RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton.

Zooplankton are important eukaryotic constituents of marine ecosystems characterized by limited motility in the water. These metazoans predominantly occupy intermediate trophic levels and energetically link primary producers to higher trophic levels. Through processes including diel vertical migration (DVM) and production of sinking pellets they also contribute to the biological carbon pump which regulates atmospheric CO2 levels. Despite their prominent role in marine ecosystems, and perhaps, because of their staggering diversity, much remains to be discovered about zooplankton biology. In particular, the circadian clock, which is known to affect important processes such as DVM has been characterized only in a handful of zooplankton species. We present annotated de novo assembled transcriptomes from a diverse, representative cohort of 17 marine zooplankton representing six phyla and eight classes. These transcriptomes represent the first sequencing data for a number of these species. Subsequently, using translated proteomes derived from this data, we demonstrate in silico the presence of orthologs to most core circadian clock proteins from model metazoans in all sequenced species. Our findings, bolstered by sequence searches against publicly available data, indicate that the molecular machinery underpinning endogenous circadian clocks is widespread and potentially well conserved across marine zooplankton taxa.

A simple guide to de novo transcriptome assembly and annotation.

A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only the information available in the RNA-seq reads. Subsequently, the sequences must be annotated in order to identify sequence-intrinsic and evolutionary features in them (for example, protein-coding regions). Although straightforward at first glance, de novo transcriptome assembly and annotation can quickly prove to be challenging undertakings. In addition to familiarizing themselves with the conceptual and technical intricacies of the tasks at hand and the numerous pre- and post-processing steps involved, those interested must also grapple with an overwhelmingly large choice of tools. The lack of standardized workflows, fast pace of development of new tools and techniques and paucity of authoritative literature have served to exacerbate the difficulty of the task even further. Here, we present a comprehensive overview of de novo transcriptome assembly and annotation. We discuss the procedures involved, including pre- and post-processing steps, and present a compendium of corresponding tools.

Ectomycorrhizal fungal diversity increases phosphorus uptake efficiency of European beech.

Increases in summer droughts and nitrogen (N) deposition have raised concerns of widespread biodiversity loss and nutrient imbalances, but our understanding of the ecological role of ectomycorrhizal fungal (ECMF) diversity in mediating root functions remains a major knowledge gap. We used different global change scenarios to experimentally alter the composition of ECMF communities colonizing European beech saplings and examined the consequences for phosphorus (P) uptake (H333 PO4 feeding experiment) and use efficiencies of trees. Specifically, we simulated increases in temperature and N deposition and decreases in soil moisture and P availability in a factorial experiment. Here, we show that ECMF α diversity is a major factor contributing to root functioning under global change. P uptake efficiency of beech significantly increased with increasing ECMF species richness and diversity, as well as with decreasing P availability. As a consequence of decreases in ECMF diversity, P uptake efficiency decreased when soil moisture was limiting. By contrast, P use efficiencies were a direct (negative) function of P availability and not of ECMF diversity. We conclude that increasing summer droughts may reduce ECMF diversity and the complementarity of P uptake by ECMF species, which will add to negative growth effects expected from nutrient imbalances under global change.