Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 138-166).

Thesis (Ph. D.)--Université de Nantes, 1970. / On cover: "Travaux du Laboratoire de geologie marine, Faculté des sciences de Nantes, 1970." At head of title: N ̊C.N.R.S.A.O. 48-52. Includes bibliographical references (p. 107-122).

Thesis (Ph.D.)--Aberdeen University, 2009. / Title from web page (viewed on Mar. 3, 2010). Includes bibliographical references.

Accurate sediment flux histories are critical data for deciphering the relative importance of climate and land use factors such as logging and road construction on sediment production and deposition. We use 210Pb activities derived from sediment cores taken on the tidal flats of the South Slough of the Coos Bay estuary to establish temporal variations in sediment accumulation rates. We determined that average deposition varied between 0.4 and 0.81 cm/yr based on two ~80 cm sediment cores. Sedimentation accumulation rates approached 2.1 cm/yr during the 1960s when a rainfall event of extreme intensity coincided with vigorous timber activity. Following this peak, a >40% reduction in peak lumber harvests in the latter part of the 20th century was accompanied by a decrease in sedimentation rates. Mean monthly rainfall during the same time period remained seasonably constant, indicating that land use is likely the key factor governing variations in sediment accumulation.

This dissertation addresses the relationship between large-scale dam removal and the nearshore ecosystem function for fish. The work is based on almost a decade’s worth of collaborative field work in the nearshore of the largest dam removal in the world recently completed on the Elwha River. The data analyzed span seven years prior to, during, and throughout the first year of each dam removal (January 2008 to November 2015). As of September 2015, approximately 2.6 million m3 of sediment material increased the area of the Elwha delta to over 150 ha. Long term study of fish in the estuary reveals fish community response to dam removal, and indicates likely interactions in the nearshore between hatchery and wild fish, including chum salmon critical to watershed recovery. Continued hatchery releases may therefore further challenge chum salmon recovery, and this interaction should be considered when planning for future watershed recovery. Community analysis revealed that, while species richness and taxonomic diversity do not appear to have a significant response to dam removal, functional diversity in the nearshore does respond significantly to dam removal. Three main shifts occurred in the nearshore: large scale and rapid creation of estuary habitats; delivery of large amounts of sediment to the delta/estuary in a short period of time, and; a shift in original habitats from tidally influenced to non-tidally influenced habitats resulted in changes in estuary function. Changes in functional diversity occur disproportionately in the new sites, which have more unstable, and so less resilient, communities. Functional diversity in the original estuary sites appears to be more resilient than in the newly created sites due to the large-scale environmental disruption that, ironically, created the new sites. However, the functional diversity at the original sites may be defined in part by management activities, including hatcheries that could mute/mask/inhibit other community responses. Further, functional diversity at the newly formed nearshore areas is predicted to stabilize as the habitats are vegetated and mature. Principal components analysis of Elwha fish community over the course of this study reveals that the fish communities of the Elwha are predictably grouped, indicating that while a few new species are observed, dam removal has not resulted in observable disruptions in fish community assemblages. And finally, nearshore habitats are critical for many forage fish species, and an emerging topic for large-scale dam removals. Forage fish spawning response to dam removal appears to be complex and may be related to multiple factors including high interannual variability in physical habitat conditions, geographic factors and complex life histories of forage fish. Habitat suitability for forage fish spawning should increase as restored ecosystem processes and newly created habitats mature and stabilize, indicating that time may be an important factor in nearshore restoration for forage fish spawning. It is therefore important to implement long-term monitoring and incorporate nearshore ecosystem process and function for multiple life history stages of nearshore species, including forage fish, into large-scale dam removal restoration and management planning. / Graduate / 2019-04-12

