Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    Data supporting the research of: Estimating architecture-based metabolic scaling exponents of tropical trees using terrestrial LiDAR and 3D modelling
    Lau Sarmiento, A.I. ; Jackson, T. ; Raumonen, P. - \ 2019
    Wageningen University & Research
    architecture-based metabolic rate - destructive harvesting - quantitative structure models - terrestrial LiDAR - WBE plant scaling exponent
    Tree architecture influences physical and ecological processes within the tree. Prior work suggested the existence of general principles which govern these processes. Among these, the West, Brown and Enquist (WBE) theory is prominent; it holds that biological function has its origin in a tree's idealized branching system network; from which scaling exponents can be estimated. The scaling exponents of the WBE theory (branch radius scaling ratio, “a” and branch length scaling ratio “b”) can be derived from branch parameters and from these, metabolic scaling rate “ö” can be derived. Until now, branch parameter values are taken from direct measurements; either from standing trees or from harvested trees. Such measurements are time consuming, labour intensive and susceptible to subjective errors. Terrestrial LiDAR (TLS) is a promising alternative, being both less biased to error, scalable, and being able to collect large quantities of data without the need of destructive sampling the trees. In this thesis we estimated scaling exponents and derived metabolic rate from TLS and quantitative structure models (TreeQSM) models from nine trees in a tropical forest in Guyana. To validate these TLS-derived scaling exponents, we compared them with scaling exponents and derived metabolic rate from field measurements at three levels: branch-level, tree-level and plot-level. For that, we destructive sampled the scanned trees and measured all branches > 10 cm. Our results show that, with some limitations, radius, length scaling exponents and architecture-based metabolic rate can be derived from 3D data of tree point clouds. However, we found that only “ö” converged between our TreeQSM modelled and manually measured dataset at both, branch-level (0.59 and 0.50 for TreeQSM and manually measured exponent, respectively) and at tree-level (0.56 and 0.51). Our results did not support the same conclusion for “a” nor “b”- neither at branch-level nor at tree-level. The “a” diverged between TreeQSM and manually measured dataset at branch-level (0:45 and 0.63) and at the tree-level (0.46 and 0.64). The “b” was the exponent which most deviated between TreeQSM and manually measured dataset at branch-level (0.42 and 0.07) and at tree-level (0.41 and 0.05). At tree-level, we found that all estimated averaged exponents deviated significantly from metabolic scaling theory predictions (“a”=1/2 ; “b” =1/3 ; “ö”=3/4 ). Our study provides an alternative method to estimate scaling exponents variation at branch-level and tree-level in tropical forest trees without the need for destructive sampling. Although this approach is based on a limited sample of nine trees in Guyana, can be implemented for large-scale plant scaling assessments. This new data might improve our current understanding of metabolic scaling without harvesting trees.
    Geometric Tree Modelling with UAV-based Lidar
    Brede, B. ; Raumonen, Pasi ; Calders, Kim ; Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Kooistra, L. - \ 2018
    Assessing biomass and architecture of tropical trees with terrestrial laser scanning
    Lau Sarmiento, Alvaro Ivan - \ 2018
    Wageningen University. Promotor(en): M. Herold, co-promotor(en): H. Bartholomeus; K. Calders. - Wageningen : Wageningen University - ISBN 9789463434720 - 157

    Over the last two decades, terrestrial light detection and ranging (LiDAR), also known as terrestrial laser scanning (TLS) has become a valuable tool in assessing the woody structure of trees, in a method that is accurate, non-destructive, and replicable. This technique provides the ability to scan an area, and utilizes specialized software to create highly detailed 3D point cloud representations of its surroundings. Although the original usage of LiDAR was for precision survey applications, researchers have begun to apply LiDAR to forest research. Tree metrics can be extracted from TLS tree point clouds, and in combination with structure modelling, can be used to extract tree volume, aboveground biomass (AGB), growth, species, and to understand ecological questions such as tree mechanics, branching architecture, and surface area. TLS can provide a robust and rapid assessment of tree characteristics. These characteristics will improve current global efforts to measure forest carbon emissions, understand their uncertainties, and provide new insight into tropical forest ecology. Thus, the main objective of this PhD is to explore the use of 3D models from terrestrial laser scanning point clouds to estimate biomass and architecture of tropical trees. TLS-derived biomass and TLS-derived architecture can potentially be used to generate significant quality data for a better understanding of ecological challenges in tropical forests.

    In this thesis, a dataset of forest inventory with TLS point clouds and destructive tree harvesting were created from three tropical regions: Indonesia, Guyana, and Peru. A total of 1858 trees were traditionally inventoried, 135 trees were TLS scanned, and 55 trees were destructively harvested. In this thesis, procedures to estimate tree metrics such as tree height (H), diameter at breast height (D), crown diameter (CD), and the length and diameter of individual branches were developed using 3D point clouds and 3D modelling. From these tree metrics, I infer AGB, develop allometric models, and estimate metabolic plant scaling of individual tropical trees. All these metrics are validated against a traditional forest inventory data and destructively harvested trees.

    Chapter 2 presents a procedure to estimate tree volume and quantify AGB for large tropical trees based on estimates of tree volume and basic wood density. The accurate estimation of AGB of large tropical trees (diameter > 70 cm) is particularly relevant due to their major influence on tropical forest AGB variation. Nevertheless, current allometric models have large uncertainties for large tree AGB, partly due to the relative lack of large trees in the empirical datasets used to create them. The key result of this chapter is that TLS and 3D modelling are able to provide individual large tree volume and AGB estimates that are less likely to be biased by tree size or structural irregularities, and are more accurate than allometric models.

    Chapter 3 focuses on the development of accurate local allometric models to estimate tree AGB in Guyana based solely on TLS-based tree metrics (H, CD, and D) and validated against destructive measurements. Current tropical forest AGB estimates typically rely on pantropical allometric models that are developed with relatively few large trees. This leads to large uncertainties with increasing tree size and often results in an underestimation of AGB for large trees. I showed in Chapter 2 that AGB of individual large trees can be estimated regardless of their size and architecture. This chapter evaluates the performance of my local allometric models against existing pantropical models and evidenced that inclusion of TLS-based metrics to build allometric models provides as good as, or even better, AGB estimates than current pantropical models.

    Chapter 4 provides an insight into the architecture and branching structure of tropical trees. In Chapter 2, I demonstrated the potential of TLS to characterize woody tree structure as a function of tree volume, but little is known regarding their detailed architecture. Previous studies have quantitatively described tree architectural traits, but they are limited to the intensity of quantifying tree structure in-situ with enough detail. Here, I analysed the length and diameter of individual branches, and compared them to reference measurements. I demonstrated that basic tree architecture parameters could be reconstructed from large branches (> 40 cm diameter) with sufficient accuracy. I also discuss the limitations found when modelling small branches and how future studies could use my results as a basis for understanding tree architecture.

    Chapter 5 describes an alternative approach to estimating metabolic scaling exponents using the branching architecture derived from TLS point clouds. This approach does not rely on destructive sampling and can help to increase data collection. A theory on metabolic scaling, the West, Brown & Enquist (WBE) theory, suggests that metabolic rate and other biological functions have their origins in an optimal branching system network (among other assumptions). This chapter demonstrates that architecture-based metabolic scaling can be estimated for big branches of tropical trees with some limitations and provides an alternative method that can be implemented for large-scale assessments and provides better understanding of metabolic scaling.

    The results from this thesis provide a scientific contribution to the current development of new methods using terrestrial LiDAR and 3D modelling in tropical forests. The results can potentially be used to generate significant quality data for a better understanding of ecological challenges in tropical forests. I encourage further testing of my work using more samples including other types of forests to reduce inherent uncertainties.

    Monitoreo climático: herramienta al servicio de la caficultura Colombiana
    Sarmiento, Ninibeth ; Ramírez, Carolina ; Jaramillo, Álvaro ; Restrepo, Alexander ; García López, Juan Carlos ; Wolters, W. ; Miguel Ayala, L. - \ 2018
    Bogota : APC Columbia - ISBN 9789588490298 - 110
    Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements
    Pfeifer, Marion ; Gonsamo, Alemu ; Woodgate, William ; Cayuela, Luis ; Marshall, Andrew R. ; Ledo, Alicia ; Paine, Timothy C.E. ; Marchant, Rob ; Burt, Andrew ; Calders, Kim ; Courtney-mustaphi, Colin ; Cuni-sanchez, Aida ; Deere, Nicolas J. ; Denu, Dereje ; Gonzalez De Tanago Meñaca, J. ; Hayward, Robin ; Lau Sarmiento, A.I. ; Macía, Manuel J. ; Olivier, Pieter I. ; Pellikka, Petri ; Seki, Hamidu ; Shirima, Deo ; Trevithick, Rebecca ; Wedeux, Beatrice ; Wheeler, Charlotte ; Munishi, Pantaleo K.T. ; Martin, Thomas ; Mustari, Abdul ; Platts, Philip J. - \ 2018
    Forest Ecosystems 5 (2018). - ISSN 2095-6355 - 14 p.
