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Plants produce different kind of secondary metabolites to protect against microbial and insect attacks. These plant secondary metabolites (PSMs) considered as bioactive compounds were used for long times in medicine and preservation of foods. As a consequence, these compounds can be present in wastewater coming from agro-alimentary, pharmaceutical and chemical industries or in vegetal wastes. The water-soluble PSMs such as saponins, polyphenols, alcoholic glycosides and bound quinones (anthraquinones) may inhibit directly the present microorganisms in the effluents. Therefore, anaerobic biodegradation processes of these solid wastes and industrial effluents may be limited by inhibition of the methanogenic archaea since they are very sensitive to this molecule type. The production of biogas can be low or nil and the organic matter contained in the effluent is not reduced. Also these compounds potentially reduce the ability to produce biofuels by biomass fermentation. These solids or effluents poured in the nature can be the basis of pollution.
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