Partitioning spatial, environmental, and community drivers of ecosystem functioning

Context: Community composition, environmental variation, and spatial structuring can influence ecosystem functioning, and ecosystem service delivery. While the role of space in regulating ecosystem functioning is well recognised in theory, it is rarely considered explicitly in empirical studies. Objectives: We evaluated the role of spatial structuring within and between regions in explaining the functioning of 36 reference and human-impacted streams. Methods: We gathered information on regional and local environmental variables, communities (taxonomy and traits), and used variance partitioning analysis to explain seven indicators of ecosystem functioning. Results: Variation in functional indicators was explained not only by environmental variables and community composition, but also by geographic position, with sometimes high joint variation among the explanatory factors. This suggests spatial structuring in ecosystem functioning beyond that attributable to species sorting along environmental gradients. Spatial structuring at the within-region scale potentially arose from movements of species and materials among habitat patches. Spatial structuring at the between-region scale was more pervasive, occurring both in analyses of individual ecosystem processes and of the full functional matrix, and is likely to partly reflect phenotypic variation in the traits of functionally important species. Characterising communities by their traits rather than taxonomy did not increase the total variation explained, but did allow for a better discrimination of the role of space. Conclusions: These results demonstrate the value of accounting for the role of spatial structuring to increase explanatory power in studies of ecosystem processes, and underpin more robust management of the ecosystem services supported by those processes

Single-cell multi-omics analysis of the immune response in COVID-19

Peer reviewedPublisher PD

Single-cell multi-omics analysis of the immune response in COVID-19

Funder: Lister Institute of Preventive Medicine; doi: https://doi.org/10.13039/501100001255Funder: University College London, Birkbeck MRC Doctoral Training ProgrammeFunder: The Jikei University School of MedicineFunder: Action Medical Research (GN2779)Funder: NIHR Clinical Lectureship (CL-2017-01-004)Funder: NIHR (ACF-2018-01-004) and the BMA FoundationFunder: Chan Zuckerberg Initiative (grant 2017-174169) and from Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194)Funder: UKRI Innovation/Rutherford Fund Fellowship allocated by the MRC and the UK Regenerative Medicine Platform (MR/5005579/1 to M.Z.N.). M.Z.N. and K.B.M. have been funded by the Rosetrees Trust (M944)Funder: Barbour FoundationFunder: ERC Consolidator and EU MRG-Grammar awardsFunder: Versus Arthritis Cure Challenge Research Grant (21777), and an NIHR Research Professorship (RP-2017-08-ST2-002)Funder: European Molecular Biology Laboratory (EMBL)Abstract: Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy

Functional trait composition of aquatic plants can serve to disentangle multiple interacting stressors in lowland streams

Historically, close attention has been paid to negative impacts associated with nutrient loads to streams and rivers, but today hydromorphological alterations are considered increasingly implicated when lowland streams do not achieve good ecological status. Here, we explore if trait-abundance patterns of aquatic plants change along gradients in hydromorphological degradation and eutrophication in lowland stream sites located in Denmark. Specifically, we hypothesised that: i) changes in trait-abundance patterns occur along gradients in hydromorphological degradation and ii) trait-abundance patterns can serve to disentangle effects of eutrophication and hydromorphological degradation in lowland streams reflecting that the mechanisms behind changes differ. We used monitoring data from a total of 147 stream reaches with combined data on aquatic plant species abundance, catchment land use, hydromorphological alterations (i.e. planform, cross section, weed cutting) and water chemistry parameters. Traits related to life form, dispersal, reproduction and survival together with ecological preference values for nutrients and light (Ellenberg N and L) were allocated to 41 species representing 79% of the total species pool. We found clear evidence that habitat degradation (hydromorphological alterations and eutrophication) mediated selective changes in the trait-abundance patterns of the plant community. Specific traits could distinguish hydromorphological degradation (free-floating, surface; anchored floating leaves; anchored heterophylly) from eutrophication (free-floating, submerged; leaf area). We provide a conceptual framework for interpretation of how eutrophication and hydromorphological degradation interact and how this is reflected in trait-abundance patterns in aquatic plant communities in lowland streams. Our findings support the merit of trait-based approaches in biomonitoring as they shed light on mechanisms controlling structural changes under environmental stress. The ability to disentangle several stressors is particularly important in lowland stream environments where several stressors act in concert since the impact of the most important stressor can be targeted first, which is essential to improve the ecological status

Partitioning spatial, environmental, and community drivers of ecosystem functioning

Context: Community composition, environmental variation, and spatial structuring can influence ecosystem functioning, and ecosystem service delivery. While the role of space in regulating ecosystem functioning is well recognised in theory, it is rarely considered explicitly in empirical studies. Objectives: We evaluated the role of spatial structuring within and between regions in explaining the functioning of 36 reference and human-impacted streams. Methods: We gathered information on regional and local environmental variables, communities (taxonomy and traits), and used variance partitioning analysis to explain seven indicators of ecosystem functioning. Results: Variation in functional indicators was explained not only by environmental variables and community composition, but also by geographic position, with sometimes high joint variation among the explanatory factors. This suggests spatial structuring in ecosystem functioning beyond that attributable to species sorting along environmental gradients. Spatial structuring at the within-region scale potentially arose from movements of species and materials among habitat patches. Spatial structuring at the between-region scale was more pervasive, occurring both in analyses of individual ecosystem processes and of the full functional matrix, and is likely to partly reflect phenotypic variation in the traits of functionally important species. Characterising communities by their traits rather than taxonomy did not increase the total variation explained, but did allow for a better discrimination of the role of space. Conclusions: These results demonstrate the value of accounting for the role of spatial structuring to increase explanatory power in studies of ecosystem processes, and underpin more robust management of the ecosystem services supported by those processes

