Correspondence: Reply to ‘Analytical flaws in a continental-scale forest soil microbial diversity study'

نویسندگان

  • Jizhong Zhou
  • Ye Deng
  • Lina Shen
  • Chongqing Wen
  • Qingyun Yan
  • Daliang Ning
  • Yujia Qin
  • Kai Xue
  • Liyou Wu
  • Zhili He
  • James W Voordeckers
  • Joy D Van Nostrand
  • Vanessa Buzzard
  • Sean T Michaletz
  • Brian J Enquist
  • Michael D Weiser
  • Michael Kaspari
  • Robert Waide
  • Yunfeng Yang
  • James H Brown
چکیده

We greatly appreciate Tedersoo’s1 interest in our recent publication2 concerning temperature effects on continental scale diversity of microbial communities in forest soils2. The Correspondence raises several questions, primarily regarding the approaches used in our study. While we welcome this debate, we disagree with the claims regarding our study design, statistical analyses and interpretations. The first concern raised in the correspondence is related to the sampling design. In contrast to most traditional microbial biogeographic studies, we sampled microbial communities at multiple spatial scales. Specifically, we focused on many replicates at a small scale, which resulted in a tradeoff for fewer samples at a large scale. This design is appropriate for addressing our research questions because soil environments are highly heterogeneous, which could mask the effects of environmental variables such as temperature on microbial distributions at continental scales. Increased sampling effort with many replicates within a site is the most effective way to mitigate the impacts of such heterogeneity on detecting patterns of microbial community diversity. We have now conducted a simulation analysis (Supplementary Table 1), which shows that large within-site sample sizes are necessary for capturing the trends between microbial diversity and temperature. Also, the experimental design with extensive sampling within a site allows us to appropriately assess the large within-site variation due to heterogeneity, which is also critical for revealing differences between microbial communities across sites. To further demonstrate this point, a similar simulation was performed using well-known published data on plant diversity and stability3. Diversity effects on stability could only be observed when the within-treatment variation was captured by more than 19 out of the 30 replicates (Supplementary Table 2). In addition, the range of temperatures (2.5–27 C) of our six forest sites is comparable to many other continental surveys for plants, animals and phytoplankton, and should be broad enough to detect the general patterns of temperature effects on ecological communities. However, we do acknowledge that the number of sites is limited, and more sites within and/or across continents should be examined to evaluate whether our results are applicable to other forest ecosystems. Thus, we pointed out this potential caveat in the original paper2. The correspondence1 also questions our regression analyses. In the original version of the study, we used univariate linear regression, multiple linear regression, nonlinear univariate regression and more complex models (original Supplementary Tables 7–9)2. We have now also conducted partial correlation analysis (Supplementary Table 3). All of these analyses indicated that temperature is generally a better predictor of microbial diversity than other environmental variables. We also performed univariate and multiple hierarchical linear model (HLM) analyses (Supplementary Tables 4 and 5), where site was used as grouping factor to account for our nested sampling design, and the degrees of freedom for the variable(s) and intercept were 4 and 120, respectively. Since heteroscedasticity and non-normality of residuals were found in many cases of our HLM analysis, variance weights were introduced to allow different variances for various sites, and the significance test was based on bootstrapping rather than parametric tests. The HLM analyses showed the same trends as univariate and multiple linear regression (original Table 9 and Supplementary Table 6, ref. 2), which further supports our original conclusion. DOI: 10.1038/ncomms15583 OPEN

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عنوان ژورنال:

دوره 8  شماره 

صفحات  -

تاریخ انتشار 2017