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

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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.

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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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Acknowledgments

The authors would like to thanks Dr. Rosario Durán and Lic. Analía Lima Raimondo (Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Uruguay) for proteins 2D gel figure, and Eng. Magela Odriozzola (BioProa Laboratory, Instituto de Ingeniería Química, Facultad de Ingeniería, UDELAR) for providing reactor scheme. The authors thanks to the following funding agencies and projects, ANII FSE 6437 and FCE 7062. A. Marone ‘s postdoctoral program was funded by the Marie Curie Intra European Fellowship WASTE2BIOHY (FP7-MC-IEF-326974) under the 7th Framework Programme of the European Community. A. Galès was funded by the French ANR Phycover project (ANR-14-CE04-0011).

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Authors and Affiliations

  1. Laboratorio de Ecología Microbiana, Departamento de Bioquímica y Genómica Microbiana, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, C.P. 11600, Montevideo, Uruguay

    Angela Cabezas, Cecilia Callejas & Claudia Etchebehere

  2. Laboratorio de Biotecnología, Facultad de Ingeniería, Universidad ORT Uruguay, Cuareim 1451, C.P. 11100, Montevideo, Uruguay

    Angela Cabezas

  3. Departamento de Engenharia Sanitária e Ambiental, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil

    Juliana Calabria de Araujo

  4. Laboratorio de Bioprocesos Ambientales, Institutito de Ingeniería Química, Facultad de Ingeniería, Universidad de la República, Herrera y Reissig 565, Montevideo, Uruguay

    Cecilia Callejas

  5. Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands

    Diana Z. Sousa

  6. Laboratoire de Biotechnologie de l’Environnement, INRA, UR0050, Avenue des Etangs, 11100, Narbonne, France

    Amandine Galès, Jérôme Hamelin, Antonella Marone & Eric Trably

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  1. Angela Cabezas
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  2. Juliana Calabria de Araujo
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  3. Cecilia Callejas
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  9. Claudia Etchebehere
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Correspondence to Claudia Etchebehere.

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Cabezas, A., de Araujo, J.C., Callejas, C. et al. How to use molecular biology tools for the study of the anaerobic digestion process?. Rev Environ Sci Biotechnol 14, 555–593 (2015). https://doi.org/10.1007/s11157-015-9380-8

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