2.1. CHCA degradation and nitrate removal properties
Strain SJ18 was grown and isolated from 2216E medium, the colony was round, translucent and white on 2216E medium solid agar plate containing 50 mg/L NAs (Fig. S1). The 16S rRNA sequencing results showed that the similarity between the degrading strains and the genus Marinobacter profundi was > 99%. The gene size of strain SJ18 was 4364528 bp, a total of 3951 genes were annotated, and the average GC content was 59.84%. Based on these characteristics, we termed this strain as Marinobacter sp. strain SJ18 (Genebank accession number: MH458950.1), and the phylogenetic tree was displayed in Fig. S2 of supplementary material.
The aerobic and anaerobic degradation of CHCA were shown in Fig. 1 (a, b). In aerobic condition, CHCA was rapidly degraded after the experiment started, and completely degraded within 60 hours. The maximum degradation rate appeared around 24 h (degradation rate was about 0.43 mg h− 1). There was no decrease of CHCA in heat-killed group, indicating abiotic factors have negligible influence on this degradation. At the same time, the TOC content dropped from 18.9 ± 0.5 to 7.0 ± 0.1 mg L− 1, and the OD600 value gradually increased with the progress of degradation, then reaching a maximum of 0.74 when the CHCA degradation was complete (about 60 h). Subsequently, the OD value gradually decreased, suggesting that strain SJ18 could utilize CHCA as the only carbon source, the cell density gradually decreased after CHCA were completely consumed. Besides, the concentration of nitrate in the experimental group gradually decreased, while the ammonium concentration increased, and no significant changes were detected on the nitrite concentration. Nitrate removal rate was > 70% throughout the process, the rate of nitrate consumption was consistent with the rate of CHCA aerobic degradation, and no nitrogen was captured during the degradation, indicating that the nitrate was reduced to ammonium, which was utilized by cells. The corresponding indicators of the blank control group did not change significantly. Under the anaerobic degradation, the CHCA was completely degraded within 84 hours, and the maximum degradation rate was about 0.37 mg h− 1 (around 36 h). It could be seen that the anaerobic degradation efficiency was lower than that of aerobic conditions. Meanwhile, the TOC concentration decreased from 18.7 ± 0.3 to 8.5 ± 0.1 mg L− 1 and the change of OD600 value was consistent with that of the aerobic group. However, the nitrite was observed to continue rise with the consumption of nitrate, and no significant changes were detected in the ammonium. In addition, the nitrite concentration level was observed to gradually decrease after the end of degradation, meanwhile, the production of nitrogen was detected at the end of the degradation (data not shown). Nitrate removal rate reached 70% and the rate of nitrate consumption was also consistent with the rate of anaerobic degradation. It could be speculated that denitrification may occurred during the anaerobic degradation of CHCA.
The fitting results of degradation curves showed that aerobic and anaerobic degradation of CHCA conformed to the pseudo-first-order kinetic reaction (Fig. S3). The reaction rate constant k = 0.0342 (R2 = 0.936) for aerobic degradation, and k = 0.0292 (R2 = 0.946) for anaerobic degradation. Pearson correlation analysis showed that both aerobic and anaerobic degradation of CHCA were significantly positively correlated with nitrate removal, with correlation coefficients of 0.871 (P < 0.05) and 0.843 (P < 0.05), respectively.
