Members of the uncultured bacterial candidate division WWE 1 are implicated in anaerobic digestion of cellulose

Rim Driss Limam,Rakia Chouari,Tianlun Li,Ahmed Landoulsi,Mouldi Saidi,Jean‐Luc Guerquin‐Kern,Ting‐Di Wu,Laurent Mazéas,Théodore Bouchez,Julien Grossin‐Debattista,Abdelghani Sghir

doi:10.1002/mbo3.144

Abstract

Clones of the WWE1 (Waste Water of Evry 1) candidate division were retrieved during the exploration of the bacterial diversity of an anaerobic mesophilic (35 ± 0.5°C) digester. In order to investigate the metabolic function of WWE1 members, a 16S rRNA gene-based stable isotope probing (SIP) method was used. Eighty-seven percent of 16S r rRNA gene sequences affiliated to WWE1 candidate division were retrieved in a clone library obtained after polymerase chain reaction (PCR) amplification of enriched DNA fraction from anaerobic municipal solid waste samples incubated with 13C-cellulose, at the end of the incubation (day 63) using a Pla46F-1390R primer pair. The design of a specific WWE1 probe associated with the fluorescence in situ hybridization (FISH) technique corroborated the abundant representation of WWE1 members in our 13C-cellulose incubations. Secondary ion mass spectrometry–in situ hybridization (SIMSISH) using an iodine-labeled oligonucleotide probe combined with high-resolution nanometer-scale SIMS (NanoSIMS) observation confirmed the isotopic enrichment of members of WWE1 candidate division. The 13C apparent isotopic composition of hybridized WWE1 cells reached the value of about 40% early during the cellulose degradation process, suggesting that these bacteria play a role either in an extracellular cellulose hydrolysis process and/or in the uptake fermentation products.

Highlights

The environmental benefits of anaerobic digestion are the production of energy-rich biogas and the reduction in the waste emission potential from municipal solid waste
Clones of the WWE1 candidate division were initially retrieved during the exploration of the bacterial diversity of an anaerobic mesophilic digester (35 Æ 0.5°C) treating sludge (Chouari et al 2005)
In such kinds of reactors, the WWE1 candidate division members were subdominants (Chouari et al 2005). To test if this group could be retrieved during anaerobic digestion of other kind of substrates, genomic DNA was extracted from municipal solid waste and mature compost of green waste batch incubations

Summary

Introduction

The environmental benefits of anaerobic digestion are the production of energy-rich biogas and the reduction in the waste emission potential from municipal solid waste. Methane production by microorganisms from anaerobic digestion can be considered as a way to gain safe and sustainable energy (McKendry 2002; Liu et al 2009). The production of methane requires a consortium of a variety of strictly anaerobic microorganisms (Ferry 1997). The microbial communities involved in this process and the impact of operational a 2013 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. MicrobiologyOpen published by John Wiley & Sons Ltd

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