    Background: Canopy structure, defined by leaf area index (LAI), fractional vegetation cover (FCover) and fraction of absorbed photosynthetically active radiation (fAPAR), regulates a wide range of forest functions and ecosystem services. Spatially consistent field-measurements of canopy structure are however lacking, particularly for the tropics. Methods: Here, we introduce the Global LAI database: a global dataset of field-based canopy structure measurements spanning tropical forests in four continents (Africa, Asia, Australia and the Americas). We use these measurements to test for climate dependencies within and across continents, and to test for the potential of anthropogenic disturbance and forest protection to modulate those dependences. Results: Using data collected from 887 tropical forest plots, we show that maximum water deficit, defined across the most arid months of the year, is an important predictor of canopy structure, with all three canopy attributes declining significantly with increasing water deficit. Canopy attributes also increase with minimum temperature, and with the protection of forests according to both active (within protected areas) and passive measures (through topography). Once protection and continent effects are accounted for, other anthropogenic measures (e.g. human population) do not improve the model. Conclusions: We conclude that canopy structure in the tropics is primarily a consequence of forest adaptation to the maximum water deficits historically experienced within a given region. Climate change, and in particular changes in drought regimes may thus affect forest structure and function, but forest protection may offer some resilience against this effect.
    Capturing forest structure and change – 5 years of laser scanning and future perspectives using UAV based LiDAR
    Bartholomeus, H.M. ; Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Herold, M. ; Brede, B. ; Kooistra, L. ; Calders, Kim - \ 2017
    In: SilviLaser 2017 Program. - Blacksburg : Virginia Tech - p. 61 - 62.
    Above-ground biomass assessment of tropical trees with Terrestrial LiDAR and 3D architecture models
    Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Bartholomeus, H.M. ; Herold, M. ; Avitabile, V. ; Raumonen, Pasi ; Martius, Christopher ; Goodman, R.C. ; Disney, Mathias ; Manuri, Solichin ; Burt, Andrew ; Calders, Kim - \ 2017
    In: SilviLaser 2017 Program. - Blacksburg : Virginia Tech - p. 123 - 124.
    Capturing forest structure using UAV based LiDAR
    Bartholomeus, H.M. ; Brede, B. ; Lau Sarmiento, A.I. ; Kooistra, L. - \ 2017
    - 2 p.
    Comparing RIEGL RiCOPTER UAV LiDAR Derived Canopy Height and DBH with Terrestrial LiDAR
    Brede, Benjamin ; Lau Sarmiento, A.I. ; Bartholomeus, Harm ; Kooistra, Lammert - \ 2017
    Sensors 17 (2017)10. - ISSN 1424-8220 - 16 p.
    In recent years, LIght Detection And Ranging (LiDAR) and especially Terrestrial Laser Scanning (TLS) systems have shown the potential to revolutionise forest structural characterisation by providing unprecedented 3D data. However, manned Airborne Laser Scanning (ALS) requires costly campaigns and produces relatively low point density, while TLS is labour intense and time demanding. Unmanned Aerial Vehicle (UAV)-borne laser scanning can be the way in between. In this study, we present first results and experiences with the RIEGL RiCOPTER with VUX ®
    ®
    -1UAV ALS system and compare it with the well tested RIEGL VZ-400 TLS system. We scanned the same forest plots with both systems over the course of two days. We derived Digital Terrain Model (DTMs), Digital Surface Model (DSMs) and finally Canopy Height Model (CHMs) from the resulting point clouds. ALS CHMs were on average 11.5 cm
    cm
    higher in five plots with different canopy conditions. This showed that TLS could not always detect the top of canopy. Moreover, we extracted trunk segments of 58 trees for ALS and TLS simultaneously, of which 39 could be used to model Diameter at Breast Height (DBH). ALS DBH showed a high agreement with TLS DBH with a correlation coefficient of 0.98 and root mean square error of 4.24 cm
    cm
    . We conclude that RiCOPTER has the potential to perform comparable to TLS for estimating forest canopy height and DBH under the studied forest conditions. Further research should be directed to testing UAV-borne LiDAR for explicit 3D modelling of whole trees to estimate tree volume and subsequently Above-Ground Biomass (AGB).
