Earth Day 2024: Leveraging Biotechnology to Combat Plastic Pollution
The environment is essential for our health and well-being, providing essential resources such as clean air, water, and fertile soil, while sustaining the ecological balance. Since its inception in 1970, Earth Day has served as an annual reminder of our obligation to protect our planet and has mobilized global efforts to address environmental issues. This year's theme, 'Planet vs. Plastic,' casts a spotlight on one of the most pressing environmental challenges of our century.
The forecast surge in plastic production, from 9.2 billion tons between 1950 and 2017 to 34 billion tons by 2050, underscores the magnitude of the challenge[1]. Plastic poses a significant environmental threat throughout its lifecycle, with its production alone accounting for 3.4% of global greenhouse gas emissions in 2019[2]. Additionally, the release of harmful additives from plastics, such as bisphenol A (BPA) and phthalates, contaminates ecosystems and poses health risks. Once discarded, plastic waste persists for hundreds or thousands of years, accumulating in landfills and infiltrating ecosystems worldwide. The widespread use of plastics has led to a staggering increase in global annual plastic waste, doubling from 156 million tons in 2000 to 353 million tons in 2019. Projections indicate that this figure could triple by 2060 (Figure 1)[2].
Figure 1: Projection of plastic waste production until 2060 (Source: OECD Global Plastics Outlook Database)
Plastic Pollution – A Global Crisis
The escalating volumes of plastic waste highlight the critical need of effective disposal and recycling strategies. According to a recent OECD report, in 2019 only 9% of plastic waste was recycled globally, while 22% was improperly managed. That year alone, widespread use of plastic, combined with inadequate disposal practices, caused 22 million tons leaking into the environment (Figure 2)[2].
Figure 2: Plastic waste leakage in 2019 (Source: OECD Global Plastics Outlook Database)
In addition, the slow degradation of plastic contributes to its continual accumulation in our environment, posing significant threats to ecosystems and biodiversity. Macroplastics, the most prevalent among leaked plastics, impact wildlife through entanglement and habit disruption. Animals often mistake plastic items for food, ingesting them and facing serious risks of injury or death (Figure 3). Reports of marine animals with stomachs full of plastic and seabirds caught in plastic fishing nets are increasingly common.
Figure 3: Seagull with disposed bag. Foto by Tim Mossholder
Furthermore, microplastics have infiltrated the food chain, traversing through trophic levels and ultimately reaching humans. Numerous studies have already documented the presence of microplastics in various human systems[3-5]. Microplastics may accumulate in tissues, triggering systemic toxicity and inflammatory responses. In the meantime, toxic chemicals released by microplastics can disrupt endocrine functions, increasing the risk of various health issues, including premature births, neurodevelopmental disorders, infertility, cardiovascular diseases, and cancers[6]. Without significant intervention, the persistent threat of plastic pollution continues to endanger animal welfare and human health.
Despite ongoing efforts to shift plastic flows from a linear to a circular model and reduce environmental leakage and accumulation, the inherent challenges of the circular process can' t be ignored. Recycled plastics often degrade in quality, contain elevated levels of toxic chemicals, and present economic and technical challenges to process. As Therese Karlsson, the science and technical advisor at the International Pollutants Elimination Network (IPEN), stated:
'Removing the mess while making more is a doomed strategy. We cannot recycle our way out.'
Addressing plastic pollution requires a multifaceted approach, encompassing prevention, advancements in recycling technologies, robust waste management strategies, and the development of alternative biobased materials.
Biotechnology: Pioneering Solutions for Plastic Pollution
Biotechnology offers promising avenues to combat plastic pollution on various levels by leveraging the power of living organism. Through biotechnological innovations, researchers are exploring enzymes and microorganisms capable of breaking down plastic waste into harmless byproducts or synthesizing biodegradable plastics from renewable resources.
Bacterial Innovations in Plastic Degradation
Bacteria, with their versatile metabolic abilities, possess the capability to break down plastics previously considered non-biodegradable. A notable discovery occurred in 2016 with the bacterium Ideonella sakaiensis, which can degrade polyethylene terephthalate (PET) through a two-step enzymatic process [7]. This was further demonstrated in a Rhodococcus strain isolated from weathered plastic. This strain was able to effectively reduce the weight of polyethylene samples by 1%, demonstrating its capabilities for plastic degradation (Figure 4) [8].
Figure 4: Degradation of polyethelene powder by a Rhodoccocus strain [10]
Further research has expanded the range of plastics that bacteria can degrade. For instance, species such as Pseudomonas putida have been engineered to break down PET[9]. In addition to single strains, consortia of bacteria have shown great promise in degrading plastics. Some bacterial consortia can simultaneously tackle different components of plastic waste, enhancing the efficiency of degradation [10]. Research into bacterial consortia is increasingly focusing on engineering these communities to optimize degradation capabilities [11].
Yeats as Catalysts in Bioplastic Production
Yeast species are increasingly recognized for their capability in synthesizing biodegradable plastics, particularly polyhydroxyalkanoates (PHAs), from renewable resources. Through genetic engineering, yeast cells can efficiently convert plant-derived substrates into PHAs, offering a sustainable alternative to conventional plastics[12]. Ongoing research aims to optimize fermentation conditions and explore novel pathways to enhance PHA production, potentially revolutionizing the plastic industry. As research progresses, yeast-based bioplastics can offer a greener and more sustainable future for plastic manufacturing.
