Collaborative Micro-biotechnology: A Technological and Social-Environmental Intervention

Author: Dylan Rees (University of Albany)
2026/07/13 | Projects

(Rees 2026; An electron microscope image of Shewanella oneidensis building an unexpected structure during an experiment that successfully synthesized cadmium sulfide, while also resulting in a large geode-like structure made mostly of cadmium oxide likely constructed and then colonized by a network of bacterial nanowire connections; a picture of bacterial agency)

Collaborative Micro-biotechnology: A Technological and Social-Environmental Intervention

This essay discusses research at the intersection of electrical engineering and microbiology, drawing on several years of work cultivating the bacterium Shewanella oneidensis MR-1 for nanomaterial synthesis and environmental biosensing. Reflecting on how engineering with microbes reshaped our own methods and assumptions, we developed a distinction between instrumental and collaborative paradigms for microbial technology development, tracing the technical trade-offs that each paradigm creates for sensor design. We extend this technical distinction into the social and ethical dimensions of engineering with microbes, using the origins of technologically valuable bacteria in polluted sites to ask: Who counts as a stakeholder in microbial biotechnology, and what obligations do engineers hold toward the communities and ecosystems those microbes come from?

As part of a multidisciplinary engineering lab at Rensselaer Polytechnic Institute beginning in 2016, I cultivated and utilized the bacterium Shewanella oneidensis MR-1, a bacterium capable of reducing a variety of metallic ions and solid-phase minerals as part of its respiratory process. Shewanella was first isolated from Lake Oneida (its namesake) in the 1980s. An interdisciplinary team of scientists discovered this bacterium after observing rapid geochemical cycling of manganese in the lake, hypothesizing that it had a biological origin (Nealson 2026). Shewanella turned out to be the manganese-reducing agent. Our lab built on existing microbiological research around Shewanella to do electronic materials research, testing Shewanella’s metal reduction capability to perform the room temperature synthesis of semiconductor materials such as cadmium sulfide and molybdenum disulfide, with applications in engineering and materials science. We wanted to demonstrate that bacteria can offer an environmentally sustainable method of creating such materials (Rees 2019; Rees 2020).

The other major thrust of our work explored the utility of Shewanella bacteria for environmental biosensing. Existing methods of detecting chemical concentrations in water rely on sensors that consume chemical reagents, and are generally designed to detect a single chemical at a time. But bacteria are in a sense elaborate multimodal biochemical sensors, and if harnessed for biosensing applications they have the potential to detect multiple target chemicals at once without the need for consumable reagents. Bacterial metabolic pathways (and Shewanella’s metabolism in particular) respond to a wide range of chemical inputs. Shewanella has demonstrated advanced chemotactic (nutrient-seeking) behavior and the ability to extrude metal-reducing appendages when the availability of electron acceptors is limited (Fredrickson 2008). As a biofilm-forming microorganism, Shewanella also organizes into colonies within which individual bacteria send biochemical signals to one another, regulating genes based upon local population density (Miller 2001). In essence, any one of these processes could be the basis of a chemical biosensor if it can be consistently measured, monitored and correlated with a chemical concentration. Furthermore, when Shewanella grows on a metallic surface, conductive proteins on its outer membrane allow it to make direct electrical contact (Gorby 2006). This has allowed scientists to use Shewanella biofilms growing on electrodes to detect chemicals such as lead, mercury, cadmium, chromium, organic pesticides (Zang 2021), and nitrates (Kelly 2023), with the potential for sending many other ions and compounds.

I. Encountering the Trouble

As trained electrical engineers, my colleagues and I were struck by how much working with microbes felt entirely unlike our prior work. Whereas electrical engineering relies on materials and methods with well-defined and predictable parameters and attempts to minimize variation and uncertainty, microbes continually resist attempts to render them into a predictable system. As bacteria grow, their biofilms develop small areas of variation from the overall experimental conditions (Cunningham, Lennox, and Ross 2010). When bacteria catalyze the precipitation of minerals, this precipitation is unpredictable as well—small variations in local surface conditions or concentrations can lead to the evolution of entirely different materials in different areas of the sample. Due to their rapid rate of reproduction and ability to perform horizontal gene transfer, bacteria also undergo relatively rapid genetic drift or genetic adaptation, such that for sufficiently long experiments, there is some uncertainty as to whether the bacterial populations present at the beginning and end of the experiment are truly the same population with the same traits (Lenski 1991). In summary, electrical engineering traditionally demands raw materials that are static in composition and behavior, and metal-reducing bacteria are anything but that.

