Nitrile-Degrading Bacteria Isolated from Compost

Abstract

Nitriles are a diverse group of organic compounds with –C≡N as functional group. Most nitriles are slightly cytotoxic but some cause severe toxic effects. More than 120 naturally occurring nitriles without considering cyanogenic glycosides are present in terrestrial and marine habitats, especially in plant components such as almonds or other fruit pits. The most common group of naturally occurring nitriles are cyanogenic glycosides, which can be found in more than 100 plant families as well as in fungi, bacteria, and animals. This group of molecules can be chemically or enzymatically hydrolyzed, leading to the release of highly toxic hydrogen cyanide and thereby act as natural defense compound (Fleming, 1999). For detoxification, two enzymatic pathways for the degradation of nitriles are known. The first one involves nitrilases (EC 3.5.5.1), a subgroup of the carbon-nitrogen hydrolase superfamily, which degrade nitriles directly to carboxylic acids and ammonia. The second one is a bi-enzymatic pathway using nitrile hydratases (NHases; EC 4.2.1.84) for the degradation of nitriles to amides and amidases (EC 3.5.1.4) for the subsequent degradation to carboxylic acids and ammonia (Gong et al., 2012). The enzymatic hydrolysis of nitriles proceeds under mild reaction conditions, whereas the chemical hydrolysis is dependent on acidic or alkaline conditions and high temperatures. The latter also results in the production of large quantities of byproducts and inorganic waste (Clouthier and Pelletier, 2012; Vergne-Vaxelaire et al., 2013). Consequently, nitrile-converting enzymes are of increasing industrial importance with respect to green chemistry. A constantly increasing number of nitrile-derived amides [e.g., acrylamides or carboxylic acids (e.g., glycolic acid)] are produced with these enzymes (Schmid et al., 2001; Panova et al., 2007). In addition, nitrilases can be used for the treatment of nitrile-polluted wastewater (Li et al., 2016) and other environmentally-friendly bioremediation processes (Gong et al., 2012). Here, we report data on the taxonomic composition of an enrichment culture with acetonitrile as nitrogen source. In addition, we present eight individual bacterial draft genome sequences of isolates obtained from this enrichment. The genome content of these isolates was analyzed with respect to genes responsible for the nitrile-degrading phenotype. Genome and average nucleotide identity analysis indicated that the isolated bacterial strains are affiliated to the species Rhodococcus erythropolis, Flavobacterium sp., Variovorax boronicumulans, Pseudomonas sp., and Pseudomonas kilonensis.