Need for Advanced Technologies
While significant advancements have been made in elucidating the roles of enzymes and microbes in the degradation and synthesis of polymers, there is still much to uncover. Culture-based methods are widely used to identify and characterize candidates but are limited by the large number of non-culturable microbial phyla, leaving a significant portion of microbial diversity unexplored. To address these limitations, researchers have turned to meta-omics, analysing collective material from samples. However, these methods currently suffers from limited resolution and overlooks heterogeneity within microbial populations. Therefore, to advance our understanding and future applications, it is crucial to develop advanced technologies capable of offering deeper insights into microbes.
VITA Platform: A Gateway to Unlocking Deeper Insights in Microbes
The rapid advancement of single-cell RNA sequencing (scRNA-seq) presents exciting opportunities for microbiology, offering new avenues to investigate gene expression and cellular heterogeneity with unprecedented precision. However, conventional scRNA-seq techniques face challenges with microbes. These challenges stem from the robustness of cell walls and the low abundance and stability of microbial mRNA. Most importantly, the absence of poly(A) tails on bacterial transcripts hinders the direct application of most scRNA-seq techniques. The launch of M20 Genomics' VITA High-Throughput Single-Cell Transcriptome Platform in 2022 marks a significant leap forward in scRNA-seq technology, offering a powerful solution to overcome the above limitations.
By leveraging random primers, the VITA platform empowers researchers to capture full-length transcriptomes across various organisms, including bacteria, fungi, and beyond. By facilitating precise analysis of gene expression at the single-cell level, the VITA platform equips researchers to identify and characterize intricate mechanisms underlying plastic degradation or synthesis.
Figure 5: VITA Products for Microbiology Research
1. Exploring Complex Bacterial Communities in a Fermentation Tank
With over 90 microorganisms, primarily bacteria, known to have plastic degradation capabilities under in vitro conditions [13], the potential to find solutions for plastic degradation is vast. It is essential to delve deep into both individual bacterial behaviours and their interactions within complex communities for advancing the understanding of underlying mechanisms and developing practical industrial processes.
In this pursuit, we utilized VITA platform to analyse a sample of fermentation sludge directly sourced from a fermenter. By replicating conditions relevant to both research and potential industrial applications, the VITA platform showcases its capacity to deliver insights crucial for advancing our understanding of processes pertinent to plastic biodegradation.
In this sample, the VITA platform captured 8,325 bacterial cells and detected 121,835 genes in total. In bacterial cells, the VITA platform achieved a median UMI count of 185 and a median gene count of 102 per cell. These results underscore the efficacy of the VITA platform to obtain high-quality data from complex bacterial communities (Table 1 and Figure 4).
Table 1: VITA platform data derived from a sample of fermentation sludge sourced from a fermenter
Figure 6: Distribution of detected genes in a sample of fermentation sludge
In this comprehensive dataset, the VITA platform identified 40 different bacterial species, with detailed insights into their relative abundance within the sample (Figure 5).
Figure 7: Species abundance in the fermentation sludge sample (Species with an abundance of <1% are displayed in white)
Identified bacterial cells in species with a relative abundance exceeding 1% were subjected to unsupervised clustering and Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction analysis. The results revealed distinct clusters corresponding to each species emerged (Figure 6).
Figure 8: UMAP projection of the most abundant species (abundance >1%) in the spent biomass sample
These results from the VITA platform on this extensive dataset provide detailed insights into their relative abundance and transcriptomic profiles. It underscores the efficacy of the VITA platform in obtaining high-quality data from complex bacterial communities used for fermentation.
2. Deciphering Yeast Communities
Addressing the pressing issue of plastic pollution requires a shift toward alternative, sustainable materials. Yeasts, known for their resilience across varied conditions and their versatility in genetic engineering, have become prominent in the production of a range of bioplastics and polymers[14].
Utilizing the VITA platform, we analysed a mixed-yeast species sample, which captured 2,339 cells, and detected a total of 10,009 genes. For yeast cells, the VITA platform achieved a median UMI count of 148 and a median gene count of 103 per cell (Table 2).
Table 2: VITA platform data derived from a sample of mixed yeast species
Employing unsupervised clustering and UMAP projection, the VITA platform identified two distinct populations in this sample. These two clusters were annotated as the yeast species Saccharomyces cerevisiae and Komagataella pastoris based on their gene expression signatures.
Figure 9: UMAP projection and species annotation of the mixed-yeast species sample
Green Horizons: M20 Genomics' Commitment to Innovations for a Sustainable Future
This Earth Day, M20 Genomics reaffirms our dedication to cultivating a sustainable future through the development of cutting-edge single-cell technologies. Our advanced VITA products enable high-throughput full-length single-cell transcriptome profiling in a broad spectrum of organisms, ranging from clinical samples to microorganisms, offering groundbreaking insights that advance the identification, characterization, and engineering of pathways and mechanisms with great potential to address plastic pollution and beyond.
Recognizing that the journey towards sustainability is a collective endeavour, M20 Genomics is steadfast in fostering collaboration to leverage technologies and innovations. Technological advancement and innovations play pivotal roles in addressing global environmental challenges. Together, we can harness their power to effect positive changes and pave the way for a sustainable world.
*To learn more about the VITA products or to join us in our mission towards a more sustainable world, please contact us at info@m20genomics.com. Together, we can make a significant impact on our planet's health and continue to innovate towards a clean future.
References:
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