    Data acquisition considerations for Terrestrial Laser Scanning of forest plots
    Wilkes, Phil ; Lau Sarmiento, Alvaro ; Disney, Mathias ; Calders, Kim ; Burt, Andrew ; Gonzalez De Tanago Meñaca, J. ; Bartholomeus, Harm ; Brede, Benjamin ; Herold, Martin - \ 2017
    Remote Sensing of Environment 196 (2017). - ISSN 0034-4257 - p. 140 - 153.
    The poor constraint of forest Above Ground Biomass (AGB) is responsible, in part, for large uncertainties in modelling future climate scenarios. Terrestrial Laser Scanning (TLS) can be used to derive unbiased and non-destructive estimates of tree structure and volume and can, therefore, be used to address key uncertainties in forest AGB estimates. Here we review our experience of TLS sampling strategies from 27 campaigns conducted over the past 5 years, across tropical and temperate forest plots, where data was captured with a RIEGL VZ-400 laser scanner. The focus is on strategies to derive Geometrical Modelling metrics (e.g. tree volume) over forest plots (≥1 ha) which require the accurate co-registration of 10s to 100s of individual point clouds. We recommend a 10 m × 10 m sampling grid as an approach to produce a point cloud with a uniform point distribution, that can resolve higher order branches (down to a few cm in diameter) towards the top of 30+ m canopies and can be captured in a timely fashion i.e. ∼3–6 days per ha. A data acquisition protocol, such as presented here, would facilitate data interoperability and inter-comparison of metrics between instruments/groups, from plot to plot and over time.
    Application of terrestrial LiDAR and modelling of tree branching structure for plant-scaling models in tropical forest trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, Christopher ; Malhi, Yadvinder ; Bentley, Lisa Patrick ; Shenkin, Alexander ; Raumonen, P. - \ 2017
    Terrestrial LiDAR and 3D Reconstruction Models for Estimation of Large Tree Biomass in the Tropics
    Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Bartholomeus, H.M. ; Herold, M. ; Raumonen, P. ; Avitabile, V. ; Martius, Christopher ; Goodman, R.M. ; Manuri, Solichin - \ 2016
    - 1 p.
    Terrestrial LiDAR and 3D Reconstruction Models for Large Individual Tree Biomass Estimation in Tropics
    Lau Sarmiento, A.I. ; Herold, M. ; Bartholomeus, H.M. ; Gonzalez de Tanago Meñaca, J. - \ 2016
    Application of Terrestrial LiDAR and Modelling of Tree Branching Structure for Plant-scaling Models in Tropical Forest Trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, Christopher ; Malhi, Yadvinder ; Bentley, Lisa Patrick ; Shenkin, Alexander ; Raumonen, P. - \ 2016
    Quantification of Tropical Forest Biomass with Terrestrial LiDAR and 3D Tree Quantitative Structure Modelling
    Gonzalez deTanago Meñaca, J. ; Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Raumonen, P. ; Avitabile, V. ; Martius, Christopher ; Joseph, Shijo - \ 2016
    Terrestrial Laser Scanning for measuring forest biomass change
    Lau Sarmiento, A.I. ; Calders, K. ; Herold, M. ; Avitabile, V. ; Raumonen, P. ; Gonzalez De Tanago Meñaca, J. ; Bartholomeus, H.M. - \ 2015
    Application of terrestrial LiDAR and modelling of tree branching structure for plant-scaling models in tropical forest trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, C. ; Malhi, Y. ; Bentley, L.P. ; Shenkin, A. ; Raumonen, P. - \ 2015
    In: Proceedings of the SilviLaser 2015 conference. - - p. 3 - 3.
    Terrestrial LiDAR and 3D tree reconstruction modeling for quantification of biomass loss and characterization of impacts of selective logging in tropical forest of Peruvian Amazon. Multi-sensor assessment, combining near and remote sensing
    Gonzalez De Tanago Meñaca, J. ; Joseph, Shijo ; Herold, M. ; Goodman, R.M. ; Bartholomeus, H.M. ; Avitabile, V. ; Raumonen, P. ; Calders, K. ; Lau Sarmiento, A.I. ; Janovec, J. - \ 2014
    Evaluation of different scan configurations for an effective field procedure on a terrestrial LiDAR scanner in tropical forest
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Gonzalez De Tanago Meñaca, J. - \ 2014
    Connecting Policy and Practice for the Conservation of Sacred Natural Sites
    Verschuuren, B. ; Wild, R. ; Verschoor, G.M. - \ 2014
    In: Indigenous Revival and Sacred Sites Conservation in the Americas / Sarmiento, F.O, Hitchner, S., New York : Berghahn Books (Environmental Anthropology and Ethnobiology ) - p. 26 - 61.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme
    Sarmiento-Ramírez, J.M. ; Voort, M. van der; Raaijmakers, J.M. ; Diéguez-Uribeondo, J. - \ 2014
    PLoS ONE 9 (2014)4. - ISSN 1932-6203 - 8 p.
