Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects

• Published in: PloS one 2015-08, Vol.10 (8), p.e0133763-e0133763
• Main Authors: Hong, Jin-Kyung, Cho, Jae-Chang
• Format: Article
• Language: English
• Subjects: Abundance; Ammonia; Ammonia - analysis; Ammonification; Ammonium; Archaea; Archaea - classification; Archaea - genetics; Archaea - isolation & purification; Archaea - physiology; Bacteria; Carbon - analysis; Carbon content; Colony Count, Microbial; Correlation analysis; Crenarchaeota; DNA Primers - genetics; Ecological effects; Ecological niches; Ecosystem; Energy Metabolism; Environmental effects; Environmental science; Gene Dosage; Gene sequencing; Genetic aspects; Genomes; Humic Substances - analysis; Mathematical models; Metabolism; Mineralization; Moisture content; Nitrogen; Nitrogen - analysis; Nitrogen content; Organic matter; Oxidation; Phosphorus - analysis; Phylogeny; Physiological aspects; Polymerase chain reaction; Primers; Prokaryotes; Real-Time Polymerase Chain Reaction; Redundancy; Regression analysis; Relative abundance; Republic of Korea; Ribosomal RNA; RNA, Archaeal - genetics; RNA, Ribosomal, 16S - genetics; rRNA 16S; Soil - chemistry; Soil Microbiology; Soils; Statistical analysis; Statistical methods; Studies; Sulfur - analysis; Temperature; Temperature effects; Terrestrial environments; Thaumarchaeota; Water; Water content
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0133763

To find environmental variables (EVs) shaping the ecological niche of the archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting thaumarchaeotal 16S rRNA gene sequences. We employed our previously developed primer, THAUM-494, which had greater coverage for Thaumarchaeota and lower tolerance to nonthaumarchaeotal taxa than previous Thaumarchaeota-directed primers. The relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to a series of statistical analyses. Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs. Negative causal relationships between RTHAUM and nutrient level-related EVs were observed in an RDA biplot. These negative relationships were further confirmed by correlation and regression analyses. Total nitrogen content (TN) appeared to be the EV that affected RTHAUM most strongly, and total carbon content (TC), which reflected the content of organic matter (OM), appeared to be the EV that affected it least. However, in the path analysis, a path model indicated that TN might be a mediator EV that could be controlled directly by the OM. Additionally, another path model implied that water content (WC) might also indirectly affect RTHAUM by controlling ammonium nitrogen (NH4+-N) level through ammonification. Thus, although most directly affected by NH4+-N, RTHAUM could be ultimately determined by OM content, suggesting that Thaumarchaeota could prefer low-OM or low-WC conditions, because either of these EVs could subsequently result in low levels of NH4+-N in soil.