The quality of water within an estuary is inseparable from the component parts; suspended particulate matter (SPM) and the balance of macro-nutrients. Long-term temporal variations and the horizontal advection of both SPM and macro-nutrient concentrations are well-constrained, but the vertical fluxes associated with micro-scale processes, such as turbulence and flocculation, are poorly constrained. The importance of three micro-scale processes on the interactions between SPM and inorganic macro-nutrients, nitrate (NO–3 ), ammonium (NH+4) and phosphate (PO3 –4 ), are examined in four field campaigns and five laboratory experiments. Field campaigns were conducted in two turbid estuaries. One field campaign was conducted in the Seine estuary, France, and three campaigns in the Tamar estuary, U.K., in order to consider the effects of seasonal variations (spring, summer and autumn). Physical conditions measured included current velocity, turbidity, turbulence and particle size, were recorded using a suite of oceanographic instrumentation. Five different laboratory studies were conducted using the same mini annular flume, with different background conditions. Inorganic macro-nutrients were measured spectrophotometrically on a continuous flow analyser (for NO – 3 and PO3 –4) and fluorimetry (NH +4). Three hypotheses are presented as potential mechanisms controlling the release and uptake of macro-nutrients from sediments. Mechanism One (M1) described an exchange process between inorganic macro-nutrients and flocculation/disaggregating particles. It was hypothesised that flocculating particles would decrease water column macro-nutrient concentrations, and vice versa. In this study, flocculation was observed in both field sites, but there was no significant relationship between flocculation and macro-nutrient concentration. Similarly, the five laboratory studies demonstrated no statistically significant relationships between flocculation and macro-nutrient concentrations. Mechanism Two (M2) hypothesised that turbulence would enhance the release portion of the exchange processes described in M1. Furthermore, it was proposed that increased turbulence would break bonds between macro-nutrients and the surface of particle faces. Turbulence was observed to limit the floc size in all experiments (both field and laboratory), but this study determined that it did not promote a significant release mechanism for inorganic macro-nutrients. However, this study observed that turbulence played a key role in the vertical distribution of PO 3 – 4 and NH +4. In both the Seine and Tamar estuaries, surface and near-bed concentrations were observed to be statistically significantly different (p = < 0.05). Finally, Mechanism Three (M3) hypothesised that increased salinity provides additional salt water cations that would enhance flocculation and M1. This study measured an increase in floc size with increasing salinity in but did not enhance the proposed M1. Instead, as with turbulence, differences in water density as a result of the salinity affected the vertical distribution of NO –3. This research concluded that micro-scale processes have no significant impact on the water-column concentration of inorganic macronutrients. Instead, it was observed that two of the three micro-scale processes, turbulence and salinity, play a key role in the vertical distribution of inorganic macro-nutrients in the Tamar and Seine estuaries.

Adaptive water resource management requires sound scientific based decisions, emanating from robust scientific data. The Department of Environmental Affairs are mandated for collaborative management of the South African coast, including estuaries, through the Integrated Coastal Management Act (Act no 24 of 2008) (ICMA). The Department Water and Sanitation is mandated through the National Water Act (Act no 36 of 1998) (NWA) to design, test and implement monitoring programmes to provide water resource data. Extensive freshwater monitoring programmes exist in South Africa but there is no standard long-term monitoring programme for estuaries. This study designed and tested a National Estuarine Monitoring Programme (NESMP) that is anchored in the NWA and the ICMA. The design was based on a review of international estuary monitoring programmes, consultation with relevant role players and five decades experience in the design, testing and implementation of water resource monitoring programmes by DWS. The main objective of this thesis is 1) to design a national estuarine monitoring programme 2) test the design of the programme for practical implementation by reflecting on collected data from case studies, and 3) design a Decision Support System to translate complex monitoring data into management information. The main objective of the NESMP is 1) to collect long-term data to determine trends in the condition of estuaries in South Africa and 2) to provide management orientated information for effective estuary management. The National Estuary Monitoring programme consists of three tiers. Tier 1 focuses on basic data including system variables and nutrient data. Tier 2 collects data required for the determination of the Ecological Water Requirements (EWR) of estuaries in accordance with a standardised method used by DWS. A tailor made monitoring programme addressing specific issues including pollution incidents and localised development pressure, making use of a combination of Tier 1 and Tier 2 components, forms Tier 3 of the NESMP. This study tested the Tier 1 components of the programme on 28 estuaries across the South African coast since 2012. However, due to space constraints, the data reflected on in this thesis, is only for case studies on the Berg and Breede estuaries between 2012 and 2016. The results indicate that the establishment and operation of the NESMP on South African estuaries making use of monthly surveys, and the deployment of permanent water quality loggers, in line with the proposed protocol, are possible. This does however require collaboration with other role players in order to share responsibility and associated resources. A tiered management structure ensures national, regional and local level implementation takes place seamlessly. A decision support system (DSS) was also designed as part of this thesis to assist with data interpretation and the creation of management orientated information. This DSS includes a measurement of the percentage exceedance of the Threshold of Potential Concern (TPC), which acts as an early warning system for water resource deterioration. This study showed that effective collaboration will ensure the sustainability of the NESMP. Implementation of the more complex and resource intensive Tier 2 and Tier 3 sampling will however need to be investigated to establish the overall success of the NESMP.