    caretta-caretta - biological-control - gut microbiota - dna-sequences - costa-rica - streptomyces - diseases - community - fungal - health
    Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora) that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.
    Acquisition of terrestrial LIDAR in tropical forest to support ecological research
    Bartholomeus, H. ; Gonzalez De Tanago Meñaca, J. ; Calders, K. ; Lau Sarmiento, A. ; Herold, M. - \ 2014
    Letter tot the editor: Iconic CO2 Time Series at Risk
    Houweling, S. ; Badawy, B. ; Baker, D.F. ; Basu, S. ; Belikov, D. ; Bergamaschi, P. ; Bousquet, P. ; Broquet, G. ; Butler, T. ; Canadell, J.G. ; Chen, J. ; Chevallier, F. ; Ciais, P. ; Collatz, G.J. ; Denning, S. ; Engelen, R. ; Enting, I.G. ; Fischer, M.L. ; Fraser, A. ; Gerbig, C. ; Gloor, M. ; Jacobson, A.R. ; Jones, D.B.A. ; Heimann, M. ; Khalil, A. ; Kaminski, T. ; Kasibhatla, P.S. ; Krakauer, N.Y. ; Krol, M. ; Maki, T. ; Maksyutov, S. ; Manning, A. ; Meesters, A. ; Miller, J.B. ; Palmer, P.I. ; Patra, P. ; Peters, W. ; Peylin, P. ; Poussi, Z. ; Prather, M.J. ; Randerson, J.T. ; Rockmann, T. ; Rodenbeck, C. ; Sarmiento, J.L. ; Schimel, D.S. ; Scholze, M. ; Schuh, A. ; Suntharalingam, P. ; Takahashi, T. ; Turnbull, J. ; Yurganov, L. ; Vermeulen, A. - \ 2012
    Science 337 (2012)6098. - ISSN 0036-8075 - p. 1038 - 1040.
    Aeolian sediment mass fluxes on a sandy soil in Central Patagonia
    Sterk, G. ; Parigiani, J. ; Cittadini, E. ; Peters, P. ; Scholberg, J.M.S. ; Peri, P. - \ 2012
    Catena 95 (2012). - ISSN 0341-8162 - p. 112 - 123.
    saltation transport - wind - environment - windbreaks - models
    The climate of Patagonia is semi-arid and characterised by frequent strong winds. Wind erosion is potentially a serious soil degradation process that impacts long-term sustainability of local agricultural systems, but the conditions and the rates of wind erosion in this region have not been studied extensively. The aim of this study was to quantify windblown mass transport on asandysoil in CentralPatagonia. Aeolianmassfluxes were measured in the valley of Sarmiento (Chubut province, Argentina) using two saltiphones and 24 Modified Wilson and Cooke (MWAC) sediment catchers. The latter were installed along three transects: (1) a control on a bare strip of land cleared of its natural vegetation, to measure the maximum wind erosion; (2) a similar transect protected by an artificial windbreak with an optical porosity of 50%; and (3) a transect in a cherry orchard protected with the same type of windbreak. Nine windstorms were recorded throughout the experimental period. Storms with wind speed peaks of 20 m s- 1 caused a total soil loss of 248 Mg ha- 1 in the control strip and heavily depleted the soil of its erodible fraction. The artificial windbreak reduced the soil loss by 51.0% on average, while no erosion was recorded in the cherry orchard. Measured maximum mass transport values were used to fit five sediment transport equations in order to select the best equation to integrate into a GIS-based wind erosion prediction system. The Kawamura (1964) equation showed the highest model efficiency and was considered to be the best sediment transport equation for the Patagonia conditions. It expresses total mass transport as a function of two empirical constants: the threshold friction velocity (u*t), and an erodibility coefficient CKa. It is concluded that wind erosion in CentralPatagonia poses a serious risk of soil degradation once the natural vegetation is removed due to overgrazing or other anthropogenic activities.
