Amongst the most threatened ecosystems on Earth, mangrove forests are also one of the more difficult to work in due to their growth in mud and open water coastal zones and their dense tangled stems, branches and prop roots. Consequently, there has been an impetus to employ remotely sensed imagery as a means for rapid inventory of these coastal wetlands. To date, the majority of mangrove maps derived from satellite imagery utilize a simple mangrove classification scheme which does not distinguish mangrove species and may not be useful for conservation and management purposes. Although more elaborate satellite based mangrove classification schemes are being developed, given their enhanced complexity they deserve additional justification for end users. The purpose of this study was to statistically examine the appropriateness of one such classification scheme based on an inventory of field data. In January of 2007 and May of 2008, 61 field sample plots were selected in a stratified random fashion based on a previous classification of a degraded mangrove forest of the Isla La Palma (Sinaloa, Mexico) using Landsat TM5 data. Unlike other previous Landsat TM based classifications of this region, which simply identified the mangrove forests as one class, the mangroves were classified (i. e. mapped) according to four conditions; healthy tall, healthy dwarf, poor condition, and dead mangroves. Within each sample plot, all mangroves of diameter of breast height (dbh) greater than 2.5 cm were identified and their height, condition and dbh recorded. An estimated Leaf Area Index (LAI) value also was obtained for each sample and the shortest distance from the center of each sample plot to open flowing water was determined using a geographic information system (GIS) overlay procedure. These data were then used to calculate mean values for the four classes as well as to determine stem densities, basal areas, and the Shannon-Wiener diversity index. In order to assess the appropriateness of this mangrove classification scheme a discriminant analysis approach was then applied to these field data. The results indicate this forest has undergone severe degradation, with decreasing mean tree heights, mean dbh and species diversity. In regards to the discriminant analysis procedure, further classification of these field plots and cross-validation based on these significant variables provided high classification accuracy thus validating the appropriateness of the satellite based image classification scheme. Moreover, the discriminant analysis indicated that the estimated LAI, mean height, and mean dbh are significant in the separation of the classification of mangrove forest condition along these field sample plots.

Given the scale and rate of mangrove loss globally, it is increasingly important to map and monitor mangrove forest health in a timely fashion. This study aims to identify the conditions of mangroves in a coastal lagoon south of the city of Mazatlán, Mexico, using proximal hyperspectral remote sensing techniques. The dominant mangrove species in this area includes the red (Rhizophora mangle), the black (Avicennia germinans) and the white (Laguncularia racemosa) mangrove. Moreover, large patches of poor condition black and red mangrove and healthy dwarf black mangrove are commonly found. Mangrove leaves were collected from this forest representing all of the aforementioned species and conditions. The leaves were then transported to a laboratory for spectral measurements using an ASD FieldSpec® 3 JR spectroradiometer (Analytical Spectral Devices, Inc., USA). R2 plot, principal components analysis and stepwise discriminant analyses were then used to select wavebands deemed most appropriate for further mangrove classification. Specifically, the wavebands at 520, 560, 650, 710, 760, 2100 and 2230 nm were selected, which correspond to chlorophyll absorption, red edge, starch, cellulose, nitrogen and protein regions of the spectrum. The classification and validation indicate that these wavebands are capable of identifying mangrove species and mangrove conditions common to this degraded forest with an overall accuracy and Khat coefficient higher than 90% and 0.9, respectively. Although lower in accuracy, the classifications of the stressed (poor condition and dwarf) mangroves were found to be satisfactory with accuracies higher than 80%. The results of this study indicate that it could be possible to apply laboratory hyperspectral data for classifying mangroves, not only at the species level, but also according to their health conditions.

