Studying marine microorganisms from space

Microorganisms are but a few micrometers in diameter and are not visible to the naked eye. Yet, the large numbers of microorganisms present in the oceans and the global impact of their activities make it possible to observe them from space. Here a few examples of how microorganisms can be studied from satellites are presented. The first case is the best known: the main pigment used in photosynthesis (chlorophyll a) can be determined from satellites. These kinds of studies have contributed a tremendous amount of understanding about the distribution and dynamics of primary production in the oceans. Two other examples will concern analysis of heterotrophic prokaryotic production and estimates of dimethyl sulfide (DMS) concentration and flux to the atmosphere. These three processes are of fundamental importance for the functioning of the biosphere. Marine microbes carry out about half of the total primary production in the planet. A substantial fraction of the respiration in the oceans is due to the activity of heterotrophic prokaryotes. Finally, the flux of DMS to the atmosphere is believed to constitute one of the mechanisms by which the biota can regulate climate. The global implications of microbial processes in the oceans can only be addressed with the help of satellites

FluorMODgui V3.0: A Graphic User Interface for the Spectral Simulation of Leaf and Canopy Chlorophyll Fluorescence

The FluorMODgui Graphic User Interface (GUI) software package developed within the frame of the FluorMOD project Development of a Vegetation Fluorescence Canopy Model is presented in this manuscript. The FluorMOD project was launched in 2002 by the European Space Agency (ESA) to advance the science of vegetation fluorescence simulation through the development and integration of leaf and canopy fluorescence models based on physical methods. The design of airborne or space missions dedicated to the measurement of solar-induced chlorophyll fluorescence using remote-sensing instruments require physical methods for quantitative feasibility analysis and sensor specification studies. The FluorMODgui model developed as part of this project is designed to simulate the effects of chlorophyll fluorescence at leaf and canopy levels using atmospheric inputs, running the leaf model, FluorMODleaf, and the canopy model, FluorSAIL, independently, through a coupling scheme, and by a multiple iteration protocol to simulate changes in the viewing geometry and atmospheric characteristics. Inputs for the FluorMODleaf model are the number of leaf layers, chlorophyll a+b content, water equivalent thickness, dry matter content, fluorescence quantum efficiency, temperature, species type, and stoichiometry. Inputs for the FluorSAIL canopy model are a MODTRAN-4 6-parameter spectra or measured direct horizontal irradiance and diffuse irradiance spectra, a soil reflectance spectrum, leaf reflectance & transmittance spectra and a excitation-fluorescence response matrix in upward and downward directions (all from FluorMODleaf), 2 PAR-dependent coefficients for the fluorescence response to light level, relative azimuth angle and viewing zenith angle, canopy leaf area index, leaf inclination distribution function, and a hot spot parameter. Outputs available in the 400-1000 nm spectral range from the graphical user interface, FluorMODgui, are the leaf spectral reflectance and transmittance, and the canopy reflectance, with and without fluorescence effects. In addition, solar and sky irradiance on the ground, radiance with and without fluorescence on the ground, and top-of-atmosphere (TOA) radiances for bare soil and surroundings same as target are also produced. The models and documentation regarding the FluorMOD project can be downloaded at http://www.ias.csic.es/fluormod

Mesonia oceanica sp. Nov., isolated from oceans during the tara oceans expedition, with a preference for mesopelagic waters

Strain ISS653T, isolated from Atlantic seawater, is a yellow pigmented, non-motile, Gram-reaction-negative rod-shaped bac-terium, strictly aerobic and chemoorganotrophic, slightly halophilic (1-15% NaCl) and mesophilic (4-37 °C), oxidase-and catalase-positive and proteolytic. Its major cellular fatty acids are iso-C15:0, iso-C15:0 2-OH, and iso-C17:0 3-OH; the major identified phospholipid is phosphatidylethanolamine and the major respiratory quinone is MK6. Genome size is 4.28 Mbp and DNA G+C content is 34.9 mol%. 16S rRNA gene sequence similarity places the strain among members of the family Flavobacteriaceae, with the type strains of Mesonia phycicola (93.2%), Salegentibacter mishustinae (93.1%) and Mesonia mobilis (92.9%) as closest relatives. Average amino acid identity (AAI) and average nucleotide identity (ANI) indices show highest values with M. mobilis (81% AAI; 78.9% ANI), M. phycicola (76% AAI; 76.3% ANI), Mesonia maritima (72% AAI, 74.9% ANI), Mesonia hippocampi (64% AAI, 70.8% ANI) and Mesonia algae (68% AAI; 72.2% ANI). Phylogenomic analysis using the Up-to-date-Bacterial Core Gene set (UBCG) merges strain ISS653T in a clade with species of the genus Mesonia. We conclude that strain ISS653T represents a novel species of the genus Mesonia for which we propose the name Mesonia oceanica sp. nov., and strain ISS653T (=CECT 9532T=LMG 31236T) as the type strain. A second strain of the species, ISS1889 (=CECT 30008) was isolated from Pacific Ocean seawater. Data obtained throughout the Tara oceans expedition indicate that the species is more abundant in the mesopelagic dark ocean than in the photic layer and it is more frequent in the South Pacific, Indian and North Atlantic oceans

