Functional rarity and evenness are key facets of biodiversity to boost multifunctionality

The functional traits of organisms within multispecies assemblages regulate biodiversity effects on ecosystem functioning. Yet how traits should assemble to boost multiple ecosystem functions simultaneously (multifunctionality) remains poorly explored. In a multibiome litter experiment covering most of the global variation in leaf trait spectra, we showed that three dimensions of functional diversity (dispersion, rarity, and evenness) explained up to 66% of variations in multifunctionality, although the dominant species and their traits remained an important predictor. While high dispersion impeded multifunctionality, increasing the evenness among functionally dissimilar species was a key dimension to promote higher multifunctionality and to reduce the abundance of plant pathogens. Because too-dissimilar species could have negative effects on ecosystems, our results highlight the need for not only diverse but also functionally even assemblages to promote multifunctionality. The effect of functionally rare species strongly shifted from positive to negative depending on their trait differences with the dominant species. Simultaneously managing the dispersion, evenness, and rarity in multispecies assemblages could be used to design assemblages aimed at maximizing multifunctionality independently of the biome, the identity of dominant species, or the range of trait values considered. Functional evenness and rarity offer promise to improve the management of terrestrial ecosystems and to limit plant disease risks.This work was funded by the British Ecological Society (SR17\1297 grant, PI: P.G.-P.) and by the European Research Council (ERC Grant Agreement #647038, BIODESERT, PI: F.T.M.). Y.L.B.-P. was supported by a Marie Sklodowska-Curie Actions Individual Fellowship within the European Program Horizon 2020 (DRYFUN Project #656035). H.S. was supported by a Juan de la Cierva-Formación grant from the Spanish Ministry of Economy and Competitiveness (FJCI-2015-26782). F.T.M. and S.A. were supported from the Generalitat Valenciana (CIDEGENT/2018/041). M.D. was supported by a Formación del Profesorado Universitario (FPU) fellowship from the Spanish Ministry of Education, Culture and Sports (FPU-15/00392). S.A. was supported by the Spanish MINECO for financial support via the DIGGING_DEEPER project through the 2015 to 2016 BiodivERsA3/FACCE‐JPI joint call for research proposals. B.K.S. research on biodiversity-ecosystem functions was supported by the Australian Research Council (DP170104634 and DP190103714). P.G.-P. was supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-024766-I). R.M. was supported by MINECO (Grants CGL2014-56567-R and CGL2017-83855-R)

Soil carbon loss by experimental warming in a tropical forest

Tropical soils contain one-third of the carbon stored in soils globally1, so destabilization of soil organic matter caused by the warming predicted for tropical regions this century2 could accelerate climate change by releasing additional carbon dioxide (CO2) to the atmosphere3,4,5,6. Theory predicts that warming should cause only modest carbon loss from tropical soils relative to those at higher latitudes5,7, but there have been no warming experiments in tropical forests to test this8. Here we show that in situ experimental warming of a lowland tropical forest soil on Barro Colorado Island, Panama, caused an unexpectedly large increase in soil CO2 emissions. Two years of warming of the whole soil profile by four degrees Celsius increased CO2 emissions by 55 per cent compared to soils at ambient temperature. The additional CO2 originated from heterotrophic rather than autotrophic sources, and equated to a loss of 8.2 ± 4.2 (one standard error) tonnes of carbon per hectare per year from the breakdown of soil organic matter. During this time, we detected no acclimation of respiration rates, no thermal compensation or change in the temperature sensitivity of enzyme activities, and no change in microbial carbon-use efficiency. These results demonstrate that soil carbon in tropical forests is highly sensitive to warming, creating a potentially substantial positive feedback to climate chang

Sprouty2 and Spred1-2 Proteins Inhibit the Activation of the ERK Pathway Elicited by Cyclopentenone Prostanoids

