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12. Novel methods to characterise spatial distribution and enantiomeric composition of usnic acids in four Icelandic lichens

Author

Xu, Maonian, Oppong-Danquah, Ernest, Wang, Xiaoyu, Oddsson, Sebastian, Abdelrahman, Asmaa, Pedersen, Simon Vilms, Szomek, Maria, Gylfason, Aron Elvar, Snorradottir, Bergthora Sigridur, Christensen, Eva Arnspang, Tasdemir, Deniz, Jameson, Cynthia J., Murad, Sohail, Andresson, Olafur Sigmar, Magnusson, Kristinn Petur, de Boer, Hugo J., Thorsteinsdottir, Margret, Omarsdottir, Sesselja, Heidmarsson, Starri, and Olafsdottir, Elin Soffia

Published
2022
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14. Historical changes in the stomatal limitation of photosynthesis : empirical support for an optimality principle

Author

Lavergne, Aliénor, Voelker, Steve, Csank, Adam, Graven, Heather, de Boer, Hugo J., Daux, Valérie, Robertson, Iain, Dorado-Liñán, Isabel, Martínez-Sancho, Elisabet, Battipaglia, Giovanna, Bloomfield, Keith J., Still, Christopher J., Meinzer, Frederick C., Dawson, Todd E., Camarero, J. Julio, Clisby, Rory, Fang, Yunting, Menzel, Annette, Keen, Rachel M., Roden, John S., and Prentice, I. Colin

Published
2020

15. Contributors

Author

Ahmad, Sayeed, primary, Akhtar, Muhammad Tayyab, additional, Alam, Md Jahangir, additional, Ata, Athar, additional, Bahadur, Shiv, additional, Bandyoypadhyay, Rajib, additional, Banerjee, Rupesh, additional, Banerjee, Sanjay K., additional, Banerjee, Subhadip, additional, Beć, Krzysztof B., additional, Bera, Sayantan, additional, Bhadra, Santanu, additional, Bhardwaj, Pardeep K., additional, Biswas, Sayan, additional, Booker, Anthony, additional, Bussmann, Rainer W., additional, Celep, Engin, additional, Chabalala, Hlupheka P., additional, Chanda, Joydeb, additional, Charoensup, Rawiwan, additional, Chattopadhyay, Debprasad, additional, Chaudhary, Sushil K., additional, Chávez-Hernández, Ana L., additional, Chik, Wai-I, additional, Choma, Irena Maria, additional, Christensen, Søren Brøgger, additional, Cordell, Geoffrey A., additional, Daley, Sharna-kay, additional, Das, Bhaskar, additional, Das, Jaydeep, additional, Das Gupta, Barun, additional, Dassarma, Barsha, additional, Dastidar, Sudarshana Ghosh, additional, de Boer, Hugo J., additional, Devi, Indira, additional, Duangyod, Thidarat, additional, Efferth, Thomas, additional, Flisyuk, Elena V., additional, Flores-Padilla, E. Alexis, additional, Ghosh, Dilip, additional, Gille, Elvira, additional, Gori, L., additional, Grabska, Justyna, additional, Guo, De-an, additional, Gupta, Arun, additional, Haldar, Pallab Kanti, additional, Harwansh, Ranjit K., additional, Heinrich, Michael, additional, Holloway, Paul, additional, Huck, Christian W., additional, Hugman, Bruce, additional, Jahangir, Muhammad, additional, Johnston, Deborah, additional, Kar, Amit, additional, Katiyar, C.K., additional, Knöss, Werner, additional, Mukherjee, Pulok Kumar, additional, Lawal, Temitope O., additional, Macovei, Irina, additional, Mahady, Gail B., additional, Mahapatra, Ananya Das, additional, Majumdar, Kalyan, additional, Matsabisa, Motlalepula Gilbert, additional, Maulik, Subir K., additional, Medina-Franco, José L., additional, Menichetti, F., additional, Mikhailovskaya, Irina Yu., additional, Miron, Anca, additional, Mitra, Achintya, additional, Mukherjee, Sonali, additional, Nahar, Lutfun, additional, Narkevich, Igor A., additional, Naz, Samina, additional, Nema, Neelesh K., additional, Nikolaichuk, Hanna, additional, Özenver, Nadire, additional, Phuneerub, Pravaree, additional, Pimpa, Rittichai, additional, Pozharitskaya, Olga N., additional, Pundir, Charu, additional, Qiao, Xue, additional, Raclariu-Manolică, Ancuța Cristina, additional, Rahman, Mukhlesur, additional, Raut, Nishikant, additional, Sampieri, A.P., additional, Sarker, Satyajit D., additional, Sener, Bilge, additional, Shaari, Khozirah, additional, Shami, Anam Amin, additional, Sharma, Nanaocha, additional, Shikov, Alexander N., additional, Sing, Dilip, additional, Skalli, Souad, additional, Tripathy, Satyajit, additional, Uppulapu, Shravan Kumar, additional, Upton, Roy, additional, Vanni, S., additional, Verpoorte, Prof. Dr. Robert, additional, Wang, Jia-bo, additional, Ye, Min, additional, Yesilada, Erdem, additional, Zhang, Hong-Jie, additional, Zhao, Chen-Liang, additional, and Zhou, Jia-jing, additional

