Nitrile-Degrading Bacteria Isolated from Compost

Egelkamp, Richard; Schneider, Dominik; Hertel, Robert; Daniel, Rolf

doi:10.3389/fenvs.2017.00056

Cited by 30 publications

(15 citation statements)

References 43 publications

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“…According to sequence similarity, nit09 is affiliated to Variovorax boronicumulans (Table 1). Nitrile-degrading abilities of this species have been described previously, but phenylacetonitrile degradation has not been mentioned (Nielsen et al 2007;Zhang et al 2012;Egelkamp et al 2017;Sun et al 2018). The molecular mass of Nit09 (36 kDa) is close to molecular masses of other known arylacetonitrilases such as the enzymes from Pseudomonas sp.…”

Section: A Novel and Stable Arylacetonitrilasementioning

confidence: 58%

“…The second one involves the degradation of nitriles to corresponding amides via nitrile hydratases (NHases) (EC 4.2.1.84) and the subsequent hydrolysis of amides to carboxylic acids and ammonia using amidases (EC 3.5.1.4). Respective enzymes are present in bacteria (Egelkamp et al 2017), filamentous fungi (Martínková et al 2009), yeasts (Rustler and Stolz 2007), and plants (Piotrowski 2008). The enzymes are used in industry for the production of Richard Egelkamp and Ines Friedrich contributed equally to this work.…”

Section: Introductionmentioning

confidence: 99%

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From sequence to function: a new workflow for nitrilase identification

Egelkamp

Friedrich

Hertel

et al. 2020

Appl Microbiol Biotechnol

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Nitrilases are industrially important biocatalysts due to their ability to degrade nitriles to carboxylic acids and ammonia. In this study, a workflow for simple and fast recovery of nitrilase candidates from metagenomes is presented. For identification of active enzymes, a NADH-coupled high-throughput assay was established. Purification of enzymes could be omitted as the assay is based on crude extract containing the expressed putative nitrilases. In addition, long incubation times were avoided by combining nitrile and NADH conversion in a single reaction. This allowed the direct measurement of nitrile degradation and provided not only insights into substrate spectrum and specificity but also in degradation efficiency. The novel assay was used for investigation of candidate nitrilase-encoding genes. Seventy putative nitrilase-encoding gene and the corresponding deduced protein sequences identified during sequence-based screens of metagenomes derived from nitrile-treated microbial communities were analyzed. Subsequently, the assay was applied to 13 selected candidate genes and proteins. Six of the generated corresponding Escherichia coli clones produced nitrilases that showed activity and one unusual nitrilase was purified and analyzed. The activity of the novel arylacetonitrilase Nit09 exhibited a broad pH range and a high long-term stability. The enzyme showed high activity for arylacetonitriles with a K M of 1.29 mM and a V max of 13.85 U/mg protein for phenylacetonitrile. In conclusion, we provided a setup for simple and rapid analysis of putative nitrilase-encoding genes from sequence to function. The suitability was demonstrated by identification, isolation, and characterization of the arylacetonitrilase. Key points • A simple and fast high-throughput nitrilase screening was developed. • A set of putative nitrilases was successfully screened with the assay. • A novel arylacetonitrilase was identified, purified, and characterized in detail.

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Section: A Novel and Stable Arylacetonitrilasementioning

confidence: 58%

Section: Introductionmentioning

confidence: 99%

From sequence to function: a new workflow for nitrilase identification

Egelkamp

Friedrich

Hertel

et al. 2020

Appl Microbiol Biotechnol

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“…In case of the nitriles, only succinonitrile, acetonitrile, and crotononitrile (Figure 2A) exhibited a positive effect on microbial growth, indicating nitrile-degrading abilities of the predominant bacterial community members. For acetonitrile, this effect was already experimentally confirmed through the successful isolation of nitrile-degrading strains from similar cultures (Egelkamp et al, 2017). All other nitrile-containing cultures revealed reduced density indicating weak or no degradation ability or tolerance levels with respect to the tested compounds.…”

Section: Discussionmentioning

confidence: 66%

Impact of Nitriles on Bacterial Communities

Egelkamp

Zimmermann

Schneider

et al. 2019

Front. Environ. Sci.

