In the marine realm, there has been considerable habitat degradation caused by multiple human disturbances that often act synergistically, strongly affecting fish and invertebrate populations and, consequently, one of the major stakeholders of these resources, fishers. However, the mechanisms underlying how marine habitats support fisheries remain understudied. In this dissertation I examined the importance of fish habitat at global, regional and local scales in two distinct systems (mangrove habitats in the tropics and rockfish habitats in inshore waters of Vancouver Island) combining a suite of different approaches. First, I explored the mangrove-fishery linkage relationship by conducting a global meta-analysis. I found strong evidence supporting the importance of mangrove area to enhance fisheries. This relationship, however, varied across countries, likely based on regional geomorphological settings and fishery management policies. Subsequently, I determined the use of mangrove and adjacent habitats by fish in a tropical lagoon system in the continental Caribbean (Colombia), systems often overlooked in the Caribbean when analyzing mangroves as fish habitat. I collected fish with gillnets at different distances from mangroves and at different sites within the same lagoon system. While fish used mangroves, fish abundance was not higher in these habitats compared to adjacent ones, as predicted. However, diversity tended to be higher in mangroves. Nevertheless, the major driver affecting abundance, diversity and biomass was salinity. That is, diversity and abundance decreased as salinity increased. Next, I used a Local Ecological Knowledge approach to explore the mangrove-fishery linkage relationship because fishers are seldom incorporated into such relationships. By conducting semi-structured interviews I found that fishers fish close to their village and to mangroves, that in addition to fishing they use mangroves for firewood and as construction material. Fishers also agreed that mangroves are important for their fishing activity, as these habitats are critical for fish and crustaceans caught in the system. Finally, I examined the importance of derived benthic parameters for rockfish abundance and distribution at large spatial scales (100s km) in inshore waters of Vancouver Island. I established that higher complexity better explains presence and higher abundance of rockfish. Furthermore, the results provided valuable information for fishery and spatial management and habitat conservation to help recover rockfish populations. All together, these findings highlight the urgency to preserve coastal marine habitats for both juvenile and adult marine organisms to sustain small-scale fisheries as a food source and for traditional purposes. While conserving habitats is a key component of a broader and more complex ecosystem approach that includes overfishing and other anthropogenic pressures, in the absence of a holistic approach the chances of success are minimal. / Graduate / 2019-04-18

Although the “genome as a blueprint” metaphor has been pervasive in biology, recent advances in molecular biology have revealed a complex network of regulatory machinery that dynamically regulated molecular processes in response to environmental conditions. However, these patterns, as well as the evolutionary processes that underlie them, remain understudied in natural conditions. In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, making landfall on salt marsh habitat dominated by the foundation species Spartina alterniflora. Despite the severe impacts to phenotype and fitness, S. alterniflora proved remarkably resilient in the face of the crude oil stress. Despite the tragedy of the Deepwater Horizon oil spill, the event represented a unique opportunity to explore the molecular mechanisms of oil tolerance in this highly resilient species. To understand how organisms regulate gene expression in natural settings and to identify best practices in genome-wide expression studies, we first surveyed a ten-year span of transcriptome-wide gene expression studies. We then confirmed the hypothesis that crude oil exposure would induce differential gene expression in affected populations, and whole-transcriptome microarray identified 3,622 genes that responded exclusively to oil stress. To confirm the function of candidate genes involved in resilience to oil stress, we used a highly-differentially expressed subset of these genes to construct gene interaction networks and identify target genes. We obtained T-DNA insertion genotypes of the emerging model grass species Brachypodium distachyon that were disrupted in these target genes for functional confirmation, but were unable to detect significant modulation of oil response through these heterologous knockouts. Finally, we isolated the phenotypic effects of crude oil exposure through greenhouse trials and found evidence that crude oil may have acted as a selective pressure, rather than an inducer of plasticity. Together, these studies identify novel patterns of gene expression in response to a severe but unpredictable stressor that has widespread impacts on a foundational salt marsh grass species. In addition, this dissertation represents a pathway to understanding functional genomics in non-model systems without extensive genomic resources.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第13262号 / 論農博第2875号 / 新制||農||1071(附属図書館) / 学位論文||R1||N5217(農学部図書室) / (主査)教授 山下 洋, 教授 澤山 茂樹, 教授 吉岡 崇仁 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

