Land use change to perennial energy crops in Northern Italy: Effects on soil organic carbon sequestration and distribution, soil enzyme activities and microbial communities.

Studies on soil organic carbon (SOC) sequestration in perennial energy crops are available for North-Central Europe, while there is insufficient information for Southern Europe. This research was conducted in the Po Valley, a Mediterranean-temperate zone characterised by low SOC levels, due to intensive management. The aim was to assess the factors influencing SOC sequestration and its distribution through depth and within soil fractions, after a 9-year old conversion from two annual systems to Miscanthus (Miscanthus × giganteus) and giant reed (Arundo donax). The 13C natural abundance was used to evaluate the amount of SOC in annual and perennial species, and determine the percentage of carbon derived from perennial crops. SOC was significantly higher under perennial species, especially in the topsoil (0-0.15 m). After 9 years, the amount of C derived from Miscanthus was 18.7 Mg ha-1, mostly stored at 0-0.15 m, whereas the amount of C derived from giant reed was 34.7 Mg ha-1, evenly distributed through layers. Physical soil fractionation was combined with 13C abundance analysis. C derived from perennial crops was mainly found in macroaggregates. Under giant reed, more newly derived-carbon was stored in microaggregates and mineral fraction than under Miscanthus. A molecular approach based on denaturing gradient gel electrophoresis (DGGE) allowed to evaluate changes on microbial community, after the introduction of perennial crops. Functional aspects were investigated by determining relevant soil enzymes (β-glucosidase, urease, alkaline phosphatase). Perennial crops positively stimulated these enzymes, especially in the topsoil. DGGE profiles revealed that community richness was higher in perennial crops; Shannon index of diversity was influenced only by depth. In conclusion, Miscanthus and giant reed represent a sustainable choice for the recovery of soils exhausted by intensive management, also in Mediterranean conditions and this is relevant mainly because this geographical area is notoriously characterised by a rapid turnover of SOC.

Isolierung, Charakterisierung und Nachweis methanogener Archaea aus laufenden Praxis-NawaRo-Biogasanlagen unter besonderer Beruecksichtigung der Gattung Methanobacterium

Im Verlauf der Forschungsarbeit wurden Proben aus fünf, mit nachwachsenden Rohstoffen (NawaRo) beschickten, landwirtschaftlichen Biogasanlagen (BGA) auf die Biozönose methanogener Archaea hin molekularbiologisch untersucht. Über „amplified rDNA restriction analysis“-Screening (ARDRA) von Bibliotheken auf Basis von 16S rRNA-Genfragmenten konnte anhand zweier beispielhafter BGA das Vorkommen von Vertretern der Gattungen Methanoculleus (Mcu.), Methanobacterium (Mb.), Methanosarcina (Msc.) und Methanosaeta (Mst.) nachgewiesen werden. Mittels denaturierender Gradienten-Gelelektrophorese (DGGE) wurde das Vorkommen dieser Mikroorganismen auch in den übrigen Anlagen gezeigt. Ergänzend dazu wurde in drei Anlagen Methanospirillum hungatei nachgewiesen. Nach Ausarbeitung gattungsspezifischer Isolierungsstrategien konnten insgesamt zehn Vertreter der Gattung Methanobacterium (Isolate Mb1 bis Mb10) und jeweils ein Vertreter der Gattungen Methanoculleus (Isolat Mcu(1)), Methanosarcina (Isolat NieKK) und Methanosaeta (Isolat Mst1.3) aus den BGA-Proben isoliert werden. Durch in silico-Abgleich der partiellen 16S rRNA-Gensequenzen wurden diese als Verwandte von Mb. formicicum MFT, Mcu. bourgensis MS2T, Msc. mazei S-6T und Mst. concilii FE mit einer Sequenzidentität > 97% identifiziert. Im Laufe weiterer molekularbiologischer Untersuchungen mittels DGGE und ARDRA-Analyse konnten die Isolate den Referenzstämmen zugeordnet werden. In Bezug auf die Gattung Methanobacterium ergaben sich jedoch leichte Abweichungen. Diese bestätigten sich in vergleichenden Analysen des genomischen Fingerabdrucks in der „specifically amplified polymorphic DNA“-PCR (SAPD-PCR), welche im Rahmen dieser Arbeit erstmalig erfolgreich auf archaeelle Organismen angewandt wurde. Hier zeigten die Isolate zwei von den Fingerabdrücken der untersuchten Referenzstämme verschiedene Hauptamplifikationsmuster. Aufgrund der Vielzahl der Isolate sowie dem signifikanten Vorkommen in qPCR-Analysen und Klonbibliotheken fokussierten sich die weiteren Arbeiten zur genauen Untersuchung dieser Abweichungen auf phylogenetische Analysen der Gattung Methanobacterium und die Entwicklung von Nachweissystemen. Die Aufklärung eines Großteils der 23S rRNA-Gensequenzen der Isolate und von ausgewählten Typstämmen ermöglichte ergänzende phylogenetische Untersuchungen zu durchgeführten 16S rRNA-Analysen. Dabei wurden die Isolate jeweils in einem eigenen Cluster abseits der meisten Referenzstämme aus der Gattung Methanobacterium positioniert. Analog zur Musterbildung im Rahmen der SAPD-Analyse zeigte sich eine Differenzierung in zwei Äste und ergab in Übereinstimmung mit den in silico-Sequenzabgleichen den höchsten Verwandtschaftsgrad mit Mb. formicicum MFT. Die Eignung der SAPD-PCR zur Ableitung spezifischer Primerpaare konnte erstmals auch für methanogene Archaea gezeigt werden. Die Ableitung zweier Primerpaare mit Spezifität für die Methanobacterium-Isolate Mb1 bis Mb10 sowie für den Typstamm Mb. formicicum MFT gelang und konnte im Rahmen eines Direkt-PCR-Nachweises erfolgreich auf Reinkulturen und Fermenterproben angewandt werden. Unter Einbezug der sequenzierten 23S rRNA-Genfragmente gelang die Erstellung von Oligonukleotid-Sonden für den Einsatz in Fluoreszenz in situ-Hybridisierungsexperimenten. Im Praxistest ergab sich für diese Sonden eine Spezifität für alle getesteten Vertreter der Gattung Methanobacterium sowie für Methanosphaera stadtmanae MCB-3T und Methanobrevibacter smithii PST.rnSomit konnten im Laufe der Arbeit die dominanten methanogenen Archaea in NawaRo-BGA in mehrphasigen Experimenten nachgewiesen, quantifiziert und auf nur wenige Gattungen eingegrenzt werden. Vertreter der vier dominanten Gattungen wurden isoliert und Nachweissysteme für Arten der Gattung Methanobacterium erstellt.rn

