Kinetics of hydrocarbon degradation in FN1 and FN4 soil microcosms
The degradation of aliphatic and aromatic hydrocarbons (HC) in FN1 and FN4 soil microcosms was monitored using GC/FID (Figure S1 and S2). In FN1 microcosm, the residual aliphatic HC content (554.98 mg/kg; 100%) decreased to 73.07% (405.51 mg/kg) after 21 days, corresponding to removal of 26.93% (149.47 mg/kg). At the end of 42 days, further decrease to 29.91% (165.98 mg/kg) in the residual aliphatic HC was observed, corresponding to removal of 70.09% (389 mg/kg) aliphatic HC (Figure S1). The residual aromatic HC content (471.56 mg/kg; 100%) decreased to 67.26% (317.19 mg/kg) after 21 days corresponding to the removal of 32.74% (154.37 mg/kg). The residual aromatic HC content decreased further at the end of 42 days, to 29.86% (140.81 mg/kg), corresponding to the removal of 70.14% (330.75 mg/kg) aromatic HC (Figure S2).
In FN4 microcosm, the residual aliphatic HC content (554.98 mg/kg; 100%) decreased to 51.27% (284.53 mg/kg) after 21 days, corresponding to removal of 48.73% (270.45 mg/kg). Further decrease in the residual aliphatic HC to 15.98% (88.66 mg/kg) was observed at the end of 42 days, corresponding to the removal of 84.02% (466.32 mg/kg) aliphatic HC (Figure S3). The residual aromatic HC content (471.56 mg/kg; 100%) decreased to 45.80% (215.98 mg/kg) after 21 days corresponding to the removal of 54.20% (255.58 mg/kg). Further decrease in the residual aromatic HC content to 17.62% (83.11 mg/kg) was observed after 42 days, corresponding to the removal of 82.38% (388.45 mg/kg) aromatic HC (Figure S4).
Significant changes in the degradation pattern of the hydrocarbon fractions were observed in FN1 and FN4 microcosms as shown in the GC fingerprints (Figures S1 and S2) and Table 1. In FN1 microcosm, the GC fingerprints of the aliphatic fractions showed complete disappearance of ethane, propane, cyclopropane, butane, methylpropane, pentane, methylbutane and tricosane fractions at the end of 42 days. Significant reductions of some fractions to <15% (hexane, octane, 2,2,4-trimethylpentane, decane, dodecane) and <30% (nonadecane, eicosane, docosane) were also observed. The GC fingerprint of the aromatic fractions revealed the disappearance of indeno(123-cd)pyrene fractions, and significant reduction to <15% of fluoranthene, benzo(a)pyrene, and dibenzo(a)anthracene fractions, respectively (Figure S1, Table 1).
In FN4 microcosm, the GC fingerprints of the aliphatic fractions revealed complete disappearance of ethane, propane, cyclopropane, butane, methylpropane, pentane, methylbutane, hexane, octane and tricosane fractions at the end of 42 days. Apart from tetradecane, all the other aliphatic fractions were significantly reduced to <10% (2,2,4-trimethylpentane, decane, dodecane) and <30% (heptane, hexadecane, heptadecane, pristane, octadecane, phytane, nonadecane, eicosane, docosane) of their initial concentrations. The GC fingerprints of the aromatic fractions revealed complete disappearance of naphthalene, fluoranthene, benzo(a)pyrene and indeno(123-cd)pyrene fractions at the end of 42 days. Substantial reduction of some aromatic fractions to <10% (dibenzo(a)anthracene), <20% (phenanthrene, benzo(b)fluoranthene, benzo(ghi)perylene), and <30% (pyrene, chrysene) at the end of 42 days were also observed (Figure S2, Table 1).
General characteristics of the metagenomes
Illumina miseq shotgun sequencing of the two metagenomes resulted in 14,232 and 22,992 sequence reads for FN1 and FN4 with a total of 4,256,742 and 6,878,221 bp, a mean sequence length of 299 bp for both metagenomes, and a mean GC content of 57.31 and 57.72%, respectively. After pre-processing step with fastp, the sequence reads in FN1 and FN4 reduced to 13,500 and 21,624 with a total of 4,035,631 and 6,465,448 bp, the same mean sequence length and GC content of 57.22% for both metagenomes. The duplication rate in FN1 and FN4 sequence reads were 5.1 and 19.3%, while the insert size peak was 468 and 209, respectively.
Structural diversity of the metagenomes
Analysis of the microbial community structure of the two metagenomes, FN1 and FN4 revealed significant differences in the taxonomic profiles generated by Kraken. In phylum classification where 14 and 8 phyla were recovered in FN1 and FN4 metagenome, the predominant phyla in FN1 are Proteobacteria (56.12%), Actinobacteria (23.79%), and Firmicutes (11.20%). In contrast, the most dominant phylum in CFMM-amended FN4 metagenome was the Firmicutes with 92.97%. Other phyla with reasonable representation in FN4 were Proteobacteria (5.47%), and Actinobacteria (0.77%). Nine phyla, which are represented in FN1 metagenome completely disappeared in FN4, while the phyla Planctomycetes, Cyanobacteria and Ignavibacteriae, not represented in FN1 were duly detected in FN4 (Figure 1).
In class delineation, 22 and 11 classes were recovered from FN1 and FN4 metagenomes. The classes Alphaproteobacteria (40.61%), Actinobacteria (24.69%) and Gammaproteobacteria (11.08%) were preponderant in FN1, while Bacilli (93.11%) massively dominate in FN4, along with reasonable representation from the classes Gammaproteobacteria (4.74%) and Actinobacteria (0.77%). Thirteen classes, which were duly represented in FN1 completely disappeared in FN4, while the classes Planctomycetia and Ignavibacteria hitherto not present in FN1 were detected in FN4 (Figure 2).
