DNA metabarcoding of deep-sea sediment communities using COI: community assessment, spatio-temporal patterns and comparison with the 18S rDNA marker

The deep sea is the largest biome on Earth, albeit it is the least studied. Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded to be potential hot-spots of biodiversity. The Mediterranean Sea hosts the 8.86% of the inventoried submarine canyons in the global ocean, like the Blanes Canyon, located in its Northwestern section. We assessed spatial (through sediment layers and along a depth gradient) and temporal (in two different seasons) patterns of biodiversity in sediment communities of the Blanes Canyon and its adjacent open slope with eDNA metabarcoding, using a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a marker. We found a total of 15,318 molecular operational taxonomic units (MOTUs), of which 10,860 could be assigned only to Eukarya. Among those assigned at lower levels, Metazoa, Stramenopiles and Archaeplastida were the dominant taxa. Within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse among the 28.2% that could be assigned to at least the phylum level. There was a trend towards decreasing diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, significantly different between zones, depths and seasons. We compared our results with the ones presented in Guardiola et al (2016), obtained using the v7 region of the 18S rRNA gene as genetic marker in the exact same samples. There were remarkable differences in the total number of MOTUs, in the most diverse taxa and in MOTU richness. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, broad spatio-temporal patterns elucidated from both datasets coincided, both markers retrieving the same ecological information. The choice of marker depends on a trade-off between marker variability, primer bias, and completeness of reference databases. Our results showed that COI can be used to accurately characterize the studied communities and to develop high-resolution bioindicators to detect ecological shifts. We also noted that COI reference databases for deep-sea organisms have important gaps, and its completeness is essential in order to successfully apply metabarcoding solutions

Functional effects of the buckwheat iminosugar D-fagomine on rats with diet-induced prediabetes

Scope: The goals of this work were to test if D-fagomine, an iminosugar that reduces body weight gain, can delay the appearance of a fat-induced prediabetic state in a rat model and to explore possible mechanisms behind its functional action. Methods and results: Wistar Kyoto rats were fed a high-fat diet supplemented with D7 fagomine (or not; for comparison) or a standard diet (controls) for 24 weeks. The variables measured were: fasting blood glucose and insulin levels; glucose tolerance; diacylglycerols as intracellular mediators of insulin resistance in adipose tissue, liver and muscle; inflammation markers (plasma IL-6 and leptin, and liver and adipose tissue histology markers); eicosanoids from arachidonic acid as lipid mediators of inflammation; and the populations of Bacteroidetes, Firmicutes, Enterobacteriales and Bifidobacteriales in feces. We found that D-fagomine reduces fat-induced impaired glucose tolerance, inflammation markers and mediators (hepatic microgranulomas and lobular inflammation, plasma IL-6, prostaglandin E2 and leukotriene B4) while attenuating the changes in the populations of Enterobacteriales and Bifidobacteriales. Conclusion: D-Fagomine delays the development of a fat-induced prediabetic state in rats by reducing low-grade inflammation. We suggest that the anti-inflammatory effect of D-fagomine may be linked to a reduction in fat-induced overpopulation of minor gut bacteria

The buckwheat iminosugar d-fagomine attenuates sucrose-induced steatosis and hypertension in rats

Scope: This study examines the long-term functional effects of D-fagomine on sucrose4 induced factors of metabolic dysfunctions and explores possible molecular mechanisms behind its action. Methods & results: Wistar Kyoto (WKY) rats were fed a 35% sucrose solution with D- fagomine (or not, for comparison) or mineral water (controls) for 24 weeks. We recorded: body weight; energy intake; glucose tolerance; plasma leptin concentration and lipid profile; populations of Bacteroidetes, Firmicutes, bacteroidales, clostridiales, enterobacteriales, and Escherichia coli in feces; blood pressure; urine uric acid and F2t isoprostanes (F2-IsoPs); perigonadal fat deposition; and hepatic histology and diacylglycerols (DAGs) in liver and adipose tissue. D-Fagomine reduced sucrose-induced hypertension, urine uric acid and F2-IsoPs (markers of oxidative stress; OS), steatosis and liver DAGs, without significantly affecting perigonadal fat deposition and impaired glucose tolerance. It also promoted excretion of enterobacteriales generated by the dietary intervention. Conclusion: D-fagomine counteracts sucrose-induced steatosis and hypertension, presumably by reducing the postprandial levels of fructose in the liver