Published
2022
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18. Orchidinae‐205: A new genome‐wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids.

Author

Veltman, Margaretha A., Anthoons, Bastien, Schrøder‐Nielsen, Audun, Gravendeel, Barbara, and de Boer, Hugo J.

Subjects
POLYSACCHARIDES, GENETIC markers, WILD animal trade, GLUCOMANNAN, TUBERS
Abstract

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost‐effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water‐soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non‐exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step‐up from traditional barcoding and universal markers, the genome‐wide custom loci targeted by Orchidinae‐205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Dietary metabarcoding of keystone sardine species reveals the importance of their ichthyoplankton prey in food webs of the Southern Brazilian Bight fisheries.

Author

de Queiroz, Anna Karolina Oliveira, Gasalla, Maria A., Laux, Marcele, Oliveira, Renato Renison Moreira, dos Anjos Santa Rosa, Fabricio, Schrøder‐Nielsen, Audun, Postuma, Felippe A., de Luna Sales, João Bráullio, de Boer, Hugo J., Mauvisseau, Quentin, and Ready, Jonathan Stuart

Subjects
KEYSTONE species, FOOD chains, FISH larvae, ICHTHYOPLANKTON, GENETIC barcoding, INDIVIDUAL retirement accounts
Abstract

Clupeiform fishes are ecologically and economically important species contributing to industrial and artisanal fisheries worldwide. They represent key links in food webs, influencing the dynamic between trophic levels. The dietary interactions of these species are poorly studied in many regions, yet essential for fisheries management. To elucidate the role of these species in food webs of the Southern Brazilian Bight pelagic fisheries, we used metabarcoding analysis of fish stomach contents of Clupeiformes and possible predators. Onboard sampling from March to September 2016 allowed for processing of 87 stomach samples representing 31 species (including 12 samples representing three species of Clupeiformes). Links between trophic levels showed the predominance of Sardinella brasiliensis and Engraulis anchoita as important dietary items of a large range of fishes (28 species belonging to 18 families) and representing the majority of the total prey read abundance assigned to clupeiform fishes (~46% and ~32%, respectively). Opisthonema oglinum contributed to the diet of 16 species in 13 families and ~18% of total read abundance of clupeiform fishes as prey. The appearance of multiple clupeiform taxa in the diet of predators that are not commonly associated with pelagic prey indicates that ecosystem‐based fisheries management should not be separated between pelagic and demersal fisheries. The diet of Clupeiformes revealed an unexpectedly large diversity of fish species and a low proportion of invertebrates (<5% of clupeiform prey reads). This was likely due to a combination of both a limitation of the metabarcoding method (primer bias and low success of invertebrate taxonomic identification) as well as a contribution of early life stages (ichthyoplankton) to the diet of these fishes. The potential role of clupeiform fish populations as a constraint to the recruitment from the ichthyoplanktonic phase of other ecologically or commercially important fishes should be considered as an important direction for future studies. [ABSTRACT FROM AUTHOR]

