Ecogenomics of the SAR11 clade Haro‐Moreno, Jose M.; Rodriguez‐Valera, Francisco; Rosselli, Riccardo ...
Environmental microbiology,
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Summary
Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenome‐assembled genomes. This fact has hampered our knowledge about their ecology and genetic ...diversity. Here we examined 175 SAR11 genomes, including 47 new single‐amplified genomes. The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic data sets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilization was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades.
Researchers working in the field of ecosystem services (ES) have long acknowledged the importance of recognising multiple values in ecosystems and biodiversity. Yet the operationalisation of value ...pluralism in ES assessments remains largely elusive. The aim of this research is to present
a taxonomy of values and valuation methods to widen the evaluative space for ES. First, we present our preanalytic positions in regards to the values and valuation of ES. Second, we review different value definitions that we deem relevant for the discussion of ES valuation. Third, we propose
a taxonomy of ES values based on different conceptions of human-nature relationships. Finally, we present a taxonomy of different methods that can be used to recognise plural values in ES. This taxonomy for a plural valuation can help ES scientists and practitioners with their aim of representing
people's multiple and context-specific ways of valuing nature. The taxonomy can also serve to pay broader attention to ES values that are overlooked or misrepresented in assessments that restrict their focus to monetary valuations.
In this paper we study Algorithmic High-Frequency Financial Markets as dynamical networks. After an individual analysis of 24 stocks of the US market during a trading year of fully automated ...transactions by means of ordinal pattern series, we define an information-theoretic measure of pairwise synchronization for time series which allows us to study this subset of the US market as a dynamical network. We apply to the resulting network a couple of clustering algorithms in order to detect collective market states, characterized by their degree of centralized or decentralized synchronicity. This collective analysis has shown to reproduce, classify and explain the anomalous behavior previously observed at the individual level. We also find two whole coherent seasons of highly centralized and decentralized synchronicity, respectively. Finally, we model these states dynamics through a simple Markov model.
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•We study non-linear coupling and emergent collective behavior in automated markets.•An information-theoretic measure of pairwise ordinal synchronization is proposed.•A couple of clustering algorithms to detect a set of daily market states is applied.•We detect two seasons of the trading year, given by their degree of centralization.•A simple Markov model is proposed to model these states dynamics.
Aedes aegypti mosquito-borne viruses including Zika (ZIKV), dengue (DENV), yellow fever (YFV), and chikungunya (CHIKV) have emerged and re-emerged globally, resulting in an elevated burden of human ...disease. Aedes aegypti is found worldwide in tropical, sub-tropical, and temperate areas. The characterization of mosquito blood meals is essential to understand the transmission dynamics of mosquito-vectored pathogens.
Here, we report Ae. aegypti and Culex quinquefasciatus host feeding patterns and arbovirus transmission in Northern Mexico using a metabarcoding-like approach with next-generation deep sequencing technology. A total of 145 Ae. aegypti yielded a blood meal analysis result with 107 (73.8%) for a single vertebrate species and 38 (26.2%) for two or more. Among the single host blood meals for Ae. aegypti, 28.0% were from humans, 54.2% from dogs, 16.8% from cats, and 1.0% from tortoises. Among those with more than one species present, 65.9% were from humans and dogs. For Cx. quinquefasciatus, 388 individuals yielded information with 326 (84%) being from a single host and 63 (16.2%) being from two or more hosts. Of the single species blood meals, 77.9% were from dogs, 6.1% from chickens, 3.1% from house sparrows, 2.4% from humans, while the remaining 10.5% derived from other 12 host species. Among those which had fed on more than one species, 11% were from dogs and humans, and 89% of other host species combinations. Forage ratio analysis revealed dog as the most over-utilized host by Ae. aegypti (= 4.3) and Cx. quinquefasciatus (= 5.6) and the human blood index at 39% and 4%, respectively. A total of 2,941 host-seeking female Ae. aegypti and 3,536 Cx. quinquefasciatus mosquitoes were collected in the surveyed area. Of these, 118 Ae. aegypti pools and 37 Cx. quinquefasciatus pools were screened for seven arboviruses (ZIKV, DENV 1-4, CHIKV, and West Nile virus (WNV)) using qRT-PCR and none were positive (point prevalence = 0%). The 95%-exact upper limit confidence interval was 0.07% and 0.17% for Ae. aegypti and Cx. quinquefasciatus, respectively.
The low human blood feeding rate in Ae. aegypti, high rate of feeding on mammals by Cx. quinquefasciatus, and the potential risk to transmission dynamics of arboviruses in highly urbanized areas of Northern Mexico is discussed.
The fungus Penicillium digitatum, the causal agent of green mould rot, is the most destructive post‐harvest pathogen of citrus fruit in Mediterranean regions. In order to identify P. digitatum genes ...up‐regulated during the infection of oranges that may constitute putative virulence factors, we followed a polymerase chain reaction (PCR)‐based suppression subtractive hybridization and cDNA macroarray hybridization approach. The origin of expressed sequence tags (ESTs) was determined by comparison against the available genome sequences of both organisms. Genes coding for fungal proteases and plant cell wall‐degrading enzymes represent the largest categories in the subtracted cDNA library. Northern blot analysis of a selection of P. digitatum genes, including those coding for proteases, cell wall‐related enzymes, redox homoeostasis and detoxification processes, confirmed their up‐regulation at varying time points during the infection process. Agrobacterium tumefaciens‐mediated transformation was used to generate knockout mutants for two genes encoding a pectin lyase (Pnl1) and a naphthalene dioxygenase (Ndo1). Two independent P. digitatum Δndo1 mutants were as virulent as the wild‐type. However, the two Δpnl1 mutants analysed were less virulent than the parental strain or an ectopic transformant. Together, these results provide a significant advance in our understanding of the putative determinants of the virulence mechanisms of P. digitatum.
Mechanochemistry, that is, the use of mechanical energy produced by milling or grinding to perform chemical transformations, was used as a green strategy using a minimal amount of solvent for the ...preparation of highly valuable formyl functionalized BODIPY dyes. The electronic properties of the meso‐aryl group play a key role in the fluorescence response of the adducts resulting from the Ugi reaction. Such an understanding of the molecular structure‐fluorescence interplay explains the brightness of these dyes in the cellular media monitored by fluorescence imaging. In the present report, we provide flow cytometry and fluorescence microscopy evidence that the novel dyes efficiently stain peripheral blood mononuclear cells (PBMCs) and Candida albicans cells without disturbing cell integrity. Moreover, it is demonstrated that by staining C. albicans cells, we can monitor the early and late steps of phagocytosis, using human monocyte‐derived macrophages. The dye series presented herein represent a novel application for formyl functionalized BODIPYs, expanding their applications in monitoring biological processes.
Mechanochemistry enables a clean, sustainable and ready access to multicomponent reaction (Ugi) adducts based on BODIPY dyes as fluorescent label. Their fluorescence response depends on the conformational freedom around the key meso position. These functionalized dyes behave as fluorescent probes, being able to stain efficiently Candida albican cells, as well as visualize phagocytosis in its early and late steps.
SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient's ...nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group.
Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as
were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.
Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.
Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on ...Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.
Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish ...pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99-100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture.
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