The Use of Archival Environmental DNA in the Laurentian Great Lakes

Description: Long-term time series data are critical in any effort to understand the timing and impact of stressors on an aquatic ecosystem and the potential resilience of that system to external pressures. These data are also critical for determining historical variability, the timing of ecological transitions that have led to present conditions, and the trajectory of change that is expected in the near-term future. For most aquatic systems, the breadth of available historical information is insufficient to identify ecological/biological transitions and their connection to altered ecosystem conditions. Combining neo-ecological with paleoecological approaches can circumvent some of these challenges by extending the historical record through information stored in the sediment. However, traditional paleoecological approaches rely on the few organisms that leave behind morphological distinct signatures and other proxies, which hampers robust assessments of biodiversity and ecosystem change. Recently, bulk environmental DNA analysis methods were developed and are now being applied to a variety of environments (e.g., water, soils, air, the built environment). In limnological settings, DNA preserved in sediment cores has proven to extend the observational record well beyond what was previously possible and provides a record for the many organisms living in these systems that do not leave behind fossils. These DNA based analyses now allow for a richer examination of the organismal history of a water body and the opportunity to make connections to current communities, including microbial communities, which have profound impacts on aquatic ecosystem functions.

As integrators of processes occurring across the landscape, lakes and estuaries are sentinels of change, recording historical human activities and climate change. For this workshop, we will focus on several areas within the Laurentian Great Lakes (LGLs) that have low dissolved oxygen levels. Low oxygen systems provide useful preservation of DNA for archival environmental DNA (aeDNA) studies, and they are often locations that have been impacted by human mediated eutrophication, and thus are a priority for ecosystem management. In the LGLs, lacustuaries, sinkholes located in Lake Huron, and the central basin of Lake Erie are notable low oxygen systems. Lacustuaries form as slack water embayments connecting rivers to lakes, and act as nutrient traps sequestering riverine inputs of nitrogen and phosphorus. Green Bay, Lake Michigan’s largest lacustuary, contains ~7% of Lake Michigan’s surface water but is responsible for ~30% of its nutrient loading. A myriad of human perturbations coupled with the physiochemical nature of embayments has led to the eutrophication of Green Bay over a period of at least 100 years. The eutrophication has led to hypoxic conditions (<2 mg/L dissolved oxygen) in near bottom waters, which now occur ~50% of the time between summer stratification and fall mixing. Karst sinkholes were discovered during acoustic surveys of Lake Huron, which has spurred a couple decades of research on these dissolved oxygen poor but sulfate rich ecosystems. These sinkholes have been studied for the microbial communities they sustain (Biddanda et al. 2009) and the carbon they store. For instance, Middle Island Sinkhole has potentially sequestered ~5 × 106 kg C and it has been shown that the majority of the carbon is derived from phytoplankton sources. Thus, because of their low oxygen levels and high exogenous carbon storage capacity, the potential for sinkholes to be useful locations to develop paleoenvironmental reconstructions via aeDNA is high. Finally, the central basin of Lake Erie has experienced extensive periods of hypoxia because of eutrophication and enhanced primary productivity, which has resulted in hypoxia being a priority area for NOAA observation networks. However, these observational records are limited to the last several decades and the understanding of pre-disturbance biological and chemical processes are lacking. Here, aeDNA may help in extending the monitoring record and providing crucial information about the dynamics of oxygen in the central basin.

We believe the analysis of aeDNA from sediments has advanced to the point where we can now effectively use it to identify past disturbances (e.g., the introduction of invasive species) and/or abrupt changes from anthropogenic stressors that can be linked to critical processes currently impacting the LGLs (e.g., hypoxia, altered food web dynamics, and changes to biogeochemical cycling). Thus, we have assembled a team of interdisciplinary scientists to document the past and present functioning of these low oxygen environments to better understand the future trajectory of coastal areas and pelagic zones in the rapidly changing LGLs. For our proposed workshop, we will engage managers, natural scientists, and social scientists to determine the potential of aeDNA from sediments as a proxy of past biodiversity change.

This workshop will scope both the basic science and management informed research questions that can be addressed in large lakes with aeDNA analysis as an emerging proxy of environmental change. We will also address the logistical challenges of retrieving sedimentary records from the LGLs, discuss the methodological challenges of working with aeDNA, and build a network of interdisciplinary large lakes focused researchers. Further, we aim to produce two products from this working group: 1) a white paper/perspectives manuscript on the scope of science that could be carried out in the LGLs using aeDNA and 2) a collaborative proposal to the cross-directorate US National Science Foundation’s Biodiversity on a Changing Planet (BoCP) program. The overarching goals of the workshop are to identify a team that will apply for a two-year BoCP Design track grant ($500,000) based on sediment coring of 3-5 locations within the LGLs, to develop creative research and technical approaches that address biodiversity change in response to anthropogenic disturbance in the LGLs, and to broaden participation within our research network. Ultimately, after the successful completion of the Design track BoCP, this group would then apply for the 5-year Implementation BoCP grant ($2,500,000). From these efforts, this working group has the potential to initiate a decade-long investigation of sediments and biodiversity change in the LGLs.