Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed

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 (δ 13C, 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 δ 15N 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

The nature of organic carbon in density-fractionated sediments in the Sacramento-San Joaquin River Delta (California)

Rivers are the primary means by which sediments and carbon are transported from the terrestrial biosphere to the oceans but gaps remain in our understanding of carbon associations from source to sink. Bed sediments from the Sacramento-San Joaquin River Delta (CA) were fractionated according to density and analyzed for sediment mass distribution, elemental (C and N) composition, mineral surface area, and stable carbon and radiocarbon isotope compositions of organic carbon (OC) and fatty acids to evaluate the nature of organic carbon in river sediments. OC was unevenly distributed among density fractions. Mass and OC were in general concentrated in mesodensity (1.6-2.0 and 2.0-2.5 g cm(-3)) fractions, comprising 84.0 +/- 1.3% of total sediment mass and 80.8 +/- 13.3% of total OC (TOC). Low-density (\u3c 1.6 g cm(-3)) material, although rich in OC (34.0 +/- 2.0% OC) due to woody debris, constituted only 17.3 +/- 12.8% of TOC. High-density (\u3e2.5 g cm(-3) /organic-poor, mineral-rich material made-up 13.7 +/- 1.4% of sediment mass and 2.0 +/- 0.9% of TOC. Stable carbon isotope compositions of sedimentary OC were relatively uniform across bulk and density fractions (delta C-13 27.4 +/- 0.5 parts per thousand). Radiocarbon content varied from Delta C-14 values of 382 (radiocarbon age 3800 yr BP) to C 94 parts per thousand(modern) indicating a mix of young and old OC. Fatty acids were used to further constrain the origins of sedimentary OC. Short-chain n-C-14-n-C-18 fatty acids of algal origin were depleted in 13C (delta C-13 37.5 to 35.2 parts per thousand) but were enriched in C-14 (Delta C-14 \u3e 0) compared to long-chain n-C-24-n-C-28 acids of vascular plant origins with higher delta C-13 (33.0 to 31.0 parts per thousand) but variable Delta C-14 values (180 and 61 %). These data demonstrate the potentially complex source and age distributions found within river sediments and provide insights about sediment and organic matter supply to the Delta

Organic geochemistry of particulate matter in the eastern tropical North Pacific Ocean: Implications for particle dynamics

Samples of marine particulate matter were collected in sediment traps and by in-situ filtration to depths of 1500 m during VERTEX II and III cruises in the eastern tropical North Pacific. Wax esters, triacylglycerols, fatty acids, sterols and steroidal ketones were analyzed in these samples to compare the compositions of organic matter associated with large sinking particulate aggregates sampled by sediment traps and with fine suspended material obtained by in-situ filtration. Distributions of specific compounds indicated that the organic chemical composition of large sinking particles and small suspended particles both in the euphotic zone and at mid-depth result from very distinct particle pools, not only in terms of particle size but also in their sources and transport mechanisms. Suspended particles in the epipelagic zone contain a mix of organic compounds derived from both phytoplankton and zooplankton sources, whereas sinking particles are dominated by zooplankton-derived compounds. In the mesopelagic zone, large, sinking particles contain organic compounds which are indicative of intensive alteration of organic matter, even though transport from the euphotic zone may have been rapid. On the other hand, it is the suspended particle pool which contains a remarkable abundance of labile organic compounds which can be attributed to undegraded phytoplankton cells rapidly delivered from surface waters. These organic geochemical results lead to a modified model of particle dynamics in which there are two distinct large, sinking particle pools which are differentially sampled by the two sampling techniques

Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system

We report measurements of seasonal variability in the C-N stable isotope ratios of plants collected across the habitat mosaic of San Francisco Bay, its marshes, and its tributary river system. Analyses of 868 plant samples were binned into 10 groups (e.g., terrestrial riparian, freshwater phytoplankton, salt marsh) to determine whether C-N isotopes can be used as biomarkers for tracing the origins of organic matter in this river-marsh-estuary complex. Variability of delta(130)C and delta(15)N was high (similar to5-10parts per thousand) within each plant group, and we identified three modes of variability: (1) between species and their microhabitats, (2) over annual cycles of plant growth and senescence, and (3) between living and decomposing biomass. These modes of within-group variability obscure any source-specific isotopic signatures, confounding the application of C-N isotopes for identifying the origins of organic matter. A second confounding factor was large dissimilarity between the delta(13)C-delta(15)N of primary producers and the organic-matter pools in the seston and sediments. Both confounding factors impede the application of C-N isotopes to reveal the food supply to primary consumers in ecosystems supporting diverse autotrophs and where the isotopic composition of organic matter has been transformed and become distinct from that of its parent plant sources. Our results support the advice of others: variability of C-N stable isotopes within all organic-matter pools is high and must be considered in applications of these isotopes to trace trophic linkages from primary producers to primary consumers. Isotope-based approaches are perhaps most powerful when used to complement other tools, such as molecular biomarkers, bioassays, direct measures of production, and compilations of organic-matter budgets

Bioreactivity of estuarine dissolved organic matter: A combined geochemical and microbiological approach

An integrated multidisciplinary study utilizing geochemical and microbial ecological approaches was conducted to characterize the origins, chemical nature, and quantities of dissolved and particulate organic matter (OM) utilized by heterotrophic bacteria in a temperate estuary. C: N, stable isotope (delta C-13), and lipid biomarker analyses revealed differences in the inferred reactivity of autochthonous versus allochthonous OM sources. Isotopic comparison of OM size fractions and bacterial nucleic acids suggests that high-molecular-weight dissolved OM (DOM) is consistently linked to bacterial biomass synthesis along the estuarine salinity gradient. Polyunsaturated fatty acids (as percent of total fatty acids, FA) were a reliable predictor of DOM decomposition in bioassays, thus providing an indicator directly linking DOM reactivity to its composition. Significant positive correlations between FA diagnostic of bacterial sources and lipid biomarker compounds diagnostic of planktonic origin indicate a systematic bacterial response to autochthonous DOM sources along the estuarine continuum. These findings further suggest that, although the geochemical signature of algal-derived OM in the dissolved phase may appear quantitatively insignificant, this fraction may nevertheless represent a principal source of bioreactive OM to heterotrophic bacteria in estuarine waters

Top-down and bottom-up controls on sediment organic matter composition in an experimental seagrass ecosystem

We tested the singular and interactive effects of resource availability (light) and community composition (food chain length and herbivore species richness) on eelgrass (Zostera marina) ecosystem properties and functioning with an experimental mesocosm system. Food chain length was manipulated through the presence or absence of blue crab (Callinectes sapidus) predators, whereas grazer species richness varied across three levels (zero, two, or four crustacean species). We found important and interacting effects of bottom-up and top-down forcings on sediment organic matter (SOM) composition. Light increased eelgrass and algal biomass and sediment organic carbon and nitrogen content. Increasing grazer diversity generally decreased algal biomass and ecosystem production but interacted with food chain length (i.e., presence of predatory crabs) and light. Predators generally increased algal biomass and ecosystem production through a trophic cascade, which was stronger at high grazer diversity and under ambient light. SOM composition, determined with fatty acid (FA) biomarkers, was sensitive to all manipulated variables. Increasing grazer species richness often decreased the contributions of FAs derived from plant and algal sources, whereas increasing light had the opposite effect. Food chain length was generally a less important determinant of SOM composition than light, although predators did increase FAs representative of heterotrophic bacteria. Overall, resource availability and epibenthic community composition strongly influenced organic matter cycling, SOM composition, and the bacterial community in seagrass-bed sediments

Isotopic compositions of lipid biomarker compounds in estuarine plants and surface sediments