Seagrass, mangrove, saltmarshes and macroalgae - the coastal vegetated habitats, offer a promising nature-based solution to climate change mitigation, as they sequester carbon in their living biomass and in marine sediments. Estimation of the macrophyte organic carbon contribution to coastal sediments is key for understanding the sources of blue carbon sequestration, and for establishing adequate conservation strategies. Nevertheless,identification of marine macrophytes has been challenging and current estimations are uncertain. In this dissertation, time- and cost-efficient DNA-based methods were used to fingerprint marine macrophytes and estimate their contribution to the organic pool accumulated in blue carbon habitats. First, a suitable short-length DNA barcode from the universal 18S gene was chosen among six barcoding regions tested, as it successfully recovered degraded DNA from sediment samples and fingerprinted marine macrophyte taxa. Second, an experiment was performed to test whether the abundance of eDNA represents the content of organic carbon within the macrophytes; results supported this notion, indicating a positive correlation (R2 = 0.85) between eDNA and organic carbon. Third, using the chosen barcode, eDNA of marine macrophyte was identified from sediments of seagrass meadows and mangrove forests in the Arabian Red Sea, to further estimate contributions to the organic carbon pools. Estimations based on eDNA were compared against estimations of organic carbon based on stable isotope analyses from the same sediments; results from both methods were similar. In addition, this research provided the first quantitative evidence of the contribution of macroalgae to coastal and oceanic carbon pools. Hitherto, macroalgae have been ignored in blue carbon assessments because their fingerprinting was challenging and there was no evidence of their carbon export. The results of this dissertation demonstrate that eDNA offers an unprecedent taxonomic discrimination, and resolve the contribution of marine macrophytes to the organic pools in blue carbon sediments.

京都大学 / 0048 / 新制・課程博士 / 博士(地球環境学) / 甲第19878号 / 地環博第152号 / 新制||地環||30(附属図書館) / 32914 / 京都大学大学院地球環境学舎地球環境学専攻 / (主査)教授 藤井 滋穂, 教授 高岡 昌輝, 准教授 田中 周平 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DFAM

The mangrove ecosystem is a marginal and complex ecosystem. Mangrove trees can tolerate heat, desiccation, high salinity, radiation, and anoxic conditions. The physiological features of mangroves help them tolerate these stressors, but their relationship with prokaryotic communities also plays a role in a productive mangrove ecosystem, mainly in nutrient cycling and biogeochemical transformation. In Saudi Arabia, a few studies were conducted to understand the microbial communities residing in the mangrove ecosystem. Most of the studies were focused on the sediments or rhizosphere of the most dominant species in the kingdom, Avicennia marina. In this study, the bacterial composition of two mangrove species (Avicennia marina and Rhizophora mucronata) and the relationship between them was explored using next generation amplicon sequencing of the V3-V4 region of the 16S rRNA. In both species, samples from four compartments were collected (sediments, rhizosphere, roots, and leaves). Both species had a similar microbial composition, with Proteobacteria and Chloroflexi being the most dominant phyla in all compartments. The lack of difference in alpha diversity measures (number of ASVs and Shannon-diversity index) between species highlights the symbiotic relationship between the trees. Previous studies have reported that A. marina has a more diverse microbial community than R. mucronata, however this difference was not significant in our samples. The multivariate analysis showed us that the microbial composition of the leaf and root samples was grouped separately from the microbial composition of sediment and rhizosphere samples, highlighting the specific microbial composition of each compartment. In addition, the enriched strains in each cluster were explored and related to the surrounding environment of the mangrove ecosystem, followed by the exploration of unique strains in each compartment using SIMPER analysis. In conclusion, this study provides the first information on the Red Sea Northern mangrove (Al-Wajh region) tree microbiomes, encompassing roots, leaves, rhizosphere, and sediments. Furthermore, by showing that some bacteria can colonize different plant compartments we contribute to disentangling their propagation channels within plants.

Mangroves provide many ecosystem services in coastal environments around the world. These include water quality improvement, creating habitats for terrestrial and aquatic species, and stabilizing shorelines. In central Florida, the red mangrove Rhizophora mangle is a common species in coastal wetlands, and recently the number of individuals successfully recruiting to intertidal oyster reefs has greatly increased, possibly because biogeochemical hot spots are present on oyster reefs due to nutrient-rich biodeposits from the live oysters. To understand how well R. mangle responds in terms of survival and growth to the suite of variables associated within these two unique habitats, I tracked 300 seedlings (n = 30 per site on 5 oyster reefs and 5 shoreline sites) that were approximately 1-year old at the start of my project. Monitoring occurred over 12 months (start: August 2022). Monthly data collection included above-ground measurements for each mangrove (survival, height, stem circumference, light availability, leaf count, herbivory, leaf area, and chlorophyll levels) of the seedlings, while below-ground measurements quantified biogeochemical properties of the soil adjacent to mangroves at each site. Survivorship declined over time for both habitats, but survivorship was greater on oyster reefs (cox regression model, p= 0.002). Results suggest greater stem circumference and ammonium concentrations at oyster reef sites. With the data gathered from this study, I determined that oyster reefs have conditions that provide better chances for long-term survival and growth for R. mangle in Mosquito Lagoon. This possibility should be considered on all subtropical estuarine systems where mangroves and intertidal oyster reefs intersect.

