Intransitivity in plant-soil feedbacks is rare but is associated with multispecies coexistence.

Although plant-soil feedback (PSF) is being recognized as an important driver of plant recruitment, our understanding of its role in species coexistence in natural communities remains limited by the scarcity of experimental studies on multispecies assemblages. Here, we experimentally estimated PSFs affecting seedling recruitment in 10 co-occurring Mediterranean woody species. We estimated weak but significant species-specific feedback. Pairwise PSFs impose similarly strong fitness differences and stabilizing-destabilizing forces, most often impeding species coexistence. Moreover, a model of community dynamics driven exclusively by PSFs suggests that few species would coexist stably, the largest assemblage with no more than six species. Thus, PSFs alone do not suffice to explain coexistence in the studied community. A topological analysis of all subcommunities in the interaction network shows that full intransitivity (with all species involved in an intransitive loop) would be rare but it would lead to species coexistence through either stable or cyclic dynamics.

The niche of a stress-tolerant specialist, Dinophysis acuminata, in a coastal upwelling system.

Dinophysis acuminata, the main cause of shellfish harvesting bans in Europe, blooms in the Galician Rías (NW Spain) throughout the upwelling season (ca. March to September). Here we illustrate rapid changes in vertical and across ría-shelf distributions of diatoms and dinoflagellates (including D. acuminata vegetative and small cells) in Ría de Pontevedra (RP) and Ría de Vigo (RV) during transitions from spin-down to spin-up phases of upwelling cycles. A subniche approach based on a Within Outlying Mean Index (WitOMI) showed that under the transient environmental conditions met during the cruise, both vegetative and small cells of D. acuminata colonized the Ria and Mid-shelf subniches, exhibiting good tolerance and extremely high marginality, in particular the small cells. Bottom-up (abiotic) control overwhelmed biological constraints, and shelf waters became a more favourable environment than the Rías. Contrasting higher biotic constraints inside the Rías were found for the small cells, with a subniche possibly controlled by unsuitable physiological status (notwithstanding the higher density) of the vegetative cell population. Results here on behaviour (vertical positioning) and physiological traits (high tolerance but very specialized niche) of D. acuminata give new insights into the ability of this species to remain in the upwelling circulation system. Higher shelf-ría exchanges in the Ría (RP) with more dense and persistent D. acuminata blooms reveal the relevance of transient event-scales and species- and site-specific characteristics to the fate of these blooms. Earlier statements about simple linear relationships between average upwelling intensities and the recurrence of Harmful algae bloom (HAB) events in the Galician Rías Baixas are questioned.

Mapping dinoflagellate blooms (Noctiluca and Alexandrium) in aquaculture production areas in the NW Iberian Peninsula with the Sentinel-2/3 satellites.

The Galician Rías (northwestern Spain) are periodically affected by harmful algal blooms (HABs), mostly dinoflagellates, which pose a challenge to aquaculture activities due to the accumulation of biotoxins in shellfish. Typically, reddish blooms in the Rías are associated with non-toxic species like Noctiluca scintillans, with a few exceptions such as Alexandrium minutum, a producer of paralytic shellfish toxins (PST). Here, a useful approach is presented for monitoring reddish blooms through satellite imagery based on three case studies, two of them belonged to monospecific blooms of red Noctiluca scintillans, and the third to a bloom of Alexandrium spp. dominated by A. tamarense. In every case, a propulsive index was evaluated using Sentinel-2A/B satellites, which provide high spatial and spectral resolutions, combined with adequate atmospheric and sunglint correction by using the ACOLITE and C2RCC processors. This approach offers a simple and feasible method to accurately and timely map blooms of red N. scintillans and Alexandrium spp. in the study area, useful to detect the distribution of reddish blooms with synoptic observations for monitoring and aquaculture management purposes. Conversely, Sentinel-3A/B satellites with a relatively coarser spatial resolution, lacking adequate visualization and mapping of the extent of small blooms, did not accurately detect bloom footprints in the coastal bay region, although this sensor displays a set of suitable multispectral bands.

RecruitNet: A global database of plant recruitment networks.

Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country, locality, responsible author, sampling dates, sampling method, and life habits of both canopy and recruit species are provided. This database will allow researchers to test ecological, biogeographical, and evolutionary hypotheses related to plant recruitment interactions. There are no copyright restrictions on the data set; please cite this data paper when using these data in publications.