Column aerosol characterization in a semi‐arid region around Marrakech during the WATERMED 2003 campaign

In the framework of the WATERMED (WATer use efficiency in natural vegetation and agricultural areas by Remote sensing in the MEDiterranean basin) project, an experimental field campaign was carried out in a semi‐arid region near Marrakech, Morocco, during March 2003. This work focused on the columnar aerosol characterization from spectroradiometric and photometric measurements of direct solar irradiance and sky radiance at ground level. The results show a high dependence of the aerosol optical properties on the air masses present in the area. Two periods with different aerosol loads were observed in the campaign. In the first, Atlantic‐origin aerosols showed a marine particle accumulation mode combined with a dominant mode corresponding to coarse particles of local origin. In the second period the synoptic situation changed towards a Saharan+Atlantic origin, the Atlantic influence persisting at altitude while at lower levels the presence of air masses proceeding from the Saharan desert was observed. This dry air carried a large quantity of mineral particles that increased the area's turbidity, leading to a substantial increase in the volume of the whole distribution, a displacement of the accumulation mode radius towards higher values and an increasingly evident spread of the coarse particle mode, although the radius remained the same as that in the first period of the campaign

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Oral Human Papillomavirus Prevalence and Genotyping Among a Healthy Adult Population in the US

IMPORTANCE In the US, oropharyngeal cancer, predominantly caused by high-risk (HR) human papillomavirus (HPV) infection, is the most frequent HPV-associated cancer, surpassing cervical cancer. However, little is known about oral HPV prevalence and genotype distribution in the general population. OBJECTIVE To assess oral HPV prevalence and factors associated with HR and low-risk infection in a general US population. DESIGN, SETTING, AND PARTICIPANTS PROGRESS (Prevalence of Oral HPV Infection, a Global Assessment) was a cross-sectional observational study conducted between November 2021 and March 2022 in 43 dental offices in the US (24 urban, 13 urban cluster, and 6 rural sites), spanning 21 states. Eligible participants were aged 18 to 60 years, visiting dental clinics for routine dental examination. Dental clinics used targeted sampling to recruit equal distributions of men and women and across age groups. EXPOSURE Participants provided an oral gargle specimen for HPV DNA and genotyping and completed behavioral questionnaires, and dentists reported oral health status. Detection of HPV DNA and genotyping was performed using the SPF10/DEIA/LiPA25 system at a central laboratory. MAIN OUTCOME Oral HPV prevalence. RESULTS Of the 3196 participants enrolled, mean (SD) age was 39.6 (12.1) years, and 55.5% were women. Oral HPV prevalence was 6.6%(95% CI, 5.7%-7.4%) for any HPV genotype, and 2.0% (95% CI, 1.5%-2.5%), 0.7%(95% CI, 0.4%-1.0%), and 1.5%(95% CI, 1.1%-1.9%) for HR, HPV-16, and 9-valent-HPV vaccine types, respectively. Among HPV-positive participants, HPV-16 was the most prevalent genotype (12.4% among men and 8.6% among women). Prevalence of HPV was higher in men than women and highest among men aged 51 to 60 years (16.8%, 6.8%, and 2.1% for any HPV, HR HPV, and HPV-16, respectively). Factors associated with HR oral infection included being male (adjusted odds ratio [AOR], 3.1; 95% CI, 1.2-8.5), being aged 51 to 60 years (AOR, 3.3; 95% CI, 1.5-7.3), having 26 or more lifetime male sex partners (AOR, 6.5; 95% CI, 2.3-18.7), and having 6 to 25 lifetime female oral sex partners (AOR, 3.4; 95% CI, 1.3-8.7). CONCLUSIONS AND RELEVANCE In this cross-sectional study, oral HPV burden was highest among older men who may be at higher risk of developing oropharyngeal cancer. In addition to male sex and older age, HR oral HPV infection was also associated with sexual behaviors, including increasing number of male sex partners and female oral sex partners

Physics demos for all UVEG degrees: a unique project in Spain

The Physics Demo Project at the University of Valencia (www.uv.es/fisicademos) has developed a collection of physics demonstrations to be used during lectures. It consists of more than 130 experimental demos about different physics topics. More than 30 professors borrow them whenever they lecture on physics in any of our 40 courses in 17 different science or technical degrees, involving 246 ECTS and more than 3500 students. Each demo kit with a simple experimental set displays a particular physics phenomenon. An on-line user guide highlights the main physics principles involved, instructions on how to use it and advices of how to link it to the theoretical concepts or to technical applications. Demo lectures (and collections) are a usual and widespread practice in many countries but not in Spain. This unique initiative aims at the recovery of this practice by involving a growing collaborative team of users and with the aid of educational innovation projects. Here we explain the project content, organization and recent developments. Our experience, together with the positive students comments, allows us to draw the following conclusions: demos introduce the real sensible world in the lecture hall, providing the necessary link between concepts and everyday life, and becoming, again, something more than "chalk and talk"