    Stomach Content of a Juvenile Bolivian River Dolphin (Inia geoffrensis boliviensis) from the Upper Madeira Basin, Bolivia
    Aliaga-Rossel, E. ; Beerman, A.S. ; Sarmiento, J. - \ 2010
    Aquatic Mammals 36 (2010)3. - ISSN 0167-5427 - p. 284 - 287.
    cetacea - iniidae
    The article presents a study about the stomach content of a juvenile Bolivian river dolphin (Inia geoffrensis boliviensis), an endemic subspecies of the Amazon River dolphin, found in the upper Madeira River basin in Bolivia. The study finds that the stomach of Bolivian river dolphin contained a mixture of partially digested fish remains and a nematode. It says that the diet of adult Bolivian river dolphins include crabs and unidentified fish species, including members of the Characidae family.
    Sweet cherry production in South Patagonia
    Cittadini, E.D. ; Sanz, C.E. ; Pugh, A.B. ; Peri, P.L. ; Szlápelis, E. ; Cárcamo, M.A. ; Kikuchi, N. ; Manavella, F.A. ; San Martino, L. ; Ñancucheo, J.A. ; Muñoz, M. ; Ridder, N. de; Keulen, H. van; Mundet, C.A. - \ 2008
    Acta Horticulturae 795 (2008). - ISSN 0567-7572 - p. 585 - 590.
    In South Patagonia, the total sweet cherry (Prunus avium L.) area has increased from 176 ha in 1997 to 507 ha in 2004, of which 232 ha are located in Los Antiguos (46°19¿ SL; 220 m elevation), 158 ha in the Lower Valley of Chubut River (LVCHR) (43°16¿ SL; 30 m elevation), 52 ha in Sarmiento (45°35¿ SL; 270 m elevation), 35 ha in Esquel (42°55¿ SL; 570 m elevation) and 30 ha in Comodoro Rivadavia (45°52¿ SL; 50 m elevation). The most common varieties are `Lapins¿, `Bing¿, `Newstar¿, `Sweetheart¿, `Stella¿, `Sunburst¿ and `Van¿ grafted on `Mahaleb¿, `Pontaleb¿, `SL 64¿, `Colt¿ or `Mazzard¿ rootstocks. Trees generally are drip-irrigated and planted at high densities, using training systems such as Tatura, central leader and modified vase (2700, 1100 and 1000 trees ha-1, respectively). Growers in Los Antiguos are more traditional, planting mainly as vase (400 to 1000 trees ha-1) or freestanding trees (280 trees ha-1) and irrigating by gravity (74% of the area). Only 4.4% of the area of Los Antiguos is frost protected, as growers rely strongly on the moderating effect of Lake Buenos Aires. Frost control systems are absent in Comodoro Rivadavia because the established orchards are located next to the sea, in an area with low risk of frost. The frost-protected area is 49% in Sarmiento, 35% in Esquel and 57% in LVCHR. Fruit are harvested from November (LVCHR) to the end of January (Los Antiguos and Esquel), and the harvest-only labour demand during the 2004/2005 season was 100,000 h. In that season, seven packinghouses exported 390 t (45% of the total production) to Europe. Most orchards have not yet reached their mature stage and new ones are being established. Therefore, fruit volumes will continue to increase and shortages of labour and packing facilities may become a constraint.
    Modelling the transformations and sequestration of soil organic matter in two constrasting ecosystems of the Andes
    Pansu, M. ; Sarmiento, L. ; Metselaar, K. ; Hervé, D. ; Bottner, P. - \ 2007
    European Journal of Soil Science 58 (2007)3. - ISSN 1351-0754 - p. 775 - 785.
