A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses
Geisen, Stefan ; Vaulot, Daniel ; Mahe, Frederic ; Lara, Enrique ; Vargas, Colomban de; Bass, David - \ 2019
BioRxiv - 34 p.
Protists – all eukaryotes besides fungi, animals, and plants - represent a major part of the taxonomic and functional diversity of eukaryotic life on the planet and drive many ecosystem processes. However, knowledge of protist communities and their diversity lags behind that of most other groups of organisms, largely due to methodological constraints. While protist communities differ markedly between habitats and biomes, they can be studied in very similar ways. Here we provide a guide to current molecular approaches used for studying protist diversity, with a particular focus on amplicon-based high-throughput sequencing (metabarcoding). We highlight that the choice of suitable primers artificially alters community profiles observed in metabarcoding studies. While there are no true ‘universal’ primers to target all protist taxa as a whole, we identify some primer combinations with a wide taxonomic coverage and provide detailed information on their properties. Although environmental protistan ecological research will probably shift towards PCR-free metagenomics or/and transcriptomic approaches in a near future, metabarcoding will remain the method of choice for in-depth community analyses and taxon inventories in biodiversity surveys and ecological studies, due its great cost-efficiency, sensitivity, and throughput. In this paper we provide a guide for scientists from a broad range of disciplines to implement protists in their ecological analyses
Twenty-three unsolved problems in hydrology (UPH)–a community perspective
Blöschl, Günter ; Bierkens, Marc F.P. ; Chambel, Antonio ; Cudennec, Christophe ; Destouni, Georgia ; Fiori, Aldo ; Kirchner, James W. ; McDonnell, Jeffrey J. ; Savenije, Hubert H.G. ; Sivapalan, Murugesu ; Stumpp, Christine ; Toth, Elena ; Volpi, Elena ; Carr, Gemma ; Lupton, Claire ; Salinas, Josè ; Széles, Borbála ; Viglione, Alberto ; Aksoy, Hafzullah ; Allen, Scott T. ; Amin, Anam ; Andréassian, Vazken ; Arheimer, Berit ; Aryal, Santosh K. ; Baker, Victor ; Bardsley, Earl ; Barendrecht, Marlies H. ; Bartosova, Alena ; Batelaan, Okke ; Berghuijs, Wouter R. ; Beven, Keith ; Blume, Theresa ; Bogaard, Thom ; Borges de Amorim, Pablo ; Böttcher, Michael E. ; Boulet, Gilles ; Breinl, Korbinian ; Brilly, Mitja ; Brocca, Luca ; Buytaert, Wouter ; Castellarin, Attilio ; Castelletti, Andrea ; Chen, Xiaohong ; Chen, Yangbo ; Chen, Yuanfang ; Chifflard, Peter ; Claps, Pierluigi ; Clark, Martyn P. ; Collins, Adrian L. ; Croke, Barry ; Dathe, Annette ; David, Paula C. ; Barros, Felipe P.J. de; Rooij, Gerrit de; Baldassarre, Giuliano Di; Driscoll, Jessica M. ; Duethmann, Doris ; Dwivedi, Ravindra ; Eris, Ebru ; Farmer, William H. ; Feiccabrino, James ; Ferguson, Grant ; Ferrari, Ennio ; Ferraris, Stefano ; Fersch, Benjamin ; Finger, David ; Foglia, Laura ; Fowler, Keirnan ; Gartsman, Boris ; Gascoin, Simon ; Gaume, Eric ; Gelfan, Alexander ; Geris, Josie ; Gharari, Shervan ; Gleeson, Tom ; Glendell, Miriam ; Gonzalez Bevacqua, Alena ; González-Dugo, María P. ; Grimaldi, Salvatore ; Gupta, A.B. ; Guse, Björn ; Han, Dawei ; Hannah, David ; Harpold, Adrian ; Haun, Stefan ; Heal, Kate ; Helfricht, Kay ; Herrnegger, Mathew ; Hipsey, Matthew ; Hlaváčiková, Hana ; Hohmann, Clara ; Holko, Ladislav ; Hopkinson, Christopher ; Hrachowitz, Markus ; Illangasekare, Tissa H. ; Inam, Azhar ; Innocente, Camyla ; Istanbulluoglu, Erkan ; Jarihani, Ben ; Kalantari, Zahra ; Kalvans, Andis ; Khanal, Sonu ; Khatami, Sina ; Kiesel, Jens ; Kirkby, Mike ; Knoben, Wouter ; Kochanek, Krzysztof ; Kohnová, Silvia ; Kolechkina, Alla ; Krause, Stefan ; Kreamer, David ; Kreibich, Heidi ; Kunstmann, Harald ; Lange, Holger ; Liberato, Margarida L.R. ; Lindquist, Eric ; Link, Timothy ; Liu, Junguo ; Loucks, Daniel Peter ; Luce, Charles ; Mahé, Gil ; Makarieva, Olga ; Malard, Julien ; Mashtayeva, Shamshagul ; Maskey, Shreedhar ; Mas-Pla, Josep ; Mavrova-Guirguinova, Maria ; Mazzoleni, Maurizio ; Mernild, Sebastian ; Misstear, Bruce Dudley ; Montanari, Alberto ; Müller-Thomy, Hannes ; Nabizadeh, Alireza ; Nardi, Fernando ; Neale, Christopher ; Nesterova, Nataliia ; Nurtaev, Bakhram ; Odongo, Vincent O. ; Panda, Subhabrata ; Pande, Saket ; Pang, Zhonghe ; Papacharalampous, Georgia ; Perrin, Charles ; Pfister, Laurent ; Pimentel, Rafael ; Polo, María J. ; Post, David ; Prieto Sierra, Cristina ; Ramos, Maria Helena ; Renner, Maik ; Reynolds, José Eduardo ; Ridolfi, Elena ; Rigon, Riccardo ; Riva, Monica ; Robertson, David E. ; Rosso, Renzo ; Roy, Tirthankar ; Sá, João H.M. ; Salvadori, Gianfausto ; Sandells, Mel ; Schaefli, Bettina ; Schumann, Andreas ; Scolobig, Anna ; Seibert, Jan ; Servat, Eric ; Shafiei, Mojtaba ; Sharma, Ashish ; Sidibe, Moussa ; Sidle, Roy C. ; Skaugen, Thomas ; Smith, Hugh ; Spiessl, Sabine M. ; Stein, Lina ; Steinsland, Ingelin ; Strasser, Ulrich ; Su, Bob ; Szolgay, Jan ; Tarboton, David ; Tauro, Flavia ; Thirel, Guillaume ; Tian, Fuqiang ; Tong, Rui ; Tussupova, Kamshat ; Tyralis, Hristos ; Uijlenhoet, Remko ; Beek, Rens van; Ent, Ruud J. van der; Ploeg, Martine van der; Loon, Anne F. Van; Meerveld, Ilja van; Nooijen, Ronald van; Oel, Pieter R. van; Vidal, Jean Philippe ; Freyberg, Jana von; Vorogushyn, Sergiy ; Wachniew, Przemyslaw ; Wade, Andrew J. ; Ward, Philip ; Westerberg, Ida K. ; White, Christopher ; Wood, Eric F. ; Woods, Ross ; Xu, Zongxue ; Yilmaz, Koray K. ; Zhang, Yongqiang - \ 2019
Hydrological Sciences Journal 64 (2019)10. - ISSN 0262-6667 - p. 1141 - 1158.
hydrology - interdisciplinary - knowledge gaps - research agenda - science questions
This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.
Climate change impacts in Sub-Saharan Africa : from physical changes to their social repercussions
Serdeczny, Olivia ; Adams, Sophie ; Baarsch, Florent ; Coumou, Dim ; Robinson, Alexander ; Hare, William ; Schaeffer, Michiel ; Perrette, Mahé ; Reinhardt, Julia - \ 2017
Regional Environmental Change 17 (2017)6. - ISSN 1436-3798 - p. 1585 - 1600.
Climate change - Impacts - Sub-Saharan Africa - Vulnerability
The repercussions of climate change will be felt in various ways throughout both natural and human systems in Sub-Saharan Africa. Climate change projections for this region point to a warming trend, particularly in the inland subtropics; frequent occurrence of extreme heat events; increasing aridity; and changes in rainfall—with a particularly pronounced decline in southern Africa and an increase in East Africa. The region could also experience as much as one meter of sea-level rise by the end of this century under a 4 °C warming scenario. Sub-Saharan Africa’s already high rates of undernutrition and infectious disease can be expected to increase compared to a scenario without climate change. Particularly vulnerable to these climatic changes are the rainfed agricultural systems on which the livelihoods of a large proportion of the region’s population currently depend. As agricultural livelihoods become more precarious, the rate of rural–urban migration may be expected to grow, adding to the already significant urbanization trend in the region. The movement of people into informal settlements may expose them to a variety of risks different but no less serious than those faced in their place of origin, including outbreaks of infectious disease, flash flooding and food price increases. Impacts across sectors are likely to amplify the overall effect but remain little understood.
Differential climate impacts for policy-relevant limits to global warming : The case of 1.5 °c and 2 °c
Schleussner, Carl Friedrich ; Lissner, Tabea K. ; Fischer, Erich M. ; Wohland, Jan ; Perrette, Mahé ; Golly, Antonius ; Rogelj, Joeri ; Childers, Katelin ; Schewe, Jacob ; Frieler, Katja ; Mengel, Matthias ; Hare, William ; Schaeffer, Michiel - \ 2016
Earth System dynamics 7 (2016)2. - ISSN 2190-4979 - p. 327 - 351.
Robust appraisals of climate impacts at different levels of global-mean temperature increase are vital to guide assessments of dangerous anthropogenic interference with the climate system. The 2015 Paris Agreement includes a two-headed temperature goal: "holding the increase in the global average temperature to well below 2 °C above pre-industrial levels and pursuing efforts to limit the temperature increase to 1.5 °C". Despite the prominence of these two temperature limits, a comprehensive overview of the differences in climate impacts at these levels is still missing. Here we provide an assessment of key impacts of climate change at warming levels of 1.5 °C and 2 °C, including extreme weather events, water availability, agricultural yields, sea-level rise and risk of coral reef loss. Our results reveal substantial differences in impacts between a 1.5 °C and 2 °C warming that are highly relevant for the assessment of dangerous anthropogenic interference with the climate system. For heat-related extremes, the additional 0.5 °C increase in global-mean temperature marks the difference between events at the upper limit of present-day natural variability and a new climate regime, particularly in tropical regions. Similarly, this warming difference is likely to be decisive for the future of tropical coral reefs. In a scenario with an end-of-century warming of 2 °C, virtually all tropical coral reefs are projected to be at risk of severe degradation due to temperature-induced bleaching from 2050 onwards. This fraction is reduced to about 90 % in 2050 and projected to decline to 70 % by 2100 for a 1.5 °C scenario. Analyses of precipitation-related impacts reveal distinct regional differences and hot-spots of change emerge. Regional reduction in median water availability for the Mediterranean is found to nearly double from 9 % to 17 % between 1.5 °C and 2 °C, and the projected lengthening of regional dry spells increases from 7 to 11 %. Projections for agricultural yields differ between crop types as well as world regions. While some (in particular high-latitude) regions may benefit, tropical regions like West Africa, South-East Asia, as well as Central and northern South America are projected to face substantial local yield reductions, particularly for wheat and maize. Best estimate sea-level rise projections based on two illustrative scenarios indicate a 50 cm rise by 2100 relative to year 2000-levels for a 2 °C scenario, and about 10 cm lower levels for a 1.5 °C scenario. In a 1.5 °C scenario, the rate of sea-level rise in 2100 would be reduced by about 30 % compared to a 2 °C scenario. Our findings highlight the importance of regional differentiation to assess both future climate risks and different vulnerabilities to incremental increases in global-mean temperature. The article provides a consistent and comprehensive assessment of existing projections and a good basis for future work on refining our understanding of the difference between impacts at 1.5 °C and 2 °C warming.
