The habitability of Earth is dependent upon the global recycling of elements essential for life, such as nitrogen, sulfur and carbon. Nutrient-cycling by micro-organisms is vital to these biogeochemical cycles because many key steps are mediated primarily, or exclusively, by microbial life. The dynamics of these cycles are highly complex, and environmental perturbations (such as changes in the oceanic oxygen concentration) can have unexpected or catastrophic effects; often causing abrupt switches between chemical states. Despite the importance of these environmental perturbations however, few theoretical models have addressed how they affect the dynamical behaviour of nutrient-cycling microbial ecosystems. In this work, we investigate the effect of environmental perturbations on microbially-mediated nutrient cycles and assess the likelihood of "sudden transitions" between chemical states of the ecosystem occurring in a variety of ecological contexts. To do this, we first use computational modelling of microbial nutrient-cycling, using a "box model" approach. We then move on to an experimental study using the microbial sulfur cycle as a model ecosystem, with freshwater pond sediment/water microcosms. These microcosms have the advantage of retaining many of the features of the real ecosystem (such as microbial diversity, spatial structure, and abiotic interactions) while allowing the controlled manipulation of environmental perturbations. We study these microcosms using a combination of chemical measurements and high-throughput sequencing of the microbial community. Finally, we return to the computational side, and attempt to reproduce chemical data from our experiments in a mathematical model containing realistic abiotic chemical interactions.

Magister Philosophiae - MPhil / This study outlines human dimensions in the hake sector in South Africa in terms of hake fish workers. The hake fish workers condition of employment, security of employment, social security issues, remunerations and their living conditions forms part of the social, economic and political dimensions in hake fisheries. The need for ensuring sustainable long-term utilisation of the hake resource and to manage, prevent and reduce all adverse effects of harvesting the hake stock through knowledge based intervention is crucial to this study. Sustainable fisheries management can use the working and living conditions of fish workers as indicators for effective management of fisheries. Fish workers issues, which include their conditions of service, contractual agreements, work safety, income, working hours and other human dimensions, may have an effect on the effective sustainable management. Ecosystems approaches takes into consideration the human dimensions and ecological consideration for effective fisheries management. Knowledge of the historical and economic importance of the hake sector is crucial for the planning and future of the fisheries. Applying the concept of the ecosystems approaches to hake fisheries management is also critical in understanding the human dimensions in hake fisheries. The qualitative methodology of field work was used in understanding the human dimensions in commercial hake fisheries. The investigation into the fish workers labour issues and living conditions through a field work highlighted that the labour issues such as type of employment (permanent or casual), conditions of employment (social security, regulated hours of work, good working conditions), stagnation in terms of promotion, remuneration and issues surrounding labour brokers are some of the social issues in the hake sector. The living conditions of fish workers, stagnation and improved remuneration should be attended to in the sector. Fish workers in the hake sector rely on wages for their livelihood. Workers’ participation in decision-making at governance level should be enhanced for effective governance in the fisheries

Riparian ecosystems are valuable to the ecological and human communities that depend on them. Over the past century, they have been subject to shifting management practices to maximize human use and ecosystem services, creating a complex relationship between water policy, management, and the natural ecosystem. This has necessitated research on the spatial and temporal dynamics of riparian vegetation change. The San Acacia Reach of the Middle Rio Grande has experienced multiple management and river flow fluctuations, resulting in threats to its riparian and aquatic ecosystems. This research uses remote sensing data, GIS, a review of management decisions, and an assessment of climate to both quantify how riparian vegetation has been altered over time and provide interpretations of the relationships between riparian change and shifting climate and management objectives. This research focused on four management phases from 1935 to 2014, each highlighting different management practices and climate-driven river patterns, providing unique opportunities to observe a direct relationship between river management, climate, and riparian response. Overall, we believe that management practices coupled with reduced surface river-flows with limited overbank flooding influenced the compositional and spatial patterns of vegetation, including possibly increasing non-native vegetation coverage. However, recent restoration efforts have begun to reduce non-native vegetation coverage.

