Revised calibration of the MBT-CBT paleotemperature proxy

The MBT-CBT proxy for the reconstruction of paleotemperatures and past soil pH is based on the distribution of branched glycerol dialkyl glycerol tetraether (brGDGT) membrane lipids. The Methylation of Branched Tetraether (MBT) and the Cyclisation of Branched Tetraether (CBT) indices were developed to quantify these distributions, and significant empirical relations between these indices and annual mean air temperature (MAT) and/or soil pH were found in a large data set of soils. In this study, we extended this soil dataset to 278 globally distributed surface soils. Of these soils, 26% contains all nine brGDGTs, while in 63% of the soils the seven most common brGDGTs were detected, and the latter were selected for calibration purposes. This resulted in new transfer functions for the reconstruction of pH based on the CBT index: pH = 7.90-1.97 × CBT (r**2 = 0.70; RMSE = 0.8; n = 176), as well as for MAT based on the CBT index and methylation index based on the seven most abundant GDGTs (defined as MBT'): MAT = 0.81-5.67 × CBT + 31.0 × MBT' (r**2 = 0.59; RMSE = 5.0 °C; n = 176). The new transfer function for MAT has a substantially lower correlation coefficient than the original equation (r**2 = 0.77). To investigate possible improvement of the correlation, we used our extended global surface soil dataset to statistically derive the indices that best describe the relations of brGDGT composition with MAT and soil pH. These new indices, however, resulted in only a relatively minor increase in correlation coefficients, while they cannot be explained straightforwardly by physiological mechanisms. The large scatter in the calibration cannot be fully explained by local factors or by seasonality, but MAT for soils from arid regions are generally substantially (up to 20 °C) underestimated, suggesting that absolute brGDGT-based temperature records for these areas should be interpreted with caution. The applicability of the new MBT'-CBT calibration function was tested using previously published MBT-CBT-derived paleotemperature records covering the last deglaciation in Central Africa and East Asia, the Eocene-Oligocene boundary and the Paleocene-Eocene thermal maximum. The results show that trends remain similar in all records, but that absolute temperature estimates and the amplitude of temperature changes are lower for most records, and generally in better agreement with independent proxy data.

Vegetation cover and radiocarbon dates of palsa and peat plateaus in the Hudson Bay Lowlands

The Holocene development of a treed palsa bog and a peat plateau bog, located near the railroad to Churchill in the Hudson Bay Lowlands of northeastern Manitoba, was traced using peat macrofossil and radiocarbon analyses. Both sites first developed as wet rich fens through paludification of forested uplands around 6800 cal. yr BP. Results show a 20th-century age for the palsa formation and repeated periods of permafrost aggradation and collapse at the peat plateau site during the late Holocene. This timing of permafrost dynamics corroborates well with that inferred from previous studies on other permafrost peatlands in the same region. The developmental history of the palsa and peat plateau bogs is similar to that of adjacent permafrost-free fens, except for the specific frost heave and collapse features associated with permafrost dynamics. Permafrost aggradation and degradation is ascribed to regional climatic, local autogenic and other factors. Particularly the very recent palsa development can be assessed in terms of climatic changes as inferred from meteorological data and surface hydrological changes related to construction of the railroad. The results indicate that cold years with limited snowfall as well as altered drainage patterns associated with infrastructure development may have contributed to the recent palsa formation.

Experiment: Marine fungi may benefit from ocean acidification

Recent studies have discussed the consequences of ocean acidification for bacterial processes and diversity. However, the decomposition of complex substrates in marine environments, a key part of the flow of energy in ecosystems, is largely mediated by marine fungi. Although marine fungi have frequently been reported to prefer low pH levels, this group has been neglected in ocean acidification research. We present the first investigation of direct pH effects on marine fungal abundance and community structure. In microcosm experiments repeated in 2 consecutive years, we incubated natural North Sea water for 4 wk at in situ seawater pH (8.10 and 8.26), pH 7.82 and pH 7.67. Fungal abundance was determined by colony forming unit (cfu) counts, and fungal community structure was investigated by the culture-independent fingerprint method Fungal Automated Ribosomal Intergenic Spacer Analysis (F-ARISA). Furthermore, pH at the study site was determined over a yearly cycle. Fungal cfu were on average 9 times higher at pH 7.82 and 34 times higher at pH 7.67 compared to in situ seawater pH, and we observed fungal community shifts predominantly at pH 7.67. Currently, surface seawater pH at Helgoland Roads remains >8.0 throughout the year; thus we cannot exclude that fungal responses may differ in regions regularly experiencing lower pH values. However, our results suggest that under realistic levels of ocean acidification, marine fungi will reach greater importance in marine biogeochemical cycles. The rise of this group of organisms will affect a variety of biotic interactions in the sea.

