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

Hong JK, Cho JC - PLoS ONE (2015)

Bottom Line: Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs.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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

RDA biplot representing the relative abundance of prokaryotic taxa and environmental variables.Solid-line arrows and dashed-line arrows represent the biplot scores of the relative abundances of prokaryotic taxa and of the environmental variables, respectively. Values in parentheses indicate the percentages of the total variation that are explained by each canonical axis.
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pone.0133763.g001: RDA biplot representing the relative abundance of prokaryotic taxa and environmental variables.Solid-line arrows and dashed-line arrows represent the biplot scores of the relative abundances of prokaryotic taxa and of the environmental variables, respectively. Values in parentheses indicate the percentages of the total variation that are explained by each canonical axis.

Mentions: The test of significance on the overall RDA results performed using 499 permutations showed that the canonical relationship between the RVs and EVs was highly significant (p = 0.018), indicating that the relative abundance of prokaryotic taxa estimated in this study and the environmental variables measured in this study were linearly related. The two canonical axes (CA-I and CA-II) shown in the RDA biplot (Fig 1) explained almost all (>99.9%) the variance in the RV data set, and the first axis (CA-I) explained the great majority (91.5%) of the variance. The relative abundance of the phylum Thaumarchaeota, RTHAUM, contributed the most (81.6%) to the first canonical axis, and the relative abundances of Archaea and Bacteria (RARCH and RBACT) respectively showed a moderate contribution (18.4%) and the smallest contribution (<0.001%) to the first canonical axis. The biplot score of RBACT on the first canonical axis was very small (/−0.010/) compared to those of RTHAUM (/+0.957/) and RARCH (/+0.455/). Among the EVs, WC, TC, TN, and TS showed biplot scores greater than 0.9 on the first canonical axis, whereas temperature, pH, and TP showed biplot scores less than 0.3. In addition, when the causal effects of temperature, pH, and TP were controlled in partial RDA, the linear relationship between EVs and RVs was significant (p < 0.05), indicating that these EVs have marginal or no effect on RVs. The angles (directions) between RVs and EVs in the RDA biplot suggested negative causal relationships of RTHAUM with nutrition level–related environmental variables (TC, TN, and TS) and with WC. RARCH was also shown to be negatively related to these four EVs (TC, TN, TS, and WC), but the causal relationships between RARCH and these EVs appeared to be less strong than the relationships between the RTHAUM and these EVs.


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

Hong JK, Cho JC - PLoS ONE (2015)

RDA biplot representing the relative abundance of prokaryotic taxa and environmental variables.Solid-line arrows and dashed-line arrows represent the biplot scores of the relative abundances of prokaryotic taxa and of the environmental variables, respectively. Values in parentheses indicate the percentages of the total variation that are explained by each canonical axis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524719&req=5

pone.0133763.g001: RDA biplot representing the relative abundance of prokaryotic taxa and environmental variables.Solid-line arrows and dashed-line arrows represent the biplot scores of the relative abundances of prokaryotic taxa and of the environmental variables, respectively. Values in parentheses indicate the percentages of the total variation that are explained by each canonical axis.
Mentions: The test of significance on the overall RDA results performed using 499 permutations showed that the canonical relationship between the RVs and EVs was highly significant (p = 0.018), indicating that the relative abundance of prokaryotic taxa estimated in this study and the environmental variables measured in this study were linearly related. The two canonical axes (CA-I and CA-II) shown in the RDA biplot (Fig 1) explained almost all (>99.9%) the variance in the RV data set, and the first axis (CA-I) explained the great majority (91.5%) of the variance. The relative abundance of the phylum Thaumarchaeota, RTHAUM, contributed the most (81.6%) to the first canonical axis, and the relative abundances of Archaea and Bacteria (RARCH and RBACT) respectively showed a moderate contribution (18.4%) and the smallest contribution (<0.001%) to the first canonical axis. The biplot score of RBACT on the first canonical axis was very small (/−0.010/) compared to those of RTHAUM (/+0.957/) and RARCH (/+0.455/). Among the EVs, WC, TC, TN, and TS showed biplot scores greater than 0.9 on the first canonical axis, whereas temperature, pH, and TP showed biplot scores less than 0.3. In addition, when the causal effects of temperature, pH, and TP were controlled in partial RDA, the linear relationship between EVs and RVs was significant (p < 0.05), indicating that these EVs have marginal or no effect on RVs. The angles (directions) between RVs and EVs in the RDA biplot suggested negative causal relationships of RTHAUM with nutrition level–related environmental variables (TC, TN, and TS) and with WC. RARCH was also shown to be negatively related to these four EVs (TC, TN, TS, and WC), but the causal relationships between RARCH and these EVs appeared to be less strong than the relationships between the RTHAUM and these EVs.

Bottom Line: Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs.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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus