Développement d'un senseur électrochimique pour le dosage des nitrates en laboratoire et en pépinière forestière

Le lessivage des nitrates, la contamination de la nappe phréatique et l’eutrophisation des cours d’eau figurent parmi les enjeux planétaires qui affectent la durabilité de l’agriculture et des ressources naturelles. Ce mémoire présente le développement d’une première génération d’un nouveau senseur électrochimique pour le dosage de précisions des nitrates. Celui-ci est basé sur la spectroscopie d’impédance électrochimique d’une membrane polymérique sélective aux ions. Grâce à cette approche, un senseur compact et abordable a été produit. Par son utilisation en solutions aqueuses et en substrats de croissance saturés, il a été montré que le senseur permettait de quantifier des ajouts contrôlés de nitrates allant de 0,6 ppm à 60 ppm. La mise en application en substrat de croissance a pu être étudiée en comparaison avec des méthodes certifiées ISO 17025 visant l’analyse de ces substrats. Le senseur a aussi montré une grande versatilité par son utilisation sur divers appareils de mesure d’impédance. En plus, il a démontré une stabilité possible suite à une implantation d’un mois directement en substrat de croissance sous les variables environnementales d’une pépinière forestière. Par l’étude du spectre d’impédance du senseur en solutions pures de différentes concentrations, il a aussi été possible de proposer le circuit électrique équivalent du système, qui met en évidence deux parcours compétitifs du courant, un au coeur de la membrane et un deuxième en solution. Les résultats de ces travaux sont au coeur de deux publications scientifiques dont le manuscrit est inclus à ce mémoire. Pour finir cette étude, des suggestions seront faites pour guider l’amélioration du senseur par le développement d’une deuxième génération de celui-ci.

Influência do uso e ocupação do solo na qualidade da água e no processo erosivo da bacia de captação do Rio Barro Preto, Coronel Vivida-PR

This study was developed in objecting to investigate the use and occupation of land in 1999, 2005, 2011 e 2015 and estimate soil degradation by laminar erosion and the relation with water quality in 2015 in the catchment basin of the Barro Preto river, Coronel Vivida – PR. For multitemporal analysis of use and occupation of land in the basin used in the Landsat 5, 7 and 8 images and Geographic Information System. The laminar erosion was estimated by the Universal Soil Loss Equation through the systematization of calculations of the factors that compose the equation in SPRING/INPE. The water quality of the studied river section was evaluated according to the Water Quality Idex and the Resolution CONAMA n. 357/2005. The multitemporal analysis of the use and occupation of land has demonstrated that basin is predominantly agricultural in all years studied, as well as the permanent preservation area presents it not regularized during the period in accordance with the Brazilian Forest Code in force. In relation the quantification of laminar soil erosion in the study period, the rainfall and runoff factor was estimated considering the rainfall data from 1986 to 2014 and resulted in a value of 11.573,47 MJ/ha.mm/a. The Dystrophic Red Latosol, Dystrophic Red Nitisol, Fluvisol and Leptosol soil erodibility factor were 0,0138, 0,0137, 0,0207, 0,0196 t.ha.h/ha.MJ.mm/a, respectively. The topographical factor has demonstrated that the catchment basin has the rough terrain because the moderate and moderate strong classes are dominant in the study area. The cover and management and support practice factors were estimated according to the multitemporal analysis of the use and occupation of land in the basin and the values ranged from 0,0006 to 0,0688. The soil losses by laminar erosion were simulated with agriculture areas with corn and soybeans in no-till. The soil losses with maize crop in no-till in 1999, 2005, 2011 and 2015 were 9.782,75, 10.592,71, 9.636,61 e 11.058,26 t/year, respectively, and soybeans crops in no-till were 15.140,01, 16.645,20, 14.662,14 e 17.049,85 t/year, respectively. In relation with water quality of the section studied river, the average of Water Quality Index during the season were 55,47, 53,09 and 49,72, for the first, second and third sample point, respectively. Indication a decrease in water quality since the source to the last sample point. It is concluded that the use and occupation of land in the catchment basin interferes in the water quality, as well as in soil degradation.

