Wageningen University and Research Centre

About: Wageningen University and Research Centre is a education organization based out in Wageningen, Netherlands. It is known for research contribution in the topics: Population & Sustainability. The organization has 23474 authors who have published 54833 publications receiving 2608897 citations.

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Abstract: Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.

Trajectories of the Earth System in the Anthropocene.

Abstract: We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a "Hothouse Earth" pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System-biosphere, climate, and societies-and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

Abstract: All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

Role of nitrifier denitrification in the production of nitrous oxide

Abstract: Nitrifier denitrification is the pathway of nitrification in which ammonia (NH 3 ) is oxidized to nitrite (NO 2 − ) followed by the reduction of NO 2 − to nitric oxide (NO), nitrous oxide (N 2 O) and molecular nitrogen (N 2 ). The transformations are carried out by autotrophic nitrifiers. Thus, nitrifier denitrification differs from coupled nitrification–denitrification, where denitrifiers reduce NO 2 − or nitrate (NO 3 − ) that was produced by nitrifiers. Nitrifier denitrification contributes to the development of the greenhouse gas N 2 O and also causes losses of fertilizer nitrogen in agricultural soils. In this review article, present knowledge about nitrifier denitrification is summarized in order to give an exact definition, to spread awareness of its pathway and controlling factors and to identify areas of research needed to improve global N 2 O budgets. Due to experimental difficulties and a lack of awareness of nitrifier denitrification, not much is known about this mechanism of N 2 O production. The few measurements carried out so far attribute up to 30% of the total N 2 O production to nitrifier denitrification. Low oxygen conditions coupled with low organic carbon contents of soils favour this pathway as might low pH. As nitrifier denitrification can lead to substantial N 2 O emissions, there is a need to quantify this pathway in different soils under different conditions. New insights attained through quantification experiments should be used in the improvement of computer models to define sets of conditions that show where and when nitrifier denitrification is a significant source of N 2 O. This may subsequently render the development of guidelines for low-emission farming practices necessary.