Les régions urbaines imposent d’intenses et multiples changements environnementaux sur les écosystèmes qu’elles contiennent et qui les entourent, et les réponses des écosystèmes à ces environnements urbains est encore relativement peu connue, même pour des processus fondamentaux comme les cycles du carbone (C) et de l’azote (N). Ce travail utilise une chronoséquence de systèmes sol-arbre d’alignement (plantations de Tilia tomentosa Moench) de 75 ans, situés à Paris, comme étude de cas principale, afin de détecter des tendances de long terme dans les cycles urbain du C et du N et d’en inférer les potentiels mécanismes sous-jacents. Un patron d’accumulation du C et du N dans les sols de rue est décrit, et nous faisons l’hypothèse que le C dérivé des racines, et le N issu des dépôts atmosphérique et apports animaux, s’accumulent dans ces sols. Ensuite, une analyse des fractions organo-minérales des sols suggère qu’il y a bien une accumulation de matière organique du sol (MOS) relativement récente. Les analyses 13C et 15N suggèrent que les racines sont un contributeur majeur à cette augmentation de la teneur en MOS et de la rétention du N exogène. Les taux de nitrification et de dénitrification potentielles augmentent avec l’âge des systèmes de rue, ce qui semble être déterminé par une augmentation des bactéries oxydant l’ammoniaque. Les dynamiques de long terme pour le C semblent caractérisées by une augmentation des apport hypogés couplée à des mécanismes de stabilisation du C racinaire. Pour le N, les sorties de N semblent contrebalancées par d’importants apports exogènes et les racines, apports dont une partie est retenue dans la biomasse végétale (racines) et la MOS. / Urban areas impose multiple and intense environmental changes on the ecosystems they contain or that surround them, and the ecosystem responses to urban environments are still poorly known, even on fundamental ecosystem processes such as carbon (C) and nitrogen (N) cycling. The dynamics of urban ecosystems, especially on the long-term, have received little attention. The present work uses a 75-year chronosequence of street soil-tree systems (plantations of Tilia tomentosa Moench) in Paris, France, as its main case study to detect long-term patterns in urban C and N cycling and infer potential underlying mechanisms. This thesis describes age-related patterns of C and N accumulation in soils, and we hypothesize that tree root-derived C and deposited N from the atmosphere and animal waste accumulate in soils. Then, an analysis of soil particle-size fractions further points towards a recent accumulation of soil organic matter (SOM), and 13C and 15N analysis suggests that tree roots are a major contributor to the increase of SOM content and N retention. Potential nitrification and denitrification rates increase with street system age, which seems driven by an increase in ammonia-oxidising bacteria. The long-term dynamics of C seem characterized by increasing belowground inputs coupled with root-C stabilization mechanisms. For N, the losses are likely compensated by exogenous inputs, part of which is retained in plant biomass (roots) and SOM.These results are then discussed in light of results obtained on Parisian black locust systems (Robinia pseudoacacia Linnæus), as well as other data, and management recommendations are proposed.

