From Bioprospecting to Biorespecting
How Soil is Catalyzing a Scientific Revolution
Biodiversity
Genetics
Ethics
The Hidden World Beneath Our Feet
What if the solution to some of humanity's greatest challenges—from antibiotic resistance to climate change—lies right beneath our feet?
Soil, that humble dirt we walk on daily, represents one of the most complex and biodiverse ecosystems on our planet. A single teaspoon of healthy soil contains thousands of different microbial species, each with unique genetic blueprints that have evolved over billions of years 5 . For decades, scientists have approached this genetic treasure trove with an extractive mindset, a practice known as "bioprospecting"—searching soil microorganisms for valuable genes, proteins, and compounds that can be turned into medicines, technologies, or industrial applications. But now, a profound shift is occurring in how we view and value this hidden biodiversity, transforming from exploitation to collaboration in a new paradigm called "biorespecting" 1 6 .
"We finally have the technology to see the microbial world that has been previously inaccessible to humans." 5
This transition isn't just about scientific methodology—it's a fundamental rethinking of the relationship between science and nature. The biorespecting approach acknowledges that genetic information contained in soil arises from entire ecosystems, including the people involved in its creation and stewardship 1 . This article explores how soil is catalyzing a transdisciplinary research revolution that brings together synthetic biology, environmental humanities, microbial ecology, and public engagement to create a more equitable and sustainable future.
Bioprospecting
The traditional approach of searching for valuable biological resources in nature, often with an extractive mindset.
Biorespecting
A new paradigm that emphasizes collaboration, reciprocity, and ethical engagement with biological resources and their sources.
Urban Soil Exploration: A Transdisciplinary Experiment
In a groundbreaking public engagement project called "Become a Biological Engineer" (BaBE), researchers from synthetic biology, environmental humanities, and microbial ecology joined forces with high-school students to explore soil microbiomes at six urban locations 1 . The project deliberately focused on urban soils—including school grounds, riverbanks, public parks, research farms, and deer parks—which have received far less scientific attention than agricultural or natural soils 1 .
The experimental design was both scientifically rigorous and collaboratively inclusive:
Site Selection
Researchers partnered with students from two schools, allowing them to collectively decide where to sample soil on their school grounds 1 .
Creative Documentation
Students worked in groups to creatively describe their sample sites, connecting with the soil on both scientific and personal levels 1 .
Comparative Analysis
Samples were also taken from four other urban locations to enable broader comparison of microbial diversity across different urban environments 1 .
This collaborative approach blurred the traditional boundaries between researcher and subject, scientist and public, setting the stage for the conceptual shift from bioprospecting to biorespecting that would emerge from the project.
Urban soil sampling provides unique insights into microbial diversity in human-dominated environments.
The Scientist's Toolkit: Decoding Soil's Genetic Secrets
Revealing Microbial Dark Matter
The BaBE project utilized cutting-edge DNA sequencing technology to unravel the genetic secrets hidden within the urban soil samples. The researchers employed nanopore-based DNA sequencing, which reads DNA sequences as they pass through nanoscale protein pores 1 . This approach allowed for real-time genetic analysis that could be shared with participants almost immediately.
Meanwhile, in a separate but methodologically related study published in 2025, Rockefeller University researchers developed advanced techniques to access what they call "microbial dark matter"—the vast majority of soil bacteria that cannot be grown in laboratory conditions 5 . Their innovative approach included:
Large DNA Fragment Isolation
They optimized a method for extracting very large, high-quality DNA fragments directly from soil, bypassing the need to culture bacteria 5 .
Long-Read Sequencing
Using emerging long-read nanopore sequencing technology, they produced continuous DNA stretches tens of thousands of base pairs long—200 times longer than previous technologies allowed 5 .
Genome Assembly
These large DNA fragments made it dramatically easier to assemble complete genomes from the complex mixture of microorganisms found in soil 5 .
Synthesis of Discoveries
Through a "synthetic bioinformatic natural products" approach, they could predict chemical structures of natural products directly from genome data and synthesize them in the lab 5 .
Essential Research Tools and Their Functions
| Tool/Reagent | Function | Significance |
|---|---|---|
| Nanopore Sequencers | Reads DNA sequences through protein pores | Enables real-time, long-read sequencing of complex soil samples without culturing 1 |
| High-Quality DNA Extraction Kits | Isolates large, intact DNA fragments from soil | Preserves long genetic sequences for better genome assembly 5 |
| Bioinformatics Software | Analyzes sequence data and assembles genomes | Converts raw genetic data into usable biological information 1 |
| Synthetic Biology Tools | Chemically synthesizes predicted natural products | Turns genetic blueprints into actual molecules for testing 5 |
| pH and Soil Testing Kits | Characterizes physical soil properties | Provides environmental context for genetic findings 1 |
The power of these technologies is demonstrated by the Rockefeller team's results: from a single forest soil sample, they generated 2.5 terabase-pairs of sequence data, uncovered hundreds of complete bacterial genomes never before seen by science (more than 99% of which were new to science), and identified two potent new antibiotic candidates 5 . This approach, which Brady describes as "isolate big DNA, sequence it, and computationally convert it into something useful," demonstrates the breathtaking potential of modern soil metagenomics 5 .
The Ethics of Discovery: Student Debates and the Birth of Biorespecting
Grappling with Benefit-Sharing
When the BaBE project students were presented with a hypothetical scenario—what if their school soil contained a valuable gene that could revolutionize medicine?—the resulting debates revealed sophisticated ethical reasoning 1 . Students were divided into groups representing different stakeholders and asked to advocate for their positions:
The Corporate Approach
Some students recognized the benefit of large sums of money being provided by multi-national companies, potentially allowing people to "move elsewhere and start a better life." 1
The Critical Perspective
Many students expressed concerns about "broken promises of large corporations they had seen in the news" and worried about what might happen to other people in the area and the local wildlife 1 .
