Applications of Paleoenvironmental Techniques in Estuarine Studies

Estuaries are, by almost any definition, variable places. Palaeoecological studies attempt to reconstruct past conditions. The validity of reconstructions is dependent on assumptions about the generality of conclusions, commonly based on a small number of samples from a limited spatial area. This Chapter summarises the main geomorphic, biogeochemical and biological processes in estuaries and provides a conceptual framework for understanding the temporal and spatial variability in factors that may affect palaeoecological evidence. We suggest that the ultimate preservation of paleo-indicators within an estuary is governed by the interaction between environmental drivers, estuarine stressors, and biogeochemical/ecological processes. We recognise that these interactions vary on temporal scales from diurnal tidal cycles to millennia, and spatially from a few square metres to whole system and latitudinal scales. We present a series of models that allow palaeoecologists to better understand the environmental context of samples collected from estuaries and make informed assessments of whether, and under what circumstances, the common assumptions may be considered valid.

Misuse of land and water resources has led to the degradation of many estuaries. As a result, present day management often focuses on developing strategies to reverse or contain these environmental impacts. However, a lack of long-term data on pre-impact conditions makes it difficult to define management goals and assess if management strategies have been, or are likely to be successful. Paleoecology is a useful tool in environmental management as it allows natural variability, pre-impact conditions, the rate, extent, direction and causes of change, and ecosystem responses to remediation and restoration attempts to be assessed. Paleoecological techniques have improved markedly during recent decades, particularly with regard to methodological advances, which allow studies to be tailored to estuarine management programs. What remains is for contemporary management approaches to consider the lessons available from historical change documented through paleoecology. This chapter outlines ways in which paleoecological approaches may be applied to estuarine management and the considerations for their integration into direct management outcomes.

In this chapter a range of sediment sampling techniques specifically suited to estuarine conditions are briefly described and discussed. Advice is provided about the selection of appropriate coring sites and techniques for a variety of conditions, including water depth, varying sediment composition, and sample analytical requirements. In the section on experimental design we briefly consider issues to do with sample replication from both a biological and geological perspective. During coring, alterations are inevitably made to the texture of the sediment, including compaction and water loss, resulting in changes to bulk density and the structure of the pore spaces, and physical disruption to layering. We comment on the nature of some of these disturbances, their dependency on sediment composition, which techniques to choose to minimise occurrence and, if necessary, how and when to make measurements to determine the amount of change caused by coring. Several factors need to be considered during the core recovery phase to ensure optimal retrieval of the core. These include use of core catchers and plugs to minimise or prevent loss of sediment during recovery. Freeze coring is recommended where the sediment-water interface is poorly defined or the sediments are particularly watery. Finally, we discuss transport and initial storage of cores.

Estuarine environments potentially provide excellent geological archives and the two radioactive isotopes ²¹⁰Pb and ¹³⁷Cs can be used to date the most recent past, under ideal circumstances as far back as 120–150 years. However, some obvious (and some less obvious) requirements need to be fulfilled for the dating-methods to be applicable and estuaries are often challenging environments in this respect. This chapter discusses some of the most common problems and includes suggestions on prudent approaches which should be considered when evaluating the applicability of the two dating methods and when calculating chronologies. The problems include among others sediment mixing, grain size affinity, post depositional mixing and choice of dating model. The discussion is illustrated with examples from tidal flat, salt marsh and fjord sediments from temperate settings but the problems are universal and should be equally relevant for estuarine settings in other climatic zones.

Radiocarbon (¹⁴C) is a radioactive cosmogenic isotope continuously produced in the upper atmosphere where it rapidly oxidises to ¹⁴CO₂. As ¹⁴CO₂, ¹⁴C enters the global carbon cycle and is incorporated into living organisms which can be radiocarbon dated following death. Radiocarbon is among the most common radiometric methods used to provide age estimates some 40–50,000 years back in time. Here, a review of the radiocarbon method covering commonly encountered problems in estuarine environments is given. Emphasis will be on methodological procedures concerning how to estimate the ¹⁴C reservoir age in these environments, including how reliably error estimates can be calculated. Subsequently, three case studies are presented, providing a short overview of investigations of ¹⁴C reservoir age variability in estuarine environments.

