Estimating taxon-specific population dynamics in diverse microbial communities

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon- specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortal- ity, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes

Soil fungal abundance and plant functional traits drive fertile island formation in global drylands

Dryland vegetation is characterized by discrete plant patches that accumulate and capture soil resources under their canopies. These “fertile islands” are major drivers of dryland ecosystem structure and functioning, yet we lack an integrated understanding of the factors controlling their magnitude and variability at the global scale.EEA BarilocheFil: Ochoa-Hueso, Raúl. Universidad Autónoma de Madrid. Department of Ecology; EspañaFil: Eldridge, David J. University of New South Wales. School of Biological, Earth and Environmental Sciences; AustraliaFil: Delgado-Baquerizo, Manuel. University of Colorado. Cooperative Institute for Research in Environmental Sciences; Estados Unidos. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Soliveres, Santiago. University of Bern. Institute of Plant Sciences; SuizaFil: Bowker, Matthew A. Northern Arizona University. School of Forestry; Estados UnidosFil: Gross, Nicolás. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; España. Institut Nationale de la Recherche Agronomique; Francia. Université La Rochelle. Centre d’étude biologique de Chizé; FranciaFil: Le Bagousse-Pinguet, Yoann. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Quero, José L. Universidad de Córdoba. Escuela Técnica Superior de Ingeniería Agronómica y de Montes. Departamento de Ingeniería Forestal: EspañaFil: García-Gómez, Miguel. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Valencia, Enrique. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; EspañaFil: Arredondo, Tulio. Instituto Potosino de Investigación Científica y Tecnológica. División de Ciencias Ambientales; MéxicoFil: Beinticinco, Laura. Universidad Nacional de La Pampa. Facultad de Agronomía; ArgentinaFil: Bran, Donaldo Eduardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Cea, Alex. Universidad de La Serena. Departamento de Biología; ChileFil: Coaguila, Daniel. Instituto de Ensino Superior de Rio Verde; BrasilFil: Dougill, Andrew J. University of Leeds. School of Earth and Environment; Gran BretañaFil: Espinosa, Carlos I. Universidad Técnica Particular de Loja. Departamento de Ciencias Naturales; EcuadorFil: Gaitan, Juan Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Suelos; ArgentinaFil: Guuroh, Reginald T. University of Cologne. Botanical Institute. Range Ecology and Range Management Group; Alemania. CSIR-Forestry Research Institute of Ghana; GhanaFil: Guzmán, Elizabeth. Universidad Técnica Particular de Loja. Departamento de Ciencias Naturales; EcuadorFil: Gutiérrez, Julio R.. Universidad de La Serena. Departamento de Biología; Chile. Centro de Estudios Avanzados en Zonas Áridas (CEAZA); Chile. Instituto de Ecología y Biodiversidad; ChileFil: Hernández, Rosa M. Universidad Experimental Simón Rodríguez. Centro de Agroecología Tropical. Laboratorio de Biogeoquímica; VenezuelaFil: Huber-Sannwald, Elisabeth. Instituto Potosino de Investigación Científica y Tecnológica. División de Ciencias Ambientales; MéxicoFil: Jeffries, Thomas. Western Sydney University. Hawkesbury Institute for the Environment; AustraliaFil: Linstädter, Anja. University of Cologne. Botanical Institute. Range Ecology and Range Management Group; AlemaniaFil: Mau, Rebecca L. Northern Arizona University. Center for Ecosystem Science and Society: Estados UnidosFil: Monerris, Jorge. Université du Québec à Montréal. Pavillon des Sciences Biologiques. Département des Sciences Biologiques; CanadáFil: Prina, Anibal. Universidad Nacional de La Pampa. Facultad de Agronomía; ArgentinaFil: Pucheta, Eduardo. Universidad Nacional de San Juan. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Biología; ArgentinaFil: Stavi, Ilan. Dead Sea and Arava Science Center, IsraelFil: Thomas, Andrew. Aberystwyth University. Department of Geography and Earth Sciences; Gran BretañaFil: Zaady, Eli. Agricultural Research Organization. Gilat Research Center. Natural Resources; IsraelFil: Singh, Brajesh K. Western Sydney University. Hawkesbury Institute for the Environment; Australia. Western Sydney University. Global Centre for Land-Based Innovation; AustraliaFil: Maestre, Fernando T. Universidad Rey Juan Carlos. Escuela Superior de Ciencias Experimentales y Tecnología. Departamento de Biología y Geología, Física y Química Inorgánica; Españ

Soil fungal abundance and plant functional traits drive fertile island formation in global drylands