    differently textured soils - high tropical andes - microbial biomass - nitrogen dynamics - clay content - turnover - carbon - simulation - decomposition - temperature
    The mechanisms linking soil respiration to climate and soil physical properties are important for modelling transformation and sequestration of C and N in the soil. We investigated them by incubating C-14 and N-15 labelled straw in soils of the dry puna (Bolivian altiplano, semi-arid shrubland at 3789 m above sea level) and the humid paramo (Venezuelan tropical alpine vegetation at 3400 m). These two ecosystems of the high Andes are comparable in terms of altitude, mean temperature and land use, but are very different regarding organic matter content, rainfall patterns and soil physical properties. Total C-14 and N-15, microbial-biomass C-14 and N-15, soil moisture and meteorological data were recorded over 2 years. Daily soil moisture was predicted from a water balance model. The data from the paramo site were used to calibrate MOMOS-6, a model of organic matter decomposition based on microbial activity and requiring only kinetic constant parameters to describe: (i) inputs to microbial biomass from plant debris and microbial metabolites, and (ii) losses from the biomass by mortality and respiration (respiration coefficient and microbial metabolic quotient qCO(2)). The simulated qCO(2)-C-14 agrees well with qCO(2)-C-14 and qCO(2) measured at the calibration site and with published data. To apply MOMOS-6 to the puna site, only the respiration coefficient of the biomass was re-estimated. The dynamics of C-14 and N-15 were very different in the two systems. In the puna, the transformation processes stop during the long dry periods, though total annual mineralization is greater than in the paramo. The change in the value of the respiration coefficient enables us to predict that the amount of C and N sequestered in the stable humus is greater in the paramo than in the puna. The data in this paper can be used to estimate values of the respiration coefficient so that MOMOS-6 can be applied to other systems.
    Factors controlling decomposition of soil organic matter in fallow systems of the high tropical Andes: A field simulation approach using 14C- and 15N-labelled plant material
    Bottner, P. ; Pansu, M. ; Sarmiento, L. ; Hervé, D. ; Callisaya-Bautista, R. ; Metselaar, K. - \ 2006
    Soil Biology and Biochemistry 38 (2006)8. - ISSN 0038-0717 - p. 2162 - 2177.
    fumigation-extraction method - microbial biomass - nitrogen - carbon - turnover - straw - calibration - dynamics - glucose - models
    N-rich (C:N = 27) and N-poor (C:N = 130) wheat straw, labelled with 14 C and 15 N, was incubated for 2 yr in two major ecosystems of the upper elevation belt of cultivation in the high Andes: the moist Paramo (precipitation = 1329 mm, altitude = 3400 m asl, Andes of Merida, Venezuela) and the dry Puna (precipitation = 370 mm, altitude = 3800 m asl, Central Altiplano, Bolivia). The experiment was installed in young (2 yr) and old (7 yr) fallow plots. The following soil analyses were performed at nine sampling occasions: soil moisture, total-C-14 and -N-15, and Microbial Biomass (MB)-C-14 and -N-15. The measured data were fitted by the MOMOS-6 model (a process based model, with five compartments: labile and stable plant material, MB, and labile (HL) and stable humus (HS)) coupled with the SAHEL model (soil moisture prediction) using daily measured and/or predicted meteorological data. The aim was to understand how (1) the climatic conditions, (2) the quality of plant material, (3) the fallow age and (4) the soil properties affect the cycling of C and N within the soil organic matter system. The fallow age (2 and 7 yr) did not affect the measured data or the model predictions, indicating that in these systems the decomposition potential is not affected by fallow length. During the short initial active decomposition phase, the labile plant material was quickly exhausted, enabling a build up of MB and of HL. During the low activity phase, that covered 4/5 of the time of exposure, the MB size decreased slowly and the HL pool was progressively exhausted as it was reused by the MB as substrate. The HL compartment was directly or indirectly the major source for the inorganic N-15 production. If the ON ratio of the added plant material increased, the model predicted (1) a reduction of the decomposition rates of the plant material (essentially the stable plant material) and (2) an increased mortality of the MB which increased the production of HL (microbial cadavers and metabolites). Thus the essential effect of the slower decomposition due to the N-poor plant material was a higher accumulation of C and N in the HL and its slower recycling by the MB during the low activity phase. The labelling experiment allows to understand the higher soil native organic matter content in Paramo soils compared to Puna. The large sequestration of organic matter generally observed in the Paramo soils can be explained by two abiotic factors: the unfavourable soil microstructure and the accumulation of free aluminium linked to the climatic and acid soil conditions, inhibiting the microbial activity physically and chemically. (c) 2006 Elsevier Ltd. All rights reserved.
    FRUPAT: A Tool to Quantify Inputs and Outputs of Patagonian Fruit Production Systems
    Cittadini, E.D. ; Keulen, H. van; Peri, P.L. - \ 2006
    In: Proceedings VIIth IS on Modelling in Fruit Research / Braun, P., - p. 223 - 230.
