Periodic Reporting for period 1 - REMAINS (REconstruction of cliMAte and hidden biodiversity in lakes: development of INnovative paleoaproacheS)
Reporting period: 2020-09-01 to 2022-08-31
Increase of temperature and biodiversity loss are major threats in the early warning systems of the planet, the high-altitude ecosystems. The analysis of sediment records provides evidence on past response of species to climatic changes, offering a unique framework to anticipate/expand our ability to manage these ecosystems. Among the commonly used paleoindicators, the analysis of cladoceran subfossils has relied on classical morphological counting. However, recent advances in mass spectrometry, which now need much lower sample sizes, and in molecular biology, with the use of sedimentary DNA, offer unprecedented opportunities to develop innovative approaches based on these REMAINS. The main goal of this project is to provide new advances to i) use cladoceran chitin as a paleothermometer and ii) establish a standard methodology to use their DNA in sediments. The intellectual merits of this proposal are threefold. First, it will use cutting-edge technology to measure subfossil chitin in lab assays, in situ calibration and validation phases. Second, it will address a new biological group not previously studied in ancient DNA. Last, by establishing new analytical methods for a very common component of lake sediments, the project will open up a new field in Paleolimnology and highlight how much hitherto untapped information is stored in paleorecords. The research approach will involve (i) the quantification of contribution of water-diet to H and O isotopes in chitin (ii) the field calibration between isotopic composition of chitin and temperature (iii) the paleothermometer validation in the sediment (iv) the establishment of a library of cladocerans by a genome skimming and (v) the development of a specific assay to identify them in sedimentary DNA. Framed in the “Environment & Climate Action” area from HORIZON 2020, the project addresses gaps in the knowledge needed to understand past changes and to protect natural resources, illustrated here by Sierra Nevada Mountains
The main activities and achievements of the present project are briefly described below.
By combining in-lab and in-field assays, we provided methodological advances to use oxygen-isotope in chitin as a paleoenvironmental proxy. These new procedural developments included: 1) Obtaining the minimum required amount of each species to obtain a stable signal of oxygen isotopes 2) Testing and using the required oxygen isotopes standards specific for polysaccharides such as chitin and 3) Operating to avoid the nitrogen interference between the nitrogen peak and the carbon monoxide peak of the cladoceran material in the mass spectrometer. These methodological insights allowed us to obtain an oxygen-isotope signal of Daphnia ephippia for the whole Holocene and part of the deglaciation in the Laguna de Río Seco (LdRS) (Sierra Nevada, Spain), which was not driven by temperature but by changes in the source (Atlantic vs. Mediterranean) and the amount of precipitation during the Holocene.
In the framework of “Investigate the advantages of DNA-based approaches over morphological techniques to unravel past diversity and track biotic interactions through time”, we established specific assays to identify cladoceran in sedimentary DNA. We found that biodiversity assessments of cladocerans using DNA were highly dependent on reference public collections, which were still biased towards planktonic and more abundant cladocerans. Rare and endemic taxa inhabiting temporary ecosystems were underrepresented. By creating our reference collection, we contributed to assigning new DNA barcodes to rare species already described in Iberia, which is crucial to allow DNA metabarcoding applications. The developed primer pair worked well in recent sedaDNA samples (surficial samples and sediment traps) but they did not show positive amplifications when using sediment core samples.
Traditional counts on cladocerans are still offering many advantages over developing techniques such as biodiversity estimations using sedaDNA. This is illustrated here by data derived from the analysis of cladoceran subfossils, which provided the longest cladoceran-based paleoecological reconstruction in the Iberian Peninsula covering the last ~8600 cal yr BP. A wetter stage was inferred between ~ 8600-5000 cal yr BP, under a stable phase for chydorid reproduction, as parthenogenesis was the main reproduction mode. An arid phase with a progressive reduction in lake level started around ~5000 cal yr BP favored species more adapted to temporary environments and triggered sexual reproduction. The increasing trend in Total Chydorid Ephippia (TCE) over the whole Holocene and particularly during the Late Holocene is in concordance with the progressive aridification and Saharan eolian dust deposition in the Sierra Nevada wetlands. Besides these hydrological signatures, morphological measurements performed on Daphnia ephippia suggested that the dorsal length of these remains might be used as an indicator of the ice-free season length, which is modulated by temperature. This new indicator of past temperatures broadly depicted a warmer period ∼ 8600-4000 cal yr BP and a colder stage ∼4000-255 cal yr BP, which is consistent with other regional and global reconstructions of temperature. Novel proxies derived from the analysis of cladocerans subfossils in the REMAINS project might be applicable to reconstruct past environmental changes in other southern-latitude alpine ecosystems.
The results of the project were presented at the following conferences: DNAqua International Conference (online, March 2021), 36th Congress of the International Society of Limnology (Berlin, August 2022), CLIVAR- Spain: Towards an integrated view of climate (Madrid, January 2023) and XXI INQUA Congress (Rome, July 2023). The fellow actively participated in several outreach activities to popularize science and science culture and also to promote gender equality in the scientific world including i) Two “Coffees with Science” (November 2021, 2022), ii) A talk during the International Day of Women and Girls in Science (February 2023) and iii) “Fossils in the City”, an activity organized by the Department within the European Researchers Night 2023.
