MOESM1 of Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
Creators: name: Vrieze, Jo De
name: Regueiro, Leticia
name: Props, Ruben
name: Vilchez-Vargas, Ramiro
name: Jáuregui, Ruy
name: Pieper, Dietmar
name: Lema, Juan
name: Carballa, Marta
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Additional file 1: Table S1. Characteristics of the substrate used for the mother reactors and the short-term stress test. Each analysis was carried out in triplicate, except for the cation measurements. Table S2 Characteristics of the inoculum used for the mother reactors. Each analysis was carried out in triplicate. Table S3 Characteristics of the inoculum used for the short-term stress test. This inoculum originated from the mixture of the three mother reactors. Each analysis was carried out in triplicate. Table S4 Overview of the P-values of the multivariate abundance model of the 79 phylotypes that had a relative abundance &gt;0.1% in at least one sample, and were present in all samples. Adjusted P-values were determined for salt concentration, time, and the DNA/RNA ratio, as well as the interaction effect between salt concentration and DNA/RNA ratio and time and DNA/RNA ratio. Highlighted P-values are considered significant at α = 0.05. Table S5 Overview of the model coefficients of the multivariate abundance model of the 79 phylotypes that had a relative abundance &gt;0.1% in at least one sample, and were present in all samples. Coefficients were determined for salt concentration, time, and the DNA/RNA ratio, as well as the interaction effect between salt concentration and DNA/RNA ratio and time and DNA/RNA ratio. A negative value indicates a negative effect of salt or time or a DNA/RNA ratio &gt; 1. Fig. S1. Evaluation of model assumptions required to allow correct inference of the multivariate regression model with (a) residuals vs. fitted, (b) scale location, and (c) normal Q–Q results. Each label colour is associated with a single phylotype. These results show that the normality of residuals and homogeneity of variance requirements are fulfilled. Fig. S2 Overview of the main operational parameters of the triplicate mother reactors, including (a) methane production, (b) pH of the reactors (■) and the substrate (●), (c) total VFA, and (d) partial alkalinity (■), total alkalinity (●), and the Ripley index (▲). Fig. S3 Cumulative methane yield of the control treatment (□), and treatments with 5 g Na+ L-1 (○), 10 g Na+ L-1 (■), and 20 g Na+ L-1 (●). Fig. S4 Total VFA, and pH and Na+ concentration in the reactors in the stress test after 14 days of operation. Average values of the triplicate reactors are presented, and error bars show standard deviations. Fig. S5 Rarefaction curves indicating the number of resolved phylotypes against sampling depth of each of the samples (both DNA and RNA) during the 14 days short-term stress test. Fig. S6 Heat map representing the microbial community of all samples on class level at a relative abundance &gt;0.1% averaged over all samples. The colour scale ranges from 0 to 60%. The different samples were labelled according to the time point (T0–T5) and salt concentration (0, 5, 10 and 20 g Na+ L-1). The inoculum sample (Inoc) at the start of the experiment as well as the feed sludge (Sludge) were also included in the heat map. Fig. S7 Heat map representing the microbial community of all samples on order level at a relative abundance &gt;0.1% averaged over all samples. The colour scale ranges from 0 to 70%. The different samples were labelled according to the time point (T0–T5) and salt concentration (0, 5, 10 and 20 g Na+ L-1). The inoculum sample (Inoc) at the start of the experiment as well as the feed sludge (Sludge) were also included in the heat map. Fig. S8 Heat map representing the microbial community of all samples on family level at a relative abundance &gt;0.1% averaged over all samples. The colour scale ranges from 0 to 60%. The different samples were labelled according to the time point (T0–T5) and salt concentration (0, 5, 10 and 20 g Na+ L-1). The inoculum sample (Inoc) at the start of the experiment as well as the feed sludge (Sludge) were also included in the heat map. Figure S9 Non-metric multidimensional scaling analysis of the Bray–Curtis dissimilarity index of the different samples on (a) DNA and (b) RNA levels. Figure S10 Overall microbial community variation between the different samples on DNA (red) and RNA (green) level, determined by the distance to the centroid. The distance to the centroid is significantly higher for the RNA samples than the DNA samples (P &lt; 0.0001). Figure S11 Box plots of the alpha diversity metrics on (a) DNA and (b) RNA levels for the different salt additions, ranging from 0 (Control) to 20 g Na+ L-1. Samples were divided in subgroups per salt concentration for comparison of the alpha diversity metrics. A significant difference between any two salt concentrations is marked with * (P &lt; 0.05), **(P &lt; 0.01), or ***(P &lt; 0.001), based on the ANOVA analysis. Figure S11 Box plots of the alpha diversity metrics on (a) DNA and (b) RNA levels for the different salt additions, ranging from 0 (Control) to 20 g Na+ L-1. Samples were divided in subgroups per salt concentration for comparison of the alpha diversity metrics. A significant difference between any two salt concentrations is marked with *(P &lt; 0.05), **(P &lt; 0.01), or ***(P &lt; 0.001), based on the ANOVA analysis.