Les écosystèmes ultramafiques (serpentiniques) de Nouvelle-Calédonie sont considérés comme des « hotspots » de la biodiversité, notamment en raison des pressions adaptatives exercées par des conditions édaphiques drastiques. En effet, ces sols, résultant de l'altération naturelle du manteau océanique, sont composés de plus de 85% d'oxydes de fer, sont déficients en N, P, K, déséquilibrés en Ca/Mg et riches en métaux lourds (Ni, Cr, Mn, Co). Dans les associations entre végétaux et microorganismes du sol, les deux partenaires jouent un rôle essentiel dans l'adaptation aux conditions édaphiques, essentiellement au niveau de la tolérance aux métaux lourds. Dans notre étude, nous avons choisi des espèces endémiques du genre Tristaniopsis (Myrtaceae) comme plantes modèles pour étudier le rôle des champignons ectomycorhiziens et des bactéries associées à l'adaptation des plantes au nickel. Pour étudier l'effet des sols ultramafiques sur la diversité des ectomycorhizes et des bactéries mycorhizosphériques, ainsi que sur les déterminants génétiques de résistance/adaptation des bactéries associées, environ 150 ectomycorhizes ont été échantillonnées à partir de quatre sites ultramafiques (trois au massif du Koniambo et un dans la forêt de Desmazures) et deux non-ultramafiques reposant sur des sols volcano-sédimentaires (site d'Arama). La caractérisation génotypique et phylogénétique des ectomycorhizes et des bactéries mycorhizosphériques obtenues a révélé la présence d'une grande diversité de champignons (principalement Cortinarius, Pisolithus, Russula, Boletellus) et de bactéries (Pseudomonas, Burkholderia, Bacillus) dans les deux types de sols, avec une richesse spécifique particulièrement élevée dans les sols ultramafiques. De plus, les bactéries mycorhizosphériques provenant des sols ultramafiques avaient des proportions significativement plus élevées d'isolats portant les gènes nreB et cnrT que celles issues des sols volcano-sédimentaires. Une forte corrélation positive a également été observée entre l'occurence de ces gènes, connus pour conférer la tolérance aux métaux lourds chez les bactéries, et la tolérance des isolats au nickel en culture pure. La récente mise en évidence de souches bactériennes mycorhizosphériques Ni-tolérantes et promotrices de la croissance de Pisolithus albus en co-culture doivent permettre d'identifier des bactéries auxiliaires de la mycorhization qui pourront être ensuite exploitées dans le cadre de programmes de revégétalisation de sites ultramafiques miniers en Nouvelle Calédonie. / New Caledonian ultramafic (serpentine) ecosystems are considered as hotspots of biodiversity, partly because of the adaptative pressure exerted by drastic edaphic conditions. Indeed these soils resulting from natural weathering of oceanic mantle could be composed of up to 85 % of iron oxides and are deficient in N.P.K., unbalance for the Ca/Mg ratio and rich in heavy metals Ni, Cr, Mn, Co. Both plant and soil microbes play a vital role in the adaptation to soil conditions mainly heavy metal uptake and tolerance. In our study, we choose endemic species of the genus Tristaniopsis (Myrtaceae) as model plant to study the role of ectomycorrhizal fungi and associated bacteria in plant adaptation to nickel. To investigate the effect of ultramafic soils on ectomycorrhiza and mycorrhizosphere bacteria diversities as well as on the genetic determinants of resistance/adaptation of associated mycorrhizosphere bacteria, 200 ectomycorrhizas were sampled from four different ultramafic sites (3 in Koniambo and 1 in Desmazures forest) vs two non-ultramafic ones from volcano-sedimentary soils (Arama). Molecular characterization of ectomycorrhiza (rRNA ITS) and associated mycorrhizosphere bacteria (16S rRNA) from these samples showed the presence of different fungi (Pisolithus albus, Russula spp., Boletellus spp.) and bacteria (Burkholderia spp., Bacillus spp., Pseudomonas spp.) that can be found in both soils. However, bacteria isolated from ultramafic soils could grow in the presence of Ni up to 20 mmol L-1 and contained cnrA and nreB genes, known to confer heavy metal tolerance, contrary to bacteria isolated from non-ultramafic soils. Moreover, we found a strong positive correlation between heavy metal tolerance and P-solubilizing ability. Further knowledge on functional diversity of ectomycorrhiza-mycorrhizosphere bacteria associations and its role in the adaptation of plants to ultramafic soils would help in the understanding of plant functioning on New Caledonian mine sites.

abstract: Climate change is increasing global surface temperatures, intensifying droughts and increasing rainfall variation, particularly in drylands. Understanding how dryland plant communities respond to climate change-induced rainfall changes is crucial for implementing effective conservation strategies. Concurrent with climate change impacts on drylands is woody encroachment: an increase in abundance of woody plant species in areas formerly dominated by grasslands or savannahs. For example, the woody plant, Prosopis velutina (velvet mesquite), has encroached into grasslands regionally over the past century. From an agricultural perspective, P. velutina is an invasive weed that hinders cattle forage. Understanding how P. velutina will respond to climate change-induced rainfall changes can be useful for management and conservation efforts. Prosopis velutina was used to answer the following question: Is there a significant interactive effect of mean soil water moisture content and pulse frequency on woody seedling survival and growth in dryland ecosystems? There were 256 P. velutina seedlings sourced from the Santa Rita Experimental Range in southern Arizona grown under four watering treatments where mean and pulse frequency were manipulated over two months. Data were collected on mortality, stem height, number of leaves, instantaneous gas exchange, chlorophyll fluorescence, biomass, and the leaf carbon to nitrogen (C:N) ratio. Mortality was low across treatments. Pulse frequency had less impact across response variables than the mean amount of water received. This may indicate that P. velutina seedlings are relatively insensitive to rainfall timing and are more responsive to rainfall amount. Prosopis velutina in the low mean soil moisture treatments lost a majority of their leaves and had greater biomass allocation to roots. Prosopis velutina’s ability to survive in low soil moisture conditions and invest in root biomass can allow it to persist as drylands are further affected by climate change. Prosopis velutina could benefit ecosystems where native plants are at risk due to rainfall variation if P. velutina occupies a similar niche space. Due to conflicting viewpoints of P. velutina as an invasive species, it’s important to examine P. velutina from both agricultural and conservation perspectives. Further analysis on the benefits to P. velutina in these ecosystems is recommended. / Dissertation/Thesis / Masters Thesis Plant Biology and Conservation 2020

Herbivores have a significant role in tundra ecosystem composition and processes. They can cause changes of vegetation composition and nutrient content that result in altered palatability of the vegetation and food availability for herbivores. The direct effect of herbivores on plant quality and quantity have been studied in detail, and recent studies have shown that present vegetation composition and soil processes might show legacies of historical grazing a century ago. This raises the question if historical grazing also has a legacy on the palatability of the vegetation. In this study, I investigated if the quality of the vegetation of the Historical Milking Grounds (HMGs) heavily grazed up until a century ago is still under influence a century after the heavy grazing has ceased. I focused on the nitrogen content and digestibility of the vegetation, since these should be two independent measures of food quality which, when evaluated together, should give a good estimate of the quality of the forage.

As the demand for distance learning increases, traditional campus-based universities continue to struggle in supporting working distance students. This has resulted in the increased phenomena of students using social media within their ecosystems of learning support. The use of formal and informal tools such as social media gives rise to boundaries which students need to cross for effective support. How social media facilitates the crossing of boundaries within ecosystems of learning support remains an unfamiliar area of research. This study employed a predominately qualitative research methods, with a small element being a quantitative method to view and investigate postgraduate distance students' ecosystem of learning support holistically. The findings of this study revealed that participants used a combination of formal and informal tools to support their learning, including social media. In particular WhatsApp, which enables the crossing of transitional, formal and informal learning contexts, hierarchical and, time and space boundaries. Recognizing social media as an important part of students' learning support ecosystem, allowed an expanded view on learning support. As such, the study highlighted a range of different learning mechanisms which occur when students cross these boundaries, with coordination being the dominant learning mechanism. In conclusion, social media (such as WhatsApp) does indeed enhance the crossing of various boundaries to support learning. However, some students do not necessarily perceive their interaction on social media as learning, which speaks to the need of legitimising social media as learning tools by institutions. This study then recommends the need for institutions to recognize and nurture the use of social media as one element of a distance learning support ecosystem for cost-effective student support strategies guided by institutional guidelines and policies.

