Panama City Fisheries Resources Office: FY 2006 Annual Report

HIGHLIGHTS FOR FY 2006 1. Captured and tagged 475 Gulf sturgeons in five Florida rivers and one bay. 2. Documented Gulf sturgeon marine movement and habitat use in the Gulf of Mexico. 3. Assisted the National Oceanic and Atmospheric Administration (NOAA) with the collection of Gulf sturgeon, implantation of acoustic tags, and monitoring of fish in a study to examine movement patterns and habitat use in Pensacola and Choctawhatchee bays post-Hurricane Ivan. 4. Provided technical assistance to Jon “Bo” Sawyer in completing a study – Summer Resting Areas of the Gulf Sturgeon in the Conecuh/Escambia River System, Alabama-Florida – for acquiring a Degree of Master of Science at Troy University, Alabama. 5. Coordinated tagging and data collection with NOAA observers aboard trawlers while collecting Gulf sturgeon during dredging operations in the coastal Gulf of Mexico. 6. Hosted the 7th Annual Gulf Sturgeon Workshop. 7. Implemented Gulf Striped Bass Restoration Plan by coordinating the 23rd Annual Morone Workshop, leading the technical committee, transporting broodfish, coordinating the stocking on the Apalachicola-Chattahoochee-Flint (ACF) river system, and evaluating post-stocking success. 8. Continued updating and managing the Freshwater Mussel Survey Database, a Geographic Information System (GIS) database, for over 800 unique sites in the Northeast Gulf (NEG) drainages in Alabama (AL), Georgia (GA), and Florida (FL). 9. Formed a recovery implementation team for listed mussels in the ACF river basin and oversaw grant cooperative agreements for 14 listed and candidate freshwater mussels in the NEG watersheds. 10. Initiated a project in the Apalachicola River to relocate mussels stranded as a result of drought conditions, and calculate river flows at which mussels would be exposed. 11. Initiated a project in Sawhatchee Creek, Georgia to determine the status of threatened and endangered (T&E) freshwater mussels and target restoration projects, population assessments, and potential population augmentation to lead toward recovery of the listed species. 12. Initiated a study to determine the age and growth of the endangered fat threeridge mussel (Amblema neislerii). 13. Provided technical assistance to the Panama City Ecological Services office for a biological opinion on the operations of Jim Woodruff Lock and Dam and its effects on the listed species and designated and proposed critical habitat in the Apalachicola River, Florida. 14. Assisted with a multi-State, inter-agency team to develop a management plan to restore the Alabama shad in the ACF river system. 15. Conducted fishery surveys on Tyndall AFB, Florida and Ft. Benning, Georgia and completed a report with recommendations for future recreational fishery needs. 16. Provided fishery technical assistance to four National Wildlife Refuges (NWR) (i.e., Okefenokee NWR, Banks Lake NWR, St. Vincent NWR, and St. Marks NWR). 17. Initiated an Aquatic Resources and Recreation Fishing Survey on Department of Defense facilities located in Region 4. 18. Identified 130 road-stream crossings on Eglin AFB for rehabilitation and elimination of sediment imputs. 19. Continued the Aquatics Monitoring Program at Eglin AFB to assess techniques that determine current status and sustainability of aquatic habitat and develop a measure to determine quality or degradation of habitat. 20. Assisted Eglin AFB Natural Resource managers in revising the installation’s Integrated Natural Resources Management Plan (INRMP) and its associated component plans. 21. Coordinated recovery efforts for the endangered Okaloosa darter including population/life history surveys, stream restoration, and outreach activities. 22. Initiated a comprehensive status review of the Okaloosa darter with analyses performed to assess available habitat, preferred habitats, range expansions/reductions/fragmentations, population size, and probability of extinction. 23. Assisted the Gulf Coastal Plain Ecosystem Partnership and the Florida Fish and Wildlife Conservation Commission (FWC) under a Memorandum of Agreement to develop conservation strategies, implement monitoring and assessment programs, and secure funds for aquatic management programs in six watersheds in northwest Florida and southeast Alabama. 24. Entered into a cooperative agreement with the U.S. Air Force to encourage the conservation and rehabilitation of natural resources at Hurlburt Field, Florida. 25. Multiple outreach projects were completed to detail aquatic resources’ conservation needs and opportunities; including National Fishing Week, Earth Day, several festivals, and school outreach.

