New approaches for the characterization of plastic-associated microbial communities and the discovery of plastic-degrading microorganisms and enzymes

Abstract

Plastics in the environment represent new substrates for microbial colonization, and recent methodological advances allow for in-depth characterization of plastic-associated microbial communities (PAMCs). Over the past several decades, discovery of plastic degrading enzymes (PDEs) and plastic degrading microorganisms (PDMs) has been driven by efforts to understand microbially-mediated plastic degradation in the environment and to discover biocatalysts for plastic processing. In this review, we discuss the evolution of methodology in plastic microbiology and highlight major advancements in the field stemming from computational microbiology. Initial research relied largely on culture-based approaches like clear-zone assays to screen for PDMs and microscopy to characterize PAMCs. New computational tools and sequencing technologies are accelerating discoveries in the field through culture-independent and multi-omic approaches, rapidly generating targets for protein engineering and improving the potential for plastic-waste management.

Computational exploration of bio-remediation solution for mixed plastic waste

“…A deep understanding of microbial biocatalysts and cellular processes is necessary for developing a large-scale biotech-based solution for management of plastic waste (Hauer, 2020; Fenner et al ., 2021; Inderthal et al ., 2021) The continued research along this direction lead to\ reporting of many microbial biocatalysts capable of degrading plastic materials along with their microbial origin, biological pathways and sequences (Gewert et al ., 2015; Emadian et al ., 2017; Wei & Zimmermann, 2017). This information has been routinely being utilized for genome mining against potential microbial degraders (Viljakainen & Hug, 2021). The available information about enzymatic families are helpful to narrow down enzyme mining efforts in metagenomics studies (Danso et al ., 2018).…”

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

“…Knowledge on the most efficient natural degradation systems could lead to identifying microbial degraders, enzymatic pathways, and metabolic interactions favoring biodegradation. Such tools would allow developing and optimizing microbial consortia for microbial-derived bioprocesses, as recycling and upcycling of agroindustrial lignocellulosic residues, plastic waste, and other pollutants ( Ohkuma et al, 2001 ; Jaiswal et al, 2020 ; Viljakainen and Hug, 2021 ). Several plant-degrading microorganisms were already identified in insect fungiculture by culture-dependent and –independent techniques, though their application in bioenergy and bioremediation waits for being fully investigated.…”

“…Together with lignocellulolytic fungal cultivars, these bacterial groups could compose biodegradation networks ( Mann and Wozniak, 2012 ; Tribedi and Sil, 2013 ; Wasi et al, 2013 ; Braña et al, 2016 ; Kowalczyk et al, 2016 ; Ebadi et al, 2017 ; Peixoto et al, 2017 ; Wilkes and Aristilde, 2017 ; Jacquin et al, 2019 ; Roager and Sonnenschein, 2019 ; Kučić et al, 2020 ; Roberts et al, 2020 ; Varjani et al, 2020 ; Gambarini et al, 2021 ; Lear et al, 2021 ; Cabral et al, 2022 ; Hou et al, 2022 ). To identify possible polymer degraders in these systems, samples from insect fungiculture environment could compose the initial inoculum for degradation assays, performed through interconnected culture-dependent and culture-independent workflows ( Figure 3 ; Shah et al, 2008b ; Viljakainen and Hug, 2021 ). This would allow to investigate the metabolic potential of the associated microbiota without threatening insect populations.…”

“…Also, total genome sequencing and annotation of polymer degrading microorganisms based on databases (reviewed in detail by Dvořák et al, 2017 ; Jaiswal and Shukla, 2020 ; Saraiva et al, 2021 ) could assist in predicting polymer-degrading enzymes. Predicted enzymes could be tested via heterologous cloning, then screening positive clones using clear-zone assay ( Nishida and Tokiwa, 1993 ; Shah et al, 2008b ; Tokiwa et al, 2009 ; Viljakainen and Hug, 2021 ; Zhu et al, 2022 ). Culture-dependent strategies have been extensively employed for identifying plastic degrading microorganisms and enzymes, and was the method that revealed Is PETase from I. sakainesis , cultured from PET-enriched environmental samples ( Yoshida et al, 2016 ).…”

“…Alterations in polymers microstructures and microporosity could be investigated through scanning electron microscopy (SEM), Fourier transformed infrared spectroscopy (FTIR), and nuclear magnetic resonance (NMR; Bernardinelli et al, 2015 ; Simmons et al, 2016 ; Alessi et al, 2018 ; Li et al, 2018 ). While advantageous for selecting and confirming polymer- degrading activity, culture-dependent methods is limited to the small fraction of microorganisms that grow in culture, and also for being laborious ( Hug et al, 2016 ; Viljakainen and Hug, 2021 ; Zhu et al, 2022 ).…”