Entwicklung und Evaluierung von Methoden zur zeitnahen Identifizierung weinrelevanter Mikroorganismen

Hefen der Gattung Saccharomyces und Milchsäurebakterien sind bei der Weinbereitung von besonderer Bedeutung. Neben der alkoholischen Gärung sind Hefen an der Ausbildung von Aromastoffen beteiligt. Milchsäurebakterien spielen eine Rolle beim biologischen Säureabbau (malolaktische Fermentation), können jedoch aufgrund ihrer Stoffwechseleigenschaft weitere Aromamodifikationen bewirken. Die Zusammensetzung der mikrobiellen Flora zu verschiedenen Zeitpunkten der Weinbereitung hat einen direkten Einfluss auf die Qualität der Weine, welche sich sowohl positiv als auch negativ verändern kann. Daher ist die zuverlässige Identifizierung und Differenzierung verschiedener Mikroorganismen auf Art- aber auch Stamm-Ebene während der Vinifikation von Bedeutung.rnDer erste Teil dieser Arbeit beschäftigte sich mit der Differenzierung von Hefearten der Gattung Saccharomyces, welche mit Hilfe konventioneller Methoden nicht eindeutig identifiziert werden können. Unter Verwendung des DNA-Fingerprintverfahrens Specifically Amplified Polymorphic DNA (SAPD)-PCR sowie der Matrix-Assisted-Laser-Desorption/Ionization-Time-Of-Flight-Mass-Spectrometry (MALDI-TOF-MS) war eine Differenzierung dieser taxonomisch sehr nah verwandten Arten möglich. Weiterhin konnten interspezifische Hybridstämme detektiert werden. In diesem Zusammenhang wurde der Hybridcharakter des Stammes NCYC 3739 (S. cerevisiae x kudriavzevii) entdeckt. Um die Elternspezies eines Hybridstamms zuverlässig zu bestimmen, sind weiterführende Genanalysen notwendig. Hierzu konnte eine Restriktionsfragmentlängenpolymorphismus (RFLP)-Analyse verschiedener genetischer Marker erfolgreich herangezogen werden.rnIm Rahmen dieser Arbeit wurde weiterhin ein Schnellidentifizierungssystem zum Nachweis weinrelevanter Milchsäurebakterien entwickelt. Mit Hilfe der Sequence Characterized Amplified Region (SCAR)-Technik konnten artspezifische Primer generiert werden, welche auf der Grundlage charakteristischer Fragmente der SAPD-PCR abgeleitet wurden. Durch die Anwendung dieser Primer in einer Multiplex-PCR-Reaktion war die Detektion verschiedener, einerseits häufig in Wein vorkommender und andererseits potentiell an der Ausbildung von Weinfehlern beteiligter Milchsäurebakterien-Arten möglich. Die ermittelte Nachweisgrenze dieser Methode lag mit 10^4 - 10^5 Zellen/ml im Bereich der Zelltiter, die in Most und Wein anzutreffen sind. Anhand der Untersuchung verschiedener Weinproben von Winzern in Rheinhessen wurde die Praxistauglichkeit dieser Methode demonstriert. rnUm die gesamten Milchsäurebakterien-Population im Verlauf der Weinbereitung zu kontrollieren, kann die Denaturierende Gradienten-Gelelektrophorese herangezogen werden. Hierzu wurden in dieser Arbeit Primer zur Amplifikation eines Teilbereichs des rpoB-Gens abgeleitet, da dieses Gen eine Alternative zur 16S rDNA darstellt. Die DNA-Region erwies sich als geeignet, um zahlreiche weinrelevante Milchsäurebakterien-Arten zu differenzieren. In einigen ersten Versuchen konnte gezeigt werden, dass diese Methode für eine praktische Anwendung in Frage kommt.rnOenococcus oeni ist das wichtigste Milchsäurebakterien während der malolaktischen Fermentation und wird häufig in Form kommerzieller Starterkulturen eingesetzt. Da verschiedene Stämme unterschiedliche Eigenschaften aufweisen können, ist es von Bedeutung, die Identität eines bestimmten Stammes zweifelsfrei feststellen zu können. Anhand der Analyse verschiedener O. oeni-Stämme aus unterschiedlichen Weinbaugebieten konnte gezeigt werden, dass sowohl die nested SAPD-PCR als auch die MALDI-TOF-MS genügend Sensitivität aufweisen, um eine Unterscheidung auf Stamm-Ebene zu ermöglichen, wobei die mittels nSAPD-PCR ermittelten Distanzen der Stämme zueinander mit deren geographischer Herkunft korrelierte.rnDie in der vorliegenden Arbeit entwickelten Methoden können dazu beitragen, den Prozess der Weinherstellung besser zu kontrollieren und so eine hohe Qualität des Endproduktes zu gewährleisten.rn

Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils

16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA:rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C:N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.

Dietary inclusion of feathers affects intestinal microbiota and microbial metabolites in growing Leghorn-type chickens.

Feather pecking in laying hens is a serious behavioral problem that is often associated with feather eating. The intake of feathers may influence the gut microbiota and its metabolism. The aim of this study was to determine the effect of 2 different diets, with or without 5% ground feathers, on the gut microbiota and the resulting microbial fermentation products and to identify keratin-degrading bacteria in chicken digesta. One-day-old Lohmann-Selected Leghorn chicks were divided into 3 feeding groups: group A (control), B (5% ground feathers in the diet), and C, in which the control diet was fed until wk 12 and then switched to the 5% feather diet to study the effect of time of first feather ingestion. The gut microbiota was analyzed by cultivation and denaturing gradient gel electrophoresis of ileum and cecum digesta. Short-chain fatty acids, ammonia, and lactate concentrations were measured as microbial metabolites. The concentration of keratinolytic bacteria increased after feather ingestion in the ileum (P < 0.001) and cecum (P = 0.033). Bacterial species that hydrolyzed keratin were identified as Enterococcus faecium, Lactobacillus crispatus, Lactobacillus reuteri-like species (97% sequence homology), and Lactobacillus salivarius-like species (97% sequence homology). Molecular analysis of cecal DNA extracts showed that the feather diet lowered the bacterial diversity indicated by a reduced richness (P < 0.001) and shannon (P = 0.012) index. The pattern of microbial metabolites indicated some changes, especially in the cecum. This study showed that feather intake induced an adaptation of the intestinal microbiota in chickens. It remains unclear to what extent the changed metabolism of the microbiota reflects the feather intake and could have an effect on the behavior of the hens.

Circulating oxidized low-density lipoprotein (LDL) is associated with risk factors of the metabolic syndrome and LDL size in clinically healthy 58-year-old men (AIR study).

OBJECTIVES Hypothetically the atherogenic effect of the metabolic syndrome may be mediated through the increased occurrence of small LDL-particles which are easily modified to atherogenic oxidized LDL (ox-LDL). The aim of this study was to test this concept by examining the association between circulating ox-LDL, LDL-particle size, and the metabolic syndrome. DESIGN AND RESULTS A population-based sample of clinically healthy 58-year-old men (n = 391) was recruited. Ox-LDL was measured by ELISA (specific monoclonal antibody, mAb-4E6) and LDL-particle size by gradient gel electrophoresis. The results showed that ox-LDL significantly correlated to factors constituting the metabolic syndrome; triglycerides (r = 0.43), plasma insulin (r = 0.20), body mass index (r = 0.20), waist-to-hip ratio (r = 0.21) and HDL (r = -0.24); (P < 0.001). Ox-LDL correlated also to LDL-particle size (r = -0.42), Apo-B (r = 0.70), LDL (r = 0.65); (P < 0.001) and, furthermore, with Apo A-1 (r = -0.13) and heart rate (r = 0.13); (P < 0.01). CONCLUSION The metabolic syndrome was accompanied by high plasma ox-LDL concentrations compared with those without the syndrome. Ox-LDL levels were associated with most of the risk factors constituting the metabolic syndrome and was, in addition related to small LDL-particle size. To our knowledge the present study is the first one to demonstrate that circulating ox-LDL levels are associated with small LDL-particle size in a population representative sample of clinically healthy middle-aged men. The high degree of intercorrelation amongst several factors makes it difficult to clarify the independent role of any specific factor.