Panama City Fisheries Resources Office: FY 2005 Annual Report

HIGHLIGHTS FOR FY 2005 1. Assisted with a study to assess hurricane impacts to Gulf sturgeon critical foraging habitat. 2. Documented Gulf sturgeon marine movement and habitat use in the Gulf of Mexico. 3. Documented Gulf sturgeon spawning with the collection of fertilized eggs in the Apalachicola River, Florida. 4. Documented Gulf sturgeon spawning with the collection of fertilized eggs in the Yellow River, Florida. 5. Assisted with benthic invertebrate survey at Gulf sturgeon marine foraging grounds. 6. Implemented Gulf Striped Bass Restoration Plan by coordinating the 22nd Annual Morone Workshop, leading the technical committee, transporting broodfish, and coordinating the stocking on the Apalachicola-Chattahoochee-Flint (ACF) river system. 7. Over 87,000 Phase II Gulf striped bass were marked with sequential coded wire tags and stocked in the Apalachicola River. Post-stocking evaluations were conducted at 45 sites in the fall and spring and 8 thermal refuges in the summer. 8. Completed fishery surveys on 4 ponds on Eglin AFB totaling 53 acres, and completed a report with recommendations for future recreational fishery needs. 9. Completed final report for aquatic monitoring at Eglin AFB from 1999 to 2004. 10. Completed a field collection of the endangered Okaloosa darter to be incorporated into a status review to be completed in FY06. 11. Provided technical assistance to the Region 4 National Wildlife Refuge (NWR) program on changes to the fishery conservation targets for the region. Also provided technical assistance to four NWRs (i.e., Okefenokee NWR, Banks Lake NWR, St. Vincent NWR, and St. Marks NWR) relative to hurricanes and recreational fishing. 12. A draft mussel sampling protocol was tested in wadeable streams in Northwest Florida and southwest Georgia, and an associated field guide, poster, and Freshwater Mussel Survey Protocol and Identification workshop were completed in FY05. 13. Implemented recovery plan and candidate conservation actions for 14 listed and candidate freshwater mussels in the Northeast Gulf Watersheds. 14. Initiated or completed multiple stream restoration and watershed management projects. A total of 7.5 stream miles were restored for stream fishes, and 11 miles of coastline were enhanced for sea turtle lighting. A total of 630 acres of wetlands and 2,401 acres of understory habitat were restored. 15. Conducted a watershed assessment to develop a threats analysis for prioritizing restoration, protection, and enhancement to natural resources of Spring Creek, Georgia and Canoe Creek, Florida. 16. Continued the formation of an Unpaved Road Interagency Team of Federal, State, and local agencies in Northwest Florida to promote stream protection and restoration from unpaved road sediment runoff. Began the development of a technical committee agreement. 17. Conducted Alabama Unpaved Road Inventory within the Northeast Gulf Ecosystem. Data collection will be completed during FY06. 18. Finalized the development of two North Florida hydrophysiographic regional curves for use by the Florida Department of Transportation (DOT) and others involved with stream restoration and protection. Initiated the development of the Alabama Coastal Plain Riparian Reference Reach and Regional Curves for use by the Alabama Department of Environmental Management (ADEM). 19. Provided technical assistance in collecting data, analysis, and thesis formulation with Troy University, Alabama, to identify the influence of large woody debris in southeastern coastal plain streams. 20. Completed pre- and post-restoration fish community monitoring at several restoration projects including Big Escambia Creek, Magnolia Creek, and Oyster Lake, Florida. 21. Established a watershed partnership for the Chipola River in Alabama and Florida and expanded development and participation in the Spring Creek Watershed Partnership, Georgia. 22. Continued to identify barriers which inhibit the movement of aquatic species within the Northeast Gulf Ecoregion. 23. Completed a report on road crossing structures in Okaloosa darter streams to guide the closure/repair/maintenance of roads to contribute to recovery of the endangered species. In cooperation with Three Rivers RC&D Council, fish passage sites identified in the report were prioritized for restoration. 24. Monitored Aquatic Nuisance Species in the Apalachicola River and tested the sterility of exotic grass carp. 25. Multiple outreach projects were completed to detail aquatic resources conservation needs and opportunities. Participated in National Fishing Week event, several festivals, and school outreach.