IgG targeting distinct seasonal coronavirus- conserved SARS-CoV-2 spike subdomains correlates with differential COVID-19 disease outcomes.

Despite SARS-CoV-2 being a "novel" virus, early detection of anti-spike IgG in severe COVID-19 patients may be caused by the amplification of humoral memory responses against seasonal coronaviruses. Here, we examine this phenomenon by characterizing anti-spike IgG responses in non-hospitalized convalescent individuals across a spectrum of COVID-19 severity. We observe that disease severity positively correlates with anti-spike IgG levels, IgG cross-reactivity against other betacoronaviruses (ß-CoVs), and FcγR activation. Analysis of IgG targeting ß-CoV-conserved and non-conserved immunodominant epitopes within the SARS-CoV-2 spike protein revealed epitope-specific relationships: IgG targeting the conserved heptad repeat (HR) 2 region significantly correlates with milder disease, while targeting the conserved S2'FP region correlates with more severe disease. Furthermore, a lower HR2-to-S2'FP IgG-binding ratio correlates with greater disease severity, with ICU-hospitalized COVID-19 patients showing the lowest HR2/S2'FP ratios. These findings suggest that HR2/S2'FP IgG profiles may predict disease severity and offer insight into protective versus deleterious humoral recall responses.

Sustained Antibody-Dependent NK Cell Functions in Mild COVID-19 Outpatients During Convalescence.

The coronavirus disease 2019 (COVID19) pandemic has left researchers scrambling to identify the humoral immune correlates of protection from COVID-19. To date, the antibody mediated correlates of virus neutralization have been extensively studied. However, the extent that non-neutralizing functions contribute to anti-viral responses are ill defined. In this study, we profiled the anti-spike antibody subtype/subclass responses, along with neutralization and antibody-dependent natural killer cell functions in 83 blood samples collected between 4 and 201 days post-symptoms onset from a cohort of COVID-19 outpatients. We observed heterogeneous humoral responses against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Overall, anti-spike profiles were characterized by a rapid rise of IgA and sustained IgG titers. In addition, strong antibody-mediated natural killer effector responses correlated with milder disease and being female. While higher neutralization profiles were observed in males along with increased severity. These results give an insight into the underlying function of antibodies beyond neutralization and suggest that antibody-mediated natural killer cell activity is a key function of the humoral response against the SARS-CoV-2 spike protein.

Therapeutic Efficacy of Human Monoclonal Antibodies against Andes Virus Infection in Syrian Hamsters.

Andes virus, an orthohantavirus endemic to South America, causes severe hantavirus cardiopulmonary syndrome associated with human-to-human transmission. No approved treatments or vaccines against this virus are available. We show that a combined treatment with 2 monoclonal antibodies protected Syrian hamsters when administered at midstage or late-stage disease.

Cytokine Profiles and Antibody Response Associated to Choclo Orthohantavirus Infection.

Background: New World Hantaviruses (NWHs) are the etiological agent underlying hantavirus cardiopulmonary syndrome (HCPS), a severe respiratory disease with high mortality rates in humans. In Panama, infections with Choclo Orthohantavirus (CHOV) cause a much milder illness characterized by higher seroprevalence and lower mortality rates. To date, the cytokine profiles and antibody responses associated with this milder form of HCPS have not been defined. Therefore, in this study, we examined immune serological profiles associated with CHOV infections. Methods: For this retrospective study, sera from fifteen individuals with acute CHOV-induced HCPS, were analyzed alongside sera from fifteen convalescent phase individuals and thirty-three asymptomatic, CHOV-seropositive individuals. Cytokine profiles were analyzed by multiplex immunoassay. Antibody subclasses, binding, and neutralization against CHOV-glycoprotein (CHOV-GP) were evaluated by ELISA, and flow cytometry. Results: High titers of IFNγ, IL-4, IL-8, and IL-10 serum cytokines were found in the acute individuals. Elevated IL-4 serum levels were found in convalescent and asymptomatic seropositive individuals. High titers of IgG1 subclass were observed across the three cohorts analyzed. Neutralizing antibody response against CHOV-GP was detectable in few acute individuals but was strong in both convalescent and asymptomatic seropositive individuals. Conclusion: A Th1/Th2 cytokine signature is characteristic during acute mild HCPS caused by CHOV infection. High expression of Th2 and IL-8 cytokines are correlated with clinical parameters in acute mild HCPS. In addition, a strong IL-4 signature is associated with different cohorts, including asymptomatic individuals. Furthermore, asymptomatic individuals presented high titers of neutralizing antibodies.

Differential CD4 T Regulatory Cell Phenotype Induced by Andes Hantavirus Glycoprotein.

Hantavirus cardiopulmonary syndrome (HCPS) caused by Andes orthohantavirus (ANDV) in South America is a public health threat due to the significant rate of mortality and the lack of a specific treatment. Interestingly, the virus does not produce cytopathic effect, thereby the strong antiviral immune response is suspected to contribute to pathogenesis, hence is important to understand the balance between protective and harmfully immunity. CD4+ T regulatory cells (Treg) are essential to control an exacerbated immune response. In human ANDV infection, little is known about CD4+ Treg cells, which may be involved in control immunopathology associated to the infection. In this report, we characterize the phenotype of memory CD4+ Tregs in a HCPS survivor's cohort. Based on the expression of CXCR3, CCR4, and CCR6, we identified different Th-like Treg populations in ANDV survival's PBMCs. In addition, the effect of ANDV-glycoprotein virus like particles (VLP) was determined. We demonstrated that memory CD4+ Treg from HCPS present a specific phenotype, showing higher frequency of PD-1 compared to healthy donors (HD). In addition, it was observed a decrease in the frequency of Th1-like memory CD4+ Treg in HCPS, important to highlight that this signature could be preserved even years after resolution of infection. Moreover, to gain insight in the mechanism involved, we evaluated whether ANDV-glycoprotein (GP) VLP could modulate CD4+ Treg. Interestingly, ANDV-GP VLP induced a decrease in the frequency of CXCR3 (Th1-like) and an increase in CCR4 (Th2-like) memory CD4+ Treg in both HD and HCPS PBMCs, indicating that ANDV-GP could specifically act over CXCR3 and CCR4 in CD4+ Treg. This report contributes to the study of human CD4+ Treg cells in ANDV infection.

Plant species abundance and phylogeny explain the structure of recruitment networks.

Established plants can affect the recruitment of young plants, filtering out some and allowing the recruitment of others, with profound effects on plant community dynamics. Recruitment networks (RNs) depict which species recruit under which others. We investigated whether species abundance and phylogenetic distance explain the structure of RNs across communities. We estimated the frequency of canopy-recruit interactions among woody plants in 10 forest assemblages to describe their RNs. For each RN, we determined the functional form (linear, power or exponential) best describing the relationship of interaction frequency with three predictors: canopy species abundance, recruit species abundance and phylogenetic distance. We fitted models with all combinations of predictor variables, from which we simulated RNs. The best functional form of each predictor was the same in most communities (linear for canopy species abundance, power for recruit species abundance and exponential for phylogenetic distance). The model including all predictor variables was consistently the best in explaining interaction frequency and showed the best performance in predicting RN structure. Our results suggest that mechanisms related to species abundance are necessary but insufficient to explain the assembly of RNs. Evolutionary processes affecting phylogenetic divergence are critical determinants of RN structure.

Two recombinant human monoclonal antibodies that protect against lethal Andes hantavirus infection in vivo.

Andes hantavirus (ANDV) is an etiologic agent of hantavirus cardiopulmonary syndrome (HCPS), a severe disease characterized by fever, headache, and gastrointestinal symptoms that may progress to hypotension, pulmonary failure, and cardiac shock that results in a 25 to 40% case-fatality rate. Currently, there is no specific treatment or vaccine; however, several studies have shown that the generation of neutralizing antibody (Ab) responses strongly correlates with survival from HCPS in humans. In this study, we screened 27 ANDV convalescent HCPS patient sera for their capacity to bind and neutralize ANDV in vitro. One patient who showed high neutralizing titer was selected to isolate ANDV-glycoprotein (GP) Abs. ANDV-GP-specific memory B cells were single cell sorted, and recombinant immunoglobulin G antibodies were cloned and produced. Two monoclonal Abs (mAbs), JL16 and MIB22, potently recognized ANDV-GPs and neutralized ANDV. We examined the post-exposure efficacy of these two mAbs as a monotherapy or in combination therapy in a Syrian hamster model of ANDV-induced HCPS, and both mAbs protected 100% of animals from a lethal challenge dose. These data suggest that monotherapy with mAb JL16 or MIB22, or a cocktail of both, could be an effective post-exposure treatment for patients infected with ANDV-induced HCPS.