The capacity of the world’s coastal ecosystems to sequester carbon dioxide (CO2), termed “Blue Carbon,” has been a major focus of research in recent decades due to its potential to mitigate climate change. Vegetated coastal ecosystems such as mangroves, seagrass beds, and salt marshes represent a global area that is one to two orders of magnitude smaller than that of terrestrial forests, yet their contribution to long-term carbon sequestration is much greater per unit-area, in part because of their high productivity and efficiency in trapping suspended matter and associated organic carbon. Despite the value that Blue Carbon (BC) systems offer in sequestering carbon, as well as providing numerous other goods and services, these habitats are being lost at critical rates and require urgent action in order to prevent further degradation and loss. Recognition of the carbon sequestration value of vegetated coastal ecosystems provides a strong argument for their protection and restoration, and global efforts are now underway to include BC ecosystems into global carbon offset budgets, focusing on their optimal management to optimize CO2 sequestration and minimize CO2 emissions. Here, BC was investigated in the Cowichan Estuary in relation to habitat type (salt marsh, eelgrass meadow, non-vegetated mudflats, and oyster shell beds), and habitat degradation. Stored organic carbon (OC) and inorganic carbon (IC) were quantified in the top 20 cm depth of sediment cores, as well as in eelgrass and salt marsh vegetation, and then extrapolated to the areal extent of each habitat type based on a high resolution 1:12,000 scale base map of the estuary. Rates of sedimentation and carbon sequestration were quantified in each habitat type using 210Pb radiometric dating, and organic matter (OM) sources and quality were assessed in each habitat type using δ13C, C/N ratios and photopigment content in the sediments. A particular focus on the lower intertidal zone allowed us to examine the potential impact of industrial activity (log transport and storage) on the estuary’s capacity for carbon storage, as a result of a reduction of suitable habitat for eelgrass and microphytobenthos (MPB). Additionally, IC was quantified in aboveground oyster shell beds and buried oyster shell to assess inorganic storage. Finally, potential valuation of Blue Carbon in the Cowichan Estuary was investigated by comparing carbon sequestration to provincial greenhouse gas (GHG) emission equivalents as well as carbon sequestration in B.C. forests. We found that the salt marsh was the most important carbon reservoir, with a mean per-hectare sediment organic carbon (SOC) stock of 49.1 ± 19.9 Mg C ha-1, total ecosystem carbon stock (TECS) of 5443.75 Mg C, and carbon accumulation rate of 74 ± 23 g C m-2 yr-1. In the other habitats, we found SOC stocks and TECS respectively 19.1 ± 3.78 Mg C ha-1 and 3651.6 ± 72.3 Mg C in the upper mudflats, 16.9 ± 4.36 Mg C ha-1 and 1058.85 Mg C in the lower mudflats, 17.9 ± 1.21 Mg C ha−1 and 324.57 Mg C in the eelgrass meadow, and 9.43 ± 1.50 Mg C ha-1 and 59.4 Mg C in the oyster beds. The eelgrass meadow had a carbon accumulation rate of 38 ± 26 g C m-2 yr-1, while the mudflats could not successfully be dated due to erosion and/or mixing. Furthermore, the salt marsh contained the highest proportion of recalcitrant, terrestrial-derived root material which was more protected from hydrodynamic forces compared to other habitats. No pattern differences were observed between the carbon reservoirs or bulk properties of the log boom area (lower mudflat) compared to the upper mudflat, and thus there was no evidence that the log booms significantly decrease carbon sequestration in the areas where they make frequent contact with the seafloor. However, decreased chlorophyll a (chl a) concentrations in the lower mudflat sediment suggests a possible detrimental impact on microphytobenthos in addition to preventing the recolonization of the seagrass Zostera marina (Z. marina). Carbon stocks in the eelgrass meadow were similar to those of the mudflats. These carbon stocks were lower than global averages but consistent with those recently reported in low Z. marina meadows in the Pacific Northwest. Evidence of significant eelgrass vegetation outwelling necessitates further investigation to elucidate the degree to which these primary products are being decomposed or buried elsewhere in the estuary or open ocean. Since approximately half of the historical salt marsh habitat is currently reclaimed for agricultural and industrial use, consideration should be given to the role of the marsh system as a carbon reservoir in future land-use policy in the Cowichan Estuary. / Graduate / 2022-04-30

Mangrove forests are unique coastal ecosystems, formed through a complex network of terrestrial, estuarine, and marine processes that have provided a diverse assortment of societal benefits across time. Compounding anthropogenic pressures are driving critical mangrove degradation worldwide, threatening the wellbeing of coastal populations historically associated with these systems. The Ciénaga Grande de Santa Marta (CGSM) in northern Colombia is the largest coastal lagoon-delta in the Caribbean. It is inhabited by stilt-house communities who have developed an intricate livelihood and cultural relationship with the mangroves. The CGSM has experienced sustained social and ecological degradation over the last 6 decades, triggered by land-use change and disruption of hydrological connections. This study integrates Social-Ecological Memory and Palaeoecology to develop a historical contextualization of the biophysical and social dimensions of environmental change in CGSM. Integration of geochemical sediment analysis, C14 radiocarbon dating, and demographic inferences from archaeological evidence revealed three distinct periods over the last 5000 years. During this time sea level rise and hydroclimatic variability shaped the transition from freshwater to prevailing marine conditions, and modulated human occupation patterns in the area around 2000 years ago. In addition, participatory reconstructions with local communities offered nuanced descriptions about the spatial, temporal and contextual aspects of the degradation process, with profound social-ecological consequences. The interdisciplinary approach of this study indicates that CGSM is a highly dynamic social-ecological system that has been changing and reconfiguring across different time scales in response to both natural and human-induced processes, and contributes to the preservation of collective memory in this unique stilt-house community. Finally, it reveals the relative effects of biophysical and social drivers on driving social-ecological change under both millennial and decadal scales.

Coastal ecosystems continue to face numerous negative impacts from human activities ranging from local nutrient enrichment to global warming. These threats have complex effects on coastal biogeochemistry, which in turn alters ecosystem ecology and climate. While sediments have long been recognized as cornerstones of marine ecosystem functioning, the impacts of anthropogenic change on benthic biogeochemical cycling remain challenging to constrain. This knowledge gap stems from technological issues as measuring marine sediment processes under natural conditions is a formidable challenge. To help move the field of sediment biogeochemistry forward, I developed a novel mass spectrometer-based system and used it to quantify dissolved gas fluxes from marine sediments. In Chapter One, I survey the field of underwater mass spectrometry from its inception three decades ago to the present. Through comprehensive descriptions of the current status of the technology, field applications to date, and future trends, I provided guidance for how to leverage this powerful new tool to measure gaseous compounds in the under sampled ocean. In Chapter Two, I review the role of permeable shelf sediments in marine nitrogen cycling. My synthesis of the small but growing body of work on nitrogen cycling in shelf sands exposed conflicting evidence surrounding the nitrogen removal capacity of permeable sediments, and I proposed targeted approaches, such as the development of noninvasive in situ technologies, to resolve these controversies. In Chapter Three, I present a newly developed flow-injection sampling system that can be coupled to a mass spectrometer to measure a range of dissolved gas species in the pore water of highly permeable sandy sediments. Rigorous calibration and validation experiments demonstrate that this novel system can quantify dissolved gas depth profiles, as well as fluxes across the sediment-water interface, in permeable sediments. Furthermore, with my prescribed design improvements, this tool promises to provide in situ data in dynamic sandy environments. In Chapter Four, I used the flow-injection mass spectrometer system to measure benthic fluxes of gaseous nitrogen and methane from cohesive sediments subjected to low oxygen conditions and varying organic matter loads. The unprecedented high temporal resolution of the gas flux data revealed the complex and dynamic effects of changing environmental conditions on the capacity of sediments to remove reactive nitrogen and regulate methane emissions. / 2024-11-08T00:00:00Z

In tropical seascapes, coral reefs often exist in proximity to marine vegetated habitats such as seagrass, mangroves, and macroalgae. This habitat mosaic offers the possibility for connection and exchange of both organisms and nutrition between habitats, mediated by biological and physical processes. This dissertation examines flows of organisms and nutrition between coral reefs and tropical vegetated habitats in the central Red Sea through 3 different mechanisms: 1) Use of multiple habitat types by tropical marine fishes, 2) Transport of algal material to coral reefs via the foraging behavior and movements of herbivorous fishes, and 3) Physical flow of water between coastal habitats. The results of this thesis suggest that coastal tropical habitats maintain a variety of ecological links at different spatial and temporal scales. A large fraction (36%) of fish species found on coral reefs are also found in at least one marine vegetated habitat in the central Red Sea, with many species mainly living in vegetated habitats as juveniles. This demonstrates the value of mangrove, seagrass, and macroalgae habitats to coral reef fishes, and suggests that many species make ontogenetic migrations between reef and non-reef habitats through their lives. Two species of herbivorous reef fishes (Naso elegans and N. unicornis) were found on coral reefs with algae in their guts which likely originated from nearby Sargassum-dominated macroalgae canopies, representing a fish-mediated, cross-habitat flux of nutrition from macroalgae habitats to coral reefs. Finally, we used a combination of remote sensing, a dye tracer study, and in-water measurements to observe water movement from shallow seagrass and mangrove habitats to nearby lagoon and coral reef habitats. Water exiting seagrass and mangrove habitats had altered concentrations of various nutrients (such as increased particulate organic carbon or decreased dissolved nutrients), suggesting that Red Sea mangroves and seagrasses change nutrient concentrations in water and the movement of water from these habitats to coral reefs could supply reefs with an allochthonous source of nutrition. These various linkages, controlled by a range of physical and biological processes, highlight the interconnected nature of tropical coastal ecosystems, and thereby the need to conserve whole habitat mosaics in the pursuit to protect coral reefs and maintain healthy and functioning coastal ecosystems.

