## 3 Mycobacterium Ecology: The Underlying Resilience Biology
### Resistance and Degradation of Recalcitrant Compounds  
NTM are seldom auxotrophic, although fatty acid auxotroph may occur sporadically. _M. avium_, _M. fortuitum_, _M. chelonae_, _M. intracellular_, and _M. scrofulaceum_ are oligotrophic [71; 111]. The growth of _M. chelonae_ and _M. fortuitum_ species in commercial sterile distilled water at 25 \({}^{\circ}\)C has been described, with a slow decline of total viable counts throughout one-year, attributed to the ability of these mycobacteria to use trace amounts of volatile or micronutrients [112]. NTM are also capable of metabolizing recalcitrant compounds acting as environmental pollutants or carcinogenic substances, such as polycyclic aromatic hydrocarbons (PAHs) (e.g., phenanthrene, naphthalene, fluorine, fluoranthene, anthracene, pyrene, benzo[a]anthracene, benzo[a]pyrene), nitrogen-containing heterocycles (e.g., morpholine), polymers (e.g., vinyl chloride), alkanes (e.g., propane), humic and fulvic acids, and sterols (e.g., cholesterol) [113; 114]. NTM are well associated with the metabolization of high molecular weight PAHs. Physiologically, they are adapted to multiply in highly concentrated PAHs environments due to different factors: (1) their hydrophobic envelope enables the transport of hydrocarbons without the need to synthesize surfactants since mycolic acids work as a biosurfactant that can be induced in response to hydrophobic substrate contact [115; 116; 117]; (2) the strong bound of PAHs to organic soil particles in oligotrophic conditions and oxygen depletion favors the proliferation of NTM [115; 116; 117]; 3) NTM biofilm formation on those soil particles enable higher accessibility to PAHs compounds [115; 116; 117]. For example, _M. vanbaelenii_ PYR-1 has been one of the most studied strains regarding PAHs degradation (Figure 2C). It was first isolated in 1988 from soil persistently exposed to PAHs. This strain holds the capacity to mineralize naphthalene, phenanthrene, fluoranthene, pyrene, 1-nitropyrene, 3-methylcholanthrene, and 6-nitrochrysene into carbon dioxide [118]. The underlying degradation of PAHs is achieved by a dioxygenase system composed of a dehydrogenase, the dioxygenase small (beta)-subunit, and the dioxygenase large (alpha)-subunit [119]. _M. vanbaalenii_ PYR-1 was also shown to degrade anthracene [120]. The metabolism of benzo[a]pyrene in this strain was also evaluated, with the initial oxidation being achieved by dioxygenases and monooxygenases. The stereo- and regioselectivity of the oxygenase involved in this pathway was confirmed [121]. _M. vanbaalenii_ PYR-1 possesses _niidAB/niidA3B3_ oxygenase that are involved in the degradation pathway of several PAHs, namely pyrene, fluoranthene, and phenanthrene, forming a phylogenetically distinct cluster from classical bacterial ring-hydroxylating oxygenase [122]. In 2006, a polyomic approach based on metabolic, genomic, and proteomic analyses was conducted to investigate the pyrene metabolism in _M. vanbaalenii_ PYR-1 strain [123]. The results suggested the degradation of pyrene to central intermediates through o-phthalate and the \(\beta\)-ketoadipate pathway [123]. A year after, a similar approach was used to investigate the metabolic pathway of fluoranthene degradation in the same strain [124]. The results point to two main metabolic pathways, with fluoranthene being initially deoxygenated, followed by a pathway bifurcation: (1) degradation via fluorene-type metabolites; (2) oxidation via acennaphthylene-type metabolites [124]. Monooxygenation of fluoranthene can also occur as a detoxification reaction [124]. The comparative and functional genomic analysis of this strain led to the detection of two genomic regions where most of the 194 genes associated with the degradation of aromatic compounds are located, being the region A (150 kb long) the larger and with an atypical mosaic structure made of several gene clusters [125].