We examined the isotopic compositions of fatty acids, sterols, and hydrocarbons isolated from three coastal macrophytes (Zostera marina, Spartina alterniflora, and Juncus roemerianus) in order to investigate the relative contribution of these vascular plants as sources of organic matter in coastal sediments such as Cape Lookout Eight, North Carolina. On average, lipid biomarker compounds extracted from the plants were depleted in C-13 by 3-5 parts per thousand relative to delta(13)C total organic carbon (TOC). However, individual compounds within each lipid class varied by up to 5.6 parts per thousand. Trends in the isotopic compositions of lipids were consistent with delta(13)C(TOC); compounds obtained from Z. marina were the most enriched in C-13 and those from J. roemerianus were the most depleted. The range in isotopic abundances and molecular compositions of the sediments was greater than that obtained from the plants, indicating that additional, presently unidentified sources of organic matter contribute to the Cape Lookout Eight sediments. Similarity between the signatures for suspended particulate matter and the sediments indicates that much of the sedimentary organic matter is derived from algal and bacterial sources. Bacterial sources of organic matter are Likely greater during summer/early fall, and incorporation of C-13-enriched bacterial biomass may contribute to observed seasonal shifts in delta(13)C(TOC) in the surficial sediments

Source-age dynamics of estuarine particulate organic matter using fatty acid delta C-13 and Delta C-14 composition

This study used a multiproxy approach to elucidate the source and age composition of estuarine particulate organic matter (POM) using bulk stable isotopes (C-13(POC)), fatty acid (FA) biomarkers, and compound specific isotopic analyses in surface waters along the Delaware River and Bay (Delaware Estuary, hereafter). C-13 values of FA (C-13(FA)) ranged more widely (-30.9 parts per thousand to -21.8 parts per thousand) than C-13(POC) (-27.5 parts per thousand to -23.5 parts per thousand), providing greater insight about POM sources along the estuary. C-13 values of C-16:0 phospholipid FA (primarily, aquatic sources) increased along the salinity gradient (-29.8 parts per thousand to -23.4 parts per thousand), while C-13(FA) values of long-chain neutral fatty acid (terrestrial sources) decreased (-28.6 parts per thousand to -30.9 parts per thousand). C-13(FA) values for C-18\u27s FA indicated the importance of marsh-derived organic matter within Delaware Estuary. Compound specific radiocarbon analysis showed the heterogeneous age structure of FA associated with POM (FA(POM)). C-14 ages of FA ranged from modern (postbomb) to 1790BP; aged FA (120BP to 1700BP) derived primarily from the watershed, whereas modern FA were produced within Delaware Estuary. C-14 ages of short-chain FA (aquatic sources) reflected differences in the age of dissolved inorganic carbon along the estuary and had older C-14 ages at the river end-member. C-14 ages of FA from terrigenous sources were older than water and sediment residence times indicating this source derived from the watershed. This study is the first to document the complex age distribution of FA(POM) along the estuarine salinity gradient and shows that inorganic carbon sources, watershed inputs and autochthonous production contribute to variation in the ages of POM

Preparing Scientists, Policy-Makers, and Managers for a Fast-Forward Future

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

Biodiversity and food web structure influence short-term accumulation of sediment organic matter in an experimental seagrass system

We tested the effects of grazer diversity and food chain length on the quantity and quality of accumulated sediment organic matter (SOM) in experimental eelgrass (Zostera marina) mesocosms. By use of a factorial manipulation of crustacean grazer species richness and predator presence, we examined the effects of epibenthic consumers on SOM composition by using stable carbon isotopes (delta C-13) and lipid biomarker compounds. Grazer species composition strongly influenced nearly all measures of SOM quantity and quality. In particular, increased densities of the grazing amphipod, Gammarus mucronatus, decreased accumulation of benthic microalgae (chlorophyll a) and the relative abundance of polyunsaturated fatty acids (FA, a proxy for labile algal organic matter) and branched FA (a proxy for bacterial biomass). On average, increasing grazer species richness decreased SOM quantity (percentage of total organic carbon). Increasing food chain length by addition of predatory blue crabs (Callinectes sapidus) resulted in a trophic cascade, increasing algal biomass and accumulation of algal organic matter in sediments, and enhancing the quality of SOM. Concomitantly, the relative proportion of bacterial branched FA increased. The identity and number of epibenthic consumers strongly influence accumulation and composition of SOM and the pathways by which it is processed, and these responses are not easily predictable from bulk measurements (delta C-13, percentage of total organic carbon) alone