Order classification revealed 53 and 28 orders in FN1 and FN4 metagenomes. The predominant orders in FN1 were Rhizobiales (26.30%), Corynebacteriales (11.06%), and Propionibacteriales (6.47%), while Bacillales (89.56%), Enterobacteriales (3.52%), and Lactobacillales (3.45%) were preponderant in FN4. Thirty orders, previously detected in FN1 completely disappeared in FN4 while the orders Pleurocapsales, Planctomycetales, Ignavibacteriales, Desulfovibrionales, and Oscillatoriales hitherto missing in FN1 were duly represented in FN4 (Figure S5).
Family delineation of FN1 and FN4 metagenomes revealed 99 and 54 families. The dominant families in FN1 were Xanthobacteraceae (10.94%), Rhizobiaceae (7.97%), and Corynebacteriaceae (7.59%), while in FN4, Bacillaceae (87.03%), Enterobacteriaceae (3.56%), and Planococcaceae (2.30%) were preponderant. Fifty-eight families previously detected in FN1 completely disappeared in FN4, while 13 families not detected in FN1 were duly represented in FN4 (Figure S6).
In genus classification, 155 and 95 genera were recovered from FN1 and FN4 metagenomes. The genera with highest representation in FN1 metagenome are Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%). In CFMM-amended FN4 metagenome, Anoxybacillus (64.58%), Bacillus (21.47%), and Solibacillus (2.39%) were preponderant. One-hundred and one (101) genera previously detected in FN1 metagenome completely disappeared in FN4, while 41 genera, hitherto not detected in FN1 were duly represented in FN4 metagenome (Figure 3).
Functional characterization of the metagenomes
Diverse hydrocarbon degradation genes were detected in FN1 metagenome as shown in Table 2. Putative genes responsible for degradation of benzoate (pcaD, mhpF, aliB, benD-xylL, benC-xylZ, badH, had, dmpD, ligC, CMLE, pcaL, acd, among others), xylene (mhpF, benD-xylL, benC-xylZ, dmpD, cymB, cmtB), chlorocyclohexane/chlorobenzene (dehH, dhaA, linC, linX, pcpC), and chloroalkane/chloroalkene (adH, dehH, dhaA, adhP) were detected. Also detected were degradative genes for toluene (bbsG, bbsC, bbsD, tsaC1), naphthalene (adH, adhP, bnsG), aminobenzoate (anthraniloyl-CoA monooxygenase, ligC, lpdB), ethylbenzene (ped, etbD), dioxin (mhpF, bphD), nitrotoluene (nemA), and several other aromatic hydrocarbons (Table 2). The benzoate and xylene degradation pathways, indicating the presence of the genes reported in this study and the reactions they catalysed in the pathways is depicted in Figure 4 and Figure 5. In FN4 metagenome, relatively few hydrocarbon degradation genes were detected. These include genes for 2-oxo-3-hexenedioate decarboxylase, 2-keto-4-pentenoate hydratase, and 2-oxopent-4-enoate/cis-2-oxohex-4-enoate hydratase involved in dioxin, xylene, and benzoate degradation. Others include putative genes for anthraniloyl-COA monooxygenase (aminobenzoate degradation), N-ethylmaleimide reductase (nitrotoluene degradation), bifunctional salicylyl-COA 5-hydroxylase/oxidoreductase (salicylate degradation), and 2-oxo-hepta-3-ene-1,7-dioic acid hydratase (hpaH) involved in 4-hydroxyphenylacetate and 2-oxopentenoate degradation.
Putative genes for uptake, transport, efflux and regulation of various inorganic nutrients and heavy metals were detected in FN1 metagenome (Table 3). These include genes for transport, uptake and regulation of phosphate/phosphonate (pstB, pstS, phnC, phoB, ompR), nitrogen (urtD, urtE, nrtC, nrtD, glnC, ntrY, ntrX), sufate/thiosulfate (cysA, cysP, ssuB, sbp) and several others. Putative genes for uptake, transport, efflux and regulation of heavy metals such as cobalt/nickel (cbiO, nikD, nikE, nrsR), iron (afuC, afuA, fhuC, fecE, fepC, fepA), molybdate/tungstate (modA, modB, modC, modF, tupC, wtpC), manganese/zinc/iron (znuC, psaB, mntB, mntA, sitB, troB, manR), and copper (nosF, cusR) were also detected (Table 3). In FN4 metagenome, putative genes for transport, uptake and regulation of inorganic nutrients such as phosphate/phosphonate (phoB, phnC, ompR), and nitrogen (narL, narP, ntrX, glnG) were detected. For heavy metals, putative genes for transport, efflux and regulation such as manR (manganese), cusR (copper), afuC (iron) and modC (molybdate) were also detected.
Worth mentioning is the detection of genes responsible for biosynthesis of biosurfactants produced by members of the microbial community in FN1 metagenome. These include rhamnosyltransferase subunit B (rhlB), a member of rhlAB gene responsible for rhamnolipid biosynthesis, and phosphatidyl-N-methylethanolamine N-methyltransferase responsible for biosynthesis of a phospholipid biosurfactant, phosphatidylethanolamine It is instructive to note that these genes were not detected in FN4 metagenome. Putative genes responsible for bacterial chemotaxis were also detected from the two metagenomes. Putative genes for bacterial chemotaxis proteins cheR, cheB, cheBR, cheY, aer, motB, and rbsB were detected in FN1 while cheB, cheY, cheV, and cheBR were detected in FN4 metagenome.