The Sundays Estuary is permanently open to the sea and has been described as channel-like along its entire length with a narrow intertidal area (mostly less than 5 - 6 m in width). The estuary experiences regular freshwater inflow with large supplies of nutrients, derived from the Orange River transfer scheme and agricultural return flow. In particular, nitrate concentrations are high as a result of fertilisers used in the Sundays River catchment area. The objectives of this study were to measure microalgal biomass and community composition and relate to flow, water quality and other environmental variables. Surveys in August 2006, March 2007, February, June and August 2008 showed that salinity less than 10 percent mostly occurred from 12.5 km from the mouth and this was also where the highest water column chlorophyll a (>20 μg l-1) was found. Different groups of microalgae formed phytoplankton blooms for the different sampling sessions, which were correlated with high chlorophyll a. These included blooms of green algae (August 2006), flagellates (March 2007), dinoflagellates (June 2008) and diatom species (February and August 2008). The dominant diatom (Cyclotella atomus) indicated nutrient-rich conditions. Green algae and diatoms were associated with low salinity water in the upper reaches of the estuary. Flagellates were dominant throughout the estuary particularly when nutrients were low, whereas the dinoflagellate bloom in June 2008 was correlated with high ammonium and pH. Maximum benthic chlorophyll a was found at 12.5 km from the mouth in February, June and August 2008 and was correlated with high sediment organic and moisture content. Benthic diatoms were associated with high temperature whereas some species in June 2008 were associated with high ammonium concentrations. The middle reaches of the estuary characterise a zone of deposition rather than suspension which would favour benthic diatom colonization. Phytoplankton cells settling out on the sediments may account for the high benthic chlorophyll a because maximum water column chlorophyll a was also found in the REI zone (where salinity is less than 10 percent and where high biological activity occurs) in the Sundays Estuary. The estuary was sampled over five consecutive weeks from March to April 2009 to identify environmental factors that support different microalgal bloom species. Phytoplankton blooms, defined as chlorophyll a greater than 20 μg l-1, were found during Weeks 1, 4 and 5 from the middle to the upper reaches of the estuary. Diatom species (Cylindrotheca closterium, Cyclotella atomus and Cyclostephanus dubius) occurred in bloom concentrations during these weeks. These diatom species are cosmopolitan and indicate brackish nutrient-rich water. Flagellates were the dominant group in Weeks 2 to 4, but positive correlations with chlorophyll a were found during Weeks 1 and 2. During the first week of this study the conditions were warm and calm (measured as temperature and wind speed) and there was a well developed bloom (38 μg l-1). There was a strong cold front from 17 to 19 March, which mixed the water column resulting in the decrease of the chlorophyll a levels (<20 μg l-1) and the bloom collapsed during Weeks 2 and 3. However, in Weeks 4 and 5 conditions were again calm and warmer, which appeared to stimulate the phytoplankton bloom. Nanoplankton (2.7 - 20 μm) was dominant during each week sampled and contributed a considerable amount (55 - 79 percent) to the phytoplankton biomass. Once again subtidal benthic chlorophyll a and water column chlorophyll a were highest 12.5 km from the mouth. Deposition of phytoplankton cells from the water column was evident in the benthic samples. The study showed that the Sundays Estuary is eutrophic and characterised by microalgal blooms consisting of different phytoplankton groups.