Panama City Fisheries Resources Office: FY 2004 Annual Report

HIGHLIGHTS FOR FY 2004 1. Completed the second of a 3-year Gulf sturgeon population estimate on the Escambia River, Florida. 2. Completed the first of a 2-year Gulf sturgeon population estimate on the Apalachicola River, Florida. 3. Conducted Gulf sturgeon presence-absence surveys in three other Florida river systems. 4. Documented Gulf sturgeon marine habitat use in the near shore waters of the Gulf of Mexico. 5. Identified environmental threats to Gulf sturgeon spawning habitat in the Choctawhatchee River, Florida. 6. Initiated a study to document Gulf sturgeon spawning with the collection of fertilized eggs in the Yellow River, Florida. 7. Implemented Gulf Striped Bass Restoration Plan by coordinating the 21st Annual Morone Workshop, leading the technical committee, transporting broodfish, and coordinating the stocking on the Apalachicola-Chattahoochee-Flint (ACF) river system. 8. Over 86,000 Phase II Gulf striped bass were marked with sequential coded wire tags and stocked in Lake Seminole and the Apalachicola River. Post-stocking evaluations were conducted at 31 sites. 9. Drafted updates to Apalachicola-Chattahoochee-Flint Striped Bass Restoration and Evaluation Five-Year Plan with partners. 10. Fishery surveys were conducted on Tyndall Air Force Base and St. Marks and St. Vincent National Wildlife Refuges. 11. Habitat evaluations and population surveys were completed at 153 Okaloosa darter stream sites. 12. Aquatic insect biomonitoring and identification of over 39,000 individual aquatic macroinvertebrates was completed and provided to Eglin Air Force Base. 13. Ten years of fishery data from Okefenokee and Banks Lake National Wildlife Refuges was analyzed with recommendations incorporated into the refuge Comprehensive Conservation Plan. 14. A draft mussel sampling protocol was tested in wadeable streams in northwest Florida and southwest Georgia. 15. Implemented recovery plan and candidate conservation actions for 14 listed and candidate freshwater mussels in the Northeast Gulf Watersheds. 16. Worked with partners in developing the Spring Creek Watershed Partnership in the Flint River basin, Georgia. 17. Multiple stream restoration and watershed management projects were initiated or completed. A total of 6.8 stream miles were restored for stream fishes, along with 56.4 miles of coastline were enhanced for sea turtle lighting. A total of 135 acres of wetlands and 58 acres of understory habitat were restored. 18. Multiple outreach projects were completed to detail aquatic resources conservation needs and opportunities. Participated in National Fishing Week event, BASS ProShops event, several festivals, and school outreach.

