I investigated the effects ofhabitat loss and subsequent restoration on invertebrate community structure and ecosystem functioning in a mined peat bog in the North Island, New Zealand. In an experimental trial, the impact of peat bog habitat loss and isolation on the invertebrate community associated with Sporadanthus ferrugineus (Restionaceae) was investigated. Potted S. ferrugineus plants were exposed to invertebrates at various distances up to 800 m from an intact habitat (the presumed source population) over 18 weeks. Invertebrates rapidly colonised the experimental plants, with all major Orders and trophic groups present on Sc ferrugineus within 6 weeks. However. with increasing distance away from the undisturbed habitat, there was a significant decrease in total richness and abundance of invertebrates associated with the potted plants. Additional tests showed that even a moderate degree of isolation (i.e. greater than 400 m) from the intact habitat caused an almost complete failure of 'Batrachedra' sp. to colonise its host plant, at least in the short-term, The density of eggs and larvae, and the average larval size of 'Batrachedra' sp. (Lepidoptera: Coleophoridae) colonising Si ferrugineus plants, as well as the proportion of Si ferrugineus stems damaged by 'Batrachedra' sp. herbivory, all decreased logarithmically with increasing distance from the intact habitat. Surprisingly, though, the rate of recovery of the insect-plant interaction following experimental habitat restoration was remarkably rapid (i.e. between 3Y2 and 6 years). After just 6 years there was no significant difference in insect-plant interactions between the intact peat bog sites and any of the experimentally restored sites up to 800 m away. These results suggest that the degree of isolation from undisturbed habitat has a major impact on the rate and patterns of restoration recovery in the invertebrate community and that some insect-plant interactions can recover rapidly from habitat loss with restoration management. Restoration of mined peat bogs in northern New Zealand is initiated by establishing a native vegetation cover to minimize further peat degradation. The effects of various restoration techniques on litter decomposition, microbial community activity and beetle community composition were investigated within an experimental trial, These treatments included translocation ofpeat bog habitat (direct transfer of islands), milled peat islands with no seed and milled peat islands with seed, and were compared with an unrestored mined site and an undisturbed peat bog. In all the response variables measured, the undisturbed peat bog sites had significantly higher decomposition rates and microbial respiration rates, and significantly higher abundance and species richness of beetles than any of the restoration treatments. Inaddition, the technique used to restore mined peatlands had a significant effect on the beetle community composition and litter decomposition processes. Despite a rapid initial change in the beetle community following habitat translocation, the direct transfer islands were still the most similar in beetle species composition to the undisturbed peat bog. Microbial activity and decomposition rates were higher in the direct transfer and mined peat surface after 6 months. However, even after 12 months, decomposition rates in the restored habitats were still far from reaching the levels recorded in the undisturbed peat bog. The results suggest that beetle community structure and ecosystem processes such as decomposition and microbial activity rates may be able to recover faster with certain restoration techniques, such as direct transfer of intact habitat islands. Subsequently, I examined long-term beetle community reassembly on islands that had been restored by creating raised areas ofprocessed peat with the addition of Leptospermum scoparium seed. Monitoring of different-aged restored islands representing the full range of restoration ages (up to 6 years) available at the peat mine, indicated that as the peat islands became older and the vegetation structure became more complex, the abundance, species richness and composition of the beetle community became increasingly similar to the community in the undisturbed peat bog. Despite this, distinct differences between the intact peat bog and older restored peat islands still persisted, even after 6 years, particularly at an individual species level. However, it is predicted that within 12 years the restored peat islands will share 100% ofbeetle species in common with the undisturbed peat bog. Taken together, these results indicate that restoration is effective in initiating the recovery of beetle assemblages and ecosystem processes (such as litter decomposition and microbial community activity) in cut-over peat bogs. However, it is estimated to take at least 12 years before pre-mining communities and functions are attained, and ongoing monitoring to develop an understanding of the longer-term dynamics of such ecosystems and processes is clearly required.