Estuarine sediments provide a valuable record of changing environmental conditions over time, although deciphering this record can be confounded by dramatic changes in sediment deposition and resuspension, and the effects of bioturbation and microbial degradation. Lipid biomarkers are commonly abundant in estuarine sediments and can provide valuable information on the sources of organic matter and how it is degraded and recycled. Terrestrial organic matter usually predominates and it is mostly derived from transport and deposition of soil-derived material. Biomarkers for this soil-derived organic material include long-chain n-alkanes, n-alkanols, n-alkan-2-ones, triterpenoids and constituents of cutin and suberin including fatty acids, ω-hydroxy fatty acids and α,ω-dicarboxylic acids (originally present as esters), and cell wall constituents including sterols and triterpenoids and lastly glycerol dialkyl glycerol tetraethers (GDGTs). Aquatic organic matter is typically characterized by high abundances of sterols, fatty acids and GDGTs, and variable amounts of specific algal markers including long-chain C₃₇ –C₄₀ alkenones, C₂₈–C₃₂ alkyl diols, C₂₀, C₂₅ and C₃₀ highly branched isoprenoid alkenes, chlorophylls and carotenoids. This chapter reviews the application of these various compounds as source-specific biomarkers and investigates the range of degradation reactions that need to be considered when using them as quantitative markers for organic matter inputs.

The sediments that are preserved in estuarine environments (saltmarsh, riverine estuaries, mangrove habitats, lagoons, isolation basins and fjords) contain organic matter that allows investigation of the provenance of that material. These data can then be used specifically to investigate past sea level/land level changes and changes in freshwater flux. Where microfossils are poorly preserved or absent, C/N and δ¹³C analyses offer an alternative method to deduce environmental histories, but they are especially useful when used in conjunction with a range of other proxies, and when local modern end-member organic variables can be measured to ‘calibrate’ the sedimentary C/N and δ¹³C. There are a wide range of C/N-δ¹³C based carbon studies, here we describe examples of studies in a variety of estuarine environments.

Understanding the history of contamination at a site may provide useful information to interpret past conditions. While organic compounds, such as pesticides, may behave quite differently in the environment compared to inorganic substances, such as metals, one common feature is that for different reasons, sediments often act as a common sink. In this sense sites with a history of deposition and little reworking are of interest to both the palaeo-environmental scientists and pollution scientists. Estuaries are often areas of significant deposition and are attractive to the historical study of anthropogenic inputs, however, sediments are also subject to a wide range of physicochemical conditions (from fresh to marine water) that fluctuate both in space and time. Changing water and sediment geochemistry influences metal binding capacity and flocculation of fine particles and for these reasons estuaries are challenging for the pollution scientist. However, methods of sediment characterization, sample preparation, and analysis have been developed over time to help understand the geochemistry that influences sources and sinks of contaminants, and their pathways through the environment. This chapter provides an extensive review of sediment contaminant characterization, including the sources, pathways and fate of contaminants in estuaries. It details analytical procedures and explores considerations when interpreting results. It has a focus on Australian estuaries but is relevant to estuaries around the world. The main aims of this review were to provide multidisciplinary researchers with a tool to further their inquiry and to encourage further studies of pollution/contamination in estuaries.

Diatoms are valuable paleo-indicators of natural processes and environmental changes caused by human activities in estuaries. They have been used to study sea level change, climate variability, floods and tsunamis, problems associated with changes in salinity and nutrients due to human activities, and to assess ecosystem responses to remediation, among others. There are many challenges such as issues of sediment disturbance and frustule preservation, as well as limitations on the development of transfer functions due to a lack of analogue sites. However, the application of diatoms to paleo-studies in a range of coastal habitats has enabled reliable and informative qualitative and quantitative reconstructions of environmental change. This chapter provides an overview of diatom estuarine ecology, different applications of diatoms to estuarine paleoecological research, their potential yet often informative limitations, and challenges going forward.