Panama City Fisheries Resources Office: FY 2003 Annual Report

HIGHLIGHTS FOR FY 2003 1. Continued a 3-year threatened Gulf sturgeon population estimate in the Escambia River, Florida and conducted presence-absence surveys in 4 other Florida river systems and 1 bay. 2. Five juvenile Gulf sturgeon collected, near the mouth of the Choctawhatchee River, Florida, were equipped with sonic tags and monitored while over-wintering in Choctawhatchee Bay. 3. Continued to examine Gulf sturgeon marine habitat use. 4. Implemented Gulf Striped Bass Restoration Plan by coordinating the 20th Annual Morone Workshop, leading the technical committee, transporting broodfish, and coordinating the stocking on the Apalachicola-Chattahoochee-Flint (ACF) river system. 5. Over 73,000 Phase II Gulf striped bass were marked with sequential coded wire tags and stocked in the Apalachicola River. Post-stocking evaluations were conducted at 31 sites. 6. Three stream fisheries assessment s were completed to evaluate the fish community at sites slated for habitat restoration by the Partners for Fish and Wildlife Program (PFW). 7. PFW program identified restoration needs and opportunities for 10 areas. 8. Developed an Unpaved Road Evaluation Handbook. 9. Completed restoration of Chipola River Greenway, Seibenhener Streambank Restoration, Blackwater River State Forest, and Anderson Property. 10. Assessments for fluvial geomorphic conditions for design criteria were completed for 3 projects. 11. Geomorphology in Florida streams initiated development of Rosgen regional curves for Northwest Florida for use by the Florida Department of Transportation. 12. Developed a Memorandum of Understanding between partners for enhancing, protecting, and restoring stream, wetland, and upland habitat in northwest Florida 13. Completed aquatic fauna and fish surveys with new emphasis on integration of data from reach level into watershed and landscape scale and keeping database current. 14. Compliance based sampling of impaired waterbodies on Eglin Air Force Base in conjunction with Florida Department of Environmental Protection for Total Maximum Daily Load development support. 15. Surveyed 20 sites for the federally endangered Okaloosa darter, provided habitat descriptions, worked with partners to implement key recovery tasks and set priorities for restoration. 16. Worked with partners to develop a freshwater mussel survey protocol to provide standard operating procedures for establishing the presence/absence of federally listed mussel species within a Federal project area. 17. GIS database was created to identify all known freshwater mussel records from the northeast Gulf ecosystem. 18. Completed recovery plan for seven freshwater mussels and drafted candidate elevation package for seven additional mussels. Developed proposals to implement recovery plan. 19. Worked with Corps of Engineers and State partners to develop improved reservoir operating policies to benefit both riverine and reservoir fisheries for the ACF river system. 20. Multiple outreach projects were completed to detail aquatic resources conservation opportunities. 21. Multiple stream restoration and watershed management projects initiated or completed (see Appendix A).

Panama City Fisheries Resources Office: FY 2002 Annual Report

HIGHLIGHTS FOR FY 2002 1. United States Senator Bob Graham assisted with a Gulf sturgeon survey. 2. Completed 3-year Gulf sturgeon population study in the Choctawhatchee River drainage. 3. Completed Gulf sturgeon potential spawning habitat survey for Northwest Florida and Southeast Alabama river systems. 4. Initiated Gulf sturgeon marine habitat and food resources study. 5. Completed Gulf sturgeon sentinel fish study. 6. Coordinated and conducted tagging of over 110,000 Phase II striped bass at Welaka and Warm Springs National Fish Hatchery. 7. Completed Okefenokee National Wildlife Refuge fishery sampling. 8. Developed a manuscript regarding the fishery of Banks Lake NWR. 9. Initiated development of a fish Index of Biotic Integrity for Florida panhandle streams. 10. Coordinated Okaloosa darter workshop. 11. Continued examining insect communities on Eglin AFB. 12. Sponsored and coordinated stream restoration workshop. 13. Provided technical assistance via Partners for Fish and Wildlife for stream restoration within the Northeast Gulf Ecosystem. 14. Finalized regional curve development in the Northern Region of Florida and secured significant funds for FY03 to expand to other regions in Florida. 15. Initiated freshwater mussel conservation in the Northeastern Gulf Ecosystem.

Nutrients and biological production in lakes

This paper is a review of studies on effects of nutrients on biological productivity and efforts made so far at restoration of nutrients in lakes. It is to provide an understanding of the basis scientific process accruing in lakes, therefore of prime importance in maintaining water quality standards for propagation of effective lake management

Problems when generating virtual models representing real objects: Hondarribia walls

[EN] This paper is based in the following project:

Limited resources? Let the habitat priority planner help!

In this time of scarce resources, coastal resource managers must find ways to prioritize conservation, land use, and restoration efforts. The Habitat Priority Planner (HPP) is a free geospatial tool created by the National Oceanic and Atmospheric Administration’s Coastal Services Center that has received wide praise for its ease of use and broad applicability to conservation strategic planning, restoration, climate change scenarios, and other natural resource management actions. Not a geographic information system (GIS) user? Don’t worry―this tool was designed to be used in a team setting. One intermediate-level GIS user can push the buttons to show quick results while a roomful of resource managers and stakeholders provide input criteria that determine the results. The Habitat Priority Planner is a toolbar for ESRI’s ArcGIS platform that is composed of three modules: Habitat Classification, Habitat Analysis, and Data Explorer. The tool calculates basic ecological statistics that are used to examine how habitats function within a landscape. The tool pre‐packages several common landscape metrics into a user‐friendly interface for intermediate GIS users. In addition, HPP allows the user to build queries interactively using a graphical interface for demonstrating criteria selections quickly in a visual manner that is useful in stakeholder interactions. Tool advocates and users include land trusts, conservation alliances, nonprofit organizations, and select National Estuarine Research Reserves and refuges of the U.S. Fish and Wildlife Service. Participants in this session will learn the basic requirements for HPP use and the multiple ways the HPP has been applied to geographies nationwide. (PDF contains 5 pages)