Coastal ecosystems comprise a relatively small area of the ocean, yet they play a disproportionate role in greenhouse gas (carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O)) and nutrient cycling. Vegetated coastal ecosystems (e.g., mangroves, salt marshes, and seagrasses) are key drivers of coastal greenhouse gas and nutrient cycling because of their environmental characteristics (e.g., shallow depths, organic matter rich sediments, etc.). My dissertation addresses the role of vegetated coastal ecosystems in greenhouse gas budgets and biogeochemical cycling. In Chapter 1, I conducted a meta-analysis to quantify the global emissions of CH4 from mangrove, salt marsh, and seagrass ecosystems. Here I show that mangrove ecosystems contribute the most CH4 out of these vegetated areas to the global marine CH4 budget. Further, while a well-known negative relationship between salinity and CH4 fluxes exists for salt marshes globally, this relationship does not hold for mangrove or seagrass meadows, suggesting that other environmental drivers are more important for predicting CH4 fluxes in these ecosystems. In Chapter 2, I present in situ fluxes of CH4 and N2O across the sediment-water interface as well as air-sea fluxes in seagrass meadows and adjacent non-vegetated sediments in two temperate coastal lagoons. Here I demonstrate that seagrass meadows can be sources or sinks of CH4 and that N2O uptake can enhance carbon sequestration in seagrass meadows by ~10%. In Chapter 3, I quantify fluxes of dissolved inorganic carbon, nitrogen, and phosphorous across the sediment-water interface in seagrass meadows and adjacent non-vegetated sediments in the same two coastal lagoons. I found that both seagrass and non-vegetated sediments exhibited dissolved inorganic carbon emission and denitrification, and that dissolved inorganic phosphorous fluxes varied by site and not with vegetation presence. This dissertation highlights the dynamic role coastal ecosystems play in biogeochemical cycling and the importance of vegetated coastal ecosystems in coastal greenhouse gas budgets. / 2024-10-03T00:00:00Z

Coral reefs have one of the highest levels of biodiversity of all ecosystems in the world and are important for both human livelihood and food security throughout many tropical countries. However, due to increased anthropogenic pressure on marine ecosystems, especially during the last couple of decades, coral reefs have become critically over-fished, and many reefs are now in a degraded state and are facing additional future threats due to further over-exploitation, chemical pollution, sedimentation, and effects of climate change. The main aim of this PhD thesis was to understand effects of anthropogenic disturbances on tropical coastal ecosystems and fish connectivity for coastal management purposes. Therefore, linkages between anthropogenic disturbance and corals were investigated (Paper I), as well as interactions between coral reef habitat and associated fish assemblage (Paper II). Furthermore, connectivity between coral reefs and other tropical coastal ecosystems was explored (Paper III), as well as fish migration to reproduction sites (Paper IV), and evaluations of spatial ecology methods (Paper V). The result showed that coral reefs that are already exposed to disturbances, such as freshwater and nutrient run-offs, may be more sensitive to climate change, in terms of increased sea surface temperatures (Paper I). In addition, there were also clear linkages between coral reef quality, in terms of coral coverage, and fish assemblages, which displayed high spatial variability and suggesting patchy recovery after the 1997/1998 bleaching and subsequent coral mass mortality event (Paper II). This highlights the importance of understanding effects of disturbances on corals, especially in terms of synergistic effects between increased water temperatures and other coastal stressors such as decreased salinity and increased nutrients; and the indirect effects of habitat degradation on the fish community. Linkages between fish and different coastal habitats were further explored. The results showed that coral reefs were strongly connected with mangrove and seagrass beds, through ontogenetic migration of fish (Paper III). Migrations to spawning sites of groupers were related to lunar activities when thousands of fish gather for reproduction purposes during new moon, which increases the risk of over-exploitation (Paper IV). The results emphasises the importance of protecting key areas such as nursing grounds and reproduction sites. Furthermore, acoustic telemetry has become an increasingly common method in studies of fish movement, and the results showed that efficiency of acoustic arrays may increase depending on deployment strategies and habitat characteristics (Paper V). In conclusion, the results from this PhD thesis emphasises the importance of protecting coral reef habitats, as well as identifying related susceptible tropical coastal areas, such as nursing grounds and reproduction sites. Indeed, a better scientific understanding of coral reef ecology and indirect and direct effects on fish assemblages are needed for efficient and accurate coastal management decisions. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.</p>