(Supplemental Table 2) Plant characteristics, GHG fluxes, and soil chemical and microbial properties in experimental treatments in Alexandra Fiord

We evaluated above- and belowground ecosystem changes in a 16 year, combined fertilization and warming experiment in a High Arctic tundra deciduous shrub heath (Alexandra Fiord, Ellesmere Island, NU, Canada). Soil emissions of the three key greenhouse gases (GHGs) (carbon dioxide, methane, and nitrous oxide) were measured in mid-July 2009 using soil respiration chambers attached to a FTIR system. Soil chemical and biochemical properties including Q10 values for CO2, CH4, and N2O, Bacteria and Archaea assemblage composition, and the diversity and prevalence of key nitrogen cycling genes including bacterial amoA, crenarchaeal amoA, and nosZ were measured. Warming and fertilization caused strong increases in plant community cover and height but had limited effects on GHG fluxes and no substantial effect on soil chemistry or biochemistry. Similarly, there was a surprising lack of directional shifts in the soil microbial community as a whole or any change at all in microbial functional groups associated with CH4 consumption or N2O cycling in any treatment. Thus, it appears that while warming and increased nutrient availability have strongly affected the plant community over the last 16 years, the belowground ecosystem has not yet responded. This resistance of the soil ecosystem has resulted in limited changes in GHG fluxes in response to the experimental treatments.

PEECE II mesocosm experiment: Dynamics of extracellular enzyme activities in seawater under changed atmospheric pCO2, 2011

As part of the PeECE II mesocosm project, we investigated the effects of pCO2 levels on the initial step of heterotrophic carbon cycling in the surface ocean. The activities of microbial extracellular enzymes hydrolyzing 4 polysaccharides were measured during the development of a natural phytoplankton bloom under pCO2 conditions representing glacial (190 µatm) and future (750 µatm) atmospheric pCO2. We observed that (1) chondroitin hydrolysis was variable throughout the pre-, early- and late-bloom phases, (2) fucoidanase activity was measurable only in the glacial mesocosm as the bloom developed, (3) laminarinase activity was low and constant, and (4) xylanase activity declined as the bloom progressed. Concurrent measurements of microbial community composition, using denaturing-gradient gel electrophoresis (DGGE), showed that the 2 mesocosms diverged temporally, and from one another, especially in the late-bloom phase. Enzyme activities correlated with bloom phase and pCO2, suggesting functional as well as compositional changes in microbial communities in the different pCO2 environments. These changes, however, may be a response to temporal changes in the development of phytoplankton communities that differed with the pCO2 environment. We hypothesize that the phytoplankton communities produced dissolved organic carbon (DOC) differing in composition, a hypothesis supported by changing amino acid composition of the DOC, and that enzyme activities responded to changes in substrates. Enzyme activities observed under different pCO2 conditions likely reflect both genetic and population-level responses to changes occurring among multiple components of the microbial loop.

Seawater conditions during the experiment in May 2011 at the sampling sites off Vulcano Island

The impacts of ocean acidification on coastal biofilms are poorly understood. Carbon dioxide vent areas provide an opportunity to make predictions about the impacts of ocean acidification. We compared biofilms that colonised glass slides in areas exposed to ambient and elevated levels of pCO2 along a coastal pH gradient, with biofilms grown at ambient and reduced light levels. Biofilm production was highest under ambient light levels, but under both light regimes biofilm production was enhanced in seawater with high pCO2. Uronic acids are a component of biofilms and increased significantly with high pCO2. Bacteria and Eukarya denaturing gradient gel electrophoresis profile analysis showed clear differences in the structures of ambient and reduced light biofilm communities, and biofilms grown at high pCO2 compared with ambient conditions. This study characterises biofilm response to natural seabed CO2 seeps and provides a baseline understanding of how coastal ecosystems may respond to increased pCO2 levels.

Prokaryotic growth and presence of metabolic products and contamination tracers in rocks samples from ODP Leg 187 sites

The microbial population in samples of basalt drilled from the north of the Australian Antarctic Discordance (AAD) during Ocean Drilling Program Leg 187 were studied using deoxyribonucleic acid (DNA)-based methods and culturing techniques. The results showed the presence of a microbial population characteristic for the basalt environment. DNA sequence analysis revealed that microbes grouping within the Actinobacteria, green nonsulfur bacteria, the Cytophaga/Flavobacterium/Bacteroides (CFB) group, the Bacillus/Clostridium group, and the beta and gamma subclasses of the Proteobacteria were present in the basalt samples collected. The most dominant phylogenetic group, both in terms of the number of sequences retrieved and the intensities of the DNA bands obtained with the denaturing gradient gel electrophoresis analysis, was the gamma Proteobacteria. Enrichment cultures showed phylogenetic affiliation with the Actinobacteria, the CFB group, the Bacillus/Clostridium group, and the alpha, beta, gamma, and epsilon subclasses of the Proteobacteria. Comparison of native and enriched samples showed that few of the microbes found in native basalt samples grew in the enrichment cultures. Only seven clusters, two clusters within each of the CFB and Bacillus/Clostridium groups and five clusters within the gamma Proteobacteria, contained sequences from both native and enriched basalt samples with significant similarity. Results from cultivation experiments showed the presence of the physiological groups of iron reducers and methane producers. The presence of the iron/manganese-reducing bacterium Shewanella was confirmed with DNA analysis. The results indicate that iron reducers and lithotrophic methanogenic Archaea are indigenous to the ocean crust basalt and that the methanogenic Archaea may be important primary producers in this basaltic environment.

