Rapid coral reef assessment using 3D modelling and acoustics: acoustic indices correlate to fish abundance, diversity and environmental indicators in West Papua, Indonesia

Background Providing coral reef systems with the greatest chance of survival requires effective assessment and monitoring to guide management at a range of scales from community to government. The development of rapid monitoring approaches amenable to collection at community level, yet recognised by policymakers, remains a challenge. Technologies can increase the scope of data collection. Two promising visual and audio approaches are (i) 3D habitat models, generated through photogrammetry from video footage, providing assessment of coral cover structural metrics and (ii) audio, from which acoustic indices shown to correlate to vertebrate and invertebrate diversity, can be extracted. Methods We collected audio and video imagery using low cost underwater cameras (GoPro Hero7™) from 34 reef samples from West Papua (Indonesia). Using photogrammetry one camera was used to generate 3D models of 4 m2 reef, the other was used to estimate fish abundance and collect audio to generate acoustic indices. We investigated relationships between acoustic metrics, fish abundance/diversity/functional groups, live coral cover and reef structural metrics. Results Generalized linear modelling identified significant but weak correlations between live coral cover and structural metrics extracted from 3D models and stronger relationships between live coral and fish abundance. Acoustic indices correlated to fish abundance, species richness and reef functional metrics associated with overfishing and algal control. Acoustic Evenness (1,200–11,000 Hz) and Root Mean Square RMS (100–1,200 Hz) were the best individual predictors overall suggesting traditional bioacoustic indices, providing information on sound energy and the variability in sound levels in specific frequency bands, can contribute to reef assessment. Conclusion Acoustics and 3D modelling contribute to low-cost, rapid reef assessment tools, amenable to community-level data collection, and generate information for coral reef management. Future work should explore whether 3D models of standardised transects and acoustic indices generated from low cost underwater cameras can replicate or support ‘gold standard’ reef assessment methodologies recognised by policy makers in marine management

Sticking With It: ER-PM Membrane Contact Sites as a Coordinating Nexus for Regulating Lipids and Proteins at the Cell Cortex

Membrane contact sites between the cortical endoplasmic reticulum (ER) and the plasma membrane (PM) provide a direct conduit for small molecule transfer and signaling between the two largest membranes of the cell. Contact is established through ER integral membrane proteins that physically tether the two membranes together, though the general mechanism is remarkably non-specific given the diversity of different tethering proteins. Primary tethers including VAMP-associated proteins (VAPs), Anoctamin/TMEM16/Ist2p homologs, and extended synaptotagmins (E-Syts), are largely conserved in most eukaryotes and are both necessary and sufficient for establishing ER-PM association. In addition, other species-specific ER-PM tether proteins impart unique functional attributes to both membranes at the cell cortex. This review distils recent functional and structural findings about conserved and species-specific tethers that form ER-PM contact sites, with an emphasis on their roles in the coordinate regulation of lipid metabolism, cellular structure, and responses to membrane stress

Agroecology: promoting the transition towards sustainability

En este artículo se define agroecología como la aplicación de los conceptos y prinicipios ecológicos al diseño y manejo de los sistemas alimentarios sostenibles. Se presentan los argumentos principales que sostienen la validez, importancia y pertinencia del enfoque agroecológico, no solo para entender los procesos involucrados en la producción de alimentos, sino para proponer alternativas que conduzcan a esos procesos para operar en sistemas sostenibles. El concepto clave, que guía el razonamiento metodológico y epistemológico en este análisis, es el de sostenibilidad. Para alcanzar sostenibilidad la metodología agroecológica no solo se ancla en la Ecología, lo cual se describe en el trabajo, sino que percibe la producción de alimentos como un proceso que involucra a los productores y consumidores interactuando en forma dinámica.In this article agroecology is defined as the application of ecological concepts and principles to the design and management of sustainable food systems. The principal arguments are presented that support the validity, importance, and application of the agroecologial focus, not only in order to understand the processes involved in food production, but also to propose alternatives that help these processes to operate in sustainable systems. The key concept that guides the methodological and epitistemalogical rationale of this analysis is sustainability. In order to achieve sustainability the agroecological methodology not only links to Ecology, as is described in the text, but perceives food production as a process involving producers and consumers operating in a dynamic interaction