A review of weed management in wheat using crop competition

Wheat occupies a principal place in the diet of humans globally, contributing more to our daily calorie and protein intake than any other crop. For this reason, preventing weed induced yield losses in wheat has high significance for world food sustainability. Herbicides and tillage play an important role in weed control, but their use has often unacceptable consequences for humans and the wider environment. Additionally, the range of herbicides effective on key weeds is dwindling due to the evolution of herbicide resistance. Elevating crop competitiveness against weeds, through a combination of wheat breeding and innovative planting design (planting density, row spacing and orientation), has strong potential to reduce weed-induced yield losses in wheat. The last decade of research has provided a solid foundation for the breeding of weed suppressive wheat cultivars, and continued research in this area should be a focus for the future. In the interim, there is cause for optimism that weeds can be effectively suppressed using existing wheat varieties, through careful cultivar selection and choice of planting design. Further research is required to define the nature of relationships between cultivar traits and competitive planting strategies, across diverse weed flora in multiple countries, sites and seasons. Investment in such innovation promises to produce benefits, not only in terms of sustained wheat yields, but also in terms of human and ecosystem health, through ameliorating chemical and sediment contamination, soil degradation, and CO2 pollution.

Comparação da eficácia de tecnologias para o controlo da perda de solo em áreas ardidas no Nordeste de Portugal aplicando modelo de erosão

As florestas exercem grande influência nos meios físico, biótico e socioeconômico, evitando a degradação do solo pela erosão, controlando a qualidade da água, fornecendo matérias-primas e alimentos, abrigando a maior parte da fauna e flora terrestre. As áreas florestais estão todavia sujeitas a significativo risco de incêndio. Como consequência dos incêndios, e entre outros impactos, o solo fica exposto à ação erosiva da chuva determinando perdas de solo muito significativas e a degradação deste recurso. Deste modo, o controle da erosão após o incêndio é essencial para a mais rápida recuperação das áreas ardidas suportada em medidas de conservação do solo eficazes. O trabalho propõe-se fazer uma avaliação quantificada da eficácia de técnicas de conservação do solo no controle da erosão em áreas ardidas, centrada em medidas de baixo custo e aplicável ao NE de Portugal, em especial o Distrito de Bragança. A metodologia de avaliação seguida inclui a construção de cenários regionais de aplicação simulada de uma seleção de medidas, mediante exploração de um modelo de erosão (Equação Universal de Perda de Solo – USLE). Através das simulações realizadas fazendo variar a distribuição de barreiras ao longo da encosta e o seu grau de retenção, foi possível avaliar a eficácia desta técnica para a redução da erosão nas condições definidas como cenários de base. Observou-se que o grau de retenção tem maior influência na redução de perda do solo do que a distância entre barreiras. Isto evidencia a necessidade de uma implementação adequada desta medida, com a instalação de barreiras de elevado grau de retenção. Aplicada apenas no primeiro ano pós-fogo, e de forma isolada, a técnica da sementeira não se mostrou suficientemente eficaz. Porém, se após um ano se realizar uma nova sementeira na área afetada, mostrou-se que pode ocorrer uma diminuição dos valores de perda de solo relativamente grande, pelo que será aconselhável a realização de uma ressementeira no ano seguinte à primeira aquando de intervenções pós-fogo com esta técnica. Uma possível combinação entre os métodos anteriores iria proporcionar uma situação ótima, como observado nos resultados das simulações efetuadas, onde a maioria dos cenários apresentou valores estimados de perda de solo menores ou iguais a 2 ton/ha.ano, limiar que separa condições de risco de erosão baixo e moderado e corresponde à tolerância de perda de solo para solos delgados e de substrato não renovável.

Degradation of lignin and other 14C-labelled compounds in compost and soil with an emphasis on white-rot fungi