Published
2024
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22. Molecular analyses of carangid fish diets reveal inter‐predation, dietary overlap, and the importance of early life stages in trophic ecology

Author

Rosa, Fabricio dos Anjos Santa, primary, Gasalla, Maria A., additional, de Queiroz, Anna Karolina Oliveira, additional, Ribas, Talita Fernanda Augusto, additional, Mauvisseau, Quentin, additional, de Boer, Hugo J., additional, Thorbek, Birgitte Lisbeth Graae, additional, Oliveira, Renato Renison Moreira, additional, Laux, Marcele, additional, Postuma, Felippe A., additional, and Ready, Jonathan Stuart, additional

Published
2024
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34. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

Author

Bachmann, Lutz, primary, Beermann, Jan, additional, Brey, Thomas, additional, de Boer, Hugo J., additional, Dannheim, Jennifer, additional, Edvardsen, Bente, additional, Ericson, Per G. P., additional, Holston, Kevin C., additional, Johansson, Veronika A., additional, Kloss, Paul, additional, Konijnenberg, Rebecca, additional, Osborn, Karen J., additional, Pappalardo, Paula, additional, Pehlke, Hendrik, additional, Piepenburg, Dieter, additional, Struck, Torsten H., additional, Sundberg, Per, additional, Markussen, Stine Svalheim, additional, Teschke, Katharina, additional, and Vanhove, Maarten P. M., additional

Published
2023
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35. Extending shared socio-economic pathways for pesticide use in Europe: Pest-Agri-SSPs

Author

Global Ecohydrology and Sustainability, Integr. Assessm. Global Environm. Change, Environmental Sciences, Nagesh, Poornima, Edelenbosch, Oreane Y., Dekker, Stefan C., Boer, Hugo J. de, Mitter, Hermine, Vuuren, Detlef P. van, Global Ecohydrology and Sustainability, Integr. Assessm. Global Environm. Change, Environmental Sciences, Nagesh, Poornima, Edelenbosch, Oreane Y., Dekker, Stefan C., Boer, Hugo J. de, Mitter, Hermine, and Vuuren, Detlef P. van

Published
2023

37. The surface-boundary layer connection across spatial scales of irrigation-driven thermal heterogeneity: An integrated data and modeling study of the LIAISE field campaign

Author

Global Ecohydrology and Sustainability, Environmental Sciences, Mangan, Mary Rose, Hartogensis, Oscar, Boone, Aaron, Branch, Oliver, Canut, Guylaine, Cuxart, Joan, de Boer, Hugo J., Le Page, Michel, Martínez-Villagrasa, Daniel, Miró, Josep Ramon, Price, Jeremy, Vilà-Guerau de Arellano, Jordi, Global Ecohydrology and Sustainability, Environmental Sciences, Mangan, Mary Rose, Hartogensis, Oscar, Boone, Aaron, Branch, Oliver, Canut, Guylaine, Cuxart, Joan, de Boer, Hugo J., Le Page, Michel, Martínez-Villagrasa, Daniel, Miró, Josep Ramon, Price, Jeremy, and Vilà-Guerau de Arellano, Jordi

Published
2023

38. A new setup to study the influence of plant growth on the consolidation of dredged cohesive sediment

Author

Coastal dynamics, Fluvial systems and Global change, Global Ecohydrology and Sustainability, Water Quality Management, Environmental Sciences, Physical Geography Research Institute, Barciela-Rial, Maria, Saaltink, Remon M., van Kessel, Thijs, Chassagne, Claire, Dekker, Stefan C., de Boer, Hugo J., Griffioen, Jasper, Wassen, Martin J., Winterwerp, Johan C., Coastal dynamics, Fluvial systems and Global change, Global Ecohydrology and Sustainability, Water Quality Management, Environmental Sciences, Physical Geography Research Institute, Barciela-Rial, Maria, Saaltink, Remon M., van Kessel, Thijs, Chassagne, Claire, Dekker, Stefan C., de Boer, Hugo J., Griffioen, Jasper, Wassen, Martin J., and Winterwerp, Johan C.

