TY - JOUR
T1 - Genomics-informed insights into microbial degradation of N,N-dimethylformamide
AU - Li, Junhui
AU - Dijkstra, Paul
AU - Lu, Qihong
AU - Wang, Shanquan
AU - Chen, Shaohua
AU - Li, Deqiang
AU - Wang, Zhiheng
AU - Jia, Zhenglei
AU - Wang, Lu
AU - Shim, Hojae
N1 - Funding Information:
Although various physicochemical methods have been used to remove DMF from wastewater (Dou et al., 2019; Zhao et al., 2018), microbial degradation is considered to be a superior alternative as it is economical, eco-friendly, and highly efficient (Dhar et al., 2020; Swaroop et al., 2009; Veeranagouda et al., 2006; Wang et al., 2020a; Zhou et al., 2018). So far, only a limited number of bacterial isolates have been discovered that are capable of utilizing DMF as the sole carbon and nitrogen source (Table 1). All isolated DMF degraders are aerobic, and mostly from the phylum Proteobacteria, particularly Alphaproteobacteria and Gamaproteobacteria, including members of Paracoccus, Methylobacterium, Mesorhizobium, Ochrobactrum, Alcaligenes, and Pseudomonas, as well as Mycobacterium (Actinobacteria) and Bacillus (Firmicutes) (Table 1). Of these bacterial isolates, some (e.g., Paracoccus sp. DMF-3, Alcaligenes sp. KUFA-1, and Pseudomonas sp. DMF 5/8) can grow on high concentration (~50 g/L) DMF solutions (Table 1). Besides Paracoccus and Bacillus, members of six other genera (i.e., Hyphomicrobium, Nitratireductor, Burkholderia, Rhodobacter, Catellibacterium, and Bradyrhizobium) were recently reported as potential DMF degraders (Kong et al., 2018a, 2019c; Li et al., 2020b). These studies were carried out to treat synthetic DMF-containing wastewater in anaerobic bioreactors, e.g., up-flow anaerobic sludge blanket and anaerobic membrane bioreactor. Recently, we developed xenobiotic degraders with DMF as carrier solvent under aerobic conditions and found that Paracoccus and Hyphomicrobium are likely the major DMF degraders (Li et al., 2020a), which is supported by identification of genes encoding N,N-dimethylformamidase (DMFase) (Li et al., 2021). In addition, members of six other genera, i.e., Achromobacter, Methyloversatilis, Nitratireductor, Pontibaca, Rhodopseudomonas, and Starkeya, carry genes encoding the large and/or small subunits of DMFase (Li et al., 2021).This work was supported by the National Natural Science Foundation of China (Grant Nos. 51409106, U1901601) and the University of Macau Multi-Year Research Grant (MYRG2018-00108-FST).
Funding Information:
This work was supported by the National Natural Science Foundation of China (Grant Nos. 51409106 , U1901601 ) and the University of Macau Multi-Year Research Grant ( MYRG2018-00108-FST ).
Publisher Copyright:
© 2021 Elsevier Ltd
PY - 2021/9
Y1 - 2021/9
N2 - Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to degrade DMF. Aerobic remediation has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest plasmids play important roles in DMF degradation in the order Rhizobiales and genus Paracoccus, but not in most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate methylamine intermediate, while around 6% of the DMF degraders that are primarily members of Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas could potentially mineralize DMF completely. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in α-, and β-Proteobacteria and Actinobacteria. Around half (446/952) of putative DMF degraders could grow with nitrate anaerobically (Pathway III), however, genes for the use of methyl-CoM to produce methane were not found. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes and plasmids form an important foundation for optimizing bioremediation of DMF-containing wastewaters.
AB - Effective degradation of N,N-Dimethylformamide (DMF), an important industrial waste product, is challenging as only few bacterial isolates are known to degrade DMF. Aerobic remediation has typically been used, whereas anoxic remediation attempts are recently made, using nitrate as one electron acceptor, and ideally include methane as a byproduct. Here, we analyzed 20,762 complete genomes and 28 constructed draft genomes for genes associated with DMF degradation. We identified 952 genomes that harbor genes involved in DMF degradation, expanding the known diversity of prokaryotes with these metabolic capabilities. Our findings suggest plasmids play important roles in DMF degradation in the order Rhizobiales and genus Paracoccus, but not in most other lineages. Degradation pathway analysis reveals that most putative DMF degraders using aerobic Pathway I will accumulate methylamine intermediate, while around 6% of the DMF degraders that are primarily members of Paracoccus, Rhodococcus, Achromobacter, and Pseudomonas could potentially mineralize DMF completely. The aerobic DMF degradation via Pathway II is more common than thought and is primarily present in α-, and β-Proteobacteria and Actinobacteria. Around half (446/952) of putative DMF degraders could grow with nitrate anaerobically (Pathway III), however, genes for the use of methyl-CoM to produce methane were not found. These analyses suggest that microbial consortia could be more advantageous in DMF degradation than pure culture, particularly for methane production under the anaerobic condition. The identified genomes and plasmids form an important foundation for optimizing bioremediation of DMF-containing wastewaters.
KW - Biodegradation pathways
KW - Denitrification
KW - Genomics
KW - Methanogenesis
KW - Plasmid
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U2 - 10.1016/j.ibiod.2021.105283
DO - 10.1016/j.ibiod.2021.105283
M3 - Article
AN - SCOPUS:85107957804
SN - 0964-8305
VL - 163
JO - International Biodeterioration and Biodegradation
JF - International Biodeterioration and Biodegradation
M1 - 105283
ER -