A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle.

All characterized members of the ubiquitous genus Acaryochloris share the unique property of containing large amounts of chlorophyll (Chl) d, a pigment exhibiting a red absorption maximum strongly shifted towards infrared compared to Chl a. Chl d is the major pigment in these organisms and is notably bound to antenna proteins structurally similar to those of Prochloron, Prochlorothrix and Prochlorococcus, the only three cyanobacteria known so far to contain mono- or divinyl-Chl a and b as major pigments and to lack phycobilisomes. Here, we describe RCC1774, a strain isolated from the foreshore near Roscoff (France). It is phylogenetically related to members of the Acaryochloris genus but completely lacks Chl d. Instead, it possesses monovinyl-Chl a and b at a b/a molar ratio of 0.16, similar to that in Prochloron and Prochlorothrix. It differs from the latter by the presence of phycocyanin and a vestigial allophycocyanin energetically coupled to photosystems. Genome sequencing confirmed the presence of phycobiliprotein and Chl b synthesis genes. Based on its phylogeny, ultrastructural characteristics and unique pigment suite, we describe RCC1774 as a novel species that we name Acaryochloris thomasi. Its very unusual pigment content compared to other Acaryochloris spp. is likely related to its specific lifestyle.

19,19'-Diacyloxy Signature: An Atypical Level of Structural Evolution in Carotenoid Pigments.

We report the isolation from the green dinoflagellate Lepidodinium chlorophorum and structural characterization of a new carotenoid termed lepidoxanthin (1), determined to be (3S,5R,6S,3'R,6'R)-5,6-epoxy-19-(2-decenoyloxy)-19'-acetoxy-4',5'-didehydro-5,6,5',6'-tetrahydro-ß,ε-carotene-3,3'-diol. Its until now unidentified 19,19'-diacyloxy substitution constitutes a chemical signature that can aid in unraveling the evolutionary course of this unicellular algae based on the proposed biosynthethic pathway.

Pigment variations in Emiliania huxleyi (CCMP370) as a response to changes in light intensity or quality.

Many studies on photoacclimation examine the pigment responses to changes in light intensity, but variations in light climate in the aquatic environment are also related to changes in spectral composition. We have employed a high-performance liquid chromatography method with improved resolution towards chlorophyll c and fucoxanthin-related xanthophylls to examine the pigment composition of Emiliania huxleyi CCMP 370 under different light intensities and spectral qualities. To maintain its photosynthetic performance, E. huxleyi CCMP370 promotes drastic pigment changes that can be either the interconversion of pigments in pools with the same basic chromophoric structure (Fucoxanthin type or chlorophyll c type), or the ex novo synthesis (Diatoxanthin). These changes are linked either to variations in light quality (Fucoxanthin related xanthophylls) or in light intensity (chlorophyll c3 /Monovinyl chlorophyll c3 , Diadinoxanthin/Diatoxanthin, ß,ɛ-carotene/ ß,ß-carotene). Fucoxanthin and 19'-hexanoyloxyfucoxanthin proportions were highly dependent on spectral conditions. Whereas Fucoxanthin dominated in green and red light, 19'-hexanoyloxyfucoxanthin prevailed under blue spectral conditions. Our results suggest that the huge pigment diversity enhanced the photoacclimative capacities of E. huxleyi to efficiently perform under changing light environments. The ubiquity and success in the global ocean as well as the capacity of E. huxleyi to form large surface blooms might be associated to the plasticity described here.

The Use of HPLC for the Characterization of Phytoplankton Pigments.

HPLC is still the technique of choice for the analysis and characterization of phytoplankton pigments. In this chapter we describe procedures for sample preparation and pigment extraction, and the use of octyl silica columns and pyridine-containing mobile phases to separate chlorophylls and carotenoids. The identification of pigments on the basis of their retention times and visible spectra, the preparation of pigment standards, and the quantitative analysis by either external or internal standard procedures are also described.