Reforming state-level coastal management and development policies: strategic retreat as an innovative, proactive and equitable coastal environmental management strategy

Atlantic and Gulf Coast shorelines include some of the most unique and biologically rich ecosystems in the United States that provide immeasurable aesthetic, habitat and economic benefits. Natural coastal ecosystems, however, are under increasing threat from rampant and irresponsible growth and development. Once a boon to local economies, complex natural forces – enhanced by global climate change and sea level rise - are now considered hazards and eroding the very foundation upon which coastal development is based. For nearly a century, beach restoration and erosion control structures have been used to artificially stabilize shorelines in an effort to protect structures and infrastructure. Beach restoration, the import and emplacement of sand on an eroding beach, is expensive, unpredictable, inefficient and may result in long-term environmental impacts. The detrimental environmental impacts of erosion control structures such as sea walls, groins, bulkheads and revetments include sediment deficits, accelerated erosion and beach loss. These and other traditional responses to coastal erosion and storm impacts- along with archaic federal and state policies, subsidies and development incentives - are costly, encourage risky development, artificially increase property values of high-risk or environmentally sensitive properties, reduce the post-storm resilience of shorelines, damage coastal ecosystems and are becoming increasingly unsustainable. Although communities, coastal managers and property owners face increasingly complex and difficult challenges, there is an emerging public, social and political awareness that, without meaningful policy reforms, coastal ecosystems and economies are in jeopardy. Strategic retreat is a sustainable, interdisciplinary management strategy that supports the proactive, planned removal of vulnerable coastal development; reduces risk; increases shoreline resiliency and ensures long term protection of coastal systems. Public policies and management strategies that can overcome common economic misperceptions and promote the removal of vulnerable development will provide state and local policy makers and coastal managers with an effective management tool that concomitantly addresses the economic, environmental, legal and political issues along developed shorelines. (PDF contains 4 pages)

Physical circulation measurements in Pamlico Sound, used to locate new oyster sanctuaries

The population of eastern oyster, C. virginica, has declined over the last century on most areas of the east and gulf coasts. North Carolina’s restoration efforts depend on the construction of subtidal oyster reefs to be used as broodstock sanctuaries in Pamlico Sound, NC. Successful restoration of the oyster population requires several thriving reefs connected as a meta-population. C. virginica has a 2-3 week larval stage, during which it gradually settles through the water column. Larvae that can travel from one reef to another during that stage form the basis of a meta-population. (PDF contains 3 pages)

Habitat enhancing marine structures: Creating habitat in urban waters

Although maritime regions support a large portion of the world’s human population, their value as habitat for other species is overlooked. Urban structures that are built in the marine environment are not designed or managed for the habitat they provide, and are built without considering the communities of marine organisms that could colonize them (Clynick et al., 2008). However, the urban waterfront may be capable of supporting a significant proportion of regional aquatic biodiversity (Duffy-Anderson et al., 2003). While urban shorelines will never return to their original condition, some scientists think that the habitat quality of urban waterfronts could be significantly improved through further research and some design modifications, and that many opportunities exist to make these modifications (Russel et al., 1983, Goff, 2008). Habitat enhancing marine structures (or HEMS) are a potentially promising approach to address the impact of cities on marine organisms including habitat fragmentation and degradation. HEMS are a type of habitat improvement project that are ecologically engineered to improve the habitat quality of urban marine structures such as bulkheads and docks for marine organisms. More specifically, HEMS attempt to improve or enhance the physical habitat that organisms depend on for survival in the inter- and sub-tidal waterfronts of densely populated areas. HEMS projects are targeted at areas where human-made structures cannot be significantly altered or removed. While these techniques can be used in suburban or rural areas restoration or removal is preferred in these settings, and HEMS are resorted to only if removal of the human-made structure is not an option. Recent research supports the use of HEMS projects. Researchers have examined the communities found on urban structures including docks, bulkheads, and breakwaters. Complete community shifts have been observed where the natural shoreline was sandy, silty, or muddy. There is also evidence of declines in community composition, ecosystem functioning, and increases in non-native species abundances in assemblages on urban marine structures. Researchers have identified two key differences between these substrates including the slope (seawalls are vertical; rocky shores contain multiple slopes) and microhabitat availability (seawalls have very little; rocky shores contain many different types). In response, researchers have suggested designing and building seawalls with gentler slopes or a combination of horizontal and vertical surfaces. Researchers have also suggested incorporating microhabitat, including cavities designed to retain water during low tide, crevices, and other analogous features (Chapman, 2003; Moreira et al., 2006) (PDF contains 4 pages)

