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.