In recent months, I have been meeting regularly with a small but global cohort of fellow soil microscopists. We’ve been discussing both the benefits and the limitations of microscopy based on our collective experiences. Our reflections have included imagining new ways to do microscope evaluations. While the current methods are useful, they can be tedious and therefore expensive and exclusive.
In a previous newsletter for my business, Rhizos, I explained how even these nuanced quantification methods are still largely qualitative due to the dynamic, living ecosystem of soil and biological amendments. The intention of this microscopy working group is to develop methods and reporting that better account for this inherent variability, while also being more practical to execute.
That’s right, we want to see if we can make microscope assessments easier to carry out, and even more accurate in the information they convey.
This is a project that we will be chipping away at this year in between our full-time work as soil consultants, compost makers and lab-technicians. Today, I’m sharing our purpose statement!
While this may seem technical, our goal is to unlock affordable, accessible microscope testing. By lowering the barrier to entry, we hope to welcome small farmers and hobbyists into these insights—empowering them to make and source better biological amendments such as compost and take an informed approach to restoring the health of the soils they steward.
They say, “create the change you wish to see in the world”, and I’d like to add: do it in community with others, because what emerges is greater than the sum of its parts. We shall see what comes of this. ✨
From the Holobiont HUB microscopy working group: Brian Vagg, Triin Savet, Andie Marsh, Renald Flores, Keisha Ernst, Sebastien d’Ursel, Tanja Dekker, and Adam Cobb
Ecological Vitality (EV)1 is an emerging concept that links organism biomass and richness2, with ecosystem processes and services. This framework promotes effective caretaking for land, soil, microbiomes, plants, and animals while enhancing meaningful field trials and community science3.
Generally, the presence and abundance of diverse organisms suggest favorable environmental conditions and food web functions4. Accurate and precise assessments of onsite biological communities5 are currently limited, hindering use of microscopy for land and soil regeneration6.
A novel protocol for Rapid Microorganism Checks (RMCs)7 will provide a new standard for practical, qualitative, and interpretable assessments of local biotic networks8. Both professionals and enthusiasts, equipped with a microscope, will be able to track key bioindicators9 of ecological well-being without the need for tediously counting organisms.
Elevate mindful microscopy10 that’s compatible with other bioscience data, demonstrating how microorganisms are the foundation of land and soil health11
Combine innovative scientific knowledge and community field experiences that enhance social collaboration and the spread of holobiont literacy12
Establish a widely-adopted approach that links thriving microbiomes and ecosystem regeneration while providing free and open-source educational materials
We’re preparing a Mindful Microscopy Primer that communicates the EV framework and explains how to complete an RMC within a few minutes. For example, we’re developing an intuitive system that allows comparisons between samples and shows trends over time.
Ultimately, our vision is to spread reliable insights through straightforward reconnaissance of the micro-world. Information provided by RMCs can be widely accessible and helpful to practitioners, supporting land and soil stewardship at every scale.
By selecting from visual references, users will benchmark the relative densities and morphological variations for micro-life subcommunities13, such as (1) fungal spores, (2) fungal filaments, (3) protozoan, and (4) nematode. These bioindicators can be estimated within a few minutes, minimizing sampling noise14 by embracing the variability and uncertainty in all living systems.
Primer 1.0 will center on compost assessments, an essential component of land and soil management. Future modules (expansions) may be added in collaboration with our practitioner community, as evidence accumulates.
Mindful microscopy opens the door to deeply compelling and authentic storytelling. By making the invisible visible, RMCs can promote a common language and illustrate how biological communities build ecosystems and support human society.
While offering guidance that’s as repeatable and reliable as possible, we recognize microscopy is only one tool in the toolkit15 and must complement other technical and social diagnostics, such as direct observations, plant health tracking, chemistry reports, molecular testing, and more.
Forthcoming materials will be open-access and non-commercial, allowing wide adoption and adaptation (like this active compost primer on Holobiont Hub). We intend that any related applications or technologies be free and transparent, inviting reasonable challenges and welcoming new discoveries to inform ongoing breakthroughs.
ecological vitality (EV) - “...the inherent capacity of nature to be healthy, robust, and full of life.” (see Lifestyle Sustainability Directory); the combination of key ecosystem factors, such as biodiversity, health, resilience, and interconnectedness
organism biomass and richness - the population (estimated abundance) and variety of species or types of a particular organism grouping, for example, nematodes
meaningful field trials and community science - communal activities, such as repeated and reported direct experiments, designed and coordinated to expand our knowledge and comprehension of regenerative practices and ecological land management
food web functions - how all organisms within an ecosystem relate to each other and create unique processes, such as the flow of energy and cycling of nutrients
biological communities - the various and interacting organisms within a sample that is collected from a larger area, such as a compost pile
land and soil regeneration - improving degraded habitat and restoring key ecosystem features, such as fertility and biodiversity
Rapid Microorganism Checks (RMCs) - a proposed method to quickly gauge each microorganism group (subcommunity) by selecting from reference images, getting an overall snapshot of samples in minutes, rather than exhaustively counting organisms
biotic networks - complex linkages between all the living parts of an ecosystem, for example, healthy soils support a multitude of interactions between individual organisms, populations, and the entire biological community
key bioindicators - microorganisms that drive ecosystem processes and food web functions by their activities and interactions, for example, the predation of bacteria and fungi by protozoa that creates a nutrient loop/cycle
mindful microscopy - a shift in thinking that focuses on dynamic functions and characteristics of the microscopic life forms that support our biosphere, instead of demanding numerical outcomes that lead to limiting judgements. For example, regarding the vast array of lifeforms that depend on soil as an energetic community that we can nurture and collaborate with, rather than merely defining and controlling
land and soil health - the capacity of soil ecosystems and landscapes to recover from stress, self-renew, and continue supporting plants, animals, and microbiomes with key processes and services, such as nutrient cycling and water filtration
holobiont literacy - a broad understanding that individual plants and animals provide a scaffolding for complex microbiomes where hosts, together with all other organisms living around, on and within their bodies, form a united community of relationships
subcommunities - a distinct group of organisms that lives within a larger biological community, for example the protozoan subcommunity found in compost
sampling noise - unavoidable variation and innate errors that reduce the accuracy and precision of all biological appraisals that are based on population samples
one tool in the toolkit - recognition that microscopy is a single approach to gathering information about biotic networks; ultimately combining different and contextually appropriate measurements is crucial to a more holistic view of biological communities
🔬 Let me know what comments or questions you might have for this working group!
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