San Francisco Bay regional sediment management strategy development

The San Francisco Bay Conservation and Development Commission (BCDC), in continued partnership with the San Francisco Bay Long Term Management Strategies (LTMS) Agencies, is undertaking the development of a Regional Sediment Management Plan for the San Francisco Bay estuary and its watershed (estuary). Regional sediment management (RSM) is the integrated management of littoral, estuarine, and riverine sediments to achieve balanced and sustainable solutions to sediment related needs. Regional sediment management recognizes sediment as a resource. Sediment processes are important components of coastal and riverine systems that are integral to environmental and economic vitality. It relies on the context of the sediment system and forecasting the long-range effects of management actions when making local project decisions. In the San Francisco Bay estuary, the sediment system includes the Sacramento and San Joaquin delta, the bay, its local tributaries and the near shore coastal littoral cell. Sediment flows from the top of the watershed, much like water, to the coast, passing through rivers, marshes, and embayments on its way to the ocean. Like water, sediment is vital to these habitats and their inhabitants, providing nutrients and the building material for the habitat itself. When sediment erodes excessively or is impounded behind structures, the sediment system becomes imbalanced, and rivers become clogged or conversely, shorelines, wetlands and subtidal habitats erode. The sediment system continues to change in response both to natural processes and human activities such as climate change and shoreline development. Human activities that influence the sediment system include flood protection programs, watershed management, navigational dredging, aggregate mining, shoreline development, terrestrial, riverine, wetland, and subtidal habitat restoration, and beach nourishment. As observed by recent scientific analysis, the San Francisco Bay estuary system is changing from one that was sediment rich to one that is erosional. Such changes, in conjunction with increasing sea level rise due to climate change, require that the estuary sediment and sediment transport system be managed as a single unit. To better manage the system, its components, and human uses of the system, additional research and knowledge of the system is needed. Fortunately, new sediment science and modeling tools provide opportunities for a vastly improved understanding of the sediment system, predictive capabilities and analysis of potential individual and cumulative impacts of projects. As science informs management decisions, human activities and management strategies may need to be modified to protect and provide for existing and future infrastructure and ecosystem needs. (PDF contains 3 pages)

Coastal management measures for the lower Maumee Watershed, Lake Erie

In January 2006 the Maumee Remedial Action Plan (RAP) Committee submitted a State II Watershed Restoration Plan for the Maumee River Great Lakes Area of Concern (AOC) area located in NW Ohio to the State of Ohio for review and endorsement (MRAC, 2006). The plan was created in order to fulfill the requirements, needs and/or use of five water quality programs including: Ohio Department of Natural Resources (DNR) Watershed Coordinator Program; Ohio EPA Great Lakes RAP Program; Ohio DNR Coastal Non-point Source Pollution Control Program; Ohio EPA Total Maximum Daily Load Program; and US Fish & Wildlife Service Natural Resources Damage Program. The plan is intended to serve as a comprehensive regional management approach for all jurisdictions, agencies, organizations, and individuals who are working to restore the watershed, waterways and associated coastal zone. The plan includes: background information and mapping regarding hydrology, geology, ecoregions, and land use, and identifies key causes and sources for water quality concerns within the six 11-digit hydrological units (HUCs), and one large river unit that comprise the Maumee AOC. Tables were also prepared that contains detailed project lists for each major watershed and was organized to facilitate the prioritization of research and planning efforts. Also key to the plan and project tables is a reference to the Ohio DNR Coastal Management Measures that may benefit from the implementation of an identified project. This paper will examine the development of the measures and their importance for coastal management and watershed planning in the Maumee AOC. (PDF contains 4 pages)