Dinoflagellates are important components of marine plankton as both primary producers and predators on bacteria and microeukaryotes. About 200 species, most of these estuarine, form a resting stage, called a cyst, as part of their life-cycle. Dinoflagellate cysts are mostly organic, composed of a very resistant material called dinosporin, and are often very well preserved in sediments. Dinoflagellate cysts have in many cases provided excellent records of changes through time in salinity, temperature and nutrients, and have also been used to reconstruct changes in sea ice cover, industrial pollution and coastal proximity through time. These environmental changes can be reconstructed from: (1) changes in dinoflagellate cyst communities; (2) changes in abundance; and (3) morphological variations in individual species. The two main methods for concentrating dinoflagellate cysts from sediment samples are palynological processing with HCl and HF, and density separation. As dinoflagellate cysts are mostly organic, they may be preserved where microfossils composed of silica or calcium carbonate are missing because of dissolution.

Estuarine settings consist of several sub-environments, each of which can be characterized by various groups of microfossils: this chapter focuses on foraminifera, testate amoebae and tintinnids. These groups of protists occur in high abundance and are present through the geological record. Thus, the remains of these protists, when preserved within estuarine sediments, can be used in palaeoenvironmental reconstructions of e.g. sea-level, post-glacial history, monitoring current pollution or investigating recovery from pollution following remediation. Here we describe these microfossil groups, introduce applications and present selected case studies.

Ostracods are microscopic, aquatic Crustacea with calcareous carapaces and are common components of estuarine ecosystems. The valves of ostracods are commonly preserved in sediment and thus can be very useful for reconstruction of palaeoenvironmental conditions. Utilising a combination of assemblage composition, ecophenotypy, taphonomy and shell chemistry (stable isotope and trace element), a great deal can be determined about estuarine formation and evolution, such as past salinity, water temperature, hydrochemistry, substrate characteristics and nutrient availability. Here, I provide an overview of how ostracods can be utilised in palaeo-studies of estuaries with examples that include hydrodynamic change, sea-level and climate variability, and the impact of pollution.

Molluscs possess a number of attributes that make them an excellent source of past environmental conditions in estuaries: they are common in estuarine environments; they typically have hard shells and are usually well preserved in sediments; they are relatively easy to detect in the environment; they have limited mobility as adults; they grow by incremental addition of layers to their shells; and they are found in all the major environments surrounding estuaries—terrestrial, freshwater, brackish, and marine waters. Analysis of molluscan assemblages can contribute information about past changes in sea level, climate, land use patterns, anthropogenic alterations, salinity, and other parameters of the benthic habitat and water chemistry within the estuary. High-resolution (from less than a day to annual) records of changes in environmental parameters can be obtained by analyzing the incremental growth layers in mollusc shells (sclerochronology). The shell layers retain information on changes in water temperature, salinity, seasonality, climate, river discharge, productivity, pollution and human activity. Isotopic analyses of mollusc shell growth layers can be problematic in estuaries where water temperatures and isotopic ratios can vary simultaneously; however, methods are being developed to overcome these problems. In addition to sclerochronology, molluscs are important to Holocene and Pleistocene estuarine palaeoenvironmental studies because of their use in the development of age models through radiocarbon dating, amino acid racemization, uranium-thorium series dating, and electron spin resonance (ESR) dating.

Corals represent a vast and detailed archive of past environmental changes in regions where instrumental data are limited and where our knowledge of multi-decadal climate variability is incomplete. In estuarine areas, coral skeletal records provide an opportunity to monitor anthropogenic impacts as well as to investigate natural environmental variability through a range of time scales, from seasonal to millennial. This paper analyzes the status of the field of coral sclerochronology (layer analysis) and geochemistry as it relates to the recovery of past records of environmental variability in estuarine settings. Coral biology, density band formation, and factors affecting the uptake of isotopic and elemental signals in the coral skeleton are explored, as they constitute important aspects in understanding corals as environmental proxies. Density bands in coral skeletons, commonly used for first-order dating, are a reliable proxy for long-term seasonal variability and to identify periods of environmental stress. The stable isotopic composition of coral carbonate has been employed to reconstruct sea-surface temperatures and salinities (δ¹⁸O), insolation changes (δ¹³C), pH variability (δ¹¹B), and water quality (δ¹⁵N), while changes in the elemental composition of corals constitute robust proxies for sea surface temperature (Sr/Ca) and riverine discharge (Ba/Ca). Additionally, changes in the trace concentration of metals, such as Pb, Cd, Al, Mn and Zn, have been used to monitor pollutants entering estuaries from urban areas and to reconstruct past changes in water quality. However, there is still controversy about the degree to which biological parameters such as metabolism and calcification rate influence the final isotopic and elemental composition of the coral lattice. As a result, a multi-proxy approach to coral-based paleoclimatology has emerged, both from the need to better understand the influences controlling coral environmental records and from recent advances in the analytical techniques for measuring the composition of coral skeletons.