Mechanistically different effects of fat and sugar on insulin resistance, hypertension and gut microbiota in rats

Insulin resistance (IR) and impaired glucose tolerance (IGT) are the first manifestations of diet-induced metabolic alterations leading to type-2 diabetes, while hypertension is the deadliest risk factor of cardiovascular disease. The roles of dietary fat and fructose in the development of IR, IGT and hypertension are controversial. We tested the long-term effects of an excess of fat or sucrose (fructose/glucose) on healthy male Wistar Kyoto (WKY) rats. Fat affects IR and IGT earlier than fructose through low-grade systemic inflammation evidenced by liver inflammatory infiltration, increased levels of plasma interleukin-6, prostaglandin E2 and reduced levels of protective short-chain fatty acids without triggering hypertension. Increased populations of gut Enterobacteriales and Escherichia coli may contribute to systemic inflammation through the generation of lipopolysaccharides. Unlike fat, fructose induces increased levels of diacylglycerols (lipid mediators of IR) in the liver, urine F2-isoprostanes (markers of systemic oxidative stress) and uric acid, and triggers hypertension. Elevated populations of Enterobacteriales and E. coli were only detected in rats given an excess of fructose at the end of the study. Dietary fat and fructose trigger IR and IGT in clearly differentiated ways in WKY rats: early low-grade inflammation and late direct lipid toxicity, respectively; gut microbiota plays a role mainly in fat-induced IR; and hypertension is independent of inflammation55 mediated IR. The results provide evidence which suggests that the combination of fat and sugar is potentially more harmful than fat or sugar alone when taken in excess

Head in the clouds, feet on the ground: how transdisciplinary learning can foster transformative change—insights from a summer school

There is a pressing need for transformative change, with a vision of long-term human well-being within planetary boundaries. The lack of progress—despite increasing awareness and action—illustrates how challenging it is to foster change in our complex global society. Education and learning are needed to enable change. Transdisciplinary learning, which meaningfully integrates diverse knowledge and perspectives, contributes to developing an integrative understanding—a necessity for tackling complex challenges. We explore how transdisciplinary learning for early-career researchers can foster transformative change and lead to increased biodiversity conservation. This paper focuses on a case study of the authors’ shared experiences during the 2021 Alternet Summer School, which focused on transformative change for biodiversity conservation and human well-being. In this introspective research, we gained insights through an online survey for participants and organizers of the summer school (n = 27). Using qualitative content analysis, we identify seven crucial elements of transdisciplinary learning which can lead to transformative change on (a) a personal level, as the learning process shifts values and helps researchers identify their roles; (b) a research level, by rethinking science and providing tools for transdisciplinary approaches, and (c) a societal level, by moving from the individual to the collective and constructing a shared vision for a sustainable future. Participants highlighted how changes on all these levels could benefit biodiversity conservation. These insights point to the benefit of transdisciplinary learning opportunities that empower young researchers to take up their part in fostering transformative change

Head in the clouds, feet on the ground: how transdisciplinary learning can foster transformative change—insights from a summer school

There is a pressing need for transformative change, with a vision of long-term human well-being within planetary boundaries. The lack of progress—despite increasing awareness and action—illustrates how challenging it is to foster change in our complex global society. Education and learning are needed to enable change. Transdisciplinary learning, which meaningfully integrates diverse knowledge and perspectives, contributes to developing an integrative understanding—a necessity for tackling complex challenges. We explore how transdisciplinary learning for early-career researchers can foster transformative change and lead to increased biodiversity conservation. This paper focuses on a case study of the authors’ shared experiences during the 2021 Alternet Summer School, which focused on transformative change for biodiversity conservation and human well-being. In this introspective research, we gained insights through an online survey for participants and organizers of the summer school (n = 27). Using qualitative content analysis, we identify seven crucial elements of transdisciplinary learning which can lead to transformative change on (a) a personal level, as the learning process shifts values and helps researchers identify their roles; (b) a research level, by rethinking science and providing tools for transdisciplinary approaches, and (c) a societal level, by moving from the individual to the collective and constructing a shared vision for a sustainable future. Participants highlighted how changes on all these levels could benefit biodiversity conservation. These insights point to the benefit of transdisciplinary learning opportunities that empower young researchers to take up their part in fostering transformative change.publishedVersio