Made available in DSpace on 2015-03-26T13:51:56Z (GMT). No. of bitstreams: 1 texto completo.pdf: 807100 bytes, checksum: 0492f1cb907f9d50a51882efd7f76fcd (MD5) Previous issue date: 2012-02-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Three thermophilic lignocellulolytic microbial communities were selected by enriched method with continual subcultivation at 55 °C. One community was selected from cow manure compost, another from decaying sugar cane bagasse, and the last one was obtained by mixing aliquots of the culture suspension from the first two. Those communities were able to degrade a cellulosic strip in three cultivation days. Evaluating the maximal day of CMCase and xylanase activity, it was observed that the mixed consortium showed the best results, with CMCase activity of 0.09 U mg-1 at the second day of cultivation, and xylanase activity of 2.86 U mg-1 at the fourth day. These enzymes were partially characterized with relation to temperature and pH of optimal activity. It was observed that CMCase showed the highest activity at 60 °C and pH 5.4, and kept 80% of its activity in a pH range of 4.5-6.5. On the other hand, the best activity for xylanase was verified at 65 °C, and in that same pH range, the enzyme kept 97% of its residual activity. Cell-free extract was concentrated by ultrafiltration. The enzymatic cocktail obtained showed CMCase activity 25-fold higher and xylanase activity 55-fold higher than the crude enzymatic extract. The cocktail was conserved by adding 50% glycerol. After storage for 60 days at 4 °C, xylanase kept 80% of the initial activity and CMCase didn t show loss of activity when kept at 25 °C for the same period. The mixed community cellular mass constitutes an inoculant able to maintain the cellulolytic phenotype after rapid freezing and storage at - 80 °C for 60 days. Fed-batch essay suggested that this community has potential to be manipulated in order to continuously hold the cellulolytic enzymes expression over time. The results evidenced the acquisition of an enzymatic cocktail from an inoculant which cellulolytic activity supported pH changes and optimal activity around 60 °C. / Três comunidades microbianas lignocelulolíticas e termofílicas foram selecionadas por subcultivo em meio de enriquecimento a 55 °C. Uma comunidade foi selecionada a partir de esterco de gado em compostagem, outra de bagaço de cana em decomposição e a terceira foi obtida a partir da mistura de alíquotas do meio de cultivo das duas anteriores. Tais comunidades apresentavam a característica de decompor uma fita de celulose em três dias de cultivo. Ao se avaliar o dia de máxima atividade CMCase e xilanase em cada comunidade, verificou-se que os melhores resultados foram encontrados no consórcio misto, com atividade de 0,09 U mg-1 para CMCase no segundo dia de cultivo e 2,86 U mg-1 para xilanase no quarto dia. Essas enzimas foram parcialmente caracterizadas em relação à temperatura e pH ótimos de atuação. Verificou-se que CMCase apresentou maior atividade a 60 °C e pH 5,4, e manteve 80% de sua atividade numa faixa de pH de 4,5 a 6,5. Já para a xilanase, a temperatura ótima foi de 65 °C e nessa mesma faixa de pH manteve uma atividade residual de 97%. O extrato livre de células foi concentrado por ultrafiltração e obteve-se um coquetel enzimático com atividade de CMCase e xilanase maior que no extrato bruto cerca de 25 e 55 vezes, respectivamente. O coquetel foi conservado pela adição de 50% de glicerol. Após 60 dias de armazenamento a 4 °C, a xilanase manteve 80% de sua atividade inicial e a CMCase não apresentou perda de atividade quando mantida a 25 °C pelo mesmo período. A massa celular da comunidade mista constitui um inoculante capaz de manter o fenótipo celulolítico após congelamento rápido e armazenamento a - 80 °C por 60 dias. Ensaio em batelada alimentada mostrou que essa comunidade apresenta potencial para ser manipulada a fim de se manter continuamente a expressão de enzimas celulolíticas ao longo do tempo. Os resultados mostraram que foi possível obter um coquetel de enzimas a partir do inoculante, cuja atividade celulolítica tolerou variações de pH e temperatura ótima em torno de 60 °C.

Os microorganismos estão entre os maiores responsáveis pela transformação dos compostos orgânicos em uma lagoa de estabilização e são a chave do sucesso deste tratamento. A utilização de técnicas de biologia molecular em conjunto é uma das melhores formas para obter resultados mais confiáveis. A estrutura da comunidade microbiana na lagoa de estabilização facultativa da estação de tratamento de esgoto doméstico do Município de Cajati foi descrita baseada nos padrões dos fragmentos do gene RNAr 16S por PCR-DGGE, CARD-FISH, biblioteca de clones de gene RNAr 16S e sequenciamento. Os padrões obtidos com o DGGE foram correlacionados com as variáveis ambientais coletadas por análise de redundância (RDA). As amostras foram coletadas em três períodos para o estudo da variação temporal, coletou-se em três profundidades (superfície, 0,7 m e 1,5 m) para o estudo espacial vertical e em nove pontos a 0,7 m de profundidade para o estudo espacial horizontal da comunidade. / Microorganisms are amongst the most responsible for the conversion of sewage organic compounds and they are the key of the treatment success. The combination of two or more molecular techniques in this kind of assessment allows getting more accurate results concerning a microbial community. The facultative stabilization pond microbial community structure of domestic sewage treatment from Cajati city was characterized based on 16S RNAr gene fragments patterns from PCR-DGGE, FISH, 16S RNAr gene clone library and sequencing. The patterns obtained by DGGE were co-related to environmental variables by redundancy analysis (RDA). The samples were collected in three intervals to study the seasonal variation, it was collected in three depth (surface, 0,7 m and 1,5 m) to the vertical assessment and in nine spots at 0,7 m depth for the horizontal assessment of the microbial community.

Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / O grande volume de Ãgua utilizado na agricultura compromete a sua disponibilidade para o consumo humano. Diante desse problema, Ã necessÃrio avaliar a utilizaÃÃo de Ãguas residuais na produÃÃo agrÃcola, como uma opÃÃo para a conservaÃÃo dos recursos hÃdricos. Ãguas residuais oriundas de campos de petrÃleo podem ser uma boa opÃÃo para irrigaÃÃo, especialmente em regiÃes de pouca e alta variabilidade de chuvas como o Nordeste brasileiro. No entanto, Ã necessÃrio avaliar os seus efeitos no solo, como acÃmulo de nutrientes e decomposiÃÃo da matÃria orgÃnica, bem como no aspecto nutricional e no crescimento das plantas. Os objetivos deste trabalho foram: i) Avaliar as mudanÃas ocorridas nos sais solÃveis e nas fraÃÃes da matÃria orgÃnica do solo e no crescimento de plantas de girassol (Helianthus annuus L.) cv. BRS 321, cultivadas em solo de textura arenosa irrigado com Ãgua residual oriunda da extraÃÃo de petrÃleo tratada por filtragem e osmose reversa; ii) Avaliar as alteraÃÃes nutricionais do girassol (Helianthus annuus) BRS 321 irrigado com Ãgua residual da extraÃÃo de petrÃleo e os efeitos sobre a produÃÃo de biomassa e de aquÃnios; e iii) Avaliar a decomposiÃÃo dos restos culturais de girassol (Helianthus annuus) cv. BRS 321 em Ãreas irrigadas com Ãgua residual da extraÃÃo de petrÃleo. O girassol foi cultivado durante trÃs perÃodos sucessivos em Ãreas irrigadas com Ãgua residual da extraÃÃo de petrÃleo tratada por filtragem (APF) e por osmose reversa (APO) ou Ãgua subterrÃnea do aquÃfero AÃu (ACA). Ao fim de cada ciclo foram determinados os valores de pH, condutividade elÃtrica (CE), a razÃo de adsorÃÃo de sÃdio (RAS) e os teores de Na, Cl, Mg, Ca, K, HCO3-, Ag, As, B, Ba, Cd, Co, Cr3+, Hg, Ni, Pb, Zn, alÃm de C nas fraÃÃes hÃmicas. Em raÃzes, parte aÃrea e aquÃnios determinaram-se os teores de N, P, K, Ca, Mg, S e Na e avaliaram-se o crescimento e o acÃmulo de biomassa. AlÃm disso, avaliou-se a decomposiÃÃo dos resÃduos da parte aÃrea das plantas de girassol. Houve alteraÃÃes nos atributos quÃmicos do solo, em destaque o acrÃscimo de sais, que foi maior nas Ãreas irrigadas com APF, e elevaÃÃo do pH, independente do tipo de Ãgua utilizado. A elevaÃÃo da salinidade e alcalinidade do solo reduziu o crescimento e o acÃmulo de biomassa das plantas. AlÃm disso, a irrigaÃÃo proporcionou alteraÃÃes nutricionais das plantas, que refletiram no crescimento e na produÃÃo de aquÃnios do girassol e na decomposiÃÃo dos resÃduos da cultura, com efeitos positivos ou negativos, conforme o tratamento da Ãgua residual. Concluiu-se que a Ãgua residual da extraÃÃo de petrÃleo utilizada na irrigaÃÃo afeta os atributos quÃmicos do solo, bem como a composiÃÃo nutricional e o desenvolvimento das plantas, principalmente quando irrigadas com a APF. AlÃm disso, a irrigaÃÃo com Ãgua residual alterou a mineralizaÃÃo dos resÃduos vegetais do girassol, mas nÃo a de decomposiÃÃo do carbono orgÃnico nas fraÃÃes hÃmicas. / The large volume of water used in agriculture compromises its availability for human consumption. Faced with this problem, it is necessary to evaluate the use of wastewater in agricultural production as an option for the conservation of water resources. Wastewater from oil fields can be a good choice for irrigation, especially in regions of low or high rainfall variability, as in the Brazilian Northeast. However, it is necessary to evaluate its effects on the soil, such as the accumulation of nutrients and decomposition of organic matter, as well as the nutritional aspect and plant growth. The aims of this study were: i) to assess the changes that take place in the soluble salts and soil organic matter fractions, and in the growth of plants of the BRS 321 cultivar of the sunflower (Helianthus annuus L.) cultivated in soil of a sandy texture and irrigated with wastewater obtained from oil extraction and treated by filtration and reverse osmosis; ii) to assess the nutritional changes in the BRS 321cultivar of the sunflower (Helianthus annuus) irrigated with wastewater from oil extraction, and the effects on biomass and achene production; and iii) to evaluate the decomposition of plant residue from the BRS 321 cultivar of the sunflower (Helianthus annuus) in areas irrigated with wastewater from oil extraction. The sunflower was grown for three successive periods in areas irrigated with wastewater from oil extraction treated by filtering (APF) and reverse osmosis (APO), or with groundwater from the AÃu aquifer (ACA). At the end of each cycle, pH values were determined, together with electrical conductivity (EC), the sodium adsorption ratio (SAR) and the levels of