By combining in-lab and in-field assays, we provided methodological advances to use oxygen-isotope in chitin as a paleoenvironmental proxy. These new procedural developments included: 1) Obtaining the minimum required amount of each species to obtain a stable signal of oxygen isotopes 2) Testing and using the required oxygen isotopes standards specific for polysaccharides such as chitin and 3) Operating to avoid the nitrogen interference between the nitrogen peak and the carbon monoxide peak of the cladoceran material in the mass spectrometer. These methodological insights allowed us to obtain an oxygen-isotope signal of Daphnia ephippia for the whole Holocene and part of the deglaciation in the Laguna de Río Seco (LdRS) (Sierra Nevada, Spain), which was not driven by temperature but by changes in the source (Atlantic vs. Mediterranean) and the amount of precipitation during the Holocene.
In the framework of “Investigate the advantages of DNA-based approaches over morphological techniques to unravel past diversity and track biotic interactions through time”, we established specific assays to identify cladoceran in sedimentary DNA. We found that biodiversity assessments of cladocerans using DNA were highly dependent on reference public collections, which were still biased towards planktonic and more abundant cladocerans. Rare and endemic taxa inhabiting temporary ecosystems were underrepresented. By creating our reference collection, we contributed to assigning new DNA barcodes to rare species already described in Iberia, which is crucial to allow DNA metabarcoding applications. The developed primer pair worked well in recent sedaDNA samples (surficial samples and sediment traps) but they did not show positive amplifications when using sediment core samples.
Traditional counts on cladocerans are still offering many advantages over developing techniques such as biodiversity estimations using sedaDNA. This is illustrated here by data derived from the analysis of cladoceran subfossils, which provided the longest cladoceran-based paleoecological reconstruction in the Iberian Peninsula covering the last ~8600 cal yr BP. A wetter stage was inferred between ~ 8600-5000 cal yr BP, under a stable phase for chydorid reproduction, as parthenogenesis was the main reproduction mode. An arid phase with a progressive reduction in lake level started around ~5000 cal yr BP favored species more adapted to temporary environments and triggered sexual reproduction. The increasing trend in Total Chydorid Ephippia (TCE) over the whole Holocene and particularly during the Late Holocene is in concordance with the progressive aridification and Saharan eolian dust deposition in the Sierra Nevada wetlands. Besides these hydrological signatures, morphological measurements performed on Daphnia ephippia suggested that the dorsal length of these remains might be used as an indicator of the ice-free season length, which is modulated by temperature. This new indicator of past temperatures broadly depicted a warmer period ∼ 8600-4000 cal yr BP and a colder stage ∼4000-255 cal yr BP, which is consistent with other regional and global reconstructions of temperature. Novel proxies derived from the analysis of cladocerans subfossils in the REMAINS project might be applicable to reconstruct past environmental changes in other southern-latitude alpine ecosystems.
The results of the project were presented at the following conferences: DNAqua International Conference (online, March 2021), 36th Congress of the International Society of Limnology (Berlin, August 2022), CLIVAR- Spain: Towards an integrated view of climate (Madrid, January 2023) and XXI INQUA Congress (Rome, July 2023). The fellow actively participated in several outreach activities to popularize science and science culture and also to promote gender equality in the scientific world including i) Two “Coffees with Science” (November 2021, 2022), ii) A talk during the International Day of Women and Girls in Science (February 2023) and iii) “Fossils in the City”, an activity organized by the Department within the European Researchers Night 2023.
The REMAINS project was designated to go beyond the state-of-the-art and provided: 1) New methodological advances to use the chitin in fossil cladocerans as an indicator of past changes; 2) The longest cladoceran-based reconstruction in Iberia; 3) The use of Total Chydorid Ephippia (TCE) as indicator of aridification and the Daphnia dorsal length as a proxy for past temperature and 4) New DNA barcodes that will improve the development of DNA metabarcoding techniques.
The outputs of the REMAINS project bring important benefits to society because they have provided knowledge about changes in past climatic conditions and identified species based on their DNA signature and offered advances. European citizens identify climate change as the third most serious problem facing the world after poverty, hunger and lack of drinking water, and armed conflicts. Climate change is also identified as one of the biggest threats to biodiversity. Placing current tendencies into longer temporal perspectives, as those acquired by the outputs of the project, is crucial to predict future changes affecting these two hot research topics and concerns of European society.
The outputs of the REMAINS project bring important benefits to society because they have provided knowledge about changes in past climatic conditions and identified species based on their DNA signature and offered advances. European citizens identify climate change as the third most serious problem facing the world after poverty, hunger and lack of drinking water, and armed conflicts. Climate change is also identified as one of the biggest threats to biodiversity. Placing current tendencies into longer temporal perspectives, as those acquired by the outputs of the project, is crucial to predict future changes affecting these two hot research topics and concerns of European society.