The Habitat-Based Microbial Recovery Index (hMRI):

A Field-Based Framework for Assessing Soil Microbial Diversity in Rewilded Forests

Research Question

We know forest soils contain vast antibiotic-producing potential, but we lack practical tools to identify which forests have habitat conditions associated with diverse microbial communities, or how to help those that don't. Can a simple index based on visible habitat features fill this gap, giving land managers and conservation practitioners both assessment capability and restoration guidance without requiring laboratory analysis?

The hMRI Approach

The Habitat-Based Microbial Recovery Index (hMRI) translates five field-measurable habitat variables—canopy cover, coarse woody debris, litter depth, plant diversity, and distance from forest edge—into a diagnostic profile to assess habitat conditions associated with soil microbial diversity. Built on 85+ peer-reviewed studies focused on temperate forests, the hMRI allows practitioners to assess habitat conditions using standard forestry tools.

Objectives

This six-week summer research project will build and validate the hMRI through five integrated objectives:

Review and Update Literature Base: Synthesizing relevant studies identifying relationships between habitat structural features and soil microbial communities. Focus on temperate forest systems with direct applicability to New England.
Construct the hMRI Model: Develop the hMRI as a five-variable diagnostic framework. Each variable is measured and reported with reference ranges. Document habitat interactions (e.g., edge × urban context, agricultural legacy) as context variables for interpretation.
Execute the Field Pilot: Apply the hMRI by quantifying habitat variables across 20+ field plots in contrasting rewilded and degraded forest sites in New England (10+ plots per site).
Validate the Model: Conduct consistency analysis to determine if the profile captures differences between site types, and evaluate against success criteria.
Translate to Practical Tool: Create a user-friendly field monitoring protocol and interpretive guide for conservation partners, including visual reference examples for each variable. Gather feedback from land trust partners to refine usability.

Methods & Timeline (6 Weeks, Summer 2026)

Weeks 1-2: Model Construction & Field Preparation:

Literature Review Update: Incorporate new relevant studies published since initial feasibility research. Focus on temperate forest meta-analyses and New England-specific data.

Reference Range Calibration: Establish reference ranges for each habitat variable using Harvard Forest LTER datasets, FIA data, and published temperate forest studies.

Field Protocol Development: Design standardized field datasheets with measurement protocols for consistent data collection.

Site Coordination: Finalize access agreements with land trusts in New England. Confirm plot locations within selected sites.

Weeks 3-4: Field Data Collection and Evaluation:

Site Selection: Work with conservation partners to access rewilded forest sites (high structural complexity, minimal recent disturbance) and degraded forest sites (low structural complexity, documented recent management).

Field Sampling: Execute standardized protocol across 20+ plots (10+ per site). Measure core variables: canopy cover, litter depth, CWD volume, distance from forest edge, plant species richness. Record context variables: edge habitat type, visible land-use history indicators, dominant tree mycorrhizal association.

Documentation: GPS coordinates, site condition photos, contextual metadata for each plot.

Measurement Reliability: Record within-plot variation for litter depth (5 measurements per plot). On a subset of plots, have a second observer independently measure variables to assess inter-observer reliability.

Profile Assessment: Compare variable measurements against reference ranges and between site types.

Success Criteria Evaluation: Evaluate results against pre-specified criteria (face validity, internal consistency, edge→interior gradient, variable distribution). Determine overall success level (full, partial, useful failure, or complete failure).

Weeks 5-6: Interpretation and Communication:

Interpretation: Contextualize findings within the literature. Examine any variables that didn't follow expected patterns.

Practitioner Review: Share draft protocol with conservation partners for feedback on clarity and usability. Revise based on input.

Visualization Development: Generate site comparison charts, variable profiles by site type, and photo reference examples.

Final Deliverables: 2,000+ word research essay, research poster, 1-page field protocol, photo reference guide, complete dataset with plot-level measurements, interpretive guide linking results to management recommendations, and notes on measurement variability.

Notes:

1. Interaction effects are qualitative. Literature documents that interactions exist but does not quantify multipliers. Context variables are recorded for interpretation, not formula adjustment.

2. Reference ranges are derived from Harvard Forest LTER, regional FIA data, and published temperate forest studies representing typical values for long-recovered temperate forests. The assumption that these ranges correspond to meaningful differences in microbial communities is supported by the literature but will not be directly lab-tested in this pilot.

4. Seasonal and temporal variation is not captured in this project. Measurements will be taken during a single summer season.

Significance:

The hMRI addresses a critical gap between ecological research and conservation practice. By translating peer-reviewed findings into a field-deployable index, this project enables evidence-based forest management without requiring expensive laboratory analysis.