Na, Cl, Mg, Ca, K, HCO3-, Ag, As, B, Ba, Cd, Co, Cr3+, Hg, Ni, Pb, Zn, and of C in the humic fractions. The concentrations of N, P, K, Ca, Mg, S and Na were determined in the roots, shoots and achenes, along with growth and the accumulation of biomass. In addition, the decomposition of shoot residue from the sunflower plants was evaluated. Changes were seen in the chemical properties of the soil, highlighting an increase in salts, which was greater in the areas irrigated with APF; a rise was also seen in pH irrespective of the type of water used. The rise in soil salinity and alkalinity reduced the growth and accumulation of plant biomass. Moreover, irrigation resulted in nutritional changes in the plants, which were reflected in the growth and production of achenes, and in the decomposition of the plant residue, having positive or negative effects according to the treatment of the wastewater. It was concluded that wastewater from oil extraction used in irrigation affects the chemical properties of the soil as well as the nutritional composition and development of the plants, especially when irrigated with APF. Furthermore, irrigation with wastewater changed the mineralisation of the sunflower plant residue, but not the decomposition of the organic carbon in the humic fractions.

O Brasil é considerado o maior produtor mundial de cana-de-açúcar, voltada para a produção de açúcar, etanol e derivados. O aproveitamento de resíduos da usina, como torta de filtro e vinhaça no condicionamento do solo pode contribuir com a manutenção da sua fertilidade. Por outro lado, a cada operação agrícola necessária para o cultivo da cana-de-açúcar está associada uma emissão de GEE que deve ser contabilizada. O objetivo desta pesquisa foi estimar a emissão dos principais GEE (CO2, N2O e CH4) pela torta de filtro, e avaliar as alterações de alguns atributos das comunidades microbianas durante o processo de decomposição. Após avaliação de uma enquete sobre o modo de utilização da torta de filtro por diversas usinas, um estudo foi desenvolvido na Usina Costa Pinto localizada em Piracicaba (SP). A torta aplicada no sulco de plantio da cana foi monitorada quanto à emissão dos gases, sendo que as concentrações dos mesmos nas amostras foram determinadas por cromatografia gasosa. Os atributos microbiológicos examinados foram a biomassa, a atividade enzimática (fosfatase ácida, alcalina e ?-glicosidase) e a estrutura da comunidade através do polimorfismo de fragmento de restrição terminal (T-RFLP). Foi observada emissão significativa dos principais GEE predominantemente da torta quando aplicada nos sulcos de plantio, com destaque para o N2O, com uma proporção doze vezes maior em massa do que o CH4, em 56 dias de experimento. Quanto aos aspectos microbiológicos, o maior valor encontrado de carbono e nitrogênio da biomassa microbiana para a dose usualmente aplicada (25 Mg ha-1), foi com dois meses de experimento, com respectivamente 484,89 ?g C g solo seco-1 e 62,95 ?g N g solo seco-1, e correlacionado pelo coeficiente de Pearson com a atividade enzimática no material. Pela técnica de T-RFLP foi possível avaliar a estrutura dos Domínios de Archaea, Bacteria e Fungi na comunidade microbiana da torta de filtro. Não houve modificação dessa estrutura ao longo do tempo analisado. Os resultados obtidos reforçam a importância dos atributos microbiológicos aliados a fatores químicos e físicos e a influência dos mesmos sobre as emissões de GEE. / Brazil is the greatest worldwide producer of sugarcane with production of sugar, ethanol and derived. Usually applied to soil as fertirrigation, filter cake and vinasse on soil conditioning have contributed to the maintenance of fertility. On the contrary, each agricultural operation is associated to GHG emissions that must be accounted for the balance of products. This work aims evaluate GHG emissions (CO2, N2O and CH4) from the filter cake, as well as evaluate the main differences in the microbiological community available within the decomposition process. After evaluation of a survey about to use the filter cake by industries, the study has been developed at Usina Costa Pinto located in Piracicaba (SP). The filter cake applied to the row of sugarcane planting have been monitored by taking regular samples of the emissions. The concentration of the three gases in the samples has been determined by gas chromatography. The microbiological aspects has been evaluated by biomass, enzymatic activity (acid phosphatase, alkaline phosphatase, and beta-glycosidase) and the community structure through terminal restriction fragment length polymorphism (T-RFLP). Significant GHG emission has been observed; mainly from the