Oxman

ALEF explores a wide breadth of ecological research at the molecular and ecosystem scales with the long-term goal of deepening our understanding of interspecies communication and overall ecosystem health.

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The project is rooted in decoding the dynamic chemical signals released by plants, bacteria, and entire ecosystems to communicate with other organisms in their vicinity. Each signal comprises the emission of biogenic volatile organic compounds (bVOCs). The ‘molecular fingerprint’ of each organism is a unique composition of bVOCs at a given time, often carrying an associated smell.

Through two main pathways—the restoration and monitoring of an ancient ecosystem and the development of synthetic biology tools for bVOC research—we collect and recreate smells from real-world, simulated, and designed ecologies. This allows us to access a rich data set that provides valuable information about species composition and the state of various ecological systems.

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Using a network of tools and technologies in both laboratory and forest environments, we generate insights into “Whole Ecologies,” with the potential to inform molecular design across domains, including horticulture and companion planting, agriculture, scent and flavor design, aromatherapy, and cosmeceuticals, prioritizing symbiotic polycultures over monocultures.

The molecular design of the foods, fragrances, and flavors of our everyday lives often relies upon producing source ingredients by modern agricultural practices of continuous monocropping. By growing the same species in the same field, year after year, monocropping yields unstable ecologies vulnerable to soil degradation, water contamination, and rampant pests and disease. The negative impact on native plant life, soil fertility, and bacterial composition, combined with high water consumption and low genetic diversity, drives the loss of wilderness and a disconnect from balanced ecosystems.

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Rather than producing and consuming mono-cultures, we pursue the study of ancient ecosystems—as well as the exploration of novel ones—that sustain diverse, internally regulated, and highly networked life-forms.

In contrast to monocultures, polycultures reflect natural ecosystems, where multiple species occupy the same region and interact in mutually beneficial ways. A greater number of species coexisting in the same ecosystem leads to greater stability, increased energy cycling, and an improved capacity to withstand climate impacts; plant distribution patterns show less randomness due to the formation of specific symbiotic relationships.

Natural ecosystems are some of the world’s biggest carbon sinks, sequestering 16 billion metric tons of carbon dioxide annually (Harris et al. 2021)—roughly 40% of global CO₂ emissions. As an ecosystem’s carbon sequestration capacity is tightly linked to its biodiversity and overall health, restoring the functionality of degraded ecosystems, while protecting the well-being of their many inhabitants, may hold the key to tackling the climate crisis.

The ALEF platform is a combination of techniques, tools, and technologies for polyculture engineering of past and future ecologies. It offers a mechanistic approach to programming, analyzing, and functionalizing large-scale, complex growth and interactions at the ecosystem scale.

Aiming to cultivate a better understanding of what constitutes a healthy ecosystem, we deploy novel sensors in laboratory and field environments to help decode, contextualize, and harness the dynamic molecular signatures of living organisms and environments.

Fueled by our growing curiosity about what constitutes a long-term and resilient ecology, we look to environments that resemble their pre-mass-human-intervention state. Among these environments, the Oak-Tulip Tree Forest holds particular significance. This mesophytic hardwood forest community once sprawled across 37% of Manhattan Island, including the location of our Hell’s Kitchen-based lab.

Extensive human activities such as logging and agriculture and the proliferation of invasive species and pests have dramatically reduced its coverage, Today, it is recorded by the Department of Environmental Conservation as occupying only 0.5% of all natural areas in New York.

Despite the precarious state of this ecosystem as a whole, individual plant species persist, with 22 of them growing in Capsule 04 in our lab—a canopy of oaks, tulip trees, American beech, black birch, and red maple; subcanopy of flowering dogwood; and understory associates of witch hazel, sassafras, and lowbush blueberries, among others. While growth in the Capsule is young, the species and conditions are designed to mirror old-growth systems, moving toward the resurrection of an ancient ecology.

The one endangered species on our list is the American Chestnut, once a dominant tree in the Northeastern US, where it made up 25% of the forest canopy. The arrival of Chestnut Blight from Japan decimated these populations, reshaping entire ecosystems. We have three saplings of the original American Chestnut preserved in their native location, where they would not survive outside.

Working with a controlled reconstruction of an ancient ecology provides an opportunity to research what factors made this collection of species thrive and remain dominant for so long. By cross-referencing data from various sensors integrated within the Capsule—including thermal and hyperspectral images and temperature and moisture levels in the air and soil—we can generate insights into how signals co-vary at the ecosystem level.

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bVOCs are also collected and cross-correlated with other quantitative metrics of ecosystem health and performance such as respiration and transpiration rates, energy dissipation, and the accumulation of biomass. Taken together, these signals can not only indicate when an ecosystem may benefit from positive interventions, but may allow us to understand new ways that we can ‘resurrect’ ancient ecosystems and promote biodiversity.

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Looking to the past to inform the future, Capsule 03 is dedicated to bVOC- based communication and continuous in vivo directed evolution. This platform comprises an array of custom bioreactors specifically designed to interact with bVOCs and engineered bacteria.

At the core of the system is a gantry setup equipped with a mechanical lung, which samples the air from each bioreactor. This allows us to transfer bVOCs between producer and sensor bacterial strains, enabling the creation and testing of biochemical communication networks.

This system is designed as a modular living computer where information would take the shape of volatile molecules in the air, instead of electrons in wire, and computations will run in engineered DNA, instead of silicon chips.

By leveraging this setup, we can explore how biochemical signals, such as those emitted by stressed plants, are captured by engineered bacteria and translated into actionable responses, both as a reporting system and as a bioremediation tool.

We are actively building bio-interactive systems where machines can control patterns of gene expression through gas-phase induction. Using gasses to regulate biological systems offers a non-invasive and transient form of communication. Unlike liquid chemicals, which often require injections that can cause physical damage and take longer to dissipate, gasses provide a quick, reversible signal.

Additionally, gas-phase induction allows for long-range signaling, making it a powerful tool for connecting distant biological systems and enabling complex interactions. Our modular computational platform represents a radical departure from existing systems that prototype bVOC interactions. As the first of its kind, it holds the promise and potential to evolve future ecologies to air-based interactions.