Climate of Central Africa: past, present and future
Tsalefac, M. ; Hiol, F.H. ; Mahe, G. ; Laraque, A. ; Sonwa, D. ; Scholte, P. ; Pokam, W. ; Haensler, A. ; Beyene, T. ; Ludwig, F. - \ 2015
In: The Forests of the Congo Basin - Forests and climate change / Wasseige, de, C., Tadoum, M., Eba'a Atyi, R., Doumenge, C., Weyrich - ISBN 9782874893551 - p. 37 - 52.
|Over 25 years of FRIEND-Water: An overview
Lanen, Henny A.J. Van; Demuth, Siegfried ; Daniell, Trevor ; Hannah, David M. ; Laaha, Gregor ; Mahe, Gil ; Tallaksen, Lena M. - \ 2014
In: Hydrology in a Changing World. - Copernicus GmbH (IAHS-AISH Proceedings and Reports ) - ISBN 9781907161414 - p. 1 - 7.
Capacity building - Databases - Dissemination - Education - Flow regimes - Hydro-extremes - International cooperation - Regional hydrology - Water resources
FRIEND-Water has been a flagship programme of the UNESCO-International Hydrological Programme (IHP) for more than 25 years. This network has delivered outstanding scientific value (research papers, conferences) and made significant contributions to international cooperation in the water sciences and associated water resources management, an objective at the core of the IHP and UNESCO mandate. An overview of major activities and outcomes from this cross-cutting programme is provided, including database progress, enhanced scientific understanding of hydrological processes across scales, development of analytical tools, education, capacity building, dissemination and cooperation with other networks. The programme is not only a network of scientists; it is also aims to be a network of several databases and institutions. Ongoing and future activities of the FRIEND-Water network are also addressed.
Standardized precipitation-evapotranspiration index (SPEI) : Sensitivity to potential evapotranspiration model and parameters
Stagge, James H. ; Tallaksen, Lena M. ; Xu, Chong Yu ; Lanen, Henny A.J. Van - \ 2014
In: Hydrology in a Changing World. - Copernicus GmbH (IAHS-AISH Proceedings and Reports ) - ISBN 9781907161414 - p. 367 - 373.
Drought - Drought Index - Meteorological Drought - Potential Evapotranspiration - Sensitivity - SPEI - SPI - Standardized Precipitation Index
The Standardized Precipitation-Evapotranspiration Index (SPEI), a variant of the WMO-recommended Standardized Precipitation Index (SPI), has significant potential as a meteorological drought index because it uses a more comprehensive measure of water availability, climatic water balance. However, inclusion of PET, a derived term, requires rigorous testing before the index gains wide acceptance. This study addresses whether the SPEI differs significantly from the SPI and tests its sensitivity to the choice of PET method by first comparing derived PET and then SPEI/SPI across 3950 gridded land cells in Europe using five commonly used PET methods with different complexity and input requirements. The SPEI was found to differ significantly from the SPI and the resulting PET and SPEI values found to group according to the PET radiation term. The mass transfer term, which integrates wind speed and humidity/pressure, was found to have a secondary effect on PET and no detectable effect on SPEI.
Future low flows and hydrological drought: How certain are these for Europe?
Alderlieste, Marcel A.A. ; Lanen, Henny A.J. Van; Wanders, Niko - \ 2014
In: Hydrology in a Changing World. - Copernicus GmbH (IAHS-AISH Proceedings and Reports ) - ISBN 9781907161414 - p. 60 - 65.