Head in the clouds, feet on the ground: how transdisciplinary learning can foster transformative change—insights from a summer school

There is a pressing need for transformative change, with a vision of long-term human well-being within planetary boundaries. The lack of progress—despite increasing awareness and action—illustrates how challenging it is to foster change in our complex global society. Education and learning are needed to enable change. Transdisciplinary learning, which meaningfully integrates diverse knowledge and perspectives, contributes to developing an integrative understanding—a necessity for tackling complex challenges. We explore how transdisciplinary learning for early-career researchers can foster transformative change and lead to increased biodiversity conservation. This paper focuses on a case study of the authors’ shared experiences during the 2021 Alternet Summer School, which focused on transformative change for biodiversity conservation and human well-being. In this introspective research, we gained insights through an online survey for participants and organizers of the summer school (n = 27). Using qualitative content analysis, we identify seven crucial elements of transdisciplinary learning which can lead to transformative change on (a) a personal level, as the learning process shifts values and helps researchers identify their roles; (b) a research level, by rethinking science and providing tools for transdisciplinary approaches, and (c) a societal level, by moving from the individual to the collective and constructing a shared vision for a sustainable future. Participants highlighted how changes on all these levels could benefit biodiversity conservation. These insights point to the benefit of transdisciplinary learning opportunities that empower young researchers to take up their part in fostering transformative change

DNA metabarcoding of deep-sea sediment communities using COI: community assessment, spatio-temporal patterns and comparison with the 18S rDNA marker

The deep sea is the largest biome on Earth, albeit it is the least studied. Among the complex ecosystems and habitats that form the deep sea, submarine canyons and open slope systems are regarded to be potential hot-spots of biodiversity. The Mediterranean Sea hosts the 8.86% of the inventoried submarine canyons in the global ocean, like the Blanes Canyon, located in its Northwestern section. We assessed spatial (through sediment layers and along a depth gradient) and temporal (in two different seasons) patterns of biodiversity in sediment communities of the Blanes Canyon and its adjacent open slope with eDNA metabarcoding, using a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) as a marker. We found a total of 15,318 molecular operational taxonomic units (MOTUs), of which 10,860 could be assigned only to Eukarya. Among those assigned at lower levels, Metazoa, Stramenopiles and Archaeplastida were the dominant taxa. Within metazoans, Arthropoda, Nematoda and Cnidaria were the most diverse among the 28.2% that could be assigned to at least the phylum level. There was a trend towards decreasing diversity in the first few cm (1 to 5) of the sediment, with only 26.3% of the MOTUs shared across sediment layers. Our results show the presence of heterogeneous communities in the studied area, significantly different between zones, depths and seasons. We compared our results with the ones presented in Guardiola et al (2016), obtained using the v7 region of the 18S rRNA gene as genetic marker in the exact same samples. There were remarkable differences in the total number of MOTUs, in the most diverse taxa and in MOTU richness. COI recovered a higher number of MOTUs, but more remained unassigned taxonomically. However, broad spatio-temporal patterns elucidated from both datasets coincided, both markers retrieving the same ecological information. The choice of marker depends on a trade-off between marker variability, primer bias, and completeness of reference databases. Our results showed that COI can be used to accurately characterize the studied communities and to develop high-resolution bioindicators to detect ecological shifts. We also noted that COI reference databases for deep-sea organisms have important gaps, and its completeness is essential in order to successfully apply metabarcoding solutions