ecoBay

Robotics and Genetic Monitoring for the Early Diagnosis of Biodiversity in Bavarian Lakes

Bavaria’s lakes are sensitive ecosystems—and they are changing. Biodiversity in freshwater ecosystems is declining, while rising temperatures, nutrient runoff, and extreme weather events create additional stress. At the same time, water monitoring often lacks the tools to capture genetic diversity quickly, reliably, and with high spatial and temporal resolution.

This is where ecoBay comes in.

The project is developing a floating autonomous robot that revolutionizes genetic biodiversity monitoring. The robot repeatedly visits defined measurement and sampling sites, continuously records limnological parameters such as temperature and oxygen levels, and takes water samples for environmental DNA and environmental RNA (eDNA/eRNA).

An AI-supported adaptive mission planning system decides in real-time which measurement sites provide the most significant information. This creates an intelligent, learning monitoring system.

From genomic and transcriptomic data, species spectra, functional activity, and genetic indicators of lake health are derived. This information is linked with water quality data and integrated into predictive models.

ecoBay is being tested on two Bavarian model lakes: Lake Ammersee and Lake Grosser Ostersee. As a project within the bayklif2 network, ecoBay strengthens the focus areas of water, biodiversity, and ecosystem health—providing standardized data and workflows for research, authorities, and other stakeholders.

Background

The decline of freshwater biodiversity is not a distant problem—it affects Bavaria directly. Lakes react sensitively to climatic changes, nutrient inputs, and hydrological fluctuations. Effective management requires reliable, timely data. However, traditional biomonitoring is often manual: time-consuming, labor-intensive, and limited to isolated points in time. The genetic diversity of a lake usually remains invisible.

Methods based on eDNA and eRNA open new possibilities. They allow for the comprehensive recording of species—including rare or elusive ones. Furthermore, they provide clues about functional activity and the physiological state of organisms.

In practice, however, standardized and automated systems that link genetic analysis with continuous water quality measurement and spatially adaptive sampling have been missing.

ecoBay builds on established eDNA/eRNA protocols (environmental DNA/RNA refers to genetic material that organisms leave in their environment, e.g., in water, soil, or air), autosampler and Environmental Sample Processor (ESP) concepts, and initial experiments with a robotic prototype. Proximity to the research stations in Wartaweil (LMU/Ammersee) and Iffeldorf (TUM/Osterseen) enables intensive preliminary studies and realistic field tests.

What has been missing until now is a robust, field-ready, and fully integrated platform that can be used even without specialized robotics expertise – ecoBay closes exactly this gap.

Methods and Objectives

ecoBay follows a clearly structured, two-stage approach:

1. Establishment of a reference base: High-resolution underwater maps are created in both model lakes, and reference and training data on habitats, water quality, and genetic diversity are collected. A static measurement field serves as a comparison system. Standardized eDNA/eRNA protocols ensure comparability.
2. Development and validation of the autonomous system: Building on this, the autonomous monitoring system is developed, tested, and validated against manual reference data.

Water and sediment samples are analyzed using metagenomics and metatranscriptomics—meaning the total DNA and RNA of all organisms in a sample is analyzed. These data are coupled with continuous sensing of parameters such as temperature, oxygen, pH value, and nutrients. Using artificial intelligence, the robot selects adaptive measurement points and dynamically optimizes its mission planning.

The goal is to develop genetic indicators of lake health and predictive models that detect changes at an early stage. ecoBay thus creates an authority-ready, scalable early-warning and monitoring solution for Bavarian lakes.

Immediate Added Value for the Free State of Bavaria

ecoBay lays the foundation for modern, future-proof monitoring of the health of Bavarian lakes.

Continuous measurements of central limnological parameters and genetic analyses via eDNA/eRNA provide high-resolution information on biodiversity and water quality—spatially differentiated and with high temporal frequency.

This supports authorities in:

• Implementing the Bavarian Water Pact (Wasserpakt Bayern),
• Fulfilling the European Water Framework Directive,
• Achieving biodiversity targets to preserve genetic diversity.

Measures can be prioritized more effectively, and their impact better evaluated. Through automation and AI-supported site selection, ecoBay relieves scarce personnel resources—effectively providing „free heads and hands“ for strategic tasks.

The platform concept is scalable and transferable to other lakes in Bavaria and beyond, creating a cornerstone for comprehensive, modern water monitoring.

Potential Synergies within bayklif2

ecoBay is closely integrated into the bayklif2 network and strengthens the consortium through standardized data, workflows, and „best practices“ from the field—ranging from permitting processes and logistics to quality assurance.

Limnological time series, habitat maps, and eDNA/eRNA data are made available according to FAIR principles via the bayklif2 data platform and NFDI4Biodiversity. Key software components are intended to be released as Open Source following successful validation.

To foster exchange and visibility, ecoBay organizes:

• The network workshop „Best Practices – From the Lab to the Field,“
• A special exhibition at the Museum of Man and Nature (Museum Mensch und Natur) in Munich,
• Dialogue formats with authorities and stakeholders (kick-off, field demonstration, user validation).

So wird der Transfer in Praxis und Verwaltung aktiv begleitet.

Langfristig kann ecoBay als Modul in bestehende Monitoringprogramme integriert und in weiteren Seen eingesetzt werden.

In the long term, ecoBay can be integrated as a module into existing monitoring programs. It tells a story of technological breakthrough: an autonomous robot on Bavaria’s lakes making genetic diversity visible—and creating a new foundation for the sustainable protection of our waters.