filter cake applied to the row of sugarcane planting especially N2O, with ratio twelve times greater than CH4 in 56 days of experiment. For microbiological aspects, the maximum of carbon and nitrogen from the microbial biomass for the treatment usually applied (25 Mg ha-1), within two months of experimentation, with respectively 484,89 ?g C g dry soil-1 e 62,95 ?g N g dry soil-1, and correlated by the coefficient of Pearson with the enzymatic activity existent in the material. The T-RFLP analysis has allowed evaluate the community structures of Archaea, Bacteria e Fungi in the microbiological community of the filter cake. Modification in the community structures was not observed over this time examined. The results obtained reinforce the importance of microbiological aspects combined with chemical and physical factors and their influence on GHG emissions.

Abstract The plant can be considered a superorganism that consists of the plant per se and numerous populations of pro- and eukaryotic microorganisms. The interactions between the plant and endophytic microorganisms colonizing plant internal tissues are typically commensalistic or mutualistic. However, information on the role of endophytes in plant defense is limited because pathways are only partly known and systemic responses are typically not seen. The aim of this thesis was to study the priming capacities of endophytic Methylobacterium sp. IMBG290 on potato (Solanum tuberosum L.). Priming of plants by non-pathogenic bacteria allows the host to save energy and to reduce time needed for development of defense reaction during a pathogen attack. Priming phenomenon was demonstrated for Methylobacterium sp. IMBG290 as an activation of salicylic acid and jasmonate/ethylene-dependent defense pathways after challenge inoculation with the pathogen. Moderate activation of plant antioxidant system may also contribute to resistance induction by the strain. The viable but nonculturable state is presumably a survival strategy observed for the majority of bacterial endophytes. Pathogen attack or environmental changes can activate these quiescent forms. Thus Methylobacterium+ sp. IMBG290 became cultivable upon plant inoculation by nonpathogenic bacteria. I observed that the composition of the endophyte community changed in response to Methylobacterium sp. IMBG290 inoculation in shoot tissues and correlated with potato disease resistance and growth promotion. Therefore, the activation of endophytic bacterial populations as a putative mechanism of plant disease resistance was proposed. Endophytes have a high agricultural potential. Growth- and resistance-promoting capacities of Methylobacterium sp. IMBG290 on potato were highly variable depending on the cultivar, pathogen, inoculum density, and environmental conditions. Context-dependent efficacy requires more attention when designing complex microbial inoculants capable influencing positively plant growth, resistance, and nutritional properties. / Tiivistelmä Kasvia voidaan pitää superorganismina, joka koostuu kasvista itsestään ja lukuisista pro-ja eukaryottisista mikrobipopulaatioista. Kasvin ja sen sisäosia asuttavien endofyyttisten mikro-organismien väliset vuorovaikutukset ovat yleensä kommensalistisia tai mutualistisia. Endofyyttien rooli kasvin puolustuksessa on kuitenkin huonosti tunnettu, koska reitit tiedetään vain osittain eikä järjestelmällisiä vasteita usein havaita. Tämän väitöskirjatyön tavoitteena oli tutkia endofyyttisen Methylobacterium sp. IMBG290-kannan kykyä vahvistaa perunan (Solanum tuberosum L.) puolustusta. Tautia aiheuttamattomat bakteerit kykenevät vahvistamaan kasvien puolustusta, mikä auttaa isäntäkasvia säästämään energiaa ja nopeuttamaan puolustusreaktiota patogeenihyökkäyksen aikana. Methylobacterium sp. IMBG290-kannan vahvistuskyvyn osoitettiin perustuvan salisyylihappo- ja jasmonaatti/etyleeni-riippuvaisten puolustusreittien aktivoimiseen patogeeni-istutuksen jälkeen. Antioksidanttijärjestelmän lievä aktivoituminen voi myös vaikuttaa kannan aiheuttamaan vastustuskyvyn lisääntymiseen. Suurimmalle osalle bakteeriendofyyteistä ‘elävä mutta viljelemätön’-olotila on luultavasti selviytymisstrategia. Patogeenihyökkäys tai muutokset ympäristössä voivat aktivoida tällaiset hiljaiset olomuodot. Methylobacterium sp. IMBG290-kanta muuttui viljeltävissä olevaan muotoon kun kasviin istutettiin tautia aiheuttamaton bakteeri. Selvitin, että endofyytti-yhteisön koostumus muuttuu vasteena Methylobacterium sp. IMBG290-kannan istuttamiseen kasvin verson solukoissa, korreloiden lisääntyneen perunan vastustuskyvyn ja kasvun kanssa. Siksi endofyyttisten bakteeripopulaatioiden aktivoitumista esitettiin uutena kasvin puolustusmekanismina. Endofyyteillä on suuret mahdollisuudet maataloudessa. Methylobacterium sp. IMBG290-kannan kasvua ja vastustuskykyä lisäävät ominaisuudet perunalla vaihtelivat lajikkeen, patogeenin, lisätyn bakteeriympin ja ympäristöolosuhteiden mukaan. Suunniteltaessa monimutkaisia bakteeriymppejä kasvien kasvin, vastustuskyvyn ja ravintosisällön lisäämiseksi, täytyy tällainen tilanteesta riippuva tehokkuus ottaa enemmän huomioon.

