Weak Phylogenetic Signal in Physiological Traits of Methane-Oxidizing Bacteria

Supplemental material to:

Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria

FigureS1: Phylogenetic tree based on partial pmoA sequences.

FigureS2: Phylogenetic tree based on 16S rRNA sequences.

TableS1:P-values of tip shuffling randomization to test the presence of phylogenetic signal in continuous-valued traits.

TableS2: The phylogenetic autocorrelation in physiological traits of MOB using the test of Abouheif (1999).

FigureS1. Phylogenetic tree based on partial pmoA sequences (391bp). The tree was constructed by maximum likelihood (1000 data resamplings) with the “GTR” substitution model. Bootstrap values (1000 data resamplings) are shown with a closed square representing bootstrap values above 70. The outgroup isNitrosococcus mobilis but not displayed in the tree.The scale bar represents 0.1 change per base position.

FigureS2. Phylogenetic tree based on 16S rRNA sequences (1399bp). The tree was constructed by maximum likelihood (1000 data resamplings) with the “GTR” substitution model. Bootstrap values (1000 data resamplings) are shown with a closed square representing bootstrap values above 70. The outgroup isNitrosococcus mobilis but not displayed in the tree.The scale bar represents 0.01 change per base position.

TableS1. Average P-values of a tip shuffling randomizations from 1000 bootstrap trees using the maximum likelihood algorithm, significant values are highlighted in bold.

Traits* / pmoA / 16S rRNA
pHopt / 0.016 ± 0.06 / 0.001 ± 0.00
pHrange / 0.237 ± 0.14 / 0.008 ± 0.01
Tempopt / 0.001 ± 0.00 / 0.002 ± 0.01
Temprange / 0.200 ± 0.05 / 0.186 ± 0.08
GC / 0.156 ± 0.15 / 0.001 ± 0.01
Speccell / 0.121 ± 0.07 / 0.402 ± 0.13
Specliter / 0.561 ± 0.08 / 0.620 ± 0.10
Kmapp / 0.511 ± 0.08 / 0.376 ± 018

*pHopt: optimal pH value for growth, pHrange: pH range for growth, Tempopt: optimal temperature for growth, Temprange: temperature range for growth, Speccell: specific affinity per cell (10-12 l cell-1 h-1), Specliter: specific affinity per liter (l g-1 h-1), Kmapp: Michaelis constant Km (apparent).

TableS2. The phylogenetic signal in physiological traits of MOB using the test of Abouheif (1999), significant P-values are highlighted in bold.

pmoA / 16S rRNA
Traits* / Obs / Std Obs / H0 / P-value / Obs / Std Obs / H0 / P-value
pHopt / 0.45 / 3.74 / greater / 0.005 / 0.50 / 4.31 / greater / 0.002
pHrange / 0.33 / 2.37 / greater / 0.002 / 0.29 / 2.10 / greater / 0.008
Tempopt / 0.44 / 3.33 / greater / 0.001 / 0.44 / 3.30 / greater / 0.003
Temprange / 0.10 / 0.77 / greater / 0.22 / 0.01 / 0.14 / greater / 0.42
GC / 0.45 / 3.47 / greater / 0.001 / 0.45 / 3.16 / greater / 0.001
Speccell / 0.08 / 0.48 / greater / 0.30 / 0.21 / 1.12 / greater / 0.15
Specliter / -0.15 / -0.81 / greater / 0.77 / 0.25 / 1.28 / greater / 0.11
Kmapp / 0.12 / 0.81 / greater / 0.20 / 0.16 / 1.13 / greater / 0.13