Les mattes de procaryotes constituent une niche écologique diversifiée. peu étudié!<..en mangrove et jamais décrjte dans les Antilles. L'objectif de cette thèse est de décrire les procaryotes filamenteux reposant sur le sédiment marin et de caractériser les interactions entre la matte, milieu et entre les différents micro-organismes. Nous avons d'abord caractérisé les micro-organismes majoritaires de la matte par le séquençage de l'ADNr 16S et des hybridations moléculaires (FISH). Il a ainsi été possible de décrire deux nouvelles espèces de Beggiatoaceae dont la structure a été étudiée par microscopie électronique. De plus, afin de caractériser l'environnement chimique de ces bactéries, des capteurs potentiométriques ont été utilisés. Ils ont permis de démontrer que les Beggiaotaceae oxydaient les sulfures en prélevant l'oxygène du milieu, tandis que des analyses de microscopie couplées à de l'EDX ont mis en évidence des réserves de soufre intracellulaires dans ces bactéries. Le séquençage de l'ADNr 16S des cyanobactéries filamenteuses a mis en évidence quatre nouvelles espèces de l'ord~e des Oscillatoriales. Deux d'entre elles, du genre Planktothricoides ont révélé une toxicité positive sur les Artemia sp:, les deux autres ont été identifiées comme proches d'Oscillatoria spongeliae, une espèce symbiotique d'éponge, bien que les coupes uItrafines d'une de ces souches aient montré une morphologie interne proche des Tychonema. L'analyse des données a permis d'étoffer les connaissances sur les communautés microbiennes de mangrove et constitue une base intéressante de travail sur la contribution des micro-organismes au fonctionnement de l'écosystème mangrove dans son ensemble / Procaryotic mats are ecological niches, occuring in many ecosystems. Those structures are little studied in marine mangrove sediment and have never been described in West Indies. The purpose ofthis thesis is to characterize the interactions between the mat and the environment, and between the different filamentous micro-organisms living into the mat. In a first place, we characterized the mainly micro-organisrns of the mat by sequencing 16S rDNA. We confirmed these sequences by molecular hybridization (FISH) with specific probes designed from sequences obtained. Thus, it was possible to describe two new Beggiatoaceae strains, whose structure has been studied by electronic microscopy. Furthemore, we used potentiometric captors in situ and in laboratory, by creating a mesocosm, in order to define the chemical environment where involved these bacteria. These experiences proved that the Beggiatoaceae of the mat oxidized the sulfur taking the oxygen from the medium, while the microscopic analysis coupled with EDX showed intracellular sulfur granules into the bacteria. The study of the filamentous cyanobacteria of the mat highlighted four new cyanobacteria strains, all studied by electronic rmcroscopy. Two of them belongs to Planktothrlcoides genus and showed positive toxicity on Artemia salina. The others species are close to Oscillatorla spongeliae, a sponge symbiont, nevertheless, one ofthem showed an intemal morphology close to Tychonema. The analysis of the different results adduces sorne knowledge about mangrove microbial communities. Furthermore, this study can be used as an interesting base to study the micro-organisms contribution in functioning mangrove ecosystem

京都大学 / 新制・課程博士 / 博士(地球環境学) / 甲第25474号 / 地環博第260号 / 新制||地環||53(附属図書館) / 京都大学大学院地球環境学舎環境マネジメント専攻 / (主査)教授 柴田 昌三, 教授 西前 出, 准教授 落合 知帆 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DGAM

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

published_or_final_version / Environmental Management / Master / Master of Science in Environmental Management