Effects of sheep and horse manure and pine bark amendments on metal distribution and chemical properties of contaminated mine soils.

Mine soils usually contain large levels of heavy metals and poor fertility conditions which limit their reclamation and the application of phyto-remediation technologies. Two organic waste materials (pine bark compost and sheep and horse manure compost), with different pHs and varying degrees of humification and nutrient contents, were applied as amendments to assess their effects on copper (Cu) and zinc (Zn) bioavailability and on fertility conditions of mine soils. Soil samples collected from two abandoned mining areas near Madrid (Spain) were mixed with 0, 30 and 60 t ha?1 of the organic amendments. The concentrations of metals among the different mineral and organic fractions of soil were determined by several extraction procedures to study the metal distribution in the solid phase of the soil affected by the organic amendments. The results showed that the manure amendment increased the soil pH and the cation exchange capacity and enhanced the nutrient levels of these soils. The pine bark amendment decreased the soil pH and did not significantly change the nutrient status of soil. Soil pH, organic matter content and its degree of humification, which were altered by the amendments, were the main factors affecting Cu fractionation. Zn fractionation was mainly affected by soil pH. The addition of manure not only improved soil fertility, but also decreased metal bioavailability resulting in a reduction of metal toxicity. Conversely, pine bark amendment increased metal ioavailability. The use of sheep and horse manure could be a cost-effective practice for the restoration of contaminated mine soils.

Molecular tools to improve chestnut management: El Bierzo as a case study

The European chestnut (Castanea sativa Mill.) is a multipurpose species that has been widely cultivated around the Mediterranean basin since ancient times. New varieties were brought to the Iberian Peninsula during the Roman Empire, which coexist since then with native populations that survived the last glaciation. The relevance of chestnut cultivation has being steadily growing since the Middle Ages, until the rural decline of the past century put a stop to this trend. Forest fires and diseases were also major factors. Chestnut cultivation is gaining momentum again due to its economic (wood, fruits) and ecologic relevance, and represents currently an important asset in many rural areas of Europe. In this Thesis we apply different molecular tools to help improve current management strategies. For this study we have chosen El Bierzo (Castile and Leon, NW Spain), which has a centenary tradition of chestnut cultivation and management, and also presents several unique features from a genetic perspective (next paragraph). Moreover, its nuts are widely appreciated in Spain and abroad for their organoleptic properties. We have focused our experimental work on two major problems faced by breeders and the industry: the lack of a fine-grained genetic characterization and the need for new strategies to control blight disease. To characterize with sufficient detail the genetic diversity and structure of El Bierzo orchards, we analyzed DNA from 169 trees grafted for nut production covering the entire region. We also analyzed 62 nuts from all traditional varieties. El Bierzo constitutes an outstanding scenario to study chestnut genetics and the influence of human management because: (i) it is located at one extreme of the distribution area; (ii) it is a major glacial refuge for the native species; (iii) it has a long tradition of human management (since Roman times, at least); and (iv) its geographical setting ensures an unusual degree of genetic isolation. Thirteen microsatellite markers provided enough informativeness and discrimination power to genotype at the individual level. Together with an unexpected level of genetic variability, we found evidence of genetic structure, with three major gene pools giving rise to the current population. High levels of genetic differentiation between groups supported this organization. Interestingly, genetic structure does not match with spatial boundaries, suggesting that the exchange of material and cultivation practices have strongly influenced natural gene flow. The microsatellite markers selected for this study were also used to classify a set of 62 samples belonging to all traditional varieties. We identified several cases of synonymies and homonymies, evidencing the need to substitute traditional classification systems with new tools for genetic profiling. Management and conservation strategies should also benefit from these tools. The avenue of high-throughput sequencing technologies, combined with the development of bioinformatics tools, have paved the way to study transcriptomes without the need for a reference genome. We took advantage of RNA sequencing and de novo assembly tools to determine the transcriptional landscape of chestnut in response to blight disease. In addition, we have selected a set of candidate genes with high potential for developing resistant varieties via genetic engineering. Our results evidenced a deep transcriptional reprogramming upon fungal infection. The plant hormones ET and JA appear to orchestrate the defensive response. Interestingly, our results also suggest a role for auxins in modulating such response. Many transcription factors were identified in this work that interact with promoters of genes involved in disease resistance. Among these genes, we have conducted a functional characterization of a two major thaumatin-like proteins (TLP) that belongs to the PR5 family. Two genes encoding chestnut cotyledon TLPs have been previously characterized, termed CsTL1 and CsTL2. We substantiate here their protective role against blight disease for the first time, including in silico, in vitro and in vivo evidence. The synergy between TLPs and other antifungal proteins, particularly endo-p-1,3-glucanases, bolsters their interest for future control strategies based on biotechnological approaches.