International audience1.Dryland vegetation is characterised by discrete plant patches that accumulate and capture soil resources under their canopies. These “fertile islands” are major drivers of dryland ecosystem structure and functioning, yet we lack an integrated understanding of the factors controlling their magnitude and variability at the global scale.2.We conducted a standardized field survey across two hundred and thirty-six drylands from five continents. At each site, we measured the composition, diversity and cover of perennial plants. Fertile island effects were estimated at each site by comparing composite soil samples obtained under the canopy of the dominant plants and in open areas devoid of perennial vegetation. For each sample, we measured fifteen soil variables (functions) associated with carbon, nitrogen and phosphorus cycling and used the Relative Interaction Index to quantify the magnitude of the fertile island effect for each function. In eighty sites, we also measured fungal and bacterial abundance (quantitative PCR) and diversity (Illumina MiSeq).3.The most fertile islands, i.e. those where a higher number of functions were simultaneously enhanced, were found at lower-elevation sites with greater soil pH values and sand content under semiarid climates, particularly at locations where the presence of tall woody species with a low specific leaf area increased fungal abundance beneath plant canopies, the main direct biotic controller of the fertile island effect in the drylands studied. Positive effects of fungal abundance were particularly associated with greater nutrient contents and microbial activity (soil extracellular enzymes) under plant canopies.4.Synthesis. Our results show that the formation of fertile islands in global drylands largely depends on: (i) local climatic, topographic and edaphic characteristics, (ii) the structure and traits of local plant communities and (iii) soil microbial communities. Our study also has broad implications for the management and restoration of dryland ecosystems worldwide, where woody plants are commonly used as nurse plants to enhance the establishment and survival of beneficiary species. Finally, our results suggest that forecasted increases in aridity may enhance the formation of fertile islands in drylands worldwide

Phylogenetic organization of bacterial activity.

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism\u27s ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.The ISME Journal advance online publication, 4 March 2016; doi:10.1038/ismej.2016.28

U.S. Natural Resources and Climate Change: Concepts and Approaches for Management Adaptation

Public lands and waters in the United States traditionally have been managed using frameworks and objectives that were established under an implicit assumption of stable climatic conditions. However, projected climatic changes render this assumption invalid. Here, we summarize general principles for management adaptations that have emerged from a major literature review. These general principles cover many topics including: (1) how to assess climate impacts to ecosystem processes that are key to management goals; (2) using management practices to support ecosystem resilience; (3) converting barriers that may inhibit management responses into opportunities for successful implementation; and (4) promoting flexible decision making that takes into account challenges of scale and thresholds. To date, the literature on management adaptations to climate change has mostly focused on strategies for bolstering the resilience of ecosystems to persist in their current states. Yet in the longer term, it is anticipated that climate change will push certain ecosystems and species beyond their capacity to recover. When managing to support resilience becomes infeasible, adaptation may require more than simply changing management practices—it may require changing management goals and managing transitions to new ecosystem states. After transitions have occurred, management will again support resilience—this time for a new ecosystem state. Thus, successful management of natural resources in the context of climate change will require recognition on the part of managers and decisions makers of the need to cycle between “managing for resilience” and “managing for change.

Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice.

Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems

Decoupling of soil nutrient cycles as a function of aridity in global drylands

18 páginas.- 10 figuras.- 72 referencias.- Online Content Any additional Methods, Extended Data display items and Source Data are available in the online version of the paper; references unique to these sections appear only in the online paper..- Puede conseguir el texto completo en el Portal de la producción científica de la Universidad Complutense de Madrid https://produccioncientifica.ucm.es/documentos/5ec78dc52999520a1d557660 .- o en lel respositorio institucional CONICET digital https://ri.conicet.gov.ar/bitstream/handle/11336/29204/CONICET_Digital_Nro.ead4e2ed-0da6-4041-814b-259e8f27bbf6_D.pdf?sequence=5&isAllowed=yThe biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems1. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes1,2,3,4,5. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability6,7,8. The increase in aridity predicted for the twenty-first century in many drylands worldwide9,10,11 may therefore threaten the balance between these cycles, differentially affecting the availability of essential nutrients12,13,14. Here we evaluate how aridity affects the balance between C, N and P in soils collected from 224 dryland sites from all continents except Antarctica. We find a negative effect of aridity on the concentration of soil organic C and total N, but a positive effect on the concentration of inorganic P. Aridity is negatively related to plant cover, which may favour the dominance of physical processes such as rock weathering, a major source of P to ecosystems, over biological processes that provide more C and N, such as litter decomposition12,13,14. Our findings suggest that any predicted increase in aridity with climate change will probably reduce the concentrations of N and C in global drylands, but increase that of P. These changes would uncouple the C, N and P cycles in drylands and could negatively affect the provision of key services provided by these ecosystems.This research is supported by the European Research Council (ERC) under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement no. 242658 (BIOCOM), and by the Ministry of Science and Innovation of the Spanish Government, grant no. CGL2010-21381. CYTED funded networking activities (EPES, Acción 407AC0323). M.D.-B. was supported by a PhD fellowship from the Pablo de Olavide University.Peer reviewe

Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function

CO2 production and the priming effect in different ecosystems

These data are from laboratory incubations of soils collected from the Merriam Powel Elevation Gradient Climate Change Experiment plots (only warming treatments). The soil was put in jars, and either had 13C-labeled glucose added or not, and CO2 production was measured over a several week period. The isotope composition of the CO2 released during the incubation was measured. This allowed us to partition CO2 production derived from the new C input (13C labeled glucose) and that from older soil organic matter (not labeled) along with CO2 concentration. From this information, priming (change of soil organic matter turnover in response to a C input) is calculated