Aquatic plants are critical components of estuarine ecosystems supporting biodiversity and a range of ecosystem services such as sediment stabilisation and denitrification. However, estuarine plants, similar to their freshwater counterparts, are in decline and under threat. The examination of remains of aquatic plants in sediment records can document the fate of the plants themselves, along with numerous natural and anthropogenic changes in estuaries, including those associated with relative sea level change, pollution and habitat degradation. In comparison with other proxies, the use of macrofossils in estuaries is in its relative infancy. However, many approaches to the examination of plant macrofossils in estuaries can be utilised from the freshwater domain where a number of advances have been made, particularly in the past decade.

Pollen and spores have an outer covering that is resistant to decay in anaerobic estuarine sediment, and their morphological and textural features, such as shape, size, aperture type and ornamentation, enable microscopic identification. Pollen analysis compares assemblages of pollen and spores in stratigraphic cores relative to the modern environment to reconstruct vegetation assemblages of past environments. Stratigraphic cores from estuarine deposits provide time-depth sequences of sediment samples, and the laboratory procedure in pollen analysis involves concentration of the pollen and spores. Microscopic examination allows identification, although it is difficult or impossible to distinguish between some genera and species, and down-core assemblages can be interpreted by comparison with those found in surface sediment samples and local and regional community structures of vegetation. Both relative abundance, and absolute concentration, are used to interpret the palaeo environment. Records have shown vegetation changes to be controlled by relative sea level change, and estuarine evolution such as progradation, infill, shoreline retreat, and by human influences. Estuarine sediments with high mixing and inorganic sediment content generally yield poorer pollen analysis records relative to estuarine sediments with an undisturbed time/depth sequence of stratigraphy and with limited reworking. Lower energy zones in central areas of wave and tide dominated estuaries have proven to be most useful for palaeo-environmental reconstruction by pollen analysis.

Modern estuaries owe their origin to post-glacial, eustatic sea level rise of the order of 120–130 m. Superimposed on this global effect are local or regional factors which need to be established for each study location, such as many Southern Hemisphere locations have shown a highstand and then a regressive stage. In the last century, sea level has been rising on many coastlines around the world, and where local or regional tectonic and/or glacio-isostatic influences prevail, relative sea level varies from global trends. The sedimentary evidence of these changes varies according to the processes dominant within an individual estuary, whether wave, tide or river dominant, or a mixture. There are two parts to sea-level reconstruction, first, determining index points to define a local sea level curve, and second, interpreting the causes of these. Sea level index points use indicators of some feature, erosional or depositional, abiotic or biotic, that formed during a period when it was under the influence of intertidal processes, and which can be dated. Quantitative transfer function approaches to achieving sea level reconstructions from estuarine deposits are shown using a case study from eastern Tasmania. Here, foraminiferal occurrences across the present intertidal marsh surface can be used to define former sea level positions in sediment cores at depth. These can be dated to provide a sea level envelope that can verify isostatic modelling results. In turn these can improve planning for future sea level change by incorporating local relative sea level trends into global projections.

Sediments provide one of the best reservoirs of information of how aquatic ecosystems have been altered by natural (climate change) and human agents over time. This information is preserved in a variety of biogenic materials including macro- and microfossils, pollen and chemical proxies, which record ecological responses to past perturbations. Chesapeake Bay, the largest estuary in the United States, is particularly well-suited to paleoenvironmental studies due to high rates of sediment accumulation, good preservation potential and historical records that can be used to corroborate evidence of change over the past several centuries. Previous paleoecological studies in Chesapeake Bay have examined how climate change and human activities have modified vegetation, species composition, sediment supply and carbon delivery over time. In this chapter, we review a variety of paleoecological approaches that have been employed to understand how the Bay ecosystem has changed over time. These proxies include microfossils (benthic foraminifera and ostracods), pollen and seeds, chemical fingerprints (stable isotopes, lipid biomarker compounds and black carbon), and mollusk shells preserved in sediment core records.