Published
2023

39. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

Author

Bachmann, Lutz, Beermann, Jan, Brey, Thomas, Boer, Hugo J, Dannheim, Jennifer, Edvardsen, Bente, Ericson, Per GP, Holston, Kevin C, Johansson, Veronika A, Kloss, Paul, Konijnenberg, Rebecca, Osborn, Karen J, Pappalardo, Paula, Pehlke, Hendrik, Piepenburg, Dieter, Struck, Torsten H, Sundberg, Per, Markussen, Stine Svalheim, Teschke, Katharina, Vanhove, Maarten PM, Bachmann, Lutz, Beermann, Jan, Brey, Thomas, Boer, Hugo J, Dannheim, Jennifer, Edvardsen, Bente, Ericson, Per GP, Holston, Kevin C, Johansson, Veronika A, Kloss, Paul, Konijnenberg, Rebecca, Osborn, Karen J, Pappalardo, Paula, Pehlke, Hendrik, Piepenburg, Dieter, Struck, Torsten H, Sundberg, Per, Markussen, Stine Svalheim, Teschke, Katharina, and Vanhove, Maarten PM

Published
2023

40. Parallels between drought and flooding: An integrated framework for plant eco-physiological responses to water stress

Author

Environmental Sciences, Sub Theoretical Biology, Sub Plant Stress Resilience, Global Ecohydrology and Sustainability, Theoretical Biology and Bioinformatics, Plant Stress Resilience, Chen, Siluo, ten Tusscher, Kirsten H. W. J., Sasidharan, Rashmi, Dekker, Stefan C., de Boer, Hugo J., Environmental Sciences, Sub Theoretical Biology, Sub Plant Stress Resilience, Global Ecohydrology and Sustainability, Theoretical Biology and Bioinformatics, Plant Stress Resilience, Chen, Siluo, ten Tusscher, Kirsten H. W. J., Sasidharan, Rashmi, Dekker, Stefan C., and de Boer, Hugo J.

Published
2023

41. A new setup to study the influence of plant growth on the consolidation of dredged cohesive sediment

Author

Barciela Rial, M. (author), Saaltink, Remon M. (author), van Kessel, Thijs (author), Chassagne, C. (author), Dekker, Stefan C. (author), de Boer, Hugo J. (author), Griffioen, Jasper (author), Wassen, Martin J. (author), Winterwerp, J.C. (author), Barciela Rial, M. (author), Saaltink, Remon M. (author), van Kessel, Thijs (author), Chassagne, C. (author), Dekker, Stefan C. (author), de Boer, Hugo J. (author), Griffioen, Jasper (author), Wassen, Martin J. (author), and Winterwerp, J.C. (author)

Abstract

Dredged cohesive sediment is progressively being used for wetland construction. However, little is known about the effect of plant growth during the self-weight consolidation of this sediment. In order to check the feasibility of such a study, a new experimental setup has been constructed. As an example, the effect of Phragmites australis on the consolidation and drainage of dredged sediment from Lake Markermeer, the Netherlands was investigated. The changes in pore water pressures at 10 cm depth intervals during a 129-day period in a column with and without plants were measured, while the water level was fixed at a constant level. Water loss via evaporation and plant transpiration was measured using Mariotte bottles and the photosynthetic processes — including plant transpiration — were measured with a LI-COR photosynthesis system. The results show that several processes initiated by Phragmites australis interfere with the physical processes involved in sediment drainage and consolidation. Phragmites australis effectively altered the pore pressure gradient via water extraction, especially between 40 and 60 cm from the bottom of the column. In this zone, daily cycles in pore pressures were observed which could directly be linked to the diurnal cycle of stomatal gas exchange. On average, water loss via evaporation and transpiration of leaves of Phragmites australis amounted to 3.9 mm day−1, whereas evaporation of bare soil amounted on average to 0.6 mm day−1. The depth-averaged hydraulic conductivity increased on average by 40% in presence of Phragmites australis. This pilot experiment confirms that the pressures sensors coupled with the new set-up enable to study pore pressure development over time and to link the effect of plant growth with alterations in water pressures profiles. A more systematic study with this set-up will in the future enable to quantify the effects of plant growth on consolidation., Environmental Fluid Mechanics

