Enhancing temporal correlations in EOF expansions for the reconstruction of missing data using DINEOF

DINEOF (Data Interpolating Empirical Orthogonal Functions) is an EOF-based technique for the reconstruction of missing data in geophysical fields, such as those produced by clouds in sea surface temperature satellite images. A technique to reduce spurious time variability in DINEOF reconstructions is presented. The reconstruction of these images within a long time series using DINEOF can lead to large discontinuities in the reconstruction. Filtering the temporal covariance matrix allows to reduce this spurious variability and therefore more realistic reconstructions are obtained. The approach is tested in a three years sea surface temperature data set over the Black Sea. The effect of the filter in the temporal EOFs is presented, as well as some examples of the improvement achieved with the filtering in the SST reconstruction, both compared to the DINEOF approach without filtering

Data Interpolating Empirical Orthogonal Functions (DINEOF): a tool for geophysical data analyses

An overview of the technique called DINEOF (Data Interpolating Empirical Orthog- onal Functions) is presented. DINEOF reconstructs missing information in geophys- ical data sets, such as satellite imagery or time series. A summary of the technique is given, with its main characteristics, recent developments and future research di- rections. DINEOF has been applied to a large variety of oceanographic variables in various domains of different sizes. This technique can be applied to a single variable (monovariate approach), or to several variables together (multivariate approach), with no complexity increase in the application of the technique. Error fields can be computed to establish the accuracy of the reconstruction. Examples are given to illustrate the capabilities of the technique. DINEOF is freely offered to download, and help is provided to users in the form of a wiki and through a discussion email list.RECOLOU

Generation of analysis and consistent error fields using the Data Interpolating Variational Analysis (Diva)

SeaDataNet

A 15-month survey of Dimethylsulfoniopropionate and Dimethylsulfoxide content in Posidonia oceanica

Posidonia oceanica is the only reported seagrass to produce significant amount of dimethylsulfoniopropionate (DMSP). It is also the largest known producer of DMSP among coastal and inter-tidal higher plants. Here, we studied (i) the weekly to seasonal variability and the depth variability of DMSP and its related compound dimethylsulfoxide (DMSO) in P. oceanica leaves of a non-disturbed meadow in Corsica, France, (ii) the weekly to seasonal variability and the depth variability of DMSP to DMSO concentration to assess the potential of the DMSP:DMSO ratio as indicator of stress, and (iii) the relationships between DMSP, DMSO, and the DMSP:DMSO ratio with potential explanatory variables such as light, temperature, photosynthetic activity (effective quantum yield of photosystem II), and leaf size. The overall average concentrations of organosulfured compounds in P. oceanica leaves were 130 ± 39 µmol.g−1 fw for DMSP and 4.9 ± 2.1 µmol.g−1 fw for DMSO. Concentrations of DMSP and DMSO in P. oceanica were overall distinctly higher and exhibited a wider range of variations than other marine primary producers such as Spartina alterniflora, phytoplankton communities, epilithic Cyanobacteria and macroalgae. Concentrations of both DMSP and DMSO in P. oceanica leaves decreased from a maximum in autumn to a minimum in summer; they changed little with depth. Potential explanatory variables except the leaf size, i.e., the leaf age were little or not related to measured concentrations. To explain the seasonal pattern of decreasing concentrations with leaf aging, we hypothesized two putative protection functions of DMSP in young leaves: antioxidant against reactive oxygen species and predator-deterrent. The similar variation of the two molecule concentrations over time and with depth suggested that DMSO content in P. oceanica leaves results from oxidation of DMSP. The DMSP:DMSO ratio remained constant around a mean value of 29.2 ± 9.0 µmol:µmol for the non-disturbed harvested meadow regardless of the time of the year, the depth or the leaf size. As suggested for the salt march plant S. alterniflora, we hypothesized the DMSP:DMSO ratio could be considered as indicator of stress in seagrasses exposed to environmental or anthropogenic stressors. More research would now be needed to confirm the functions of DMSP and DMSO in seagrasses and how the DMSP:DMSO ratio will vary under various disturbances.FCT: 57/2016, UID/Multi/04326/2019.info:eu-repo/semantics/publishedVersio

Was the last bacterial common ancestor a monoderm after all?

