Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

Mangot, Jean-François et al.-- 12 pages, 7 figures, 2 tables, supplementary information https://dx.doi.org/10.1038/srep41498Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questionsThis work was supported by the US NSF grants DEB-1031049 and OCE-821374 (to M.E.S.), by the ANR French projects Oceanomics (ANR-11-BTBR-0008, to C.V.), France Génomique (ANR-10-INBS-09, to P.W.), and Prometheus (ANR-09-PCS-GENM_217, to O.J.), by the EU project SINGEK (H2020-MSCA-ITN-2015-675752, to R.M.), and by the Spanish project MEFISTO (CTM2013-43767-P, MINECO). J.-F.M. was supported by a Marie Curie Intra-European Fellowship (PIEF-GA-2012-331190, EU). R.L. was supported by Juan de la Cierva (JCI-2010-06594, MINECO) and Ramón y Cajal fellowships (RYC-2013-12554, MINECO)Peer Reviewe

Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity

International audienceRecent advances in next-generation sequencing (NGS) technologies spur progress in determining the microbial diversity in various ecosystems by highlighting, for example, the rare biosphere. Currently, high-throughput pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used to characterize bacterial and archaeal communities, and rarely to characterize protist communities. In addition, although taxonomic assessment through phylogeny is considered as the most robust approach, similarity and probabilistic approaches remain the most commonly used for taxonomic affiliation. In a first part of this work, a tree-based method was compared with different approaches of taxonomic affiliation (BLAST and RDP) of 18S rRNA gene sequences and was shown to be the most accurate for near full-length sequences and for 400 bp amplicons, with the exception of amplicons covering the V5-V6 region. Secondly, the applicability of this method was tested by running a full scale test using an original pyrosequencing dataset of 18S rRNA genes of small lacustrine protists (0.2-5 mm) from eight freshwater ecosystems. Our results revealed that i) fewer than 5% of the operational taxonomic units (OTUs) identified through clustering and phylogenetic affiliation had been previously detected in lakes, based on comparison to sequence in public databases; ii) the sequencing depth provided by the NGS coupled with a phylogenetic approach allowed to shed light on clades of freshwater protists rarely or never detected with classical molecular ecology approaches; and iii) phylogenetic methods are more robust in describing the structuring of under-studied or highly divergent populations. More precisely, new putative clades belonging to Mamiellophyceae, Foraminifera, Dictyochophyceae and Euglenida were detected. Beyond the study of protists, these results illustrate that the tree-based approach for NGS based diversity characterization allows an in-depth description of microbial communities including taxonomic profiling, community structuring and the description of clades of any microorganisms (protists, Bacteria and Archaea)

Disruptive life events and health:longitudinal evidence from a large cohort in the Netherlands

Events that happen in individuals’ lives can have far-reaching consequences in many different life domains, for instance on one’s health and health behaviours. Some events, such as finding a partner or having a child, are usually perceived as “positive” by those who experience them, and can have a positive effect on health. Yet, other “disruptive” or stressful events -for instance the death of a partner or losing your job- may lead to poorer health, and/or increase unhealthy behaviours, such as alcohol abuse, to cope with stress. Moreover, this may be true for individual events, such as unemployment, which affect specific individuals (and those around them), but also for collective events that affect millions of people, like the Covid-19 pandemic did. We used a large sample of individuals from the northern provinces of the Netherlands to study the impact of unemployment and the Covid-19 pandemic on health. Results show that individuals who were unemployed for more than a few months, or several times, had higher risk of abusing alcohol (binge drinking). Regarding the Covid-19 pandemic, depression and anxiety symptoms clearly increased in the population during the preventive lockdowns, and the negative effect accumulated over time. In fact, those who experienced several disruptive events (for instance, having precarious working conditions as well as having previous mental health issues), suffered the most negative impact in terms of mental and physical health

The association between unemployment trajectories and alcohol consumption patterns. Evidence from a large prospective cohort in The Netherlands

Unemployment is expected to influence alcohol consumption, but studies show mixed results, partly because most studies concentrate on current employment status. However, unemployment could be particularly consequential if it is part of a trajectory of employment precariousness. Moreover, the association between unemployment and alcohol consumption may not be homogeneous across the population, but differ by subgroups (e.g. socioeconomic status). This study longitudinally analyses the association between different employment trajectories and alcohol consumption, and examines if the association is moderated by socioeconomic status (SES), partner status, age and gender. Four waves of data of the Lifelines Cohort study are used. Sample consists of individuals from 18-50 years old, active in the labor market (n = 104,766) from the northern provinces of the Netherlands. Employment trajectories are defined by employment status in each wave, duration of unemployment, and number of exposures to unemployment. Drinking patterns are divided into "abstainers", "moderate drinking" (1.5 drinks/day) and "binge drinking" (>5 drinks/occasion; 4 for women). The associations are estimated with multinomial logistic regression models. Results show that recent, long-term unemployment (> 6 months) is associated with higher rates of heavy drinking (RRR = 1.26 [95 % CI 1.03-1.54]), whereas short-term unemployment does not show any association with the outcome. Being continuously unemployed throughout the observation period shows a strong association with binge drinking (RRR = 1.43 [95 % CI 1.06-1.93]), as well as reporting 2 or more long unemployment spells (RRR = 1.49 [95 % CI 1.21-1.83]). The group of abstainers (77.95 % women) have significantly lower SES, and poorer health than their peers. For some individuals, recent unemployment increases the likelihood for abstinence (RRR = 1.23 [95 % CI 1.00-1.51]). Evidence suggests that length of unemployment is key in order to grasp its effects in terms of changing drinking patterns