published_or_final_version / Zoology / Doctoral / Doctor of Philosophy

published_or_final_version / Zoology / Master / Master of Philosophy

Les forêts de mangrove contribuent de manière significative au flux d'énergie, au cycle des nutriments et du carbone dans l'océan côtier, étant un puits pour le CO2 atmosphérique. Les forêts de mangroves sont très productives et stockent une quantité élevée de carbone à la fois dans leurs sols et dans leur biomasse.Au cours de la décomposition de la litière, les nutriments et le carbone peuvent être recyclés ou exportés vers les écosystèmes adjacents par l'action des marées. La mangrove de Can Gio (Ho Chi Minh Ville, Vietnam), dégradée par l'épandage de défoliants pendant la guerre du Vietnam, a pu être restaurée grâce à la replantation et à la régénération naturelle. À ce jour, la forêt de mangrove de Can Gio est la plus grande forêt de mangrove contiguë au Vietnam, et est devenue la première réserve biosphère UNESCO dans ce pays. L'objectif principal de cette thèse était de caractériser le cycle du carbone dans la forêt de mangrove tropicale.Les résultats de cette thèse ont permis de:- Développer des équations allométriques permettant d’estimer la biomasse aérienne de la forêt plantée de mangroves de l’espèceRhizophora apiculatadans le sud du Vietnam;- Calculer les stocks de carbone totaux dans différents peuplements de mangrove se développant sous le climat tropical du sud du Vietnam;- Caractériser les taux de décomposition de la litière et évaluer la dynamique des nutriments et des métaux traces au cours des processus de dégradation de la litière, ainsi que l'évolution de δ13C pendant la décomposition;- Déterminer la variabilité saisonnière des flux de CO2 à différentes interfaces: sol-air, eau-air et tronc-air, et caractériser les profils de concentration en CO2 dans la canopée. / Mangrove forests significantly contribute to energy flow, nutrient and carbon cycling in the coastal ocean, being a sink for atmospheric CO2. Mangroves forests are highly productive and store high amount of carbon both in their soils and in their biomass. During leaf litter decomposition, nutrients and carbon can be recycled or exported to adjacent ecosystems by the tidal action. Can Gio mangrove, degraded by the spraying of defoliants during the Vietnam War, successfully recovered through replantation and natural regeneration after 40 years. To date, the Can Gio mangrove forest is the largest contiguous mangrove forest in Vietnam, and became the first Mangrove Biosphere Reserve in this country. The main objective of this PhD thesis was to characterize carbon cycling within the Can Gio mangrove forest, which is a tropical one.The results of this PhD thesis allowed to: - Develop allometric equations and to estimate the aboveground biomass of Rhizophora apiculata Blume planted mangroves forest in Southern Vietnam; - Calculate the total carbon stocks in different mangrove stands developing under the tropical climate of Southern Vietnam; - Characterize the leaf litter decomposition rates, and assess nutrients and trace metals dynamics during litter decay processes, as well as the evolution of δ13C during decay; - Determine the seasonal variability CO2 fluxes at different interfaces: soil-air, water-air and trunk-air, and to characterize CO2 concentrations profiles in the canopy.

