Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion.

Jo De Vrieze,Dietmar H Pieper,Juan M Lema,Marta Carballa,Ruy Jáuregui,Ramiro Vilchez-Vargas,Ruben Props,Leticia Regueiro

doi:10.1186/s13068-016-0652-5

Abstract

BackgroundThe microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.ResultsThe application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation.ConclusionsThis research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0652-5) contains supplementary material, which is available to authorized users.

Highlights

The microbial community in anaerobic digestion is mainly monitored by means of diversity was observed between the total (DNA)-based meth‐ ods
Methane production slowly increased to a final value of 173 ± 27 mL CH4 L−1 d−1 on day 42 (Additional file 1: Figure S2a), which corresponded with a chemical oxygen demand (COD) conversion efficiency of 49.5 ± 7.8%
The treatments with 10 and 20 g Na+ L−1 clearly had a much lower methane production, with values of 0.32 ± 0.14 and 0.08 ± 0.01 L CH4 L−1, respectively. These values corresponded with a COD conversion to CH4 of 18.2 ± 7.9 and 4.9 ± 0.8%, indicating severe inhibition of methanogenesis. These results were confirmed by the increase in volatile fatty acid (VFA) concentration to 1.24 ± 0.33 and 1.12 ± 0.46 g COD L−1 in the reactors with 10 and 20 g Na+ L−1, respectively, while no VFA were detected in the control and the treatment with 5 g Na+ L−1 (Additional file 1: Figure S4a)

Summary

Introduction

The microbial community in anaerobic digestion is mainly monitored by means of DNA-based meth‐ ods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. The difference between microbial community response on DNA (total com‐ munity) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated. Anaerobic digestion (AD) contains a complex microbial community that produces biogas from organic waste streams. The stability of the AD process is mainly monitored based on the conventional parameters, such as pH, volatile fatty acid (VFA) concentrations, alkalinity, and biogas. Microbial community evenness [12,13,14] and dynamics [8, 15, 16], whether or not influenced by a suitable inoculum [17], reflect the microbial community structure and organization, and

Methods

Results

Discussion

Conclusion