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

"Où peut-on trouver des microbes, et comment survivent-ils dans ces lieux ?" sont des questions essentielles afin de comprendre la vie sur Terre. Les populations bactériennes du sol sont connues pour jouer un rôle important dans les cycles biogéochimiques, l'entretien des sols, les effets climatiques et l'agriculture.Dans ce travail, j'ai utilisé la technique de pyroséquençage, via le produit d’une PCR d’ADNr 16S amplifiée extraite d’ADN totale, afin de révéler les populations bactériennes présentes dans quatre environnements inhabituels et oligotrophes différents:A. Les écosystèmes saumâtres sont largement distribués sur Terre et sont représentés par des systèmes aquifères salés et des sols salins. Nous avons examiné la composition bactérienne des sédiments des estuaires, sols saumâtres et des échantillons de sol sablonneux de la région de Camargue, échantillonnés pendant deux années consécutives. Les membres appartenant au phylum Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria et Actinobactéries ont été trouvés principalement dans les sols et sédiments. Nous avons constaté que les membres de ces groupes bactériens étaient associés principalement à des bactéries halophiles, sulfatoréductrices (SRB), nitratoréductrices et coliformes, dont leurs proportions ont probablement été affectées par la salinité et leurs localisations géographiques.B. Les bactéries associées à la rhizosphère des plantes sont connues pour jouer un rôle essentiel dans les cycles biogéochimiques, la nutrition des plantes et la lutte biologique contre les maladies végétales. Nous avons examiné les populations bactériennes de la rhizosphère du riz (Oryza sativa) en fin de croissance dans la région de la Camargue en 2013 et 2014. Les populations bactériennes les plus abondantes se sont révélées être des membres appartenant au phylum Proteobacteria, Acidobacteria, Chloroflexi et Gemmatimonadetes. Les genres bactériens auxquels appartiennent ces différents phylums sont connus pour participer dans des processus biogéochimiques du sol, tel que la nitrification, la dénitrification, l'oxydation, ainsi que comme agents de control biologique. Les proportions bactériennes trouvées varient considérablement en fonction de leur localisation géographique et selon l’année d’échantillonnage.C. Nous avons examiné les sols de surface de "Padza de Dapani" situés sur l'île de Mayotte au large de la côte est de l'Afrique, car cette région n’est pas un vrai désert, mais y ressemble due à l’érosion du sol. Les sols de Mayotte sont acides, oligotrophes et minéralisées, et leur population bactérienne principale appartient aux phylums des Actinobactéries, Proteobacteria et Acidobacteria. Un fait intéressant, les membres des genres Acinetobacter, Arthrobacter, Burkholderia et Bacillus sont prédominants dans nos échantillons, comme observé dans des déserts (asiatiques) chauds et jouant probablement un rôle dans la minéralisation des sols, expliquant la désertification.D. Les régions arides de la Terre constituent > de 30% de la surface continentale et les sols oligotrophes sont soumis à des facteurs environnementaux difficiles tels que la faible pluviométrie moyenne annuelle, l'exposition aux UV et les grandes fluctuations de température. Nous avons examiné les populations bactériennes présentes dans la rhizosphère des plantes pionnières et les sols de surface du désert de Jizan d'Arabie Saoudite. Les phylums bactériens les plus abondants appartiennent aux groupes des Bacteroidetes, Proteobacteria et Firmicutes qui diffèrent entre la rhizosphère des plantes étudiées par rapport à la surface du sol, à l'exception de la plante "Panicum Turgidum" qui contient des proportions élevées (70%) des membres appartenant au genre Flavobacterium. / “What microbes are where, and how do they live there” is now an essential question to understand life on Earth, even when comparing seemingly similar ecosystems in different locations. Soil bacterial populations are known to play important roles in biogeochemical cycles, soil maintenance, climatic effects and agriculture. I used pyrosequencing of PCR amplified 16S rDNA from total extracted DNA in order to reveal the bacterial populations living in four different unusual and oligotrophic environments: A. Saline areas are widely distributed on Earth’s and are represented by both saline lakes and saline soils. We examined the bacterial composition of estuary sediments, brackish and sandy soil samples from the Camargue region (Rhône delta in southern France) sampled in two consecutive years. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria and Actinobacteria phyla were found principally in saline sediment and soil samples. We found that members from these phyla were associated principally to halophilic bacteria, sulphate reducing bacteria (SRB), nitrate reducing bacteria and coliforms, and that their varying proportions were likely affected by salinity and geographical location. B. Bacterial populations associated with the rhizosphere of plants are known to play essential roles in biogeochemical cycles, plant nutrition and disease biocontrol. We examined the bacterial populations of the rhizosphere of rice (Oryza sativa) growing in the Camargue region in 2013 and 2014. The most abundant bacterial populations were found to be members belonging to the Proteobacteria, Acidobacteria, Chloroflexi and Gemmatimonadetes phyla. The genera members belong these phyla were found to participate in soil biogeochemical processes such as nitrification, denitrification, oxidation, as well as act as biocontrol agents. The bacterial populations were found to significantly vary by geographical location as well by year of collection. C. We examined the surface soils from “Padza de Dapani” on the island of Mayotte off the east coast of Africa, as this region is not a true (hot) desert, but resembles one due to extensive soil erosion. In the acidic, oligotrophic and mineralized soil samples from Mayotte, members of the Actinobacteria, Proteobacteria and Acidobacteria phyla dominated the bacterial populations. Interestingly, members of the genera Acinetobacter, Arthrobacter, Burkholderia and Bacillus were found to be predominant in our samples, as is also observed in hot (Asian) deserts and may play roles in soil mineral weathering, thus helping to understand desertification processes. D. Earth’s arid regions comprise >30% of the continental surface and the oligotrophic soils are subjected to harsh environmental factors such as low average annual rainfall, high UV exposure and large temperature fluctuations. We examined the bacterial populations present in the rhizosphere of pioneer plants and surface soils in the Jizan desert of Saudi Arabia. The most abundant bacterial phyla belonged to the Bacteroidetes, Proteobacteria and Firmicutes phyla that were different between the rhizosphere of plant versus these from surface sand, with the exception of the plant “Panicum Turgidum”, which contain in its rhizosphere high proportions (70%) of members belonging to the Flavobacterium genus.