How to use molecular biology tools for the study of the anaerobic digestion process?

  • Angela Cabezas
  • Juliana Calabria de Araujo
  • Cecilia Callejas
  • Amandine Galès
  • Jérôme Hamelin
  • Antonella Marone
  • Diana Z. Sousa
  • Eric Trably
  • Claudia Etchebehere
Review paper

Abstract

Anaerobic digestion is used with success for the treatment of solid waste, urban and industrial effluents with a concomitant energy production. The process is robust and stable, but the complexity of the microbial community involved in the process is not yet fully comprehensive. Nowadays, the study of this complex ecosystem is facilitated by the availability of different molecular tools, but it is very important to choose the adequate tool to answer specific questions. The aim of this review is to describe different molecular techniques, indicate the questions that can be addressed by each technique, enumerate their limitations and give practical advices for their use. Examples of how the molecular tools have been used to address various questions in anaerobic digestion are presented. The key point now is to apply all this information to improve anaerobic digestion. The integration of concepts of microbial-ecology, environmental-engineering, modeling and bioinformatics is currently necessary.

Keywords

Anaerobic digestion Bioreactor Molecular biology Microbial ecology Function Microbial resource management 

Abbreviations

AD

Anaerobic digestion

ANOSIM

Analysis of similarity

ANOVA

Analysis of variance

ARDRA

Amplified ribosomal DNA restriction analysis

BES

2-Bromoethanesulphonic acid

BONCAT

Biorthogonal non-canonical amino acid tagging

CE-SSCP

Capillary electrophoresis Single Strand Conformation Polymorphism

CCA

Canonical correspondence analysis

CLSM

Confocal laser scanning microscopy

CNV

Copy number variation

DIET

Direct interspecies electron transfer

DGGE

Denaturing gradient gel electrophoresis

DNA

Desoxyribo nucleic acid

EGSB

Expanded granular sludge blanket

FISH

Fluorescent in situ hybridization

HIT

Hydrogen interspecies transfer

MAR-FISH

Micro auto radiographic fluorescent in situ hybridization

NanoSIMS

Nanoscale secondary ion mass spectrometry

NGS

Next generation sequencing

NMDS

Nonmetric multidimentional scaling

NPMANOVA

Non parametric multivariate ANOVA

OLR

Organic loading rate

OTU

Operational taxonomic unit

PCA

Principal component analysis

PCoA

Principal coordinate analysis

PCR

Polymerase chain reaction

qPCR

Quantitative polymerase chain reaction

RISA

Ribosomal intergenic spacer analysis

RNA

Ribo nucleic acid

rRNA

Ribosomal RNA

SAO

Syntrophic acetate oxidizers

SIMSISH

Secondary ion mass spectrometry combined with FISH

SIP

Stable isotope probing

SSCP

Single Strand Conformation Polymorphism

ssDNA

Single strand DNA

T-RFLP

Terminal-Restriction Fragment Length Polymorphism

T-RF

Terminal-Restriction Fragment

UASB

Upflow anaerobic sludge blanket

VSS

Volatile suspended solids

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Angela Cabezas
    • 1
    • 2
  • Juliana Calabria de Araujo
    • 3
  • Cecilia Callejas
    • 1
    • 4
  • Amandine Galès
    • 6
  • Jérôme Hamelin
    • 6
  • Antonella Marone
    • 6
  • Diana Z. Sousa
    • 5
  • Eric Trably
    • 6
  • Claudia Etchebehere
    • 1
  1. 1.Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica MicrobianaInstituto de Investigaciones Biológicas Clemente EstableMontevideoUruguay
  2. 2.Laboratorio de Biotecnología, Facultad de IngenieríaUniversidad ORT UruguayMontevideoUruguay
  3. 3.Departamento de Engenharia Sanitária e AmbientalUniversidade Federal de Minas GeraisBelo HorizonteBrazil
  4. 4.Laboratorio de Bioprocesos Ambientales, Institutito de Ingeniería Química, Facultad de IngenieríaUniversidad de la RepúblicaMontevideoUruguay
  5. 5.Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
  6. 6.Laboratoire de Biotechnologie de l’EnvironnementINRA, UR0050NarbonneFrance

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