Bioaccesibilidad de elementos traza en suelos de parques infantiles. Aplicación al análisis de riesgo

En este trabajo doctoral se evaluó la bioaccesibilidad in vitro para As, Co, Cr, Cu, Ni, Pb y Zn (en la fracción menor de 100μm) por tres procedimientos distintos en 32 muestras de suelo superficial, recogidas en 16 parques infantiles de la ciudad de Madrid.. Dos de los métodos de extracción (SBET y extracción con HCl a pH=1.5) reproducen únicamente la fase gástrica, mientras que otro (RIVM) tiene en cuenta un proceso completo de digestión (gástrico+intestinal). La bioaccesibilidad (%) se definió frente a las concentraciones pseudototales de los elementos traza estudiados (agua regia), utilizando un modelo de regresión lineal pasando por el origen. Los dos métodos gástricos ofrecieron resultados similares y consistentes con datos de otros estudios, siendo el orden de bioaccesibilidad As ≈ Cu ≈ Pb ≈ Zn > Co > Ni > Cr, con rangos entre el 63 y el 7%. Para el procedimiento RIVM (gástrico + intestinal) se obtuvieron valores de un orden similar a los obtenidos en fase gástrica para los elementos As, Cu, Pb y Zn (muy similares para el Zn, algo superiores para Cu y Pb, y algo inferiores para As). Por el contrario, la bioaccesibilidad de Co y Cu es, en este caso, muy superior a la resultante de los ensayos en fase gástrica. El orden de bioaccesibilidad es Co ≈ Cu ≈ Pb > As ≈ Cr ≈ Zn, con rangos entre el 42 y el 69%. Los resultados de los tres procedimientos evaluados correlacionan muy intensamente para los elementos traza As, Cu, Pb y Zn, existiendo intensas correlaciones entre casi todos los elementos estudiados para las dos fases gástricas, no siendo así en el ensayo de digestión completa. Se estudiaron algunas propiedades físico-químicas de los suelos muestreados, así como su composición en algunos elementos mayoritarios con el objeto de evaluar su influencia sobre la bioaccesibilidad. Se observa una dependencia de la bioaccesibilidad (%) de distintos elementos respecto a algunas propiedades de los suelos estudiados, tales como: contenido en Fe, Ca (carbonatos) y P, materia orgánica y pH. El contenido en Fe resulta ser muy relevante en cuanto a la bioaccesibilidad obtenida. En todos los casos correlaciona negativamente con el porcentaje de bioaccesibilidad siendo más significativo este fenómeno en el caso de las extracciones en fase gástrica. Se sugiere que dada la baja solubilización de los óxidos de hierro en los medios extractantes empleados hay una fuerte adsorción de complejos aniónicos (metal-anión cloruro) sobre la superficie de estos óxidos de Fe, con la consiguientes disminución de la bioaccesibilidad. En cuanto al contenido en calcio (carbonatos) este dato parece muy relevante si nos referimos a la bioaccesibilidad del As. Efectivamente el As aparece ligado al Ca del suelo y su solubilización en medios ácidos implicaría un aumento de la bioaccesibilidad del As, mientras que su precipitación al pasar a pH básico (fase intestinal) provocaría una disminución de la bioaccesibilidad. La materia orgánica sólo se ha demostrado relevante respecto a los contenidos pseudototales para el Zn. Para el porcentaje de bioaccesibilidad es significativo para muchos elementos en los ensayos en fase gástrica. La influencia del pH de los suelos estudiados sólo parece ser muy significativo en el caso del Cr. Los valores altamente homogéneos del pH de los suelos estudiados sin duda hacen que este parámetro no resulte significativo para más elementos, tal como se desprende de estudios anteriores. ABSTRACT A total of 32 samples of superficial soil were collected from 16 playground areas in Madrid. The in vitro bioaccessibility of As, Co, Cr, Ni, Pb and Zn (fraction below 100μm) was evaluated by means of three extraction processes. Two of them (SBET and HCl-extraction, pH=1.5) simulate the gastric enviroment, while the other one (RIVM) reproduces a gastric+intestinal digestion sequence. Bioaccessibility (%) was compared against pseudo-total concentrations of trace elements studied (aqua regia) with a linear regression model (forced to intercept the origin) Both gastric methods offered very similar and consistent results with data from other studies, with bioaccessibilities following the order: As ≈ Cu ≈ Pb ≈ Zn > Co > Ni > Cr, and ranging from 63% to 7% The values obtained through RIVM (gastric+ intestinal) method are similar to those obtained in gastric environment for elements: As, Cu, Pb and Zn (very similar to Zn, to a higher extent Cu and Pb, and to a lower extent As). On the contrary the bioaccessibility obtained for elements Co and Cu is considerable higher than in gastric environment sequence. Bioaccessibilities follows the order Co ≈ Cu ≈ Pb >As ≈ Cr ≈ Zn, ranging between 42 and 69%. The three procedures used correlate very intensively to trace elements As,Cu, Pb and Zn, existing strong correlations between almost all elements studied for the two gastric environment, not in the case of the complete digestion sequence. Some soil physical – chemical properties selected were studied, as well as their composition in some main elements in order to assess their influence on bioaccessibility. A dependence was observed between different elements bioaccesibility (%) and some soil properties, such as: Fe, Ca (carbonate) content and P, organic matter and pH. Fe content becomes very relevant regarding the bioaccessibility obtained. In all cases it correlated negatively with bioaccessibility percentage being more significant this phenomenon in gastric environment extractions. It is suggested that given the low solubility of iron oxide in the extractant media used there has to be a strong adsorption of anionic complexes (metal – chloride anion) on these Fe oxides surface, with a consequent decrease of bioaccessibility. Regarding calcium (carbonate) content this data seems very relevant referred to As bioaccessibility. Indeed, As appears to be bound to soil Ca and its solubilisation in acid media would increase As bioaccessibility, while its precipitation at basic pH (intestinal environment) would cause a reduction in bioaccessibility. The influence of organic matter only seemed significant for Zn “total” content, while it is significant in terms of gastric bioaccessibility for many elements. Soil pH only seems to be very significant in case of Cr. The highly homogeneous values for soil pH makes the influence of this parameter negligible for the other elements, unlike what has been observed in several previous studies.