Plants and animals have evolved unique morpho-physiological adaptions to cope with the harsh and steep environmental gradients that characterise the mangrove ecosystem. However, the capacity of these two main components of the system to thrive, and the extraordinary productivity of mangrove forests in extreme conditions, has been overlooked in terms of the role of the microbiome. By combining approaches that included molecular microbial ecology, biogeochemical analyses, microscopy, raman spectroscopy and microsensor measurements, this thesis aimed to investigate the potential role of bacterial symbiosis in the adaptation of mangrove crabs to their environment and subsequently how these different animals modify their environment. Finally, with a field-based approach monitoring microbial communities, sediment metabolism and plant performance, the thesis aimed to investigate the plant/animal/bacterial dynamics in relation to seasonal environmental changes to contribute to understand the mangrove plant productivity paradox of high productivity under conditions of limited nutrents. Crab species were associated with distinct gill-bacteria communities, that produced carotenoids, according with their level of terrestrial adaptation. These carotenoids may be involved in protecting the gills from oxidative stress during air exposure. The main groups of ecosystem engineering crabs in mangroves had significant but diverse effects on the sediment environment and microbiome predominantly related to their ecology (i.e. filter feeder vs herbivore). Burrows increase aerobic microbial activity in the immediate burrow wall with a cascade effect on sediment microbial communities and nutrient distribution observed consistently across mangroves in different locations and with diverse environmental conditions. Microorganisms play an important role in adapting crabs on their evolutionary path to land and could contribute to the success of their colonization. At high population densities, of more than 50 individuals per square meter in some mangroves, these crabs deeply impact the functioning of the mangrove ecosystem, affecting microbial networks and nutrient recycling in the sediment, which may ameliorate conditions for plant growth. The microbiome is an understudied component of mangroves that lies at the basis of the functioning of these systems, influencing the success of the animal inhabitants (ecosystem engineers) that deeply modify the sediment microbiome, therefore influencing ecosystem functioning and resilience and, potentially, the success of the plants themselves (ecosystem architects).

In Palm Beach County, S. terebrans burrows into grounded roots and trunks of R. mangle causing collapse. This is contrary to previous studies suggesting this species burrows only into free-hanging roots. Nutrients and C. virginica cover may affect S. terebrans abundance and distribution. Surveys show burrowing significantly varies among sites, but not between free-hanging and grounded roots. Nutrients vary by site, but neither N nor P was correlated with burrowing. Nutrient treated roots showed no colonization pattern associated with N or P. Lignin varied among sites, but didn’t affect burrowing. Finally, C. virginica limited colonization in the portion of R. mangle tissue it covered. The location of C. virginica on the seaward/landward side was not predictive of burrowing. R. mangle height and leaves were not negatively affected by cover treatment or burrowing. Results highlight the need for additional research to determine the influence of environmental factors on this species interaction. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