Les mangroves sont de plus en plus mentionnées comme outil de bioremédiation potentiel dans le traitement des eaux usées (EU). Actuellement, les effets des rejets d’EU sur la macrofaune, et plus particulièrement sur les crabes de mangrove, ne sont pas clairs. Ces espèces sont dites ingénieurs de cet écosystème, notamment grâce à leur activité de bioturbation qui permet, entre autres, l’infiltration des EU dans le sédiment via leurs terriers. L’objectif ont donc été d’étudier l’impact du rejet d’EU domestiques sur la physiologie (osmorégulation, métabolisme et balance oxydative) de 3 espèces de crabe (2 Sesarmidae et 1 Ocypodidae) par une approche combinant expérimentations en laboratoire et sur le terrain en utilisant un site pilote expérimental sur l’île de Mayotte. Ces crabes qui vivent dans la zone intertidale ont un mode de vie bimodal et font fréquemment face à des salinités variables. Ils sont de bons hyper-hypo-osmorégulateurs et sont adaptés à cette vie à l’interface entre terre et eau aussi bien au niveau de la régulation ionique que de la respiration. Les résultats indiquent que la densité des terriers diminue dans les zones d’écoulement des EU et que la communauté des espèces est modifiée avec la dominance de Parasesarma guttatum (PG) qui n’est pas une espèce bioturbatrice. Les EU induisent donc une modification potentielle du fonctionnement de l’écosystème. PG diminue son métabolisme alors que les deux autres espèces étudiées l’augmentent significativement. Immergées dans les EU, les trois espèces étudiées présentent des atteintes de la fonction osmorégulatrice (activité de la Na+/K+-ATPase et épaisseur d’épithélium branchiale) et de la balance oxydative (formation d’espèces réactives de l’oxygène dans l’hémolymphe et enzymes antioxydantes des branchies) en laboratoire mais des effets moins marqués sont observés chez les crabes maintenus in situ dans des terriers artificiels. Les biomarqueurs étudiés peuvent ainsi être utilisés pour mesurer l’état physiologique des crabes soumis à des rejets d’EU domestiques. Ces atteintes qui entraînent des coûts métaboliques supplémentaires peuvent mener à la réduction de leur fitness, contribuant à expliquer les observations écologiques. De plus, les résultats montrent que les crabes violonistes sont les plus sensibles, suivis des deux Sesarmidae alors que PG semble mieux adapté pour éviter les EU. Si aucun dysfonctionnement majeur n’a été observé à l’échelle de l’écosystème jusqu’à présent, il convient de maintenir un suivi régulier de ces espèces, en tenant compte de leur spécificité en termes d’activité bioturbatrice et de santé physiologique. / Mangroves are increasingly proposed as a bioremediation tool for wastewater (WW) treatment. However, this practice can impact mangrove crabs which are key engineer species of the ecosystem through their bioturbation activities. Their burrows are directly involved in the bioremediation process allowing WW infiltration in the sediment. This study aimed to determine the effects of WW on the physiology (osmoregulation, bioenergetics, oxidative balance) of 3 species of crabs (2 Sesarmidae and 1 Ocypodidae) with laboratory and in situ experiments (burrow density and caging experiment in an experimental area with controlled WW releases on a mangrove located on the island of Mayotte). These crabs inhabit the intertidal area of variable salinity with a bimodal life (aquatic and terrestrial). They are good hyper-hypo-osmoregulators and well adapted to terrestrial life both in terms of osmotic and aerial breathing capacities. Burrow density decreases in flat areas where WW flows and crab community is altered with a marked dominance of Parasesarma guttatum (PG) (a species with no bioturbation activity). This change may induce drastic alterations of the ecosystem functioning. The bioenergetic response of PG is totally different from the other studied species. PG decreases its metabolic rate in WW but the other species have increased metabolic activity. Moreover, after laboratory exposure the 3 species show impairments in their osmoregulatory capacity (Na+/K+-ATPase activity and epithelium gill thickness) and oxidative balance (reactive oxygen species formation in haemolymph and antioxidant enzyme activity in gills) due to WW exposure in laboratory conditions. In situ, encaged crabs showed a similar but reduced pattern. These effects could decrease their fitness and may also explain the observed ecological changes. The biomarkers used in this study may be a useful tool to monitor crab populations. Moreover, our results show that fiddler crabs are the most sensitive to WW followed by other Sesarmidae. PG seems better adapted to avoid WW exposure. Even if no major dysfunction is observed at the ecosystem level yet, WW release should be carefully monitored nevertheless with an emphasis on crab bioturbation activity and their physiological health according to species sensitivity.