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Climate change is leading to habitat shifts that threaten species persistence throughout California's unique ecosystems. Baseline biodiversity data would provide opportunities for habitats to be managed under short-term and long-term environmental change. Aiming to provide biodiversity data, the UC Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program to be a citizen and community science biomonitoring initiative that uses environmental DNA (eDNA, DNA shed from organisms such as from fur, feces, spores, pollen or leaves). Now with results from 1,000 samples shared online, California biodiversity patterns are discoverable. Soil, sediment and water collected by researchers, undergraduates and the public reveal a new catalog of thousands of organisms that only slightly overlap with traditional survey bioinventories. The CALeDNA website lets users explore the taxonomic diversity in different ways, and researchers have created tools to help people new to eDNA to analyze community ecology patterns. Although eDNA results are not always precise, the program team is making progress to fit it into California's biodiversity management toolbox, such as for monitoring ecosystem recovery after invasive species removal or wildfire.

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.

Molecular forensic techniques to trace DNA from surfaces and sediments have played important roles in conservation and species protection for decades, but their application in the field of ecology is not as well established. In the 1990s, forensic sequencing was applied to non-human samples, illuminating how DNA shed in the environment can be used to track species, populations, and individuals, with implications for animal conservation and management cases. Concurrently, molecular markers such as DNA barcodes were increasingly being published for systematics and biodiversity surveys. Now, forensic techniques are being applied as metabarcoding and metagenomics for ecology and conservation, taking advantage of massive biodiversity DNA reference databases to trace and characterize everything in environmental samples from individuals to whole communities, revealing the provenance and timing of events. Sequencing environments across space and time provides key ecosystem biometrics that point to the causes—and often the culprits—of ecological change. Ecological forensics broadens translational research opportunities in conservation, policy, and environmental justice. This chapter specifically focuses on the increased use of environmental DNA (eDNA), which can be collected from soil, sediment, water, or air, in forensic ecological research from real-time to deep time. The rise of this new subdiscipline has the potential to shape the future of biodiversity management and discovery globally.

Ecological systems are subjected to multiple stressors that can interact in complex ways resulting in "ecological surprises". We examine the pivotal role of 'control' assignment in the categorization of stressors into five classes: additive, +synergistic, -synergistic, +antagonistic, and -antagonistic. We demonstrate if an alternate treatment can reasonably be considered the experimental control, nonlinear interaction classifications change, both in sign (+/-) and in direction (synergistic/antagonistic). Further, switching of interaction classifications is not predictable as changing control can result in multiple possible alternate nonlinear classifications. To explore the magnitude of this problem, we evaluate publications gathered for a recent meta-analysis to 1) explore rationales for choice of controls and 2) quantify how frequently it is reasonable to reassign the control. We found controls were designated with a variety of implicit and explicit justifications, with two overall rationales: 1) controls based on 'natural' conditions (historic, current, or future); 2) controls based on direction of impact, such that stressors always have negative impacts. We reasoned that control re-assignment was justified if an alternate treatment met one of these rationales. Of the 844 interactions classified in the meta-analysis, we determined >95% could be reassigned. Based on these findings, we recommend a new approach to meta-analyses, where the 'control' is strictly and consistently defined by the authors of the meta-analysis. These controls should be based on their broader question, rather than following the common practice of defaulting to controls assigned by the authors of each study, as we found these rationales vary broadly based on the specific questions of each study. Consistent control designation within the ecological or toxicological framework of each meta-analysis may provide deeper and more consistent insight into the nature of interactive effects between multiple stressors. Gaining this insight is crucial because stressor interactions are certain to increase in the Anthropocene.

Global change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring California’s biodiversity through environmental DNA (eDNA)—DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.

Beginning in the mid 20th Century the Chesapeake Bay began to show the first signs of eutrophication, with seasonal depletion of free oxygen in bottom waters (hypoxia). Eutrophication is driven largely by external loading of phosphorus (P) and nitrogen (N). These nutrients maintain high levels of phytoplankton productivity and subsequent transfer of fixed carbon to the sediments. That carbon fuels heterotrophs that uptake free oxygen in the bottom waters at a faster rate than it can be replenished during seasonal stratification, resulting in periods of persistent hypoxia and anoxia. Aerobic and anaerobic decomposition of the settled plankton and detritus drives the release of remineralized nutrients such as orthophosphate (P). Episodic and seasonal mixing events transport the N and P to better illuminated surface waters where it supports blooms of phytoplankton, which will settle and continue the positive feedback loop of eutrophication. To better understand the role of sediments in the ongoing stress caused by eutrophication in the Chesapeake Bay we incubated sediment cores at temperatures to model an in situ seasonal cycle. We measured oxygen concentrations and P levels to estimate the release of orthophosphate to the overlying waters under various oxygen conditions. During oxic conditions the net flux of orthophosphate was from the water column into the sediments. Anoxia drove P flux from the sediments back to the water column. These results indicate internal P loading during periods of anoxia by the sediments to the water column may lead to continued eutrophication.