2.2 Degradation intermediates and pathways of CHCA
In order to explore the aerobic and anaerobic degradation pathway of CHCA, samples at 0, 36, 60 and 84 hours were selected for intermediate products detection by GC-MS. Results showed that several intermediate products were captured, the cyclohexenecarboxylic acid (m/z = 198, 183) were found in both aerobic and anaerobic groups based on mass spectral database. The appearance of cyclohexenecarboxylic acid product indicated that CHCA might lose two electrons through dehydrogenation and form a carbon-carbon double bond on the cyclohexane ring. This degradation method is generally considered to be typical β-oxidation and appears in most aromatic or cycloalkane pollutants (Kung et al. 2014, Whitby 2010). Moreover, the presence of glycerol (m/z = 205, 147, 73) was detected in the aerobic group, and the production of lactic acid (m/z = 191, 147, 117) was found in the anaerobic group. Glycerol and lactic acid are presumed to be the oxidative hydrolysis products of fatty acids under anaerobic conditions, respectively. This would imply that cyclohexenecarboxylic acid could open the ring by hydrolysis and eventually form short-chain fatty acids. Unfortunately, no specific fatty acid products were captured during the degradation process. This might be due to the fact that fatty acids were readily available to microorganisms, resulting in their short-lived during degradation, and this speculation has been confirmed in some reports. Quesnel et al. found that the intermediate product cyclohexanoic acid existed for a short period of time during the study of the biodegradation process of cyclohexanoic acid and could not be captured (Quesnel et al. 2011). Although the product after ring opening was not captured, it could be basically confirmed that CHCA was mainly biodegraded through β-oxidation.
The whole genome sequencing was also used to explore the degradation process of CHCA. The COG, GO and KEGG databases of strain SJ18 were analyzed to predict the biological process, function genes and degradation pathways for the CHCA under aerobic and anaerobic conditions. The COG analysis results (see Fig. S4) showed the function genes classification including energy production and conversion, amino acid transport and metabolism, carbohydrate transport and metabolism, coenzyme transport and metabolism, lipid transport and metabolism, cell wall/membrane/envelope biogenesis were significantly enriched. Based on GO analysis (Fig. S5), the enriched genes mainly include cellular process, metabolic process, binding, catalytic activity, nitrogen utilization, antioxidant activity, enzyme regulator activity, transporter activity and other functions in the genome of strain SJ18. The KEGG annotation results (Fig. 3) showed that the pathway of membrane transport, coenzyme metabolism, carbohydrate metabolism and amino acid metabolism were also enriched. In addition, the more detailed pathway such as ABC transporters, fatty acid degradation and biosynthesis, degradation of ketone bodies, pyruvate metabolism and styrene degradation, chlorocyclohexane and chlorobenzene degradation, benzoate degradation, toluene degradation, naphthalene degradation pathway were also obviously enriched in the strain SJ18. Some genes associated with CHCA degradation in these pathways were analyzed, the long-chain acyl-CoA synthase (fadD), benzoate 1,2-dioxygenase (benA), catechol 1,2-dioxygenase (catA), 3-hydroxyacyl-CoA dehydrogenase (HADH), hydroxycyclohexene carboxylic acid dehydrogenase (benD), alcohol dehydrogenase (adh) and 3-hydroxy-3-methylglutaryl coenzyme a lyase (hmgL) genes involved in the genome of strain SJ18, which have been confirmed to participated in the β-oxidation and the metabolism process of alkanes and polcyclic aromatic hydrocarbons in aerobic and anaerobic conditions (Boll et al. 2014, Cameron et al. 2019, Kung et al. 2013, McKew et al. 2021). It could be inferred that those function genes may play an important role in the biodegradation of CHCA.
According to the above results, the aerobic and anaerobic degradation pathways of CHCA were inferred (Fig. 4). First, two hydrogen atoms were removed by the dehydrogenase, forming a carbon-carbon double bond (cyclohexenecarboxylic acid) on the cyclohexane ring. For aerobic degradation, the cyclohexenecarboxylic acid was ring-opened to formed fatty acids by specific dioxygenases (such as benzoate 1,2-dioxygenase or catechol 1,2-dioxygenase) with the participation of oxygen. Under anaerobic conditions, cyclohexenecarboxylic acid was hydrolyzed and dehydrogenated to sequentially generate 1-hydroxy-cyclohexanecarboxylic acid and cyclohexanonecarboxylic acid, and those products were subsequently hydrolyzed and opened to form short-chain fatty acids. Finally, glycerol and lactic acid were formed through multiple β-oxidation under aerobic and anaerobic conditions, respectively.