The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized Bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox, a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). This public toolbox is designed for researchers without a specific training in bioinformatics (launched by a single command line). Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. All the workflows are based on Singularity containers and Nextflow to increase reproducibility. The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales (Cyanobacteria). This study is published at https://doi.org/10.1093/gigascience/giad022GENER

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.

peer reviewed[en] BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales

Study of the ecology, population structure and dynamic of the macroalgae Codium elisabethae in Faial (Azores) with underwater visible imagery.

Codium elisabethae O.C. Schmidt is a dark green globose macroalgae isolating an internal sea water volume in a lumen. Codium elisabethae is endemic to the Macaronesian region and is very similar to Codium bursa C. Agardh whose distribution range spans the West-European, North-Western African and Mediterranean coasts and which was proposed as a potential indicator of coastal environmental changes based on the study of its ecology, revealing its long lifespan. Until recently, relatively little was known on Codium elisabethae as compared to the more widespread Codium bursa. To fill this gap, the present research aimed at producing an accurate description of the ecology and population dynamics of Codium elisabethae occupying the rocky shores of the Monte da Guia Special Area of Conservation (SAC)/Natura 2000 network (Faial, Azores). To achieve this, two reference sites were selected for long term monitoring: a sheltered no-go reserve exhibiting a dense Codium elisabethae population (Caldeirinhas), and a location experiencing more exposed conditions holding a sparser population (Ponta Furada). First, environmental conditions experimented by benthic organisms were extensively quantified and interpretated in regard to topographical particularities of each site. The study of reproduction dynamics showed a persistent summer fertility and an important vegetative reproduction. Important nutrient concentration ratio was found between the Codium elisabethae lumen water and surrounding sea water (mean ratios: nitrates: 5.7; ammonium: 3.4; phosphates: 3.1). In situ counting’s and size measurements revealed much higher densities of young recruits in the site of the Caldeirinhas (order of 20 ind/m²) than in the one of Ponta Furada (order of 1/m), for both summer and winter. Secondly, underwater visible imagery was exploited as an efficient and non-invasive alternative to classical in situ population estimation. Between August 2003 and November 2005, fifteen seabed photo coverages were collected by scuba-divers. Subsequent image processing consisted in mosaicing, interactive identification, and automatic change detection methods. This allowed quantifying the seasonal fluctuations of population structures (density, percentage cover and biomass) and of population dynamics (growth, recruitment, mortality and primary production). Chi-square tests of image-derived estimates and in situ measurements confirmed the validity of a centimeter precision for the estimation of population structure of individuals above 4 cm diameter. Important variability of population structure and density was observed within the sites at small spatial scales. Significant differences of population structure and dynamics parameters are demonstrated between two close-by but contrasting coastal habitats. Population density showed a sharp reduction in autumn 2003 and did not recover fully in spring and summer 2004. During the following year, population of the protected site maintained density and biomass, while at the exposed site population density dropped. In contrast with conclusions from earlier studies on the Azorian Codium elisabethae and on the Mediterranean Codium bursa, the present study revealed higher biomass (34 - 730 g dry wt.m-²), growth rates (up to 2.5 cm/month in summer) and primary production (0.53 – 11.5 g dry wt.m-².day-1), and demonstrated the seasonal fluctuations of these parameters for the studied Azorian Codium elisabethae population. The lifespan of Codium elisabethae was estimated to reach at least 7 years in the SAC of Monte da Guia based on an integration of average seasonal growth rates measured by imagery on extended population samples. This study demonstrates the high potential of registered underwater photomosaics time-series for long term surveys of macroalgae populations. This work provides also a strong framework to further developments and applicability to other species, which should be helpful to strengthen our current understanding of benthic ecosystem processes