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome characterization in a shark (Doane et al., 2017; skin microbiome of the common thresher shark). A comparative characterization of microbiomes sampled from different shark species and anatomical locations will allow an understanding of the differences in microbiomes that may be explained by variance in shark habitat and diet. Florida leads as shark bite capitol of the world, with 778 unprovoked bites recorded since 1837, or 4-5 average bites per year. With only a few bites a year, there is not a lot of opportunities to study these bites. What can be studied, however, is how the microbial environment in shark’s teeth is composed. To understand overall microbiome composition, and if microbiomes are distinct from the environment, or specific by species or anatomical location (henceforth location), we characterized microbiomes from the teeth, gill, skin, and cloacal microbiomes of 8 shark species in south Florida (nurse, lemon, sandbar, Caribbean reef, Atlantic sharpnose, blacktip, bull, and tiger) using high throughput DNA sequencing of the 16S rRNA gene V4 region. There was a significant difference in microbial community richness among species, sample location, but not the interaction between species and location. Microbial diversity by location was significantly different for both the Shannon index and Inverse Simpson index. Samples examined by species had no significant difference in microbial community diversity overall for both Shannon and Inverse Simpson indexes. Microbial community diversity of samples by location and species combined significantly differed when submitted to an analysis of variance with the Shannon index, but not the Inverse Simpson index. Teeth microbial communities showed the most diversity based on both Shannon and Inverse Simpson indices. Teeth microbiomes are distinct but also share taxa with the water they inhabit, including potentially pathogenic genera such as Streptococcus (8.0% ± 9.0%) and Haemophilus (2.9% ± 3.3%) in the Caribbean reef shark. The lemon shark teeth hosted Vibrio (10.8% ± 26.0%) and the Corynebacterium genus (1.6%±5.1%). The Vibrio genus (2.8% ± 6.34%), Salmonella enterica (2.6% ± 6.4%), and the genus Kordia (3.1% ± 6.0%) are found in the nurse shark teeth microbial community. Strikingly, the Vibrio genus was represented in the sandbar shark (54.0% ± 46.0%) and tiger shark (5.8% ±12.3%) teeth microbiomes. One OTU related to traditionally non-pathogenic family Phyllobacteriaceae appear to be driving up to 32% of variance in teeth microbiome diversity. We conclude that south Florida sharks host distinct microbiomes from the surrounding environment and vary among species due to differences in microbial community richness. Future work should focus on bacteria found in shark teeth to determine if those present are pathogenic and could provide insights to bite treatment.

This diploma thesis has been carried out as a part of the project Utilization of long term (passive) sampling methods combined with in situ microcosms for assessment of (bio)degradation potential (PASSES). In the frame of the project groundwater remediation took place in the premises of Farmak a.s. in Olomouc using a pilot photooxidation unit and efficiency of the remediation was monitored through passive and active sampling methods. Pilot photooxidation unit is a technology based on the H2O2/UV-C photochemical oxidation of organic pollutants. In this work optimization tests of the pilot photooxidation unit were performed. The residence time of the groundwater in the photoreactors, required for its sufficient decontamination from pharmaceuticals and aromatic hydrocarbons, was 2.5 hours. 91% degradation of the pharmaceuticals and 80% degradation of aromatic hydrocarbons were reached during this interval. Although the removal efficiency of the pharmaceuticals by the photooxidation unit was high, the pilot photooxidation unit was not able to effectively remove the pharmaceuticals at the studied locality. By comparing the results of the pharmaceuticals from active and passive groundwater sampling during the remediation attempt, passive Polar Organic Chemical Integrative Sampler (POCIS) was found to be...