Europe - Forcing - Future - Hydrological drought - Low flow - Runoff - Uncertainty
Climate data from a re-analysis dataset (WFD, 1971-2000) and three GCMs (1971-2100) for two emissions scenarios were used to: (i) explore future low flows and hydrological drought characteristics, and (ii) estimate how uncertainty in forcing propagates into these characteristics. Runoff was obtained through a multi-model mean from large-scale models forced with WFD and GCMs. Low flow and drought characteristics in two transects across Europe were intercompared for 1971-2000 to estimate forcing uncertainty, and for two future time frames to quantify climate change impact and to compare impact with forcing uncertainty (signal-noise ratios). Annual flow was projected to decrease (maximum 30%), but forcing uncertainty is larger (minimum 35%). Drought duration was predicted to increase (50-180%) with low forcing uncertainty (<10%). Similar observations were made for future deficit volumes. This study shows that future droughts can be predicted with higher certainty than low flows and that multi-forcing is required.
Do changes in environmental and fishing pressures impact marine communities? An empirical assessment
Rochet, M.J. ; Trenkel, V.M. ; Carpentier, A. ; Coppin, F. ; Sola, L.G. ; Leaute, J.P. ; Mahe, J.C. ; Maiorano, P. ; Mannini, A. ; Murenu, M. ; Piet, G.J. ; Politou, C.Y. ; Reale, B. ; Spedicato, M.T. ; Tserpes, G. ; Bertrand, J.A. - \ 2010
Journal of Applied Ecology 47 (2010)4. - ISSN 0021-8901 - p. 741 - 750.
compensatory dynamics - indicators - shelf - eutrophication - ecosystems - mechanisms - management - fisheries - metrics - trends
1. The development of ecosystem approaches to environmental management implies the need to account for multiple pressures on ecosystems. Trends in multiple metrics that respond differently to changes in major environmental pressures need to be combined to evaluate the impacts of fishing and environmental changes on fish communities. 2. An exploited fish community is viewed as a three-level food chain in which the two upper levels, or functional groups, are targeted by fishing fleets, while the lowest level is subject to environmental variation. Qualitative modelling is used to predict changes at the two upper levels, that is, top-down vs. bottom-up perturbations. Abundance and length metrics are calculated from survey data for 14 Mediterranean and East-Atlantic groundfish shelf communities at both population and functional group levels. The joint likelihood of time trends in metrics is used to evaluate the evidence for different causes of changes. 3. A wide diversity of impacts is found to have equal evidence at the population level within each community. Consistency between the impacts identified and changes in pressures known from independent information is found at the functional group and community level. The results suggest that there is some compensation between species within functional groups. 4. Synthesis and applications. The method can be used to conduct an integrated assessment of community dynamics subject to multiple pressures. Joint trends in metrics provide evidence of which known pressures are having an impact on the community, and thus, which management actions should be taken to mitigate these changes.
Low flow and drought studies : the Northern European (NE) FRIEND experience
Tallaksen, L. ; Demuth, S. ; Lanen, H.A.J. van - \ 2007
In: Climatic and anthropogenic impacts on the variability of water resources. - Paris : Unesco - p. 99 - 106.
watervoorraden - klimaat - klimaatverandering - conferenties - menselijke invloed - water resources - climate - climatic change - conferences - human impact
|Solid-phase synthesis, conformational analysis, and biological activity of the AVR9 elicitor peptides of the fungal tomato pathogen Cladosporium fulvum.
Mahe, E. ; Vossen, P. ; Hooven, H.W. van den; Le-Nguyen, D. ; Vervoort, J. ; Wit, P.J.G.M. de - \ 1998
Journal of peptide research 52 (1998). - ISSN 1397-002X - p. 482 - 495.
Correlation between binding affinity and necrosis-inducing activity of mutant AVR9 peptide elicitors.
Kooman-Gersmann, M. ; Vogelsang, R. ; Vossen, P. ; Hooven, H.W. van den; Mahe, E. ; Honee, G. ; Wit, J.G.M. de - \ 1998
Plant Physiology 117 (1998). - ISSN 0032-0889 - p. 609 - 618.
|Measuring income disparities between (and within) farm households and non-farm households by means of the individual welfare function of income.
Kingma, D. ; Oskam, A.J. - \ 1987
In: Income disparities among farm households and agricultural policy / Leon, Y., Mahe, L., Kiel : Wissenschaftsverlag Vauk - p. 25 - 42.