SUMMARY Mangrove ecosystems thrive in (sub)tropical, intertidal areas where adaptations like vivipary and the hydrochorous dispersal of propagules become an absolute necessity. As propagule dispersal and early growth allow for the replenishment of existing stands and colonization of new habitats, many authors recognize the importance of these stages in structuring mangrove populations and communities. However, when it comes to the actual propagule dispersal and recruitment mechanisms, there is an apparent lacuna in the current understanding of mangrove ecology. The period between the mature propagule falling from the parental mangrove tree and the early growth of the established seedling, under various possible circumstances, remains in the dark. In this study we focus on this particular period by investigating both the places where these propagules end up as the pathways their dispersal units follow. And we go one step further. Mangrove forests are being destroyed worldwide at a threatening pace despite their tremendous asset to coastal human communities and associated biological species. The effect of human-induced (cutting and mangrove conversion to aquaculture ponds) as well as indirectly and/or ‘naturally’ evolving disturbances (sea level rise) on propagule hydrochory occupies an important place in this study. Dispersal of water-buoyant propagules of the family Rhizophoraceae and Acanthaceae (now including the Avicenniaceae) was studied in Gazi Bay (Kenya), Galle and the Pambala-Chilaw Lagoon Complex (Sri Lanka). The study sites differ both in tidal regime and vegetation structure, covering an interesting variety of ecological settings to examine propagule dispersal. Field data and experiments ranging from micro/ mesotopographical measurements and successive propagule counts to hydrodynamic and propagule dispersal experiments were collected or executed in situ. Two main methodological approaches were employed. Firstly, the question on mechanisms of propagule recruitment was addressed by statistically investigating the effect of microtopography, top soil texture and above-ground-root complexes on the stranding and self-planting of propagules (Chapter 2&3). Afterwards, suitability maps were created using Geographical Information Systems (GIS) to assess whether a particular mangrove stand has the ability to succesfully rejuvenate. Furthermore, the effect of degradation (tree cutting) (Chapter 2&3), sea level rise (Chapter 2&4) and microtopography-altering burrowing activities of the mangrove mud lobster Thalassina anomala (Chapter 3), was incoporated in the GIS-analyses. Secondly, the combined set-up of hydrodynamic modelling and ecological dispersal modelling was developed to simulate propagule dispersal pathways influenced by dispersal vectors (tidal flow, fresh water discharge, wind), trapping agents (retention by vegetation or aerial root complexes) and seed characteristics (buoyancy, obligated dispersal period) (Chapter 5&6). This type of approach provided the possibility to explore propagule dispersal within its ecological context, but was also applied to an implication of shrimp pond area restoration (Pambala-Chilaw Lagoon Complex, Sri Lanka) (Chapter 5) and to evaluate changes in propagule dispersal when sea level rises (Gazi Bay, Kenya) (Chapter 6). The main findings regarding propagule recruitment indicate that propagules are not distributed equally or randomly within a mangrove stand, yet species-specific distribution for anchorage occurs. Characteristics of the environment (microtopography, top soil texture and above-ground root complex) influence propagule recruitment in a way that complex root systems (e.g. pencil roots and prop roots) facilitate the entanglement of dispersal units and a more compact soil texture (like clay and silt) and a predominant flat topography creates suitable areas for stranding and self-planting of propagules. This combines effects of existing vegetation and abiotic factors on mangrove propagule establishment. Since propagule dispersal is not solely determined by species-specific propagule characteristics (e.g. buoyancy, longevity, etc.), I emphasize that propagule sorting by hydrochory has to be viewed within its ecological context. Propagule retention by vegetation and wind as a dispersal vector, deserve a prominent role in studies on propagule dispersal. The significance of dense vegetation obstructing long distance dispersal (LDD in its definition of this work), mainly in inner mangrove zones, supports our main finding that propagule dispersal is largely a short distance phenomenon. ‘Largely’ is here understood as quantitatively, not excluding epic colonization events of rare but important nature. In accordance with the Tidal Sorting Hypothesis (TSH) of Rabinowitz (1978a), smaller, oval-shaped propagules were found to disperse over larger distances than bigger, torpedo-shaped propagules. We can however not fully support the TSH because (1) these differences are no longer valid when comparing between torpedoshaped propagules of different sizes and (2) propagule dispersal is not always directed towards areas more inland, but can be strongly concentrated towards the edges of lagoons and channels Anthropogenic pressure on mangrove ecosystems, more specifically clear-felling or mangrove conversion to aquaculture ponds, imposes limitations on propagule recruitment due to reduced propagule availability and a decrease in suitable stranding areas where the architecture of certain root complexes, like prop roots and pencil roots, function as propagule traps. These types of pressure appear to have more severe consequences on propagule dispersal than the effect of sea level rise on mangroves. Mangrove forests, which are not situated in an obviously vulnerable setting, can be resilient to a relative rise in sea level if a landward shift of vegetation assemblages and successful early colonization is not obstructed by human-induced pressures. Also, and this renders mangrove forests vulnerable in spite of their intrinsic resilience, when the ‘capital’ of forest is severely reduced or impoverished as happens extensively worldwide, the ‘interest’ on this capital, understood as propagule availability, delivery and trapping, will not allow them to efficiently cope with sea level rise, putting sustainability of mangrove ecosystem services and goods at risk. In a larger framework of mangrove vegetation dynamics, knowledge on propagule dispersal will benefit management strategies for the conservation of mangroves worldwide, besides its fundamental interest to fully fathom the ecology of this particular marine-terrestrial ecotone formation.

