alex-bagnoud/anammoxbellefontaine

Anammox distribution in Bellefontaine

This github repository details the statistical analyses carried out in the paper Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils written by Alexandre Bagnoud, Sylvia Guye-Humbert, Brigitte Schloter-Hai, Michael Schloter and Jakob Zopfi and published in FEMS Microbiology Ecology, Volume 96, Issue 2 in February 2020 (https://doi.org/10.1093/femsec/fiz191).

This work describes the distribution, diversity and activity of anammox along a sharp soil gradient, from an amended pasteure to an ombrotrophic peatbog. The aim of the statistical analysis presented here is to understand which environmental parameters are controlling anammox distribution in this soil system.

Note: the phylogenetic analyses of this article are presented in another repository.

Files:

This repository inlcude the following files:

• amx_matrix.csv includes the complete data set for this analysis
• Script_with_complete_output.md is the markdown version of the R script, with the complete output.
• Script_with_short_output.md is the markdown version of the R script, with a simplified consol output, for a better readability
• Script.R is the R script used for this analysis.

Description of variables of data matrix:

Here is the exhaustive list of all the variables in amx_matrix.csv and their description:

• SampleID: Unique sample identifier. The first digit correspond to the soil (1 to 4) and the second digit to the sample number in the soil profile.
• Soil: Soil type, 1 to 4.
• Depth: Depth of the sample in the soil profile. Unit : cm.
• AMXcopiesNb: Number of anammox 16S rRNA genes detected. Unit : copies g^-1 of dry soil.
• AOBcopiesNb: Number of bacterial amoA genes detected. Unit : copies g^-1 of dry soil.
• AOBcopiesNb: Number of archaeal amoA genes detected. Unit : copies g^-1 of dry soil.
• DaysBelowWaterTable: Number of days per year that a soil sample is spending below the water table. Unit : day.
• LOI: Loss on ignition of soil samples. Unit : % (g g^-1).
• N: Nitrogen in soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Unit : % (g g^-1).
• C: Carbon in soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Unit : % (g g^-1).
• FeIISoil: Concentration of Fe(II) extracted from soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Unit : umol g^-1 of dry soil.
• FeIIISoil: Concentration of colloidal Fe(III) extracted from soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Unit : umol g^-1 of dry soil.
• pHSoil: pH H₂O of soil samples.
• NH4Soil: Concentration of NH₄⁺ extracted from soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 4. Unit : umol g^-1 of dry soil.
• NO3Soil: Concentration of NO₃^- extracted from soil samples. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 4. Unit : umol g^-1 of dry soil.
• avNH4Water: Average concentration of NH₄⁺ in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avNO2Water: Average concentration of NO₂^- in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avNO3Water: Average concentration of NO₃^- in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avpHWater: Average pH in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1.
• avO2Water: Average concentration of O₂ in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : mg l^-1.
• avFeIIWater: Average concentration of Fe(II) in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avFeIIIWater: Average concentration of colloidal Fe(III) in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avSIIWater: Average concentration of S(-II) in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• avSO4water: Average concentration of SO₄^2- in interstitial water samples during an annual cycle. Some values were interpolated by linear combination in order to match the depth of other variables. Not measured in Soil 1. Unit : umol l^-1.
• NitrifRate: Nitrification rates measured in vitro for few samples per soil type. Unit : umol NH₄⁺ g^-1 dry soil h^-1.
• BOD: Biological oxygen demand, measured during 5 days for samples from Soil 3 only. Unit : mg O₂ g^-1 dry soil.

Note: Concentration of NO₂^- extracted from soil samples was not included in the data set, as this value is null for all observations.