Plant trait characteristics vary with size and eutrophication in European lowland streams

1. Previous studies investigating community-level relationships between plant functional trait characteristics and stream environmental characteristics remain scarce. Here, we used community-weighted means to identify how plant traits link to lowland stream typology and how agricultural intensity in the catchment affects trait composition. 2. We analysed plant trait characteristics in 772 European lowland streams to test the following two hypotheses: (i) trait characteristics differ between plant communities in small and medium-sized streams, reflecting adaptations to different habitat characteristics, and (ii) trait characteristics vary with the intensity of agricultural land use in the stream catchment, mediated either directly by an increase in productive species or indirectly by an increase in species that efficiently intercept and utilize light. 3. We found that the communities in small streams were characterized by a higher abundance of light-demanding species growing from single apical meristems, reproducing by seeds and rooted to the bottom with floating and/or heterophyllous leaves, whereas the community in medium-sized streams was characterized by a higher abundance of productive species growing from multi-apical and basal growth meristems forming large canopies. 4. We also found indications that community trait characteristics were affected by eutrophication. We did not find enhanced abundance of productive species with an increasing proportion of agriculture in the catchments. Instead, we found an increase in the abundance of species growing from apical and multi-apical growth meristems as well as in the abundance of species tolerant of low light availability. The increase in the abundance of species possessing these traits likely reflects different strategies to obtain greater efficiency in light interception and utilization in nutrient-enriched environments. 5. Synthesis and applications. Our findings challenge the general assumption of the EU Water Framework Directive compliant assessment systems that plant community patterns in streams reflect the nutrient preference of the community. Instead, light availability and the ability to improve interception and utilization appeared to be of key importance for community composition in agricultural lowland streams. We therefore suggest moving from existing approaches building on species-specific preference values for nutrients to determine the level of nutrient impairment to trait-based approaches that provide insight into the biological mechanisms underlying the changes. We recommend that existing systems are critically appraised in the context of the findings of this study

Water Framework Directive Intercalibration Technical Report: Northern Lake Benthic invertebrate ecological assessment methods

One of the key actions identified by the Water Framework Directive (WFD; 2000/60/EC) is to develop ecological assessment tools and carry out a European intercalibration (IC) exercise. The aim of the Intercalibration is to ensure that the values assigned by each Member State to the good ecological class boundaries are consistent with the Directive’s generic description of these boundaries and comparable to the boundaries proposed by other MS. In total, 83 lake assessment methods were submitted for the 2nd phase of the WFD intercalibration (2008-2012) and 62 intercalibrated and included in the EC Decision on Intercalibration (EC 2013). The intercalibration was carried out in the 13 Lake Geographical Intercalibration Groups according to the ecoregion and biological quality element. In this report we describe how the intercalibration exercise has been carried out in the Northern Lake Benthic invertebrate group.JRC.H.1-Water Resource

Impacts of hydromorphological degradation and disturbed sediment dynamics on ecological status. Deliverable 3.1 of REFORM (REstoring rivers FOR effective catchment Management), a collaborative project (large-scale integrating project) funded by the European Commission within the 7th Framework Programme under Grant Agreement 282656.

There is an acknowledged need among stakeholders that new hydromorphological metrics are required to facilitate site remediation and for reporting at national and European levels. Pressure/ impact data were assembled from across Europe. The task was challenging, but useful information was gathered. For each major hydromorphological pressure, the physical response gradients of rivers was summarised as diagnostic diagrams. For the first time we provide evidence that metrics indicating HYMO impact could be developed from monitoring data on fish and macrophytes. For the first time we demonstrate the potential to derive metrics sensitive to fine sediment. We provide evidence that phytobenthos (diatoms), invertebrates and macrophytes have the potential to be used in combined metrics. We found that many existing macroinvertebrate metrics lack specificity and can provide false positive responses to HYMO pressure, suggesting that disentanglement of multi-stressor responses is critical to good diagnosis. There is evidence that aquatic habitats protected under the Habitats Directive will be increasingly vulnerable to hydrological pressures with the changing climate. Frequently, overlooked topics such as sediment quality and groundwater issues ought to supplement or be included in HYMO assessments due to their potential for explaining variance in biological datasets. Land-use data on a spatial scale beyond the reach scale (corridor and catchment) relates to site-specific macroinvertebrate metrics and could be a more robust way of assessing impacts

Single-cell multi-omics analysis of the immune response in COVID-19

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy

Single-cell multi-omics analysis of the immune response in COVID-19.

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy