Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.     

Covariations between pupil diameter and supplementary eye field activity suggest a role in cognitive effort implementation

In both human and nonhuman primates (NHP), the medial prefrontal region, defined as the supplementary eye field (SEF), can indirectly influence behavior selection through modulation of the primary selection process in the oculomotor structures. To perform this oculomotor control, SEF integrates multiple cognitive signals such as attention, memory, reward, and error. As changes in pupil responses can assess these cognitive efforts, a better understanding of the precise dynamics by which pupil diameter and medial prefrontal cortex activity interact requires thorough investigations before, during, and after changes in pupil diameter. We tested whether SEF activity is related to pupil dynamics during a mixed pro/antisaccade oculomotor task in 2 macaque monkeys. We used functional ultrasound (fUS) imaging to examine temporal changes in brain activity at the 0.1-s time scale and 0.1-mm spatial resolution concerning behavioral performance and pupil dynamics. By combining the pupil signals and real-time imaging of NHP during cognitive tasks, we were able to infer localized cerebral blood volume (CBV) responses within a restricted part of the dorsomedial prefrontal cortex, referred to as the SEF, an area in which antisaccade preparation activity is also recorded. Inversely, SEF neurovascular activity measured by fUS imaging was found to be a robust predictor of specific variations in pupil diameter over short and long-time scales. Furthermore, we directly manipulated pupil diameter and CBV in the SEF using reward modulations. These results bring a novel understanding of the physiological links between pupil and SEF, but it also raises questions about the role of anterior cingulate cortex (ACC), as CBV variations in the ACC seems to be negligible compared to CBV variations in the SEF.

Ultrafast functional imaging reveals short- and long-term covariations between pupil diameter and activity in the Supplementary Eye Field (SEF) of awake behaving non-human primates, yielding a novel understanding of the physiological links between the pupil and SEF.     

Male sex chromosomal complement exacerbates the pathogenicity of Th17 cells in a chronic model of central nervous system autoimmunity

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Rewired phenolic metabolism and improved saccharification efficiency of a Zea mays cinnamyl alcohol dehydrogenase 2 (zmcad2) mutant

Lignocellulosic biomass is an abundant byproduct from cereal crops that can potentially be valorized as a feedstock to produce biomaterials. Zea mays CINNAMYL ALCOHOL DEHYDROGENASE 2 (ZmCAD2) is involved in lignification, and is a promising target to improve the cellulose-to-glucose conversion of maize stover. Here, we analyzed a field-grown zmcad2 Mutator transposon insertional mutant. Zmcad2 mutant plants had an 18% lower Klason lignin content, whereas their cellulose content was similar to that of control lines. The lignin in zmcad2 mutants contained increased levels of hydroxycinnamaldehydes, i.e. the substrates of ZmCAD2, ferulic acid and tricin. Ferulates decorating hemicelluloses were not altered. Phenolic profiling further revealed that hydroxycinnamaldehydes are partly converted into (dihydro)ferulic acid and sinapic acid and their derivatives in zmcad2 mutants. Syringyl lactic acid hexoside, a metabolic sink in CAD-deficient dicot trees, appeared not to be a sink in zmcad2 maize. The enzymatic cellulose-to-glucose conversion efficiency was determined after 10 different thermochemical pre-treatments. Zmcad2 yielded significantly higher conversions compared with controls for almost every pre-treatment. However, the relative increase in glucose yields after alkaline pre-treatment was not higher than the relative increase when no pre-treatment was applied, suggesting that the positive effect of the incorporation of hydroxycinnamaldehydes was leveled off by the negative effect of reduced p-coumarate levels in the cell wall. Taken together, our results reveal how phenolic metabolism is affected in CAD-deficient maize, and further support mutating CAD genes in cereal crops as a promising strategy to improve lignocellulosic biomass for sugar-platform biorefineries.     

The Diversity and Functions of Choline Sulphatases in Microorganisms

Choline sulphates have two putative roles in microorganisms: as a reservoir of C, N and S and as osmoprotectants. Although there is no established connection to date regarding the relative distribution of these two functions in microbial communities, this information is crucial in determining the role of choline sulphate in soils, particularly in cultivated soils where S is limiting. Therefore, in order to establish such a connection, the diversity of choline sulphatase (betC) genes was investigated in this study using numerous fully sequenced microbes available in GenBank. Our genomic analyses revealed unequivocally that the betICBA operon is restricted to Rhizobiaceae family members, which live under symbiotic conditions that prevent elemental depletion. Together with the uniform genetic organisation of the betICBA operon in Rhizobiaceae, BetC appears to be both utilised for osmoprotection or S replenishment. In contrast, betC in a wide variety of free-living microbes (including fungi, archaea and bacteria) was found in a cassette encoding only BetC and a choline sulphate transporter, a configuration that appears to be responsible for fulfilling elemental S requirements. Lastly, the relatively high number of BetC sequences available allowed the identification of a specific signature sequence that discriminates between these two functions and also globally defines some conserved motifs in microbial choline sulphatases. Due to the widespread presence of BetC in microbes and the wide repartition of the betC cassette system, the potential importance of choline sulphatase in global S recycling requires further clarification.     

ENVIRONMENTAL VISCOSITY DOES NOT AFFECT THE EVOLUTION OF COOPERATION DURING EXPERIMENTAL EVOLUTION OF COLICIGENIC BACTERIA

Cooperation should be favored under environmental conditions allowing the preferential interaction of cooperators among themselves and limiting interactions with defectors. Bacteria cooperating to kill competitors by secreting a toxin evolved during several hundred generations in two environments: a viscous environment that should promote cooperator assortment, and a nonviscous environment that should not allow such preferential interaction. A quantitative decrease in cooperation was observed in all populations, but as expected, cooperation was maintained at a higher level in the viscous environment. Mutants that are resistant against but not producing the toxin were identified at a low frequency in a few populations from the viscous environment and at a high frequency in all the populations from the nonviscous environment. The underlying mutations were identified. Relative fitness of the cooperator and mutant genotypes were obtained with bacteria that were isogenic, except for the identified mutations. Competition experiments indicated that cooperation is not favored by environmental viscosity as imposed in our system and suggested that when it comes to cooperation, environmental viscosity should be considered not only in terms of individual movement, but also in terms of the distribution of the public good.     

Differential Influence of Life Cycle on Growth and Toxin Production of three Pseudo‐nitzschia Species (Bacillariophyceae)

We used a multistrain approach to study the intra‐ and interspecific variability of the growth rates of three Pseudo‐nitzschia species – P. australis, P. fraudulenta, and P. pungens – and of their domoic acid (DA) production. We carried out mating and batch experiments to investigate the respective effects of strain age and cell size, and thus the influence of their life cycle on the physiology of these species. The cell size – life cycle relationship was characteristic of each species. The influence of age and cell size on the intraspecific variability of growth rates suggests that these characteristics should be considered cautiously for the strains used in physiological studies on Pseudo‐nitzschia species. The results from all three species do not support the hypothesis of a decrease in DA production with time since isolation from natural populations. In P. australis, the cellular DA content was rather a function of cell size. More particularly, cells at the gametangia stage of their life cycle contained up to six times more DA than smaller or larger cells incapable of sexual reproduction. These findings reveal a link between P. australis life cycle and cell toxicity. This suggest that life cycle dynamics in Pseudo‐nitzschia natural populations may influence bloom toxicity.