Chlorophyll c(CS-170) isolated from Ostreococcus sp. is [7-methoxycarbonyl-8-vinyl]protochlorophyllide a.

The controversial molecular identification of the so-called chlorophyll cCS-170 has been settled. Despite its relevance as a potential biomarker in the study of eukaryotic picophytoplankton, the structure of this chlorophyll remained so far uncertain. A full characterization by NMR, UV-vis, and ESI-MS is reported, revealing this chlorophyll as [7-methoxycarbonyl-8-vinyl]-protochlorophyllide a.

Genetic regulation of cold-induced albinism in the maize inbred line A661.

In spite of multiple studies elucidating the regulatory pathways controlling chlorophyll biosynthesis and photosynthetic activity, little is known about the molecular mechanism regulating cold-induced chlorosis in higher plants. Herein the characterization of the maize inbred line A661 which shows a cold-induced albino phenotype is reported. The data show that exposure of seedlings to low temperatures during early leaf biogenesis led to chlorophyll losses in this inbred. A661 shows a high plasticity, recovering resting levels of photosynthesis activity when exposed to optimal temperatures. Biochemical and transcriptome data indicate that at suboptimal temperatures chlorophyll could not be fully accommodated in the photosynthetic antenna in A661, remaining free in the chloroplast. The accumulation of free chlorophyll activates the expression of an early light inducible protein (elip) gene which binds chlorophyll to avoid cross-reactions that could lead to the generation of harmful reactive oxygen species. Higher levels of the elip transcript were observed in plants showing a cold-induced albino phenotype. Forward genetic analysis reveals that a gene located on the short arm of chromosome 2 regulates this protective mechanism.

Characterization of [8-ethyl]-chlorophyll c3 from Emiliania huxleyi.

We report herein the isolation and complete characterization of a member of the chlorophyll c family, designated as [8-ethyl]-chlorophyll c(3) ([8-ethyl]-chl c(3)). Structural elucidation of this pigment rested on the analysis of mono- and bidimensional NMR, UV-VIS spectroscopy and ESI-MS data, and the configuration at the 13(2) position on chiral HPLC analysis.

Characterizing the pregnancy immune phenotype: results of the viral immunity and pregnancy (VIP) study.

PURPOSE: The increased risk of morbidity and mortality from certain microbial infections and the demonstrated improvements in the clinical course of some autoimmune diseases support the existence of pregnancy-related alterations in immune status. Elucidating the changes in innate and adaptive immunity during gestation may improve pregnancy outcomes and facilitate the development of targeted therapies for autoimmune diseases. METHOD: The Viral Immunity and Pregnancy (VIP) study evaluated over 50 subjects longitudinally at three time points during pregnancy and at two time points post-delivery. Leukocyte enumeration was performed; functional responses of NK cells and CD4 T cells were analyzed, and soluble factors such as cytokines, defensins, and steroid hormones were measured in maternal blood. RESULTS: In comparison to the post-partum period, the latter part of pregnancy was characterized by significant increases in blood phagocytes and pDCs and decreases in the number and activity of NK and T cells. Alterations were found in antimicrobial proteins and serum cytokines. CONCLUSIONS: These data show that pregnancy is not a period of immunosuppression but an alteration in immune priorities characterized by a strengthening of innate immune barriers and a concomitant reduction in adaptive/inflammatory immunity in the later stages of pregnancy.

Peripheral blood cytokine profiling during pregnancy and post-partum periods.

PROBLEM: Pregnancy requires that the maternal immune system adapt to prevent rejection of the fetal semi-allograft. This immunologic adaptation may contribute to pregnancy-related alterations in disease susceptibility and severity of infections from viral pathogens such as influenza virus. METHOD OF STUDY: As part of a larger study investigating the maternal systemic immune response during pregnancy, peripheral blood was collected three times during pregnancy and twice post-partum to measure serum levels of 23 cytokines, chemokines, and growth factors. This longitudinal study design allowed each woman's post-partum blood draw to serve as her own comparison, thus controlling for interpersonal variability in expression levels. RESULTS: When compared to the post-partum samples, significant pregnancy-related changes in IFNγ, TNFα, VEGF, GCSF, Eotaxin, and MCP-1 expression were observed. These changes have significant immunologic effects in vivo and in culture. CONCLUSION: Pregnancy-associated changes to steady state serum cytokines may have important immunologic consequence.