extracted from upland field soils. Twelve experimental upland field plots containing four different soil types, i.e., Cumulic Andosol, Low-humic Andosol, Yellow Soil and Gray Lowland Soil, were maintained under three different fertilizer management systems for 8 years (chemical fertilizer, rice husks and cow manure, and pig manure, respectively). Two-way ANOVA and RDA analyses showed that the copy number and PCR-DGGE profile of archaeal 16S rRNA gene were affected mainly by soil type, especially between Andosol and non-Andosol, but were also influenced by fertilizer type. Among several soil chemical properties, total N content showed a significant correlation to archaeal community. Sequence analyses showed that most of the major DGGE bands corresponded to uncultured Crenarchaeota of Group I.1b that contained ammonia-oxidizing archaea (AOA). These sequences were separated into two clusters in the phylogenetic tree and each lineage showed a different response to total N content.

Seasonal Transition of Active Bacterial and Archaeal Communities in Relation to Water Management in Paddy Soils

“…The reaction mixture comprised 2× SYBR Green PCR Master Mix, 0.2 μM forward and reverse primer pairs ((357F and 520R for bacteria (41); A364a and A934b for archaea (15), 0.5 μg/μl BSA, and DNA or cDNA as a template. The PCR conditions were as follows: initial denaturation at 95°C for 10 min, followed by 40 cycles of 95°C for 30 s, 58°C for 30 s, and 72°C for 30 s (for bacteria) or 40 cycles of 94°C for 30 s, 66.5°C for 30 s, and 72°C for 50 s (for archaea).…”

“…PCR amplification and DGGE were performed as described previously (41, 15). PCR product size was confirmed by electrophoresis on 1.5% agarose gel stained with ethidium bromide, and amplicons were purified using the Wizard SV Gel and PCR CleanUp System (Promega, Madison, WI, USA).…”

Ecological Perspectives on Microbes Involved in N-Cycling

“…Many ecosystem ecologists have focused on the N cycle or the dynamics of N transformation in various ecosystems because N (along with H, C, O, S and P), as a major component of proteins and nucleic acids, is an essential element for life and its supply can limit primary productivity in many natural terrestrial and marine ecosystems (12, 122). The N cycle has also been the focus of debate in nitrogen-rich ecosystems, such as fertilized agricultural fields or eutrophic rivers and coasts that are affected by anthropogenic N input (48, 53, 85, 90, 101, 110, 114, 115, 134, 135). Wastewater treatment systems are also examples of artificial ecosystems in which N removal is frequently studied (29, 78, 116, 121).…”

Rediscovery of the Microbial World in Microbial Ecology

“…Characterization of biological processes by microbial communities will be an increasingly important issue for defining ecosystem metabolisms (20, 38, 68). Analysis of community-level responses against disturbance or change in environmental parameters is a practical approach to find out the key members and interspecies relationships within microbial communities (9, 12, 14, 26, 30, 53). At present, several software/web tools are available for data analysis, e.g.…”