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Nitriles are organic molecules with-C≡N as functional group and often toxic for living organisms. Detoxification can occur via nitrilases that degrade nitriles directly to carboxylic acids and ammonia, or with nitrile hydratases and amidases that convert nitriles to amides and subsequently to carboxylic acids and ammonia. Despite the knowledge of enzymatic degradation pathways, the influence of these compounds on the composition of bacterial communities is unknown. The tolerances of four phylogenetically different bacterial strains without known nitrile detoxification systems (Agrobacterium tumefaciens, Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli) to the toxic effects of nine nitriles and the corresponding carboxylic acids were determined. Based on these results, the effect of nitriles on diversity and composition of compost-derived bacterial communities was monitored over time by 16S rRNA gene amplicon-based and metagenome analyses. Acetone cyanohydrin, 2-phenylpropionitrile, and pyruvonitrile exhibited a lethal, phenylacetonitrile, 4-hydroxybenzonitrile, and cyclohexanecarbonitrile a growth-suppressing and succinonitrile, acetonitrile, and crotononitrile a growth-promoting effect on the studied communities. Furthermore, each nitrile had a specific community-shaping effect, e.g., communities showing growth-suppression exhibited high relative abundance of Paenibacillus. In general, analysis of all data indicated a higher resistance of Gram-positive than Gram-negative bacterial community members and test organisms to growth-suppressing nitriles. More than 70 putative nitrilase-encoding and over 20 potential nitrile hydratase-encoding genes were identified during analysis of metagenomes derived from nitrile-enrichments, underlining the high yet often unexplored abundance of nitrile-degrading enzymes.

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“…30 µm thickness) using a DM2700P Leica Microscope coupled to a DFC550 digital camera. Carbonate textures have been classified following Dunham (1962) and Embry III and Klovan (1971).…”

Section: Petrographic Analysismentioning

confidence: 99%

“…Illumina PE sequencing of the amplicons and further processing of the sequence data was performed in the Göttingen Genomics Laboratory (Göttingen, Germany). After Illumina MiSeq processing, sequences were analyzed as described in Egelkamp et al (2017) with minor modifications. In brief, paired-end sequences were merged using PEAR v0.9.10 (Zhang et al, 2014); sequences with an average quality score below 20 and containing unresolved bases were removed with QIIME 1.9.1 (Caporaso et al, 2010).…”

Section: Data Analysis and Pipelinementioning

confidence: 99%

Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge

Rincón-Tomás¹,

Duda

Somoza

et al. 2019

Biogeosciences

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Abstract. Azooxanthellate cold-water corals (CWCs) have a global distribution and have commonly been found in areas of active fluid seepage. The relationship between the CWCs and these fluids, however, is not well understood. This study aims to unravel the relationship between CWC development and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz, Atlantic Ocean). This region is comprised of mud volcanoes (MVs), coral ridges and fields of coral mounds, which are all affected by the tectonically driven seepage of hydrocarbon-rich fluids. These types of seepage, for example, focused, scattered, diffused or eruptive, is tightly controlled by a complex system of faults and diapirs. Early diagenetic carbonates from the currently active Al Gacel MV exhibit δ13C signatures down to −28.77 ‰ Vienna Pee Dee Belemnite (VPDB), which indicate biologically derived methane as the main carbon source. The same samples contain 13C-depleted lipid biomarkers diagnostic for archaea such as crocetane (δ13C down to −101.2 ‰ VPDB) and pentamethylicosane (PMI) (δ13C down to −102.9 ‰ VPDB), which is evidence of microbially mediated anaerobic oxidation of methane (AOM). This is further supported by next generation DNA sequencing data, demonstrating the presence of AOM-related microorganisms (ANMEs, archaea, sulfate-reducing bacteria) in the carbonate. Embedded corals in some of the carbonates and CWC fragments exhibit less negative δ13C values (−8.08 ‰ to −1.39 ‰ VPDB), pointing against the use of methane as the carbon source. Likewise, the absence of DNA from methane- and sulfide-oxidizing microbes in sampled coral does not support the idea of these organisms having a chemosynthetic lifestyle. In light of these findings, it appears that the CWCs benefit rather indirectly from hydrocarbon-rich seepage by using methane-derived authigenic carbonates as a substratum for colonization. At the same time, chemosynthetic organisms at active sites prevent coral dissolution and necrosis by feeding on the seeping fluids (i.e., methane, sulfate, hydrogen sulfide), allowing cold-water corals to colonize carbonates currently affected by hydrocarbon-rich seepage.

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Nitrile-Degrading Bacteria Isolated from Compost

Cited by 30 publications

References 43 publications

From sequence to function: a new workflow for nitrilase identification

From sequence to function: a new workflow for nitrilase identification

Impact of Nitriles on Bacterial Communities

Cold-water corals and hydrocarbon-rich seepage in Pompeia Province (Gulf of Cádiz) – living on the edge

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