The Fraser Estuary was investigated five times under varying flow regimes. The surface distribution of dissolved manganese consistently exhibited a maximum value at a salinity ranging from 4 to 12 ppt. Experimental results and field data suggest this peak does not result from the desorption nor dissolution of riverborne suspended particulate manganese. The excess metal is derived from the estuarine bottom sediments. Desorption or dissolution of manganese from the estuarine bottom sediments resuspended due to the advancing salt wedge enhances the dissolved manganese concentration in the bottom waters, especially in the toe of the salt wedge. This manganese enrichment may also be influenced to a lesser extent by the concurrent release of some interstitial water with enriched dissolved manganese concentrations due to the in situ reduction of amorphous manganese oxides. The subsequent entrainment and mixing of water from the toe of the salt wedge into the outflowing river water causes a downstream increase in the dissolved manganese content, and eventually determines the peak manganese concentration and salinity. Further downstream mixing with saline waters having relatively low manganese levels causes surface concentrations to decrease. Thus, the dissolved manganese distribution can be explained in terms of two conservative dilution curves which intersect at the manganese peak. The dissolved oxygen generally behaves conservatively in both the surface and bottom waters of the Fraser Estuary. The removal of alkalinity may occur at low salinity, however, alkalinity exhibits conservative behaviour through most of the salinity range. The surface distribution of pH can be replicated theoretically only when mixing in the surface is considered as a two step process. The alkalinity behaves conservatively in the surface waters of the Strait of Georgia. The pH and dissolved oxygen display seasonal variations related to primary productivity and mixing processes. The distribution of dissolved manganese in surface waters of the Strait of Georgia is determined mainly by the dilution of Fraser River water. Bottom waters have enhanced dissolved manganese concentrations due to reductive remobi1ization of manganese from the sediments. Concentrations of dissolved manganese at mid-depths are determined by seasonal variations in the stability of the water column. Depth profiles of suspended particulate manganese indicate increasing concentrations with depth. This may result from the oxidative precipitation of manganese and/or the resuspension of bottom sediments. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Recent evidence indicates that some of California’s coastal estuaries are contaminated with the chemical 4-nonylphenol (4-NP). Tissue burdens of 4-NP detected in the intertidal arrow goby (Clevelandia ios) in California are among the highest recorded worldwide, however, it remains unknown whether these fish are impacted by this 4-NP contamination. 4-NP is an established endocrine disrupting compound with estrogenic properties that can alter reproductive function. Furthermore, evidence that estrogens can modulate iono- and osmo-regulatory function in fishes implies that estuarine fishes exposed to 4-NP may also experience an impaired ability to maintain hydromineral balance. In Chapter 1 of this research, the time course of detectable xenoestrogen biomarker responses including gene transcripts encoding vitellogenins (vtgA and vtgC), choriogenins (chgL and chgHm), and estrogen receptors esr1 and esr2a were examined using quantitative real-time reverse transcription PCR (qRT-PCR) in adult male arrow gobies exposed to either 4-NP or E2. Specifically, adult gobies were treated with 4-NP at 10 μg/L (low 4-NP dose), or 4-NP at 100 μg/L (high 4-NP dose), ethanol vehicle (negative control), or 17β-estradiol (E2) at 50 ng/L (positive control) for 21 days. This 21 day exposure period was following by a 21 day depuration period to assess the time pattern of biomarker recovery. Results from these experiments indicated that 4-NP can induce increases in relative mRNA levels encoding vitellogenins, choriogenins, and estrogen receptor esr1 – but not esr2a – in the liver within 72 hrs, and that these transcriptional changes return to pre-exposure levels within 12 days of the termination of 4-NP or E2 exposure. In sum, these findings validate the use of mRNA levels for several estrogen-responsive genes as accurate biomarkers for short-term 4-NP exposure in the arrow goby. In Chapter 2, I evaluated the effects of 4-NP and E2 exposures on the osmoregulatory ability of C. ios. I exposed adult arrow gobies to 4-NP (10 μg/L or 100 μg/L) or E2 (50 ng/L) for 14 days, and then transferred the fish from a 33 ppt salinity (control) environment to either 20 ppt, or 5 ppt conditions. Whole body water content was then measured, and the relative mRNA levels for the ion channels Na+/K+/2Cl--cotransporter1 (nkcc1) and Na+/H+ exchanger-3 (nhe3), and the aquaporin water channel aquaporin-3 (aqp3) were quantified in the gill epithelium by qRT-PCR. Results showed that fish treated with 4-NP exhibited higher whole body water content, suggesting that 4-NP exposure results in excessive water uptake during hypoosmotic challenge. 4-NP treated gobies also exhibited elevated nkcc1 and reduced nhe3 and aqp3 mRNAs in the gill even prior to transfer of fish from the 33 ppt acclimation salinity. At 6 hrs after salinity transfer, transcripts encoding nkcc1 remained elevated in the gill epithelium of 4-NP treated gobies transferred to 20 ppt or maintained at 33 ppt (salinity control), while nhe3 and aqp3 mRNAs were still less abundant in gills of these fish. These findings point to impaired maintenance of water balance in gobies exposed to 4-NP, with those changes in fluid homeostasis possibly mediated in part by changes in gill ionic regulation. Taken as a entirety, the findings provided by this research reinforces accumulating data showing the potential for 4-NP to disrupt reproductive physiology in vertebrates, and points to the possibility that 4-NP may impair the ability of fish to regulate ion and water balance under changing salinity conditions.