PeECE III - Pelagic Ecosystem CO2 Enrichment Study, Raunefjord, Bergen, Norway, 2005

The effects of CO2-induced seawater acidification on plankton communities were also addressed in a series of 3 mesocosm experiments, called the Pelagic Ecosystem CO2 Enrichment (PeECE I-III) studies, which were conducted in the Large-Scale Mesocosm Facilities of the University of Bergen, Norway in 2001, 2003 and 2005, respectively. Each experiment consisted of 9 mesocosms, in which CO2 was manipulated to initial concentrations of 190, 350 and 750 µatm in 2001 and 2003, and 350, 700 and 1050 µatm in 2005. The present dataset concerns PeECE III.

Mejora de la eficacia de Penicillium oxalicum como agente de biocontrol en enfermedades de plantas hortícolas

Actualmente, la reducción de materias activas (UE) y la implantación de la nueva Directiva comunitaria 2009/128/ que establece el marco de actuación para conseguir un uso sostenible de los plaguicidas químicos y la preferencia de uso de métodos biológicos, físicos y otros no químicos, obliga a buscar métodos de control menos perjudiciales para el medio ambiente. El control biológico (CB) de enfermedades vegetales empleando agentes de control biológico (ACB) se percibe como una alternativa más segura y con menor impacto ambiental, bien solos o bien como parte de una estrategia de control integrado. El aislado 212 de Penicillium oxalicum (PO212) (ATCC 201888) fue aislado originalmente de la micoflora del suelo en España y ha demostrado ser un eficaz ACB frente a la marchitez vascular del tomate. Una vez identificado y caracterizado el ACB se inició el periodo de desarrollo del mismo poniendo a punto un método de producción en masa de sus conidias. Tras lo cual se inició el proceso de formulación del ACB deshidratando las conidias para su preservación durante un período de tiempo mayor mediante lecho fluido. Finalmente, se han desarrollado algunos formulados que contienen de forma individual diferentes aditivos que han alargado su viabilidad, estabilidad y facilitado su manejo y aplicación. Sin embargo, es necesario seguir trabajando en la mejora de su eficacia de biocontrol. El primer objetivo de esta Tesis se ha centrado en el estudio de la interacción ACB-patógeno-huésped que permita la actuación de P.oxalicum en diferentes patosistemas. Uno de los primeros puntos que se abordan dentro de este objetivo es el desarrollo de nuevas FORMULACIONES del ACB que incrementen su eficacia frente a la marchitez vascular del tomate. Las conidias formuladas de PO212 se obtuvieron por la adición conjunta de distintos aditivos (mojantes, adherentes o estabilizantes) en dos momentos diferentes del proceso de producción/secado: i) antes del proceso de producción (en la bolsa de fermentación) en el momento de la inoculación de las bolsas de fermentación con conidias de PO212 o ii) antes del secado en el momento de la resuspensión de las conidias tras su centrifugación. De las 22 nuevas formulaciones desarrolladas y evaluadas en plantas de tomate en ensayos en invernadero, seis de ellas (FOR22, FOR25, FOR32, FOR35, FOR36 y FOR37) mejoran significativamente (P=0,05) el control de la marchitez vascular del tomate con respecto al obtenido con las conidias secas de P.oxalicum sin aditivos (CSPO) o con el fungicida Bavistin. Los formulados que mejoran la eficacia de las conidias secas sin aditivos son aquellos que contienen como humectantes alginato sódico en fermentación, seguido de aquellos que contienen glicerol como estabilizante en fermentación, y metil celulosa y leche desnatada como adherentes antes del secado. Además, el control de la marchitez vascular del tomate por parte de los formulados de P. oxalicum está relacionado con la fecha de inicio de la enfermedad. Otra forma de continuar mejorando la eficacia de biocontrol es mejorar la materia activa mediante la SELECCIÓN DE NUEVAS CEPAS de P. oxalicum, las cuales podrían tener diferentes niveles de eficacia. De entre las 28 nuevas cepas de P. oxalicum ensayadas en cámara de cultivo, sólo el aislado PO15 muestra el mismo nivel de eficacia que PO212 (62-67% de control) frente a la marchitez vascular del tomate en casos de alta presión de enfermedad. Mientras que, en casos de baja presión de enfermedad todas las cepas de P. oxalicum y sus mezclas demuestran ser eficaces. Finalmente, se estudia ampliar el rango de actuación de este ACB a OTROS HUÉSPEDES Y OTROS PATÓGENOS Y DIFERENTES GRADOS DE VIRULENCIA. En ensayos de eficacia de P. oxalicum frente a aislados de diferente agresividad de Verticillium spp. y Fusarium oxysporum f. sp. lycopersici en plantas de tomate en cámaras de cultivo, se demuestra que la eficacia de PO212 está negativamente correlacionada con el nivel de enfermedad causada por F. oxysporum f. sp. lycopersici pero que no hay ningún efecto diferencial en la reducción de la incidencia ni de la gravedad según la virulencia de los aislados. Sin embargo, en los ensayos realizados con V. dahliae, PO212 causa una mayor reducción de la enfermedad en las plantas inoculadas con aislados de virulencia media. La eficacia de PO212 también era mayor frente a aislados de virulencia media alta de F. oxysporum f. sp. melonis y F. oxysporum f. sp. niveum, en plantas de melón y sandía, respectivamente. En ambos huéspedes se demuestra que la dosis óptima de aplicación del ACB es de 107 conidias de PO212 g-1 de suelo de semillero, aplicada 7 días antes del trasplante. Además, entre 2 y 4 nuevas aplicaciones de PO212 a la raíces de las plantas mediante un riego al terreno de asiento mejoran la eficacia de biocontrol. La eficacia de PO212 no se limita a hongos patógenos vasculares como los citados anteriormente, sino también a otros patógenos como: Phytophthora cactorum, Globodera pallida y G. rostochiensis. PO212 reduce significativamente los síntomas (50%) causados por P. cactorum en plantas de vivero de fresa, tras la aplicación del ACB por inmersión de las raíces antes de su trasplante al suelo de viveros comerciales. Por otra parte, la exposición de los quistes de Globodera pallida y G. rostochiensis (nematodos del quiste de la patata) a las conidias de P. oxalicum, en ensayos in vitro o en microcosmos de suelo, reduce significativamente la capacidad de eclosión de los huevos. Para G. pallida esta reducción es mayor cuando se emplean exudados de raíz de patata del cv. 'Monalisa', que exudados de raíz del cv. 'Desirée'. No hay una reducción significativa en la tasa de eclosión con exudados de raíz de tomate del cv. 