2.3 Nitrate metabolism pathway during CHCA degradation
The changes of nitrate, nitrite and ammonium during CHCA degradation were described in section 3.1. Nitrate reduction to ammonia and denitrification were considered to be involved in the aerobic and anaerobic degradation, respectively. Hence, the transformation of nitrate was further elucidated with the assistance of genome sequencing. The genome sequence of the strain was compared with the KEGG database, and the nitrogen metabolism pathway of strain SJ18 was obtained, as shown in Fig. 5. The results showed that a total of seven of nitrogen-related genes were found, include nitrate reductase (NarGHI), nitrate assimilation reduction catalytic subunit (NasAB), nitrite reductase (NirS), nitrite reductase subunits (NirBD), nitric oxide reductase (NorBC), nitrous oxide reductase (NosZ) and nitrite oxidoreductase (NxrAB). Among them, NarGHI, NirS, NorBC and NosZ genes were considered as common denitrification genes that could carry out the complete denitrification process, and the genes NarGHI and NirBD could convert nitrate to ammonium by dissimilatory reduction. (Lu et al. 2011, Marchant et al. 2017). However, NarGHI gene was oxygen-sensitive and the expression of NarGHI was inhibited under aerobic conditions (Zhang et al. 2018). Thus, the nitrate cannot be converted to nitrite under aerobic conditions due to the missing of NapAB gene (periplasmic nitrate reductase, which can reduce nitrate to nitrite under aerobic conditions). Instead, the reduction of nitrate was achieved by the catalytic subunit of nitrate assimilation reduction (NasAB). Referring to the inorganic nitrogen chemical indicators and genomic results, the transformation process of nitrate in CHCA aerobic and anaerobic biodegradation was proposed: in aerobic condition, nitrate as an electron donor was transported from extracellular to intracellular through nitrate transporter (Nrt), then NasAB reduces nitrate to nitrite, and subsequently, nitrite was reduced to ammonium with the action of NirBD. Finally, ammonium could be processed into glutamate by glutamine synthase (glnA) and glutamate dehydrogenase (gudB/rocG), and subsequently participated in glutamate metabolism. Under anaerobic condition, NarGHI catalyzes the reduction of nitrate to formed nitrite, the NirS was involved in the reduction of nitrite to nitric oxide (NO), and then, NorBC was participated in the reduction of NO to nitrous oxide (N2O), which in turn reduced N2O to nitrogen (N2) by NosZ.
In general, strain SJ18 not only has the ability to reduce nitrate to ammonia, such as dissimilated nitrate reduction to ammonia pathway (DNRA) and assimilated nitrate reduction to ammonia pathway (ANRA), but also has the denitrification. During the process of nitrate removal, the first step of the DNRA pathway was denitrification, which relied on NarGHI to reduce nitrate. In ANRA pathway, the NasAB was used to assimilate and reduce nitrate to nitrite. However, due to the NirA or NIT-6 coding gene missing, the strain SJ18 was unable to reduced nitrate to ammonium through the ANRA pathway. Therefore, the nitrite produced in the first step of ANRA need to be further metabolized through other nitrogen metabolism pathways, such as the denitrification or the DNRA pathway. In addition, strain SJ18 also has the ability to encode nitrite oxidoreductase, and the nitrite could be nitrified to form nitrate.
Overall, the metabolic pathways of nitrate in aerobic and anaerobic biodegradation were obviously different. Under aerobic conditions, nitrate was gradually consumed with the degradation of CHCA, while the cell growth (OD value increased) was observed. Indicating the nitrate was converted to ammonium through ANRA and DNRA pathways, subsequently, the produced ammonium was used for cells growth. During anaerobic degradation, the concentration of nitrite increased rapidly as nitrate was consumed, and nitrogen was detected in the end. The denitrification was speculated to be an important pathway of nitrate metabolism under anaerobic conditions. The accumulation of nitrite in the degradation system might be due to the rate of nitrate reduction (coding gene, NarGHI) step was much faster than the nitrite reduction (NirS), nitric oxide reduction (NorBC) or nitrous oxide reduction (NosZ) steps.