Based on the feature of high-altitude permafrost topography and the diverse microbial ecological communities of the Qinghai-Tibetan Plateau, soil samples from thirteen different collection points around Qinghai lake were collected to screen for extremophilic strains with the ability to degrade phenol, and one bacterial strain recorded as TIBETAN4 that showed effective biodegradation of phenol was isolated and identified. TIBETAN4 was closely related to Kocuria based on its observed morphological, molecular and biochemical characteristics. TIBETAN4 grew well in the LB medium at pH 7–9 and 0–4% NaCl showing alkalophilicity and halophilism. The isolate could also tolerate up to 12.5 mM phenol and could degrade 5 mM phenol within 3 days. It maintained a high phenol degradation rate at pH 7–9 and 0–3% NaCl in MSM with 5 mM phenol added as the sole carbon source. Moreover, TIBETAN4 could maintain efficient phenol degradation activity in MSM supplemented with both phenol and glucose and complex water environments, including co-culture Penicillium strains or selection of non-sterilized natural lake water as a culture. It was found that TIBETAN4 showed enzymatic activity of phenol hydroxylase and catechol 1,2-dioxygenase after induction by phenol and the corresponding genes of the two enzymes were detected in the genome of the isolate, while catechol 2,3-dioxygenase or its gene was not, which means there could be a degradation pathway of phenol through the ortho-pathway. The Q-PCR results showed that the transcripts of both the phenol hydroxylase gene and catechol 1,2-dioxygenase gene were up-regulated under the stimulation of phenol, demonstrating again that the strain degraded phenol via ortho-degradation pathway.

As a typical filamentous fungus, Aspergillus species are highly adaptive to diverse ecological habitats, represented by their occurrence in both terrestrial and marine environments; this could plausibly be ascribed to their preeminent biological diversity and metabolic variability. In this context, marine-derived Aspergillus fungi have recently attracted great interest as a promising potential source of biologically active compounds. The present study depicts the genomic and chemical profiles of M7, a strain of Aspergillus terreus isolated from mussels in the South China Sea; the crude extracts of its soybean fermentation exhibit potent growth-inhibitory properties against A. baumannii and P. aeruginosa. Subsequently, functional genomics analysis based on sequences implied a considerable biosynthetic potential of the strain, which is substantiated by the 75 biosynthetic gene clusters (BGCs) identified via genome mining; the majority (49 BGCs) were functionally unknown. Representatively, the putative biosynthetic pathways of terramide A and terramide B, the bacteriostatic products obtained through chemical separation and characterized from the fermentation, could not be allocated to any known BGC, highlighting the metabolic potency and diversity of this strain. Meanwhile, based on a comprehensive analysis of fermentation conditions, we confirmed that the presence of environmental iron was inversely correlated with antimicrobial characteristics of the strain M7, presumably due to the interference in the biosynthetic pathway or bioactive mechanisms of the antimicrobial components, e.g., terramide A and B. Our observations provide genomic and biochemical insight into the metabolic and ecological novelties of this strain, underpinning the diversity of biosynthetic flexibility and adaptive strategies of marine Aspergillus fungi.

Due to the specific properties of the marine environment, marine microorganisms have exclusive physicochemical characteristics that are different from those of terrestrial microorganisms, which can produce various secondary metabolites (SMs) with considerable structural diversity and biological activity. In this study, three strains of coepiphytic Aspergillus with potential antibacterial activities, A7 (Aspergillus flavus), B27 (Aspergillus flavipes), and R12 (Aspergillus sydowii), were isolated from the South China Sea. Via the Illumina MiSeq sequencing platform, the genomes of the three strains were sequenced, and genome comparison showed the highest diversity of the biosynthetic gene clusters (BGCs) in A7. In addition, a comparison of physiological and genomic characteristics between A7 and other A. flavus strains demonstrated the superior environmental adaptability of A7, which is apparently consistent with the genetic richness of BGCs. By assigning reads to known BGCs, putative BGCs were allocated in A7 that corresponded to various SMs, including naphthopyrone, pyranonigrin E, and cyclopiazonic acids. Based on gene homology analysis, we surmise that a region is involved in the biosynthesis of ustiloxin-like RiPPs, a less thoroughly studied SM in fungi. Our results provide genetic information for the investigation of marine Aspergillus spp., which may help to elucidate their chemical diversity and adaptive strategies.