Organic matter in soils and sediments derives from a mixture of biological origins, often making it difficult to determine inputs from individual sources. Complicating the determination of source inputs to soil and sedimentary organic matter (OM) is the fact that physical and microbial processes have likely modified the initial composition of these sources. This study focused on identifying the composition of watershed-derived OM to better understand inputs to inland waters and improve our ability to resolve between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts. We surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Multiple classes of organic proxies—including sterols, fatty acids (FA), lignin phenols and stable carbon and nitrogen isotope values (δ¹³C, δ¹⁵N)—were measured in soils, vegetation, charcoal, and freshwater plankton to characterize representative source endmembers. Sterols—including 27-nor-24-cholesta-5,22-dien-3β-ol, cholesta-5,22-dien-3β-ol, 24-methylcholesta-5,22-dien-3β-ol and cholesta-5-en-3β-ol, and positive δ¹⁵N values—were associated with aquatic OM (plankton, suspended particulate OM), whereas lignin phenols, long chain FA, and diacids characterized terrigenous sources (soils, charcoal, vegetation). Trends in organic carbon and biomarker signatures in soil samples showed a response to environmental disturbance (i.e., mining, agriculture) through an inverse relationship between OM content and land use. Results from this study demonstrate the utility of multi-biomarker studies for distinguishing between OM from different sources and land uses, offering new insights for biogeochemical studies in aquatic systems.

Uncertainties in understanding ecosystems increase the risk that management will fail to achieve desired results. Adaptive management is a structured, iterative application of science-based knowledge to reduce uncertainties and build flexibility into decision-making. However, adaptive management is more easily planned than implemented, and it is only beginning to be applied in the California’s Sacramento–San Joaquin Delta. We draw from two assessments of adaptive management in the Delta and examples of its use elsewhere to suggest how the process can be facilitated. Although a highly structured adaptive-management process may not always be needed, several elements are essential. Adaptive management should begin by clearly identifying the problem, goals, and objectives; recognizing uncertainties; identifying decision points and alternative approaches; recognizing when adjustments are needed and having the flexibility to make them; and considering societal and political constraints. Model complexity should be matched to that of the system and management needs; experiments can help unravel causal relationships. Monitoring, analyses, and syntheses require comprehensive data-management systems. More frequent and organized communications among scientists, managers, stakeholders, and decision-makers are necessary. We propose the establishment of an “Adaptive Management Team” to coordinate efforts across the management spectrum of the Delta and to provide guidance and link individual projects to shared approaches and experiences. Reliable long-term support will be needed to assess results of management actions, adjust approaches where improvement is likely, and strive toward the legislated goals of enhancing the Delta ecosystem while also providing reliable water supplies to much of California, and doing both these things in a manner that protects values of the Delta as a place where people live and work.

Ecosystems in the Sacramento–San Joaquin Delta are changing rapidly, as are ecosystems around the world. Extreme events are becoming more frequent and thresholds are likely to be crossed more often, creating greater uncertainty about future conditions. The accelerating speed of change means that ecological systems may not remain stable long enough for scientists to understand them, much less use their research findings to inform policy and management. Faced with these challenges, those involved in science, policy, and management must adapt and change and anticipate what the ecosystems may be like in the future. We highlight several ways of looking ahead—scenario analyses, horizon scanning, expert elicitation, and dynamic planning—and suggest that recent advances in distributional ecology, disturbance ecology, resilience thinking, and our increased understanding of coupled human–natural systems may provide fresh ways of thinking about more rapid change in the future. To accelerate forward-looking science, policy, and management in the Delta, we propose that the State of California create a Delta Science Visioning Process to fully and openly assess the challenges of more rapid change to science, policy, and management and propose appropriate solutions, through legislation, if needed.

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.