TY - JOUR A1 - Patterson, Jenelle A. A1 - He, Hai A1 - Folz, Jacob S. A1 - Li, Qiang A1 - Wilson, Mark A. A1 - Fiehn, Oliver A1 - Bruner, Steven D. A1 - Bar-Even, Arren A1 - Hanson, Andrew D. T1 - Thioproline formation as a driver of formaldehyde toxicity in Escherichia coli JF - Biochemical Journal N2 - Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate. KW - formaldehyde KW - thiazolidine-4-carboxylic acid KW - thioproline KW - Xaa-Pro aminopeptidase Y1 - 2020 U6 - https://doi.org/10.1042/BCJ20200198 SN - 1470-8728 SN - 0006-2936 VL - 477 IS - 9 SP - 1745 EP - 1757 PB - Portland Press CY - London ER - TY - JOUR A1 - Dennis, Alice B. A1 - Ballesteros, Gabriel I. A1 - Robin, Stéphanie A1 - Schrader, Lukas A1 - Bast, Jens A1 - Berghöfer, Jan A1 - Beukeboom, Leo W. A1 - Belghazi, Maya A1 - Bretaudeau, Anthony A1 - Buellesbach, Jan A1 - Cash, Elizabeth A1 - Colinet, Dominique A1 - Dumas, Zoé A1 - Errbii, Mohammed A1 - Falabella, Patrizia A1 - Gatti, Jean-Luc A1 - Geuverink, Elzemiek A1 - Gibson, Joshua D. A1 - Hertaeg, Corinne A1 - Hartmann, Stefanie A1 - Jacquin-Joly, Emmanuelle A1 - Lammers, Mark A1 - Lavandero, Blas I. A1 - Lindenbaum, Ina A1 - Massardier-Galata, Lauriane