Puu, ruohokasvit ja näistä tehdyt tuotteet kuten mekaanisesta massasta valmistettu sanomalehtipaperi sisältävät ligniiniä, joka hajoaa yleensä hyvin hitaasti luonnossa. Valkolahosienet hajottavat ligniiniä tehokkaimmin, ja koska niiden tuottamat entsyymit hajottavat myös muita vaikeasti hajoavia yhdisteitä, voidaan valkolahosienten avulla mahdollisesti puhdistaa saastuneita maita. Tässä työssä haluttiin selvittää, säilyttävätkö valkolahosienet (Abortiporus biennis, Bjerkandera adusta, Dichomitus squalens, Phanerochaete chrysosporium, Phanerochaete sordida, Phlebia radiata, Pleurotus ostreatus, Trametes hirsuta ja Trametes versicolor) aktiivisuutensa ja kasvavatko ne maassa. Aktiivisuutta mitattiin seuraamalla sienten synteettisen ligniinin (14C-DHP) hajotuskykyä. T. versicolor (silkkivyökääpä) osoittautui tehokkaimmaksi ligniinin hajottajaksi ja sen pentakloorifenolin (PCP) hajotuskykyä tutkittiin erillisessä kokeessa. Entiset tai pitkään käytössä olleet saha-alueet ovat yhä saastuneet puun käsittelyaineista peräisin olevilla kloorifenoleilla. Biohajoavien muovien kehitystyö sekä kompostoinnin yleistyminen jätteiden käsittelymenetelmänä ovat luoneet tarpeen materiaalien biohajoavuuden määrittämiseen. Euroopan standardisoimisjärjestön (CEN) kontrolloidussa kompostitestissä biohajoavuus määritetään materiaalin hajoamisen aikana muodostuvan hiilidioksidin perusteella. Hiilidioksidin tuotto mitataan sekä näytettä sisältävästä kompostista että kompostista ilman näytettä, ja tällöin oletetaan, että kompostin orgaaninen aines molemmissa komposteissa (tausta) tuottaa yhtä paljon hiilidioksidia. Testin puutteeksi saattaa osoittautua kompostissa tai maassa esiintyvä "priming effect". Tällä tarkoitetaan materiaalin lisäämisen jälkeen esiintyvää epänormaalin suurita tai pientä hiilidioksidin muodostusta, minkä seurauksena testin tulosksena saatava biohajoavuus on virheellinen. Ligniinin hajotessa muodostuu enemmän humusta kuin hiilidioksidia, koska ligniini on humuksen tärkein lähtöaine. Näin ollen ligniiniä sisältävät paperituotteet saattavat testin mukaan vaikuttaa biologisesti hajoamattomilta. Valkolahosienet hajottivat 4-23% ligniinistä hiilidioksidiksi ja T. versicolor 29% PCP:sta. Kompostissa ligniini hajosi hiilidioksidiksi 58°C:ssa huomattavasti vähemmän (8%) kuin lämpötiloissa 35°C ja 50°C (23-24%). Kompostin todennäköisesti tärkeimpien ligniinin hajottajien, termofiilisten sienten, tyypillinen optimilämpötila on 45°C, eivätkä ne ole enää aktiivisia 58°C:ssa. Sekä maassa että kompostissa ligniini sitoutui kuitenkin suurimmaksi osaksi humukseen. Valkolahosienet hajottivat sekä humukseen sitoutunutta ligniiniä että PCP:ia, mutta kompostin sekapopulaatio ei tähän pystynyt, ja ligniiniä sitoutui humukseen yhä enemmän kompostoinnin aikana. T. versicolor hajotti PCP:ia tehokkaasti, eikä se tuottanut myrkyllisiä kloorianisoleja, joita jotkut valkolahosienet saattavat muodostaa kloorifenoleista. Priming effect ilmiötä tutkittiin eri ikäisissä ja kypsyydeltään erilaisissa komposteissa. Kompostit erosvat toisistaan myös hajoamattoman jätteen määrän ja mikrobipopulaation suhteen. Negatiivinen priming effect havaittiin kaikissa epästabiileissa komposteissa (ikä enintään 6 kk), ja sen lisäksi yhdessä näistä komposteista positiivinen priming effect kokeen lopussa. Stabiileissa komposteissa (ikä vähintään 6 kk) ilmiötä ei sen sijaan havaittu. Epästabiileissa komposteissa biohajoavuudelle saadut tulokset eivät siis ole luotettavia. Työn tulosten perusteella valkolahosienet, ja erityisesti T. versicolor, ovat lupaavia saastuneen maan puhdistukseen, joskin sienirihmaston mahdollisuudet säilyä aktiivisena maan alkuperäisen mikrobipopulaation kanssa täytyy vielä selvittää. Kompostin sekapopulaatio, joka ei sisällä valkolahosieniä, hajotti ligniiniä yllättävän tehokkaasti termofiilisille sienille sopivissa lämpötiloissa, vaikka ligniini sitoutuikin pääasiallisesti humukseen. Kompostin kypsyys osoittautui tärkeäksi tekijäksi kontrolloidun kompostitestin onnistumisen kannalta. Priming effect ilmiön välttämiseksi on varmistettava, että testissä käytetty komposti on riittävän kypsä. Kompostien mikrobipopulaation koostumusta kompostoinnin eri vaiheissa tulisi tarkemmin selvittää, koska stabiilien ja epästabiilien kompostien ero aiheutui todennäköisesti populaatioiden rakenteessa vallitsevista eroista. Näin myös priming effect ilmiön syyt voitaisiin selittää paremmin.

Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.