Em suas várias nuanças a geografia se apresenta como uma ciência interdisciplinar, com interface em muitos segmentos do conhecimento. As ramificações geográficas fazem com que esta ciência seja plural na tradicionalidade acadêmica, nos permitindo trabalhar questões cronológicas, biológicas, humanas e da natureza, como será apresentado nesta tese. A questão que fundamenta este trabalho pauta-se na necessidade de compreender os fatores externos e internos que alteram a vida do ser humano no ecossistema manguezal do Rio Jordão sob a hipótese de que, a ausência de políticas públicas gera problemas ambientais e sociais. O que será realizado ao detectar da comunidade suas correlações com o manguezal em cena. A ação degradadora do homem vai aniquilando aos poucos o ecossistema do manguezal, isso nos faz perceber que as peculiaridades inerentes ao povo vivente desta comunidade também perde sua especificidade. Consequentemente, a atividade pesqueira perde força porque a comunidade local vai sendo removida, comprometendo assim a conservação de sua cultura. O pescador passa para a condição de cidadão, usuário urbano, um simples morador a somar-se ao sistema vicioso da cultura uniformizada, característica dos centros urbanos. O eixo da tese trata inicialmente de compreender a localização da área de pesquisa e da ocupação territorial do estado envolvendo o tema; tem consequência com a realização da caracterização do manguezal em questão e do ser humano nele habitante; apresentação da análise bibliográfica; justificativas, finalidades, metodologia do trabalho, identificar as externalidades e internalidades relacionadas ao ecossistema em questão e as alterações que os moradores do manguezal em estudo sofrem/causam. Com a caracterização da bacia hidrográfica do Rio Jordão, não foi apenas delimitada a área de estudo, mas interpretou-se também a dinâmica no sistema de bacia, neste caso, possibilitou-se conhecer melhor o entorno do rio, o manguezal e focar-se especificadamente nas questões relacionadas com as comunidades quando detectamos a correlação em que os moradores percebem entre o ecossistema do manguezal e suas próprias vidas. Contudo, os capítulos desta tese expressam uma vontade, a de trazer da população habitante da bacia do rio Jordão, informações tributárias a este ecossistema. / Geography, presented here as an interdisciplinary science, with interface in a lot of segments of the knowledge. Its branches make this science a plural science in the academic traditionalism. It allows us to work issues on chronologic, biologic, human and nature as it will be presented in this study. A question that bases this work line is the theory of the necessity to understand the external and internal factors that change lives of the people and the mangrove ecosystems of Jordan River that can be detected from the community and its correlations with the mangrove. The degenerating action of the man is destroying the mangrove ecosystem and this makes us realize that the inherent peculiarities of those people also lose their individualization. Consequently the fish activity loses the strength because the local community is forced to change their life styles, committing the upkeeping of their culture. The fisherman becomes a city citizen, a urban user, an ordinary person who comes to add to the vicious cycle of the unifying culture, what is a characteristic of the urban centres. The main idea of this study is to deal initially with the understanding the location of the area in study, and the territorial occupation of the state involving this subject. It has consequence with the practice of the mangrove characteristics and its inhabitants. A presentation of a bibliographic analysis, justification, purpose, methodology of the study, identification of the internal and external factors related to the ecosystem and the changes that the inhabitants from the mangrove have to deal with. With the characterization of hydrographical basin of the Jordan river, it wasnt only marked the area of study but it was also interpreted the dynamics of the basin system and in this case, the possibility of knowing the river better and to focus on questions connected with community when we detected the correlation between the inhabitants and the ecosystem and the mangrove, and their own existence. However, the chapters of study express a strong will of bringing to the population who live in the Jordan River basin, information about this ecosystem.