'San Pedro'. Para G. rostochiensis la reducción en la tasa de eclosión de los huevos se obtiene con exudados de la raíz de patata del cv. 'Desirée'. El tratamiento con P. oxalicum reduce también significativamente el número de quistes de G. pallida en macetas. Con el fin de optimizar la aplicación práctica de P. oxalicum cepa 212 como tratamiento biológico del suelo, es esencial entender cómo el entorno físico influye en la capacidad de colonización, crecimiento y supervivencia del mismo, así como el posible riesgo que puede suponer su aplicación sobre el resto de los microorganismos del ecosistema. Por ello en este segundo objetivo de esta tesis se estudia la interacción del ACB con el medio ambiente en el cual se aplica. Dentro de este objetivo se evalúa la INFLUENCIA DE LA TEMPERATURA, DISPONIBILIDAD DE AGUA Y PROPIEDADES FÍSICO-QUÍMICAS DE LOS SUELOS (POROSIDAD, TEXTURA, DENSIDAD...) SOBRE LA SUPERVIVENCIA Y EL CRECIMIENTO DE PO212 en condiciones controladas elaborando modelos que permitan predecir el impacto de cada factor ambiental en la supervivencia y crecimiento de P. oxalicum y conocer su capacidad para crecer y sobrevivir en diferentes ambientes. En las muestras de suelo se cuantifica: i) la supervivencia de Penicillium spp. usando el recuento del número de unidades formadoras de colonias en un medio de cultivo semi-selectivo y ii) el crecimiento (biomasa) de PO212 mediante PCR en tiempo real. En los resultados obtenidos se demuestra que P. oxalicum crece y sobrevive mejor en condiciones de sequía independientemente de la temperatura y del tipo de suelo. Si comparamos tipos de suelo P. oxalicum crece y sobrevive en mayor medida en suelos areno-arcillosos con un bajo contenido en materia orgánica, un mayor pH y una menor disponibilidad de fósforo y nitrógeno. La supervivencia y el crecimiento de P. oxalicum se correlaciona de forma negativa con la disponibilidad de agua y de forma positiva con el contenido de materia orgánica. Sólo la supervivencia se correlaciona también positivamente con el pH. Por otro lado se realizan ensayos en suelos de huertos comerciales con diferentes propiedades físico-químicas y diferentes condiciones ambientales para ESTUDIAR EL ESTABLECIMIENTO, SUPERVIVENCIA Y DISPERSIÓN VERTICAL Y MOVILIDAD HORIZONTAL DE PO212. P. oxalicum 212 puede persistir y sobrevivir en esos suelos al menos un año después de su liberación pero a niveles similares a los de otras especies de Penicillium indígenas presentes en los mismos suelos naturales. Además, P. oxalicum 212 muestra una dispersión vertical y movilidad horizontal muy limitada en los diferentes tipos de suelo evaluados. La introducción de P. oxalicum en un ambiente natural no sólo implica su actuación sobre el microorganismo diana, el patógeno, si no también sobre otros microorganismos indígenas. Para EVALUAR EL EFECTO DE LA APLICACIÓN DE P. oxalicum SOBRE LAS POBLACIONES FÚNGICAS INDIGENAS PRESENTES EN EL SUELO de dos huertos comerciales, se analizan mediante electroforesis en gradiente desnaturalizante de poliacrilamida (DGGE) muestras de dichos suelos a dos profundidades (5 y 10 cm) y a cuatro fechas desde la aplicación de P. oxalicum 212 (0, 75, 180 y 365 días). El análisis de la DGGE muestra que las diferencias entre las poblaciones fúngicas se deben significativamente a la fecha de muestreo y son independientes del tratamiento aplicado y de la profundidad a la que se tomen las muestras. Luego, la aplicación del ACB no afecta a la población fúngica de los dos suelos analizados. El análisis de las secuencias de la DGGE confirma los resultados anteriores y permiten identificar la presencia del ACB en los suelos. La presencia de P. oxalicum en el suelo se encuentra especialmente relacionada con factores ambientales como la humedad. Por tanto, podemos concluir que Penicillium oxalicum cepa 212 puede considerarse un óptimo Agente de Control Biológico (ACB), puesto que es ecológicamente competitivo, eficaz para combatir un amplio espectro de enfermedades y no supone un riesgo para el resto de microorganismos fúngicos no diana presentes en el lugar de aplicación. ABSTRACT Currently, reduction of active (EU) and the implementation of the new EU Directive 2009/128 which establishing the framework for action to achieve the sustainable use of chemical pesticides and preference of use of biological, physical and other non-chemical methods, forces to look for control methods less harmful to the environment. Biological control (CB) of plant diseases using biological control agents (BCA) is perceived as a safer alternative and with less environmental impact, either alone or as part of an integrated control strategy. The isolate 212 of Penicillium oxalicum (PO212) (ATCC 201888) was originally isolated from the soil mycoflora in Spain. P. oxalicum is a promising biological control agent for Fusarium wilt and other tomato diseases. Once identified and characterized the BCA, was developed a mass production method of conidia by solid-state fermentation. After determined the process of obtaining a formulated product of the BCA by drying of product by fluid-bed drying, it enables the preservation of the inoculum over a long period of time. Finally, some formulations of dried P. oxalicum conidia have been developed which contain one different additive that have improved their viability, stability and facilitated its handling and application. However, further work is needed to improve biocontrol efficacy. The first objective of this thesis has focused on the study of the interaction BCA- pathogen-host, to allow P.oxalicum to work in different pathosystems. The first point to be addressed in this objective is the development of new FORMULATIONS of BCA which increase their effectiveness against vascular wilt of tomato. PO212 conidial formulations were obtained by the joint addition of various additives (wetting agents, adhesives or stabilizers) at two different points of the production-drying process: i) to substrate in the fermentation bags before the production process, and (ii) to conidial paste obtained after production but before drying. Of the 22 new formulations developed and evaluated in tomato plants in greenhouse tests, six of them (FOR22 , FOR25 , FOR32 , FOR35 , FOR36 and FOR3) improved significantly (P = 0.05) the biocontrol efficacy against tomato wilt with respect to that obtained with dried P.oxalicum conidia without additives (CSPO) or the fungicide Bavistin. The