Draft Genome Sequence of a Cladosporium Species Isolated from the Mesophotic Ascidian Didemnum maculosum

0s and 1s in marine molecular research: a regional HPC perspective

High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus

Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs), that can be detected in a variety of environments including the human body, adversely affecting global health. Bioremediation is an emerging field for the detoxification and removal of environmental pollutants, with novel biocatalysts appropriate for this task being in high demand. In this study, a biobank of novel fungal strains isolated as symbionts of marine invertebrates was screened for their ability to remove 2,4,5-trichlorobiphenyl (PCB29). The most efficient strains were studied further for their ability to express laccase activity, the most commonly associated extracellular activity involved in the removal of aromatic pollutants and encoded in fungi by the enzymatic class of multicopper oxidases (MCOs). The strain expressing the highest laccase activity, Cladosporium sp. TM138-S3, was cultivated in the presence of copper ions in a 12 L bioreactor and two enzymes exhibiting laccase activity were isolated from the culture broth through ion-exchange chromatography. The two enzymes, Lac1 and Lac2, were biochemically characterized and showed similar characteristics, although an improved ability to remove PCB29 (up to 71.2%) was observed for Lac2 in the presence of mediators. In parallel, we performed RNAseq of the strain growing in presence and absence of PCB29 and reconstructed its transcriptome assembly. Functional annotation allowed identifying the MCO repertoire of the fungus, consisting of 13 enzymes. Phylogenetic analysis of Ascomycete MCOs further allowed classifying these enzymes, revealing the diversity of laccase activities in Cladosporium sp. TM138-S3.

Degradation Mechanism of 2,4-Dichlorophenol by Fungi Isolated from Marine Invertebrates

2,4-Dichlorophenol (2,4-DCP) is a ubiquitous environmental pollutant categorized as a priority pollutant by the United States (US) Environmental Protection Agency, posing adverse health effects on humans and wildlife. Bioremediation is proposed as an eco-friendly, cost-effective alternative to traditional physicochemical remediation techniques. In the present study, fungal strains were isolated from marine invertebrates and tested for their ability to biotransform 2,4-DCP at a concentration of 1 mM. The most competent strains were studied further for the expression of catechol dioxygenase activities and the produced metabolites. One strain, identified as Tritirachium sp., expressed high levels of extracellular catechol 1,2-dioxygenase activity. The same strain also produced a dechlorinated cleavage product of the starting compound, indicating the assimilation of the xenobiotic by the fungus. This work also enriches the knowledge about the mechanisms employed by marine-derived fungi in order to defend themselves against chlorinated xenobiotics.