Structural equation modelling reveals plant-community drivers of carbon storage in boreal forest ecosystems

Boreal forest ecosystems are important drivers of the global carbon (C) cycle by acting as both sinks and sources of atmospheric CO₂. While several factors have been proposed as determining the ability of boreal forest to function as C sinks, little is known about their relative importance. In this study, we applied structural equation modelling to a previously published dataset involving 30 boreal-forested islands that vary greatly in their historic fire regime, in order to explore the simultaneous influence of several factors believed to be important in influencing above-ground, below-ground and total ecosystem C accumulation. We found that wildfire was a major driver of ecosystem C sequestration, and exerted direct effects on below-ground C storage (presumably through humus combustion) and indirect effects on both above-ground and below-ground C storage through altering plant-community composition. By contrast, plant diversity influenced only below-ground C storage (and even then only weakly), while net primary productivity and decomposition had no detectable effect. Our results suggest that while boreal forests have great potential for storing significant amounts of C, traits of dominant plant species that promote below-ground C accumulation and the absence of wildfire are the most important drivers of C sequestration in these ecosystems.     

Muskoxen Modify Plant Abundance,Phenology, and Nitrogen Dynamics in a High Arctic Fen

Ecosystems - Herbivores are key drivers of vegetation dynamics in most ecosystems. However, the effect of high arctic herbivores on vegetation dynamics throughout a growing season is not well...     

Autophagy–virus interplay in plants: from antiviral recognition to proviral manipulation

Autophagy is a conserved self-cleaning and renewal system required for cellular homeostasis and stress tolerance. Autophagic processes are also implicated in the response to ‘non-self’ such as viral pathogens, yet the functions and mechanisms of autophagy during plant virus infection have only recently started to be revealed. Compelling evidence now indicates that autophagy is an integral part of antiviral immunity in plants. It can promote the hypersensitive cell death response upon incompatible viral infections or mediate the selective elimination of entire particles and individual proteins from compatible viruses in a pathway similar to xenophagy in animals. Several viruses, however, have evolved measures to antagonize xenophagic degradation or utilize autophagy to suppress disease-associated cell death and other defence pathways like RNA silencing. Here, we highlight the current advances and gaps in our understanding of the complex autophagy–virus interplay and its consequences for host immunity and viral pathogenesis in plants.     

Resilience of ecosystem processes: a new approach shows that functional redundancy of biological control services is reduced by landscape simplification

Functional redundancy can increase the resilience of ecosystem processes by providing insurance against species loss and the effects of abundance fluctuations. However, due to the difficulty of assessing individual species’ contributions and the lack of a metric allowing for a quantification of redundancy within communities, few attempts have been made to estimate redundancy for individual ecosystem processes. We present a new method linking interaction metrics with metabolic theory that allows for a quantification of redundancy at the level of ecosystem processes. Using this approach, redundancy in the predation on aphids and other prey by natural enemies across a landscape heterogeneity gradient was estimated. Functional redundancy of predators was high in heterogeneous landscapes, low in homogeneous landscapes and scaled with predator specialisation. Our approach allows quantifying functional redundancy within communities and can be used to assess the role of functional redundancy across a wide variety of ecosystem processes and environmental factors.     

New mitochondrial primers for metabarcoding of insects,designed and evaluated using in silico methods

Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime ) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.     

MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements

In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome‐scale studies to characterize both model and non‐model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome‐wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site‐associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms—enabling the exploration of diverse evolutionary and conservation questions.     

BiP Inducer X: An ER Stress Inhibitor for Enhancing Recombinant Antibody Production in CHO Cell Culture

Prolonged endoplasmic reticulum (ER) stress reduces protein synthesis and induces apoptosis in mammalian cells. When dimethyl sulfoxide (DMSO), a specific monoclonal antibody productivity (q_mAb)‐enhancing reagent, is added to recombinant Chinese hamster ovary (rCHO) cell cultures (GSR cell line), it induces ER stress and apoptosis in a dose‐dependent manner. To determine an effective ER stress inhibitor, three ER stress inhibitors (BiP inducer X [BIX], tauroursodeoxycholic acid, and carbazole) are examined and BIX shows the best production performance. Coaddition of BIX (50 μm ) with DMSO extends the culture longevity and enhances q_mAb. As a result, the maximum mAb concentration is significantly increased with improved galactosylation. Coaddition of BIX significantly increases the expression level of binding immunoglobulin protein (BiP) followed by increased expression of chaperones (calnexin and GRP94) and galactosyltransferase. Furthermore, the expression levels of CHOP, a well‐known ER stress marker, and cleaved caspase‐3 are significantly reduced, suggesting that BIX addition reduces ER stress‐induced cell death by relieving ER stress. The beneficial effect of BIX on mAb production is also demonstrated with another q_mAb‐enhancing reagent (sodium butyrate) and a different rCHO cell line (CS13‐1.00). Taken together, BIX is an effective ER stress inhibitor that can be used to increase mAb production in rCHO cells.     

Quantifying long‐term recurrence in planktonic microbial eukaryotes

How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long‐term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV‐III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long‐term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non‐recurrent changes characterize the dynamics of microbial assemblages.     

A Framework for Development and Communication of Absolute Environmental Sustainability Assessment Methods

An absolute environmental sustainability assessment (AESA) addresses whether a production or consumption activity can be considered environmentally sustainable in an absolute sense. This involves a comparison of its environmental pressure to its allocated environmental carrying capacity. AESA methods have been developed in multiple academic fields, each using their own set of concepts and terms with little communication across the fields. A recent growing interest in using AESA methods for decision support calls for a better common understanding of the constituents of an AESA method and how it can be communicated to scientific peers and to potential users. With this aim, we develop a framework for AESA methods, composed of a succession of four assessment steps and involving six methodological choices that must be made by the method developer or the user. We then use the framework to analyze and compare five selected AESA methods that focus on the release of phosphorus and nitrogen to the environment. In this manner, we show that the framework is able to systematically differentiate AESA methods that initially appear to be similar. Intended users of the framework include (1) method developers communicating new AESA methods to academic peers or potential method users and (2) researchers comparing a group of existing AESA methods and communicating their differences to their peers and to potential users looking for guidance on method selection.     

Quality Assessment and Circularity Potential of Recovery Systems for Household Plastic Waste

Plastic recycling is promoted in the transition toward a circular economy and a closed plastic loop, typically using mass‐based recycling targets. Plastic from household waste (HHW) is contaminated and heterogeneous, and recycled plastic from HHW often has a limited application range, due to reduced quality. To correctly assess the ability to close plastic loops via recycling, both plastic quantities and qualities need to be evaluated. This study defines a circularity potential representing the ability of a recovery system to close material loops assuming steady‐state market conditions. Based on an average plastic waste composition including impurities, 84 recovery scenarios representing a wide range of sorting schemes, source‐separation efficiencies, and material recovery facility (MRF) configurations and performances were assessed. The qualities of the recovered fractions were assessed based on contamination and the circularity potential calculated for each scenario in a European context. Across all scenarios, 17% to 100% of the generated plastic mass could be recovered, with higher source‐separation and MRF efficiencies leading to higher recovery. Including quality, however, at best 55% of the generated plastic was suitable for recycling due to contamination. Source‐separation, a high number of target fractions, and efficient MRF recovery were found to be critical. The circularity potential illustrated that less than 42% of the plastic loop can be closed with current technology and raw material demands. Hence, Europe is still far from able to close the plastic loop. When transitioning toward a circular economy, the focus should be on limiting impurities and losses through product design, technology improvement, and more targeted plastic waste management.