The decomposition of organic substrates represents an important part of the global carbon cycle and affects its global change through CO2 release. In temperate forests, deadwood represents a large carbon stock, its amount and decomposition is crucial for ecosystem biodiversity and functioning. The fungi are omnipresent powerful decayers in all terrestrial ecosystems. Their ability to decompose all deadwood compounds, mainly lignocellulose, is highly important. Without fungi, the wood decompositions and the release of withheld nutrients back to nutrient cycles couldn't be performed. While many studies were concerned with the estimation of decomposition rates of deadwood, still deeper knowledge about microbial decomposition processes and the diversity of saproxylic species and their interaction is needed. The fungi are still underrepresented in dead wood studies. This study had two main objectives. First was to describe the fungal community on downed deadwood of Fagus sylvatica and Abies alba in natural forest of Salajka in the Czech Republic, to reflect the substrate changes during the different decay stages, and to link the enzyme activities to fungal community composition and their described ecophysiologies. Second aim was to describe the fungal communities on standing and downed dead logs of...

Le réchauffement régional de l'ouest de la Péninsule Antarctique (WAP) combiné à la diminution attendue de glace de mer et à l'apparition printanière du trou d'ozone pourrait modifier la composition et la structure de la communauté microbienne. De plus, ces variations environnementales pourraient modifier le potentiel de la WAP en tant que puits de CO2. Dans ce contexte, cette thèse visait à évaluer les effets combinés du changement climatique sur la production primaire et sur la composition et la structure de la communauté microbienne de la WAP. Cette thèse visait également à évaluer le rôle de la structure, de la composition, de la production primaire et de la respiration de la communauté microbienne sur les échanges de CO2 entre l'atmosphère et l'océan. Cette étude a premièrement permis de décrire les variations de l'étendue de glace de mer, de l'épaisseur de la couche d'ozone et de la température de surface de l'eau dans la WAP au cours des 30 dernières années (1972-2007) et notamment d'observer le retrait de plus en plus précoce de la glace de mer en relation avec le réchauffement des eaux de la WAP. L'évolution de ces paramètres environnementaux offre une nouvelle fenêtre temporelle de production primaire. Ainsi, cette étude a permis de montrer que la production primaire annuelle a augmenté de 1997 à 2007, et ceci, en relation avec l'anomalie de glace de l'hiver précédent. En effet, la production primaire journalière était négativement et positivement corrélée avec, respectivement, l'étendue de glace de mer et la température de l'eau de septembre à novembre et de février à mars, suggérant que le réchauffement régional de la WAP favorise plus de production primaire durant le printemps et l'automne. En revanche, le retrait précoce de la glace de mer en coïncidence avec l'apparition printanière du trou d'ozone a provoqué l'augmentation de la photoinhibition au printemps (avec 11,6 ± 2,8 % de la production primaire journalière en moyenne). En conséquence, le changement climatique régional de la WAP a, à la fois, un effet positif et un effet négatif sur la production primaire. Cette étude a également permis de décrire la dynamique de la communauté microbienne marine dans l'archipel de Melchior (dans la WAP) de l'automne au printemps 2006. En raison des conditions environnementales extrêmes, l'abondance et la biomasse de la communauté microbienne étaient faibles durant l'automne et l'hiver et dominées par les petites cellules (< 2 µm) et donc par un réseau trophique microbien. En effet, la biomasse phytoplanctonique était faible durant l'automne et l'hiver (avec une concentration moyenne en chlorophylle a, Chl-a, de 0,3 et 0,13 µg l-1, respectivement). La biomasse phytoplanctonique a augmenté au printemps (avec un maximum de Chl-a de 1,13 µg l-1), mais, en dépit des conditions de croissance favorables, est restée faible et le phytoplancton était toujours dominé par de petites cellules (2-20 µm) et donc par le réseau trophique microbien ou multivore. De plus, la disparition précoce de glace de mer durant le printemps 2006 a exposé les eaux de la WAP à de fortes radiations ultraviolettes B (RUVB, 280-320 nm), qui ont eu un effet négatif sur la communauté microbienne des eaux de surface. Cette étude a également mis en évidence la relation existante entre les échanges CO2 et d'O2 entre l'atmosphère et l'océan dans la WAP et la biomasse, la composition, la production primaire et la respiration de la communauté microbienne. Il existait tout d'abord une relation positive entre la concentration en Chl-a et la proportion de diatomées