Published
2023
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49. Carbon isotopic ratios of modern C$_3$ and C$_4$ vegetation on the Indian peninsula and changes along the plant-soil-river continuum - implications for vegetation reconstructions

Author

Kirkels, Frédérique M.S.A., De Boer, Hugo J., Hernández, Paulina Concha, Martes, Chris R.T., van der Meer, Marcel T.J., Basu, Sayak, Usman, Muhammed O., and Peterse, Francien

Abstract

The large difference in the fractionation of stable carbon isotopes between C$_3$ and C$_4$ plants is widely used in vegetation reconstructions, where the predominance of C$_3$ plants suggests wetter and that of C$_4$ plants drier conditions. The stable carbon isotopic composition of organic carbon (OC) preserved in soils or sediments may be a valuable (paleo-)environmental indicator, based on the assumption that plant-derived material retains the stable carbon isotopic value of its photosynthetic pathway during transfer from plant to sediment. In this study, we investigated the bulk carbon isotopic values of C$_3$ and C$_4$ plants ($\delta ^{13}$ C) and of organic carbon ($\delta ^{13}$ C$_{org}$) in soils, river suspended particulate matter (SPM) and riverbed sediments to gain insight into the control of precipitation onC$_3$ and C$_4$ plants ($\delta ^{13}$ C values and to assess changes in $\delta ^{13}$ C$_{org}$ values along the plant–soil–river continuum. This information allows us to elucidate the implications of different $\delta ^{13}$ C end-members on C$_3$/C$_4$ vegetation reconstructions. Our analysis was performed in the Godavari River basin, located in the core monsoon zone in peninsular India, a region that integrates the hydroclimatic and vegetation changes caused by variation in monsoonal strength. The basin has distinct wet and dry seasons and is characterised by natural gradients in soil type (from clay-rich to sandy), precipitation (∼ 500 to 1500 mm yr$^{-1}$) and vegetation type (from mixed C$_3$/C$_4$ to primarily C$_3$) from the upper to the lower basin. The $\delta ^{13}$C values of Godavari C$_3$ plants were strongly controlled by mean annual precipitation (MAP), showing an isotopic enrichment of ∼ 2.2 ‰ from ∼ 1500 to 500 mm yr$^{-1}$. Tracing $\delta ^{13}$C$_{org}$ values from plant to soils and rivers revealed that soils and riverbed sediments reflected the transition from mixed C$_3$ and C$_4$ vegetation in the dry upper basin to more C$_3$ vegetation in the humid lower basin. Soil degradation and stabilisation processes and hydrodynamic sorting within the river altered the plant-derived $\delta ^{13}$C signal. Phytoplankton dominated the $\delta ^{13}$C$_{org}$ signal carried by SPM in the dry season and year-round in the upper basin. Application of a linear mixing model showed that the %C$_4$ plants in the different subbasins was ∼ 7 %–15 % higher using plant end-members based on measurement of the Godavari vegetation and tailored to local moisture availability than using those derived from data compilations of global vegetation. Including a correction for the $^{13}$C enrichment in Godavari C$_3$ plants due to drought resulted in maximally 6 % lower estimated C$_4$ plant cover. Our results from the Godavari basin underline the importance of making informed choices about the plant $\delta ^{13}$C nd-members for vegetation reconstructions, considering characteristics of the regional vegetation and environmental factors such as MAP in monsoonal regions., Biogeosciences, 19 (17), ISSN:1726-4170

Published
2022

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