As we developed the microbial nanomaterial synthesis side of our work—considering how our process might scale industrially—our thoughts turned to optimization and yield. We sought to produce as much of exactly the material or electrochemical signal we wanted, as efficiently and consistently as possible, under known and reproducible conditions. Though such challenges are a part of nanomaterial synthesis in general, the dynamic behavior of bacteria made the experiments unusually difficult to optimize according to traditional metrics. Experiments produced our desired crystal structures alongside other, more baffling ones that we could not reproduce with a new experiment. Certain environmental variables, such as light, would affect the experiment when we did not expect them to. Bacteria colonized our substrates in visibly different ways each time we ran the experiment. One could say that the bacteria had goals that differed from our own as electrical engineers.

At first we interpreted differences between experimental results in terms of purely physical variables as we had been trained to do: pH, temperature, chemical concentration and so on. But the strongest determining factor in experimental outcomes, uniting all these variables, was the biological state of the bacteria on both an individual and community scale. In interpreting our results we found ourselves adopting first a technical language (electron donor and acceptor limitation, log or stationary phase) and later a colloquial and affective language already familiar to many biologists (Yanai 2020). Were the bacteria stressed? Were they happy? In describing our efforts to influence these bacterial affective states using tools such as voltage, lactate concentration or quorum sensing molecules, we often reached for the phrase “talking to microbes”. This phrase sometimes raised eyebrows among our collaborators, but captured the fact that we were attempting to interpret and respond to bacterial bioelectrochemical signals by producing new signals legible to the bacteria. It also had the effect of describing our research as a collaboration with nonhuman living agents—the implications of which we increasingly considered alongside the technical work.

In terms of human-microbial communication, one might cast the traditional biological sciences as an act of listening to and understanding living organisms without intervention, and the biological engineering sciences (such as synthetic biology) as the opposite—an attempt to dictate the behavior of an organism as much as possible. Our research attempted to solve engineering problems using the self-organizing behavior of bacteria as agents rather than biochemical machines, making our work an act of two-way communication. As we conducted literature reviews to understand related and prior work, we became interested in seeing which prior research resembled dictation to microorganisms and which resembled collaboration with them.

II. Instrumental vs. Collaborative Paradigms

Working with a colleague in Science and Technology Studies (STS) who performed an ethnographic study of our lab, we proposed two distinct paradigms for microbiological technological development—the instrumental and the collaborative. The instrumental approach employs a living organism in an engineering context by applying traditional engineering constraints and demands from top to bottom, seeing its attributes as targets for further optimization and engineering to meet human-defined criteria. By contrast, the collaborative approach tries as much as possible to see the organism as an agent with its own goals tied to an ecosystem function and context, then aligning a human-defined technological goal with that context. These distinctions led to publications including this article, and a publication in STS developed through collaborative engagements with our lab (Stanton 2026).

These instrumental and collaborative categories provide a framework to better understand many other potential and existing biotechnologies, representing our attempt to combine insights from the practice of the life sciences (Szymanski 2018) with those of the critical humanities, especially STS (Tironi 2020). Upon further examination, this collaborative tendency is also found in existing disciplines. In wastewater treatment, for instance, operators sometimes refer to their plants as 'bug farms'—large microbial populations whose thriving and the plant's effective operation are, in practice, the same thing (City of Wabasha 2023; Wastewater Treatment Expert 2022). The collaborative approach demands attention to the full ecology and relationships of the organisms involved: what conditions allow them to thrive, how they interact, and how humans can control the system with macroscopic interventions (nutrients, dissolved oxygen), while also allowing microscopic dynamics to self-organize. In this manner, a collaborative approach to development looks for technological solutions in the complexity of the living system itself rather than seeing such complexity as an impediment to technological goals.

III. Technical Implications

In the context of our group’s biosynthesis and biosensing work, it became clear that instrumental and collaborative approaches offered distinct technical advantages and disadvantages. An instrumental approach is easily translatable to metrics that can be communicated, replicated, optimized, and published. For instance, when developing an electrochemical biosensor using Shewanella bacteria, we can derive more immediately legible experimental results by removing all other bacteria from the experimental enclosure and growing the bacteria in a minimal chemically-defined liquid medium, even if these conditions do not match the natural ecosystem in which such bacteria would otherwise thrive. These conditions reflect the engineered goals of optimization and control.