Sprouty and Spred proteins have been widely implicated in the negative regulation of the fibroblast growth factor receptor-extracellular regulated kinase (ERK) pathway. In considering the functional role of these proteins, we explored their effects on ERK activation induced by cyclopentenone prostanoids, which bind to and activate Ras proteins. We therefore found that ectopic overexpression in HeLa cells of human Sprouty2, or human Spred1 or 2, inhibits ERK1/2 and Elk-1 activation triggered by the cyclopentenone prostanoids PGA1 and 15d-PGJ2. Furthermore, we found that in HT cells that do not express Sprouty2 due to hypermethylation of its gene-promoter, PGA1-provoked ERK activation was more intense and sustained compared to other hematopoietic cell lines with unaltered Sprouty2 expression. Cyclopentenone prostanoids did not induce Sprouty2 tyrosine phosphorylation, in agreement with its incapability to activate tyrosine-kinase receptors. However, Sprouty2 Y55F, which acts as a defective mutant upon tyrosine-kinase receptor stimulation, did not inhibit cyclopentenone prostanoids-elicited ERK pathway activation. In addition, Sprouty2 did not affect the Ras-GTP levels promoted by cyclopentenone prostanoids. These results unveil both common and differential features in the activation of Ras-dependent pathways by cyclopentenone prostanoids and growth factors. Moreover, they provide the first evidence that Sprouty and Spred proteins are negative regulators of the ERK/Elk-1 pathway activation induced not only by growth-factors, but also by reactive lipidic mediators

Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

BACKGROUND: Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25–30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS: We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS: Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS: Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing

Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases.

BACKGROUND: Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS: We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS: Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS: Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing

Climate change legacies contrastingly affect the resistance and resilience of soil microbial communities and multifunctionality to extreme drought

1. Soil microbial communities largely determine the ability of soils to provide multiple functions simultaneously (i.e. soil multifunctionality; multifunctionality hereafter). However, a major research challenge is understanding how soil microbial communities and associated multifunctionality resist and recover from extreme climate events such as droughts, and how the legacy of past climatic conditions may constrain such responses. 2. Here, we used soils subjected to 7 years of reduced rainfall (~35% reduction), warming (3°C temperature increase) and their combination to assess climate change legacies on the resistance and resilience of both soil fungal and bacterial communities and multifunctionality to a subsequent extreme drought event (2 weeks at 3% water-holding capacity). At the end of the extreme drought, and 1, 15 and 60 days after rewetting, we assessed bacterial and fungal community composition, richness and abundance, as well as a multifunctionality index based on eight functions related with soil carbon (C), nitrogen (N) and phosphorous (P) cycling. 3. Climate change legacies influenced the resistance and resilience of bacterial and fungal abundance to extreme drought, but not those of community composition, richness and multifunctionality. The resistance of bacterial and fungal abundance showed opposite responses to warming and reduced rainfall. Specifically, climate change legacies increased the resistance of fungal abundance, whereas they reduced that of bacterial abundance. The resistance and resilience of multifunctionality to extreme drought were not related to the resistance or resilience of bacterial and fungal communities. Yet, the resistance of multifunctionality was related to that of Chytridiomycota, whereas its resilience was related to that of Proteobacteria. 4. Overall, our results indicate that climate change legacies affected the resistance and resilience of soil bacterial and fungal abundance to a subsequent extreme drought event, but not those of their community composition, richness and multifunctionality. Our results provide new insights on how climate change legacies contrastingly influence the resistance and resilience of soil microbial communities and multifunctionality. Furthermore, our findings highlight the role that specific microbial taxa play in maintaining soil multifunctionality and recovering from extreme drought events predicted under anthropogenic climate change.This research was funded by the European Research Council (ERC Grant agreement 647038 [BIODESERT]). M.D. was supported by a FPU fellowship from the Spanish Ministry of Education, Culture and Sports (FPU-15/00392) and by the BIODESERT project. P.G.-P. is supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-024766-I). S.A. was supported by the Spanish MINECO via the DIGGING_DEEPER project through the 2015-2016 BiodivERsA3/FACCE-JPI joint call for research proposals. The B.K.S. lab on soil biodiversity and ecosystem functions is supported by the Australian Research Council (DP 190103714). F.T.M. and S.A. acknowledge support from the Generalitat Valenciana (CIDEGENT/2018/041)