Aislamiento y evaluación de cepas nativas de Trichoderma spp., como promotor de desarrollo radicular

La investigación consistió en aislar, identificar y aplicar diferentes cepas de Trichoderma, multiplicadas por fermentación liquida. Los aislados fueron obtenido de cuatro provincias de la Amazonia Ecuatoriana de tres cultivos. Las cepas de Trichoderma fueron seleccionadas mediante un screenning, el cual consistió en sumergir las semillas de maíz en una solución 1x107 de esporas por tratamiento y se dejó en reposo por una hora. Las inoculaciones se realizaron previo a la siembra cada 15 días, hasta los 60 días. Posteriormente a la primera inoculación de los tratamientos, se evaluó la altura de planta, longitud y diámetro de raíces, como resultado, se determinó que todos los tratamientos que incluían Trichoderma lograron un crecimiento notable en las raíces a diferencia del control. Se concluye que los aislados MSPP-01-03 y MSPP-02-05 actúan como promotores del crecimiento radical de plantas de maíz.The research consisted of isolating, identifying, and applying different strains of Trichoderma, multiplied by liquid fermentation. The isolates were obtained from four provinces of the Ecuadorian Amazon from three crops. The Trichoderma strains were selected by screening, which consisted of submerging the corn seeds in a 1x107 solution of spores per treatment and left to rest for one hour. Inoculations were performed before sowing every 15 days until 60 days. After the first inoculation of the treatments, the plant height, length, and diameter of roots were evaluated, as a result, it was determined that all the treatments that included Trichoderma achieved remarkable growth in the roots in contrast to the control. It is concluded that the isolates MSPP-01-03 and MSPP-02-05 act as promoters of root growth of maize plants

Horizon scanning the application of probiotics for wildlife

The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called ‘probiotics for wildlife’ is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife

Conversion of forest to agriculture increases colored dissolved organic matter in a subtropical catchment and adjacent coastal environment

Land-ocean dissolved organic matter (DOM) transport is a significant and changing term in global biogeochemical cycles which is increasing as a result of human perturbation, including land-use change. Knowledge of the behavior and fate of transported DOM is lacking, particularly in the tropics and subtropics where land-use change is occurring rapidly. We used Parallel Factor (PARAFAC) Analysis to investigate how land-use influenced the composition of the DOM pool along a subtropical land-use gradient (from near-pristine broadleaf forest to agri-urban settings) in Belize, Central America. Three humic-like and two protein-like components were identified, each of which was present across land uses and environments. Land-use mapping identified a strong (R2 = 0.81) negative correlation between broadleaf forest and agri-urban land. All PARAFAC components were positively associated with agri-urban land-use classes (cropland, grassland, and/or urban land), indicating that land-use change from forested to agri-urban exerts influence on the composition of the DOM pool. Humic-like DOM exhibited linear accumulation with distance downstream and behaved conservatively in the coastal zone whilst protein-like DOM exhibited nonlinear accumulation within the main river and nonconservative mixing in coastal waters, indicative of differences in reactivity. We used a hydrodynamic model to explore the potential of conservative humics to reach the region's environmentally and economically valuable coral reefs. We find that offshore corals experience short exposures (10 ± 11 days yr−1) to large (∼120%) terrigenous DOM increases, whilst nearshore corals experience prolonged exposure (113 ± 24 days yr−1) to relatively small (∼30%) terrigenous DOM increases

Global transpiration data from sap flow measurements : the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.Peer reviewe

Sloan Digital Sky Survey IV: mapping the Milky Way, nearby galaxies, and the distant universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median ). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July

An upper limit to the photon fraction in cosmic rays above 10^19 eV from the Pierre Auger Observatory

An upper limit of 16% (at 95% c.l.) is derived for the photon fraction in cosmic rays with energies above 10^19 eV, based on observations of the depth of shower maximum performed with the hybrid detector of the Pierre Auger Observatory. This is the first such limit on photons obtained by observing the fluorescence light profile of air showers. This upper limit confirms and improves on previous results from the Haverah Park and AGASA surface arrays. Additional data recorded with the Auger surface detectors for a subset of the event sample, support the conclusion that a photon origin of the observed events is not favoured

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July