Nonetheless, the collaborative approach offers potential technical advantages of its own. If one develops a microbial sensor that fully depends on the experimental conditions developed in the lab, deploying it in the field will require a 'lab in a jar' approach—transporting the chemically-defined medium and otherwise-sterile experimental environment to the field and interfacing it with the outside environment using a semipermeable membrane. Since the unpredictability of this environment is by definition a threat to the sensor’s operation, this setup is fragile by nature. Alternatively, consider a biosensor architecture built around a bacterial biofilm in direct, unmediated contact with its environment, including a chemically complex growth medium and a range of other microbial species. Real sensing performance—fast response, broad chemical sensitivity, sensitivity to trace concentrations—is most easily realized with direct contact (Zhao 2026). But direct contact means the biofilm is no longer an enclosed, well-characterized population of a single species; wild bacteria will colonize it, community composition will drift, and the sensor's 'active ingredient' becomes an open, evolving consortium rather than a fixed reagent. While an instrumental approach responds to environmental biosensing problems by enforcing containment, the collaborative approach instead treats the open, mixed-species biofilm as the sensor. In optimizing such a sensor, the engineer must relinquish individual control of the microorganism and instead attempt to interface with the biofilm as a micro-ecosystem that can be influenced using population-level variables (current and voltage among these).

Teaching engineers to think and design with such systems requires new modes of thinking beyond traditional engineering education. One might focus on the insights of engineers who have pioneered such collaborative approaches (such as the aforementioned sewage treatment plant operators) or look to adopt definitions of optimization and yield used by permaculturalists and forest gardeners or the Indigenous land stewards that inspired them (Jacke 2005). Our lab and interdisciplinary engagements are increasingly aligned toward these aims.

IV: Social Implications

As scholars in STS have argued previously, microbes are situated “in a web of material, socio-economic, ecological, and historical settings that shape the nature of those relations” with other human and non-human entities (Cañada 2025: 6). In the context of our lab’s work, this is most clearly illustrated through the origin stories of some of the bacteria regarded as most valuable to nanotechnology and biosensing. Bacteria such as Acidithiobacillus ferrooxidans are capable of bio-leaching metal ions from solid rock, freeing them for potential use in nanosynthesis processes. These bacteria were originally isolated from acid mine drainage sites, where they evolved in an environment of direct exposure to the highly acidic and heavy metal-laden wastes of the mining industry. Employing such bacteria technologically requires us to understand the degraded environments from which the bacteria arose. Meanwhile, the traditional engineering design process identifies the needs of a customer or client, then develops, tests and iterates design concepts based on the client’s needs (Ulrich 2020). Who is the client for a microbial technology sourced from a mine drainage site? It could easily be the entity that produced the pollution, attempting to comply with cleanup regulations through bioremediation. It could also be a surrounding community facing a public health crisis due to the mine drainage and seeking bioremediation and/or monitoring solutions.

Regardless, Acidithiobacillus and other technologically-relevant bacteria, especially those originating from pollution, represent deep entwinements between microbes, human beings, geology, time, and place (Bonelli 2021). Such entwinements raise questions with regard to engineering ethics and policy which must be investigated through practice as with the technical questions raised earlier. In the case of our research group, the following questions arose: Given that distinct microbial populations tend to arise at polluted sites, can technologies developed with these microbes empower the affected communities through community-led biosensing and/or bioremediation research? If so, what role does the engineer play in such research, and what role is played by the community and its expertise? What stewardship or ownership over this microbial technology should be afforded to the communities most affected? Work to attempt to answer these questions is ongoing (Sawyer 2023).

Conclusion

This essay has considered how engineering with Shewanella and related bacteria surfaced technical, ethical, and social questions that a purely instrumental approach to biotechnology tends to submerge, and has argued that a collaborative paradigm can yield both better-performing sensors and more accountable relationships with the communities and environments from which useful microbes are drawn. The collaborative approach we describe has no settled vocabulary. Following Haraway, we call it staying with the trouble, as holobiants that live and evolve alongside microbes (Haraway 2016). Reconsidering microbial technologies as partnerships reframes the engineer not as the sole author of a design, but as one party among several, each with legitimate claims on how the resulting technology is used and governed. We see this as part of a broader responsibility crisis in biotechnology, and offer the instrumental/collaborative distinction as one small contribution toward addressing it.

Author Bio:

J. Dylan Rees is a Visiting Assistant Professor in the Department of Electrical and Computer Engineering at the University at Albany. He is also an active member of the Society for the Social Studies of Science who has co-authored papers, Making and Doing sessions, and panel talks with researchers in the field of STS.

Published: 07/13/2026