In this study,we used mangrove phytoremediation ecotechniques to treat polycyclic aromtic hydrocarbons (pyrene) contaminated soil. First, we compared the four species of mangroves in Taiwan, Kandelia candel Druce, Rhizophora stylosa Griff, Avicennia marina Vierh and Lumnitzera racemosa Willd, inoculated by endomycorrhizae in no contaminated soils. According to the experimental results, the four species of mangroves could be colonized by Glomus aggregatum and Glomus mosseae. In colonization rate and colonization intensity, Glomus aggregatum were found higher than those of Glomus mosseae. For the degradation efficiencies of pyrene in soils, according to the experimental results, we found that the Lumnitzera racemosa Willd exhibited best growing conditions among the four species. The degradation rates for all tests systems pyrene were measured above 90% . In accordance with passed study, the species of Kandelia candel Druce presented effective efficiencics for pyrene degradation. The speacis of Lumnitzera racemosa Willd and Kandelia candel Druce were planted in the artifical pyrene contaminated soils, which were incubated in a greenhouse , while the control systems without vegetation were used for comparison. After 90 days of incubation, the experimental result showed that the soils planted with Lumnitzera racemosa Willd and Kandelia candel Druce were found able to enhance the microbial and dehydrogenase activities. The addition of Glomus aggregatum could help plants to prevent from the stress of pyrene. The addition of salinity into the siols was a pressure for mangroves so the mangroves, incoculated by endomycorrhizae showed stronger dependence on mycorrhizal fungi than those in the siols of no salinity. In salty siol, mangroves exhibited high effective degradation rates for pyrene. In the siols for the illumination groups, the pyrene degradation rates for all test systems were measured about 85%. The siols for the dark groups showed that the average pyrene degradation rates were about 70%.

Ammonia/ammonium-oxidizing prokaryotes (AOPs) play a crucial role in nitrogen transformation in the natural ecosystems including mangrove wetlands. The objectives of the present study were to investigate the spatial and temporal distribution of AOPs in the mangrove wetland sediments in subtropical Hong Kong and their ecophysiology. When AOP communities and abundances in a natural coastal mangrove wetland and a constructed freshwater wetland were compared, the constructed freshwater wetland contained a broader range of phylotypes, higher diversity, more complex community structures, and more uneven abundances of AOPs than the mangrove wetland. Typha angustifolia affected the community structures of all AOPs and enhanced their abundances in the rhizosphere. Both Phragmites australis and Cyperus malaccensis showed some effects on the community structures of ammonia-oxidizing bacteria (AOB), but little effects on those of anaerobic ammonium oxidizing (anammox) bacteria or ammonia-oxidizing archaea (AOA). Kandelia obovata had no detectable effect on any group of the AOPs due to their smaller size. AOPs in oxic and anoxic sediments of a protected mangrove wetland were investigated in both winter and summer. Seasonality had little effect on community structure and abundance of anammox bacteria. AOA community structures were stable between the two seasons, but AOA abundance was significantly higher in winter than summer. The community structures of AOB were different between winter and summer, but the abundance in winter was apparently higher than that in summer. Sediment type had a noticeable influence on community structure and abundance of anammox bacteria. No apparent difference in AOA community structures between the different types of sediments in winter was observed, but the oxic sediments showed obviously different AOA community structures from anoxic sediments in summer. Sediment type had little effect on AOB community structures, but AOB abundance in oxic sediments was obviously lower than anoxic ones in both seasons. Addition of acetate or leaf litter into sediment inhibited the growth of anammox bacteria in laboratory incubation. The inhibition of anammox bacteria by acetate was more pronounced than by leaves. Acetate and leaf litter did not affect AOA community structures, but promoted their growth. Both acetate and leaf litter affected the AOB community structures and promoted their growth in the early phase of the incubation. The promoting effects by leaf litter were more obvious than by acetate. Allylthiourea effectively inhibited the growth of both AOA and AOB in laboratory incubation, but only slightly for anammox bacteria. Acidic condition altered AOB community structure, but affected anammox bacteria and AOA slightly. Alkaline condition strongly affected community structures of anammox bacteria and AOA, but slightly for AOB. Alkaline condition inhibited the growth of anammox bacteria, but promoted AOA and AOB slightly. Increase in salinity resulted in higher diversity of anammox bacteria, and AOA and AOB might have species specific preference for salinity. High salinity promoted anammox bacteria growth; inhibited AOA for 5-10 days, but promoted them afterward; and promoted AOB. Totally, this study revealed new and specific information on the spatial and temporal distribution of AOPs in mangrove wetland and factors affecting their ecophysiology. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Thesis (M. Env. Sc.)--University of Adelaide, Mawson Graduate Centre for Environmental Studies, 1998. / Includes bibliographical references (leaves 65-71).