    A software called FRUPAT was developed for calculating input and output coefficients (Technical Coefficients) of fruit production systems in South Patagonia. FRUPAT combined locations (Río Chubut valley; Sarmiento valley; Los Antiguos valley; Río Chico valley), edaphic environment (good quality soil with water-table depth exceeding 2 m; good quality soil with water-table depth between 1 and 2 m; low water holding capacity soil without water-table influence), fruit-tree crops (sweet cherry; plum; peach; apple; walnut), training systems (tatura; central leader; vase), irrigation systems (drip; furrow) and frost control systems (sprinkler irrigation; heating; passive) that provided 1080 multi-annual fruit production activities. Parameters have been identified as default values and most of those can be easily modified by the user. Relevant inputs and outputs can be estimated, such as gross value of product, expenditures, financial result, biocide use, N-fertiliser surplus and labour. As an example of how FRUPAT can be used, some results are presented for a single physical environment (good quality soil with water-table depth exceeding 2 m, in the Río Chubut valley) using sprinkler irrigation as frost control method. First, 5 crops under a single production technique (vase with furrow irrigation) are compared in terms of their monetary technical coefficients. Subsequently, results of sweet cherry under different production techniques (3 training systems with 2 irrigation systems) are presented. Finally, the time course of gross value of product, total expenditures, financial result and cumulative financial result are analyzed for a single activity (sweet cherry, trained as tatura under drip irrigation). FRUPAT may be used as a stand-alone tool for simple analysis as demonstrated here or as an intermediate step for linear programming
    Comparison of five soil organic matter decomposition models using data from a 14C and 15N labeling field experiment
    Pansu, M. ; Bottner, P. ; Sarmiento, L. ; Metselaar, K. - \ 2004
    Global Biogeochemical Cycles 18 (2004). - ISSN 0886-6236 - p. 1 - 11.
    fumigation-extraction method - microbial biomass - sensitivity-analysis - agricultural soils - nitrogen dynamics - carbon - turnover - temperature - calibration - straw
    Five alternatives of the previously published MOMOS model (MOMOS-2 to -6) are tested to predict the dynamics of carbon (C) and nitrogen (N) in soil during the decomposition of plant necromass. 14C and 15N labeled wheat straw was incubated over 2 years in fallow soils of the high Andean Paramo of Venezuela. The following data were collected: soil moisture, total 14C and 15N and microbial biomass (MB)-14C and -15N, daily rainfall, air temperature and total radiation. Daily soil moisture was predicted using the SAHEL model. MOMOS-2 to -4 (type 1 models) use kinetic constants and flow partitioning parameters. MOMOS-2 can be simplified to MOMOS-3 and further to MOMOS-4, with no significant changes in the prediction accuracy and robustness for total-14C and -15N as well as for MB-14C and -15N. MOMOS-5 (type 2 models) uses only kinetic constants: three MB-inputs (from labile and stable plant material and from humified compounds) and two MB-outputs (mortality and respiration constants). MOMOS-5 did not significantly change the total-14C and -15N predictions but markedly improved the predictive quality and robustness of MB-14C and -15N predictions (with a dynamic different from the predictions by other models). Thus MOMOS-5 is proposed as an accurate and ecologically consistent description of decomposition processes. MOMOS-6 extends MOMOS-5 by including a stable humus compartment for long-term simulations of soil native C and N. The improvement of the predictions is not significant for this 2-year experiment, but MOMOS-6 enables prediction of a sequestration in the stable humus compartment of 2% of the initially added 14C and 5.4% of the added 15N
    Colonización, deforestación, protección y recuperación del bosque montano nuboso en la Reserva Forestal Los Santos
    Kappelle, M. ; Omme, L. van; Juárez, M. ; Cleef, A.M. - \ 1999
    In: Entendiendo las Interfaces Ecológicoas para la Gestión de los Paisajes Culturales en los Andes : III Simposio Internacional de Desarollo Sustentable de MontaAas, Quito, South America / Sarmiento, F., Hidalgo, J., Andean Mountain Association - p. 199 - 2007.
    Colonization, deforestacion, protection y recuperation del bosque montano nuboso en la Reserva Forestal Los Santos, Costa Rica
    Kapelle, M. ; Omme, L. van; Juarez, M. ; Cleef, A. - \ 1999
    In: in: III Simposio Internacional de Desarolle Sustentable de Montanas: Entendiedo las Interfaces Ecologicas para la Cestion de los Paisajes Culturales en los Andes. Andean Mountain Association - CEPEIGE & The University of Geogia, CLACS. Editorial CEPEIGE, Quito / F. Sarmiento & J. Hidalgo (eds.), 1999. - [S.l.] : [s.n.], 1999 - p. 199 - 207.
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