We aimed to reconstruct the changes in salinity on the inner continental shelf adjacent to the Río de la Plata estuary (RdlP) over the past 1200 years. A 10-m-long sediment core was retrieved from the RdlP-mud-depocenter, and was analyzed for diatoms and TC, TN, δ¹³C, δ¹⁵N. The results showed a constant high sedimentation rate of 8 mm per year⁻¹. We identified four zones (Z1–Z4 from oldest to youngest), which contained different diatom assemblages. The basal section (1005 cm) contains only freshwater species (Aulacoseira and Stephanodiscus) indicating permanent freshwater conditions. Z1 and Z2 (1200–500 cal years BP) are dominated by marine species (Coscinodiscus radiatus, Thalassiosira eccentrica and T. oestrupii var. venrickae), suggesting marine conditions. Z3 (500–80 cal years BP) contains mostly freshwater taxa (Aulacoseira and Eunotia), implying an influence of freshwater discharge from RdlP. Z4 (since 1930 AD) indicates more estuarine conditions, as revealed by higher abundance of marine and marine-brackish species (Cyclotella and Actinocyclus). We concluded that changes in climatic forcing were the main factors determining variations in salinity. A weak El Niño/La Niña Southern Oscillation (ENSO) activity and a northerly wind system during the Medieval Warm Period would probably have transported Brazilian waters into the Uruguayan coastal system. In contrast, stronger ENSO activity and the establishment of a southerly wind system during the Little Ice Age would have displaced the RdlP low salinity plume towards the north. Biological and geochemical proxies suggest a human influence over the past 80 years, most probably via changes in nutrient input and catchment modification.

Paleoecological analyses of biotic assemblages from cores collected throughout south Florida’s estuaries indicate gradually increasing salinities over approximately the last 2000 years, consistent with rising sea level. Around the beginning of the twentieth century these gradual patterns of change began to shift, corresponding to the beginning of human alteration of the environment via canal construction, railroad construction and other land use changes. Between 1950 and 1960, at a time of significant construction of water management structures another distinctive shift in the biological assemblages occurred. Analysis of the assemblages provides essential information on long-term patterns of change in the estuaries and provides a basis for predicting future trajectories of change. Paleosalinity estimates derived from the cores are providing input to linear regression models to determine related freshwater flow into the estuaries of south Florida. These analyses are being used to help establish performance measures and targets for the Comprehensive Everglades Restoration, established following an Act of Congress in 2000. Restoration of south Florida’s ecosystems is slated to be a 30–50 year effort that will require detailed knowledge of past decadal to centennial-scale changes in climate, freshwater flow and salinity. This historical perspective provides information that allows land managers to set realistic and sustainable goals for restoration, and provides insight into the potential response of south Florida’s ecosystem to various future scenarios of global change.

The past of the Baltic Sea has been intensively investigated using a wealth of techniques. By far the largest number of studies has focused on sea level and salinity changes, driven by global climate and isostatic crustal rebound after the Baltic Sea emerged underneath the Weichselian Ice Sheet ca. 15,000 cal. years BP. The post-glacial history of the Baltic has included both freshwater and brackish water stages depending on the connection of the Baltic Sea with the world’s oceans. As the Baltic is one of the most polluted sea areas in the world, many studies have also focused on both the long-term trends in nutrients and productivity and the relatively recent anthropogenic eutrophication. The long-term changes in the trophic state of the Baltic Sea have been found to be linked to changes in climate, which controls freshwater discharge from the catchment and weathering rates, as well as marine water inflow from the North Sea. The productivity of the Baltic Sea has followed major climate patterns: it was high during warm periods and lower during phases of deteriorating climate. Recent eutrophication of the Baltic Sea can mainly be explained by a marked increase in discharge of nutrients caused by a growing population and changes in the agricultural practice, although long-term climate variability also plays a part. Signs of recovery have recently been detected, however, the Baltic Sea is still far from its pre-industrial trophic state.