Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces

Partenogenesis inducida en Musa spp. para la obtención de plantas haploides

Tesis (M. Sc) -- CATIE, Turrialba (Costa Rica), 1991En la actualidad el mejoramiento de los materiales diploides en musáceas es la etapa indispensable en el mejoramiento del banano y el plátano. Una de estas miras es la obtención de líneas homocigotas. La obtención de plantas homocigotas, aunque posible a través de autofecundaciones, demoraría de ocho a diez años. Por consiguiente, la partenogénesis inducida a través de la polinización con polen irradiado, podría constituir una alternativa más rápida. Este método consiste en la formación de plantas haploides, cuyo lote de cromosomas se puede duplicar con colchicina para formar plantas homocigotas. Con base en ésto, se plantearon los siguientes objetivos: encontrar un método que permita evaluar el porcentaje de germinación del polen de Musa acuminata ssp burmanicoides y de Musa balbisiana tipo TANI determinar si el polen de estas subespecies es capaz de germinar después de ser sometido a diferentes dosis de radiación gamma determinar si el polen así tratado es capaz de estimular el desarrollo de la semilla sin que ocurra la fertilización analizar histológicamente el desarrollo de las semillas obtenidas, después de polinizar con el polen sometido a diferentes dosis de radiación determinar la utilidad de la técnica de polinización con polen irradiado, en la formación de plantas haploides en Musa spp. El polen de M. acuminata ssp burmannicoides y de M. balbisiana tipo TANI, fue irradiado con diferentes dosis de radiación gamma, para polinizar plantas de M. acuminata ssp burmannicoides. El polen fue capaz de germinar después de ser irradiado a cualquiera de las dosis utilizadas. En todos los tratamientos se logró la formación de semillas. El estudio histológico permitió determinar los intervalos de radiación más apropiados para el desarrollo de los embriones. En estas dosis se logró obtener plantas completas a través del rescate de embrión. Para la determinación del nivel de ploidia de las plantas obtenidas, se utilizaron dos métodos: primero se evaluó el número de cromosomas realizando un cariotipo el otro método fue el análisis de citometría en flujo, el cual consistió en evaluar el volumen de ADN de los núcleos. Muchas de las plantas evaluadas fueron encontradas diploides. Sin embargo en las plantas obtenidas en el tratamiento 5 Kr (M. acuminata ssp burmannicoides por M. balbisiana tipo TANI), se encontró una planta haploide con 11 cromosomas (n=11) y en el tratamiento 7 Kr (M. acuminata ssp burmannicoides por M. acuminata ssp burmannicoides), se encontró otra planta haploide con 11 cromosomas (n=11)

Soil organic carbon pool under native tree plantations in the Caribbean lowlands of Costa Rica

[EN] We evaluated the soil organic carbon (SOC) pool and selected physico-chemical soil variables in a plantation with native tree species established in a degraded pasture of the Caribbean lowlands of Costa Rica. Studies on the rate and accumulation of aboveground biomass and C have been conducted in native tree plantations of Costa Rica. However, more studies on the SOC pool are needed since only few works provide information on the subject. The tree plantation was established in 1991 on a 2.6 ha. degraded pasture (Ischaemum sp.) Four species were selected: Vochysia guatemalensis Smith, Calophyllum brasiliense Cambess, Stryphnodendron excelsum Poeppig et Endl. and Hieronyma alchorneoides Allemao. Average SOC concentration ranged from 44.9 to 55.2 g kg−1 (0–10 cm), and decreased with depth up to 12.7–16.8 g kg−1 (40–50 cm). The highest SOC pool was measured under H. alchorneoides and V. guatemalensis, i.e. 131.9 and 119.2 Mg C ha−1, respectively, whereas in the pasture it was 115.6 Mg C ha−1. The SOC pool has not changed significantly under the tree species evaluated 14 years after establishment. A multivariate ordination technique named between-within class principal component analysis was used to determine the factors and trend that explain the variability in the data. The effect of vegetation in the SOC and selected soil variables measured in this study was only detected for H. alchorneoides. The information presented herein about the depth distribution of the SOC fraction improves our knowledge for further developing prediction models.Financial support for this study was provided by the US Department of Energy. We also thank the assistant in the field provided by Juan Hugo. Thanks to H. Arrieta for kindly permit the use of lab facilities at EARTH during field work, and Y. Raut is acknowledged for his help in C:N determinations at OSU lab. The useful comments provided by two anonymous referees are also highly appreciated.Peer reviewe