Reforming state-level coastal management and development policies: strategic retreat as an innovative, proactive and equitable coastal environmental management strategy

Atlantic and Gulf Coast shorelines include some of the most unique and biologically rich ecosystems in the United States that provide immeasurable aesthetic, habitat and economic benefits. Natural coastal ecosystems, however, are under increasing threat from rampant and irresponsible growth and development. Once a boon to local economies, complex natural forces – enhanced by global climate change and sea level rise - are now considered hazards and eroding the very foundation upon which coastal development is based. For nearly a century, beach restoration and erosion control structures have been used to artificially stabilize shorelines in an effort to protect structures and infrastructure. Beach restoration, the import and emplacement of sand on an eroding beach, is expensive, unpredictable, inefficient and may result in long-term environmental impacts. The detrimental environmental impacts of erosion control structures such as sea walls, groins, bulkheads and revetments include sediment deficits, accelerated erosion and beach loss. These and other traditional responses to coastal erosion and storm impacts- along with archaic federal and state policies, subsidies and development incentives - are costly, encourage risky development, artificially increase property values of high-risk or environmentally sensitive properties, reduce the post-storm resilience of shorelines, damage coastal ecosystems and are becoming increasingly unsustainable. Although communities, coastal managers and property owners face increasingly complex and difficult challenges, there is an emerging public, social and political awareness that, without meaningful policy reforms, coastal ecosystems and economies are in jeopardy. Strategic retreat is a sustainable, interdisciplinary management strategy that supports the proactive, planned removal of vulnerable coastal development; reduces risk; increases shoreline resiliency and ensures long term protection of coastal systems. Public policies and management strategies that can overcome common economic misperceptions and promote the removal of vulnerable development will provide state and local policy makers and coastal managers with an effective management tool that concomitantly addresses the economic, environmental, legal and political issues along developed shorelines. (PDF contains 4 pages)

On-chip integrated label-free optical biosensing

This thesis investigates the design and implementation of a label-free optical biosensing system utilizing a robust on-chip integrated platform. The goal has been to transition optical micro-resonator based label-free biosensing from a laborious and delicate laboratory demonstration to a tool for the analytical life scientist. This has been pursued along four avenues: (1) the design and fabrication of high-$Q$ integrated planar microdisk optical resonators in silicon nitride on silica, (2) the demonstration of a high speed optoelectronic swept frequency laser source, (3) the development and integration of a microfluidic analyte delivery system, and (4) the introduction of a novel differential measurement technique for the reduction of environmental noise.

The optical part of this system combines the results of two major recent developments in the field of optical and laser physics: the high-$Q$ optical resonator and the phase-locked electronically controlled swept-frequency semiconductor laser. The laser operates at a wavelength relevant for aqueous sensing, and replaces expensive and fragile mechanically-tuned laser sources whose frequency sweeps have limited speed, accuracy and reliability. The high-$Q$ optical resonator is part of a monolithic unit with an integrated optical waveguide, and is fabricated using standard semiconductor lithography methods. Monolithic integration makes the system significantly more robust and flexible compared to current, fragile embodiments that rely on the precarious coupling of fragile optical fibers to resonators. The silicon nitride on silica material system allows for future manifestations at shorter wavelengths. The sensor also includes an integrated microfluidic flow cell for precise and low volume delivery of analytes to the resonator surface. We demonstrate the refractive index sensing action of the system as well as the specific and nonspecific adsorption of proteins onto the resonator surface with high sensitivity. Measurement challenges due to environmental noise that hamper system performance are discussed and a differential sensing measurement is proposed, implemented, and demonstrated resulting in the restoration of a high performance sensing measurement.

The instrument developed in this work represents an adaptable and cost-effective platform capable of various sensitive, label-free measurements relevant to the study of biophysics, biomolecular interactions, cell signaling, and a wide range of other life science fields. Further development is necessary for it to be capable of binding assays, or thermodynamic and kinetics measurements; however, this work has laid the foundation for the demonstration of these applications.