The Equity Consideration
While many felt strongly that "some personal benefits were warranted as they had discovered this valuable resource," making medicine free to everyone was "deemed unfair" 1 .
These student discussions highlighted the core tensions in environmental research: How should benefits from natural resources be shared? Who has the right to profit from genetic information? What responsibilities do we have to the ecosystems and communities from which we learn?
Student Perspectives on Soil Resource Use
| Stakeholder Position | Key Arguments | Underlying Values |
|---|---|---|
| Multi-national Company | Large financial investments deserve returns; economic development benefits community | Utilitarianism; market-based logic |
| Local Community | Resources from our land should primarily benefit local residents; historical connection to place | Distributive justice; rights-based approach |
| Scientific Community | Knowledge should be freely shared; open science accelerates progress | Communalism; scientific progress |
| Environmental Group | Soil ecosystem protection must be prioritized; intrinsic value of nature | Environmental ethics; conservation |
| Government Regulator | Need balanced approach; fair rules for all parties | Procedural justice; compromise |
From Extraction to Collaboration: Understanding the Paradigm Shift
The student debates, combined with transdisciplinary discussions among researchers, catalyzed a profound shift in how the project team conceptualized their work. They began moving from "bioprospecting" to what they termed "biorespecting" 1 .
Bioprospecting: An Extractive Legacy
The bioprospecting metaphor has its roots in extractive industries like mining, framing nature as a resource to be exploited for human benefit 1 . This approach has historical connections to colonial practices of taking biological materials without appropriate recognition or benefit-sharing, sometimes referred to as "biopiracy" 1 . Even when conducted ethically, the bioprospecting framework emphasizes one-way transactions where knowledge is taken on the scientist's terms without wider engagement or reciprocity 1 .
The limitations of bioprospecting become particularly evident in the context of international regulations like the Nagoya Protocol on Access and Benefit-sharing, which struggles to address the challenges posed by digital sequence information (DSI) generated through modern DNA sequencing techniques 1 .
Biorespecting: A New Ethical Framework
Biorespecting represents a radical rethinking of this relationship. It acknowledges that genetic information in soil arises from entire ecosystems, including the people involved in its creation and stewardship 1 . This approach:
- Recognizes Complexity: Views soil ecosystems as collaborative partners rather than raw materials 1
- Emphasizes Reciprocity: Ensures that knowledge use is accountable to its source ecosystems 1
- Promotes Benefit-Sharing: Helps improve the wellbeing of future generations through equitable practices 1
- Values Relationships: Creates ongoing connections between researchers, communities, and ecosystems 1
Comparing Scientific Approaches to Soil Biodiversity
| Aspect | Bioprospecting Model | Biorespecting Model |
|---|---|---|
| Core Metaphor | Mining, extraction | Collaboration, reciprocity |
| Relationship to Nature | Resource to be exploited | Partner in knowledge creation |
| Primary Goal | Discovery of valuable genetic material | Understanding ecosystems and equitable benefit-sharing |
| Community Engagement | Often minimal or transactional | Essential and collaborative |
| Ethical Foundation | Utility and profit | Care and responsibility |
| Legal Framework | Nagoya Protocol (focused on physical transfer) | Evolving to address Digital Sequence Information |
As the BaBE project demonstrates, this shift isn't merely theoretical—it transforms how research is designed, conducted, and applied. When researchers acknowledge that "knowledge can arise from ecosystems and communities," they recognize the obligation to reciprocate with care and benefit-sharing 1 .
The Future of Biorespecting: Implications for Science and Society
The implications of the biorespecting paradigm extend far beyond soil science. This approach has relevance for any field that draws knowledge from natural systems or traditional communities. The transition from bioprospecting to biorespecting comes at a critical time, as technological advances like long-read DNA sequencing are dramatically expanding our ability to access genetic information from environmental sources 5 .
Digital Sequence Information
The biorespecting framework offers a roadmap for navigating the ethical challenges posed by DSI, especially in microbial ecology 1 .
Medical Discoveries
Recent discoveries from soil microbes include new antibiotic candidates like erutacidin and trigintamicin that show potency against drug-resistant bacteria 5 .
Global Equity
Biorespecting ensures that as we unlock soil's potential, we do so in ways that are equitable and accountable to ecosystems and communities 1 .
The Potential of Soil Microbes
From a single forest soil sample, researchers generated 2.5 terabase-pairs of sequence data and identified hundreds of complete bacterial genomes new to science 5 .
Cultivating a New Relationship with Nature
Soil, once viewed as mere dirt, is now recognized as both a catalyst for transdisciplinary collaboration and a mirror reflecting our relationship with the natural world.
The journey from bioprospecting to biorespecting represents more than just a change in terminology—it signals a fundamental shift in how humanity conceives of its place in the natural order.
As we continue to face global challenges like climate change, biodiversity loss, and antibiotic resistance, the wisdom of the biorespecting approach becomes increasingly clear. By acknowledging that genetic information is not merely a resource to be extracted but rather a gift from complex ecosystems that includes responsibilities and relationships, we open the door to more sustainable, equitable, and collaborative forms of scientific practice.
The soil beneath our feet has always held life-saving secrets. Now, it's also teaching us how to be better students of nature and better partners in the great, interconnected web of life. As we learn to respectfully listen to what soil has to tell us, we may find solutions not just to scientific and medical challenges, but to the deeper ethical questions about how to live in right relationship with our planet.