dans la communauté phytoplanctonique. De plus, il existait une corrélation négative significative entre la Chl-a et le ΔpCO2. La production primaire nette de la communauté (NCP) était principalement contrôlée par la production primaire et était négativement et positivement reliée avec le ΔpCO2 et le pourcentage de saturation de l'O2, respectivement, suggérant que la production primaire joue un rôle majeur dans les échanges de CO2 et d'O2 entre l'atmosphère et l'océan dans la WAP. Par ailleurs, le ΔpCO2 moyen au cours des trois années étudiées était de -20,04 ± 44,3 µatm, menant à un puits de CO2 potentiel durant l'été et l'automne dans la région. Le sud de la WAP était un puits potentiel de CO2 (-43,60 ± 39,06 µatm) durant l'automne alors que le nord de la WAP était principalement une source potentielle de CO2 durant l'été ou l'automne (-4,96 ± 37,6 et 21,71 ± 22,39 µatm, respectivement). Les plus fortes concentrations en Chl-a mesurées dans le sud de la WAP pourraient expliquer cette distribution spatiale. / Regional warming in the western Antarctic Peninsula (WAP), along with the expected decrease in sea-ice cover and the seasonal ozone layer breakdown could modify the composition and the structure of the microbial community. In addition, these environmental changes could modify the potential of the WAP as a CO2 sink. In this context, this thesis aimed at evaluating the combined effects of regional climatic changes on the primary production and the composition and structure of the microbial community in the WAP. In a second time, this thesis aimed at evaluating the role of the microbial community structure, composition, primary production and respiration on air-sea CO2 gas exchanges.First, the variations in sea-ice cover, stratospheric ozone layer thickness and sea surface temperature over the last 30 years (1972-2007) were described. Related to the warming of WAP waters, the retreat of sea-ice was happening earlier each decade in the WAP. The observed changes in these environmental parameters offer a new temporal window for primary production. Indeed, the annual primary production increased from 1997 to 2007, in relation with the sea-ice cover anomaly for the previous winter. In addition, daily primary production was negatively and positively correlated to, respectively, sea-ice cover and sea-water temperature from September to November and from February to March, suggesting that regional warming favoured more primary production during spring and fall. On the contrary, the early retreat of sea-ice in spring, in coincidence with the spring ozone layer breakdown, led to an increase in photoinhibition (with an average of 11.6 ± 2.8 % of the daily primary production being photoinhibited). Therefore, regional climatic changes in the WAP had both a positive and a negative impact on primary production.The microbial community variability was also described in the Melchior Archipelago (in the WAP) from fall to spring 2006. Because of the extreme environmental conditions, the microbial community abundance and biomass were low in fall and winter and the community was dominated by small cells (< 2 µm), hence by a microbial food-web. Indeed, phytoplanktonic biomass was low during fall and winter (with respective chlorophyll a concentration, Chl-a, of 0.3 and 0.13 µg l-1). Phytoplankton biomass increased in spring (with a maximum Chl-a of 1.13 µg l-1) but, despite favourable growth conditions, phytoplankton was still dominated by small cells (2-20 µm), hence by a microbial or multivorous food-web. In addition, the early retreat of sea-ice in the spring 2006 exposed the WAP waters to strong ultraviolet B radiations (UVBR, 280-320 nm) that had a negative impact on the microbial community in surface waters.Finally, the relationship between air-sea CO2 and O2 exchanges in the WAP with the phytoplankton community biomass and composition and with the microbial community primary production and respiration was described. A positive relationship existed between Chl-a and the proportion of diatoms in the phytoplankton community. In addition, a negative relationship existed between Chl-a and ΔpCO2. The net community production (NCP) was mainly controlled by primary production and was negatively and positively related to ΔpCO2 and the %O2 saturation, respectively, suggesting that primary production was the main driver of air-sea CO2 and O2 gas exchanges in the WAP. In addition, the average ΔpCO2 for the summers and falls 2002 to 2004 was -20.04 ± 44.3 µatm, leading to a potential CO2 sink during this period in the WAP. The southern WAP was a potential CO2 sink (-43.60 ± 39.06 µatm) during fall while the northern part of the Peninsula was mainly a potential CO2 source during summer and fall (-4.96 ± 37.6 and 21.71 ± 22.39 µatm, respectively). The higher Chl-a concentrations measured in the southern WAP may explain this spatial distribution.