Roles for mannitol and mannitol dehydrogenase in active oxygen-mediated plant defense

Reactive oxygen species (ROS) are both signal molecules and direct participants in plant defense against pathogens. Many fungi synthesize mannitol, a potent quencher of ROS, and there is growing evidence that at least some phytopathogenic fungi use mannitol to suppress ROS-mediated plant defenses. Here we show induction of mannitol production and secretion in the phytopathogenic fungus Alternaria alternata in the presence of host-plant extracts. Conversely, we show that the catabolic enzyme mannitol dehydrogenase is induced in a non-mannitol-producing plant in response to both fungal infection and specific inducers of plant defense responses. This provides a mechanism whereby the plant can counteract fungal suppression of ROS-mediated defenses by catabolizing mannitol of fungal origin.

Abrogation of disease development in plants expressing animal antiapoptotic genes

An emerging topic in plant biology is whether plants display analogous elements of mammalian programmed cell death during development and defense against pathogen attack. In many plant–pathogen interactions, plant cell death occurs in both susceptible and resistant host responses. For example, specific recognition responses in plants trigger formation of the hypersensitive response and activation of host defense mechanisms, resulting in restriction of pathogen growth and disease development. Several studies indicate that cell death during hypersensitive response involves activation of a plant-encoded pathway for cell death. Many susceptible interactions also result in host cell death, although it is not clear how or if the host participates in this response. We have generated transgenic tobacco plants to express animal genes that negatively regulate apoptosis. Plants expressing human Bcl-2 and Bcl-xl, nematode CED-9, or baculovirus Op-IAP transgenes conferred heritable resistance to several necrotrophic fungal pathogens, suggesting that disease development required host–cell death pathways. In addition, the transgenic tobacco plants displayed resistance to a necrogenic virus. Transgenic tobacco harboring Bcl-xl with a loss-of-function mutation did not protect against pathogen challenge. We also show that discrete DNA fragmentation (laddering) occurred in susceptible tobacco during fungal infection, but does not occur in transgenic-resistant plants. Our data indicate that in compatible plant–pathogen interactions apoptosis-like programmed cell death occurs. Further, these animal antiapoptotic genes function in plants and should be useful to delineate resistance pathways. These genes also have the potential to generate effective disease resistance in economically important crops.