The soil organic carbon in particle-size separates under different regrowth forest stands of north eastern Costa Rica

11 páginas, 4 figuras, 6 tablas.-- Ecological management and sustainable development in the humid tropics of Costa Rica.Despite the importance of the secondary forest (SF) in tropical areas, few studies have quantified the soil organic carbon (SOC) pool in Costa Rica. Most of the studies conducted to date in this country have focused mainly on changes in the soil C pool following conversion of forests to pastures, which is the predominant land use in the tropics. The aim of this study was to measure SOC concentration and pool in particle-size fractions down to 50 cm depth in four SF stands regenerating from different intensities of prior land use in loamy sand and sandy loam soils of northeast Costa Rica: (i) a gallery forest (GF), (ii) a 15-year-old SF enriched with commercially planted native trees (15SF), (iii) a 25-year-old SF (25SF), and (iv) an abandoned Theobromma cacao plantation >60 years old (60SF). Additional objectives were (1) to determine the relationship of SOC concentration with selected physical and chemical soil properties, and (2) to establish the key determinants of the depth distribution of SOC in order to identify meaningful trends in the SOC pool. The SOC pool was highest under the 60SF (221.4 Mg C ha−1) followed by the 15SF (212.1 Mg C ha−1), the 25SF (195.9 Mg C ha−1) and the lowest in the GF (183.5 Mg C ha−1). The SOC concentration decreased significantly from 59.7 to 94.1 g kg−1 in the 0–10 cm layer down to 31.0 to 45.5 g kg−1 in the 40–50 cm layer in all forest stands. The fine silt + clay fraction contained the highest values of SOC concentration in all forest stands. Soil texture and the age of the SF were identified as the main factors that explained the variability in SOC. The age of SF stand influenced the distribution of size class aggregates and SOC.This work was funded by the US Department of Energy. The first author thanks “Fundación ARAID” (Spain) for financial support during manuscript preparation.Peer reviewe

The soil C pool in different agroecosystems derived from the dry tropical forest of Guanacaste, Costa Rica

11 páginas, 6 figuras, 6 tablas.-- Ecological management and sustainable development in the humid tropics of Costa Rica.Inventories of soil C pools are still lacking from tropical sites. Our objective was to assess total C and N concentrations in the different mineral soil fractions down to 50 cm depth in relation to selected physical and chemical properties of 5 ecosystems at La Flor Sustainable Center in Guanacaste, Costa Rica. The ecosystems studied were a derived savanna with scattered trees, a gallery forest, an abandoned Mango indigofera L. plantation, a Citrus sp. plantation, and a Saccharum officinarum L. (sugarcane) plantation. Significant differences were found for the main fixed factor ecosystem for all variables analyzed (ANOVA). The TSC concentration was significantly higher in the sugarcane plantation compared to the rest of land use systems. The TSC concentration decreased significantly with increase in depth in all ecosystems and ranged from 20.3–38.3 to 4.3–20.9 g kg−1 in the 0–10 and 40–50 cm depth, respectively. In all cases, the clay + silt fraction ( Curatella savanna > Mango and Citrus plantations > gallery forest. A principal component analysis (PCA) performed with all variables studied showed that the ordination of land uses (ecosystems) in the factorial plane defined by the first two axes was significant (Monte Carlo permutation test, P < 0.0001). The highest TSC pool down to 50 cm depth was obtained in the sugarcane plantation (160 Mg C ha−1) while less C was found in the rest of ecosystems, i.e. from 66 (gallery forest) to 80 Mg C ha−1 (Curatella savanna). The TSC concentration obtained in the sugarcane plot is likely the result of the incorporation of surface residues into the soil that would have otherwise been lost through burning, which is the current practice in the region. Further studies on C stabilization in the clay fraction are thus needed to test the hypothesis of soil C enrichment due to residue management. Finally, trade-offs are to be considered for both preservation of the fragile dTf and the productivity of derived land uses that increases soil C at the same time.Financial support during field work was provided by the US Department of Energy. The first author thanks Fundación ARAID-GA (Spain) for financial support.Peer reviewe