Editorial: Harnessing synthetic biology for ecosystem sustainability and biodiversity conservation

Ecosystem sustainability and biodiversity conservation are threatened by habitat destruction and climate change, resulting in a global loss of biodiversity. Levin and Budisa envisioned a convergence of synthetic biology (SynBio) and metagenomics as a new approach to understanding complex biological systems, and perhaps even developing engineered strategies for community-level engineering. Recent studies have shown that synthetic biology can play a pivotal role in mitigating ecosystem degradation by characterizing how microbial communities are impacted by pollutants and/or climate change.

Flores-Orozco et al. (2023) used a metagenomic approach to investigate the impact of common manure treatments on the microbial communities in manures from different dairy farms, including one in which the dairy cows had not been treated with antibiotics. The analyses documented the presence and abundance of antimicrobial resistance genes (ARGs), bactericides, and heavy metal resistance genes (BacMet), and mobile genetic elements (MGEs) in these microbial communities, and determined that mesophilic anaerobic digestion (MAD) reduced the numbers of ARGs, BacMet, and MGEs to a greater extent than aerobic storage and solid-liquid separation treatments.

McCorquodale-Bauer et al. used metagenomics to investigate the effect of three different biological wastewater treatments on the microbial community and the ‘resistome’, the type and numbers of antibiotic resistance genes (ARGs) encoded by microbes in the community. The results indicated that each biological treatment significantly reduced ARGs and metal resistance genes (MRGs). A network analysis identified eight bacterial genera strongly associated with these ARGs. Analyses revealed a strong correlation between the iron (Fe) concentration in the water and total ARG abundance, as well as between total metal concentration (across eight measured metals) and antibiotic resistance genes, suggesting that high Fe and metal concentrations may favor facultative bacteria that carry ARGs, by providing an electron donor for anaerobic respiration. This study suggests that phytoextraction of metals, including Fe, may play a significant role in reducing ARG abundance in treated water columns.

Stanley et al., Stanley et al. (2025) investigated the use of Engineered Floating Wetlands (EFWs) for phytoremediation and biodegradation of bitumen and heavy crude oil containing Polycyclic Aromatic Hydrocarbons (PACs) in a freshwater lake. Metagenomics was used to assess the impacts of a controlled conventional heavy crude oil spill on changes in the microbial community of the EFW plant roots. Taxonomic profiles of the top 40 ASVs included the presence of organisms previously identified to have PAC/hydrocarbon degrading potential. These studies indicate that the dominant taxa of EFW microbial communities can shift drastically in response to oil or environmental conditions, which may be valuable for the secondary remediation of oil spills.

Although SynBio was originally developed as a set of tools for engineering of microbes and their enzymes, it is now possible to engineer expression of heterologous proteins in specific plant tissues and subcellular compartments (Chartrand-Pleau et al., 2025), and engineer microbial communities, creating a new discipline that may be called ‘synthetic microbial ecology’. The contribution by San Román et al. provides an overview of strategies for the design of microbial communities and the optimization of their functions, which could include engineering microorganisms for bioremediation, developing metabolic models to understand microbial interactions, and creating renewable biocatalysts for water reclamation. The prospect of engineering microbial communities (as opposed to single organisms) has emerged as a promising approach to applied microbial ecology (Großkopf and Soyer, 2014; McCarty and Ledesma-Amaro, 2019; Shong et al., 2012). Communities enable stable functional compartmentalization and division of labor (Beck et al., 2022; Wang et al., 2022; Roell et al., 2019). Communities are often able to resist invasions by invasive species, as exemplified by the stability of human intestinal and vaginal microbial communities (Pagar et al., 2024; Marciel-Fiuza et al., 2023). Strategies for engineering microbial communities include: Trait-based approaches; Directed evolution; Environmental engineering; and Modelling and computer-assisted design San Román et al.

However, the application of SynBio to engineering of microbial communities faces a number of critical issues. In 1974, concerns about biohazards of recombinant DNA experiments led to calls for a moratorium on cloning and further recombinant DNA technologies. In 1975, a conference held at the Asilomar State Beach Conference Centre in California brought together molecular biologists, lawyers, doctors, and government officials to discuss the potential risks and ethical concerns of the then-new field of recombinant DNA (rDNA) technology. The main concerns were: 1) Biosafety Risks of Recombinant DNA; and 2) Defining Risk Levels. The Asilomar Conference on Recombinant DNA (Berg et al., 1975; Berg, 2008) was a landmark event in the history of science and bioethics. Synthetic microbial ecology now faces the same kinds of questions.

The contribution of Keiper and Atanassova outlines a strategic plan to support the Convention on Biological Diversity (CBD), proposed at the Kunming-Montreal Global Biodiversity Framework (KMGBF), in December 2022. The CBD is a multilateral treaty with three main objectives: the conservation of biological diversity; the sustainable use of its components; and the fair and equitable sharing of benefits arising from genetic resources. The KMGBF proposal includes a “biosafety” target, that reflects the CBD obligations for Parties to implement biosafety measures, and measures for handling biotechnology and distributing its benefits. The KMGBF proposal explicitly recognizes the benefits of biotechnology/synthetic biology and recommends them as tools that can be used to develop “…solutions for implementation and mainstreaming” for ecosystems. However, biosafety and defining risk are key issues that remain to be established. The inclusion of a biosafety target in the KMGBF protocol has ignited hope for renewed recognition of the potential for biotechnology to contribute to global environmental goals. Further discussions about biosafety and risk mitigation will impact the application of biotechnology/synthetic biology tools for ecosystem sustainability and biodiversity conservation in the coming years.

The applications of SynBio to ecosystem sustainability and biodiversity conservation can, and should be, extended to challenges in environmental sustainability in developing countries, where there are significant gaps in the accessibility of these technologies. Baluku et al. (2026) assessed the awareness, perceptions and barriers of SynBio among 140 students, lecturers and researchers from 17 countries in Africa. They highlight the need to strengthen academic curricula, expand access to affordable training platforms, invest in laboratory infrastructure and promote a biosecurity and biosafety regulations framework to support the growth of synthetic biology research in Africa.

Synthetic biology combines natural and artificial components of life and applies interdisciplinary engineering principles to advance biotechnology and enable a deeper understanding of complex interactions in ecosystems. Metagenomics has significantly improved our understanding of how microorganisms’ collective functions emerge from the intricate interactions between their genetic and metabolic potentials and the environment, and has enabled valuable applications in environmental sustainability, such as analyzing antimicrobial resistance in waste management, bioremediation of oil spills, and the degradation of plastics.

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Footnotes

Edited and Reviewed by: Daniela Bittencourt, Brazilian Agricultural Research Corporation (EMBRAPA), Brazil