formulations that improve the efficiency of dried conidia without additives are those containing as humectants sodium alginate in the fermentation bags, followed by those containing glycerol as a stabilizer in the fermentation bags, and methylcellulose and skimmed milk as adherents before drying. Moreover, control of vascular wilt of tomatoes by PO212 conidial formulations is related to the date of disease onset. Another way to further improve the effectiveness of biocontrol is to improve the active substance by SELECTION OF NEW STRAINS of P. oxalicum, which may have different levels of effectiveness. Of the 28 new strains of P. oxalicum tested in a culture chamber, only PO15 isolate shows the same effectiveness that PO212 (62-67 % of control) against tomato vascular wilt in cases of high disease pressure. Whereas in cases of low disease pressure all strains of P. oxalicum and its mixtures effective. Finally, we study extend the range of action of this BCA TO OTHER GUESTS AND OTHER PATHOGENS AND DIFFERENT DEGREES OF VIRULENCE. In efficacy trials of P. oxalicum against isolates of different aggressiveness of Verticillium spp. and Fusarium oxysporum f. sp. lycopersici in tomato plants in growth chambers, shows that the efficiency of PO212 is negatively correlated with the level of disease caused by F. oxysporum f. sp. lycopersici. There is not differential effect in reducing the incidence or severity depending on the virulence of isolates. However, PO212 cause a greater reduction of disease in plants inoculated with virulent isolates media of V. dahlia. PO212 efficacy was also higher against isolates of high and average virulence of F. oxysporum f. sp. melonis and F. oxysporum f. sp. niveum in melon and watermelon plants, respectively. In both hosts the optimum dose of the BCA application is 107 conidia PO212 g-1 soil, applied on seedlings 7 days before transplantation into the field. Moreover, the reapplication of PO212 (2-4 times) to the roots by irrigation into the field improve efficiency of biocontrol. The efficacy of PO212 is not limited to vascular pathogens as those mentioned above, but also other pathogens such as Oomycetes (Phytophthora cactorum) and nematodes (Globodera pallida and G. rostochiensis). PO212 significantly reduces symptoms (50 %) caused by P. cactorum in strawberry nursery plants after application of BCA by dipping the roots before transplanting to soil in commercial nurseries. Moreover, the exposure of G. pallida and G. rostochiensis cysts to the conidia of P. oxalicum, in in vitro assays or in soil microcosms significantly reduces hatchability of eggs. The reduction in the rate of G. pallida juveniles hatching was greatest when root diffusates from the `Monalisa´ potato cultivar were used, followed by root diffusates from the `Désirée´ potato cultivar. However, no significant reduction in the rate of G. pallida juveniles hatching was found when root diffusates from the ‘San Pedro” tomato cultivar were used. For G. rostochiensis reduction in the juveniles hatching is obtained from the root diffusates 'Desirée' potato cultivar. Treatment with P. oxalicum also significantly reduces the number of cysts of G. pallida in pots. In order to optimize the practical application of P. oxalicum strain 212 as a biological soil treatment, it is essential to understand how the physical environment influences the BCA colonization, survival and growth, and the possible risk that can cause its application on other microorganisms in the ecosystem of performance. Therefore, the second objective of this thesis is the interaction of the BCA with the environment in which it is applied. Within this objective is evaluated the INFLUENCE OF TEMPERATURE, WATER AVAILABILITY AND PHYSICAL-CHEMICAL PROPERTIES OF SOILS (POROSITY, TEXTURE, DENSITY...) ON SURVIVAL AND GROWTH OF PO212 under controlled conditions to develop models for predicting the environmental impact of each factor on survival and growth of P. oxalicum and to know their ability to grow and survive in different environments. Two parameters are evaluated in the soil samples: i) the survival of Penicillium spp. by counting the number of colony forming units in semi-selective medium and ii) growth (biomass) of PO212 by real-time PCR. P. oxalicum grows and survives better in drought conditions regardless of temperature and soil type. P. oxalicum grows and survives more in sandy loam soils with low organic matter content, higher pH and lower availability of phosphorus and nitrogen. Survival and growth of P. oxalicum negatively correlates with the availability of water and positively with the organic content. Only survival also correlated positively with pH. Moreover, trials are carried out into commercial orchards soils with different physic-chemical properties and different environmental conditions TO STUDY THE ESTABLISHMENT, SURVIVAL, VERTICAL DISPERSION AND HORIZONTAL SPREAD OF PO212. P. oxalicum 212 can persist and survive at very low levels in soil one year after its release. The size of the PO212 population after its release into the tested natural soils is similar to that of indigenous Penicillium spp. Furthermore, the vertical dispersion and horizontal spread of PO212 is limited in different soil types. The introduction of P. oxalicum in a natural environment not only involves their action on the target organism, the pathogen, but also on other indigenous microorganisms. TO ASSESS THE EFFECT OF P. oxalicum APPLICATION ON SOIL INDIGENOUS FUNGAL COMMUNITIES in two commercial orchards, soil samples are analyzed by Denaturing Gradient Gel Electrophoresis polyacrylamide (DGGE). Samples are taken from soil at two depths (5 and 10 cm) and four dates from the application of P. oxalicum 212 (0, 75, 180 and 365 days). DGGE analysis shows that differences are observed between sampling dates and are independent of the treatment of P. oxalicum applied and the depth. BCA application does not affect the fungal population of the two soil analyzed. Sequence analysis of the DGGE bands confirms previous findings and to identify the presence of BCA on soils. The presence of P. oxalicum in soil is especially related to environmental factors such as humidity. Therefore, we conclude that the 212 of strain Penicillium oxalicum can be considered an optimum BCA, since it is environmentally competitive and effective against a broad spectrum of diseases and does not have any negative effect on soil non-target fungi communities.

Effects of forage type on diversity in bacterial pellets isolated from liquid and solid phases of the rumen content in sheep and goats.

Two sheep and two goats, fitted with a ruminal cannula, received two diets composed of 30% concentrate and 70% of either alfalfa hay (AL) or grass hay (GR) as forage in a two-period crossover design. Solid and liquid phases of the rumen were sampled from each animal immediately before feeding and 4 h post-feeding. Pellets containing solid associated bacteria (SAB) and liquid associated bacteria (LAB) were isolated from the corresponding ruminal phase and composited by time to obtain 2 pellets per animal (one SAB and one LAB) before DNA extraction. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal DNA was used to analyze bacterial diversity. A total of 78 and 77 bands were detected in the DGGE gel from sheep and goats samples, respectively. There were 18 bands only found in the pellets from sheep fed AL-fed sheep and 7 found exclusively in samples from sheep fed the GR diet. In goats, 21 bands were found only in animals fed the AL diet and 17 were found exclusively in GR-fed ones. In all animals, feeding AL diet tended (P < 0.10) to promote greater NB and SI in LAB and SAB pellets compared with the GR diet. The dendrogram generated by the cluster analysis showed that in both animal species all samples can be included in two major clusters. The four SAB pellets within each animal species clustered together and the four LAB pellets grouped in a different cluster. Moreover, SAB and LAB clusters contained two clear subclusters according to forage type. Results show that in all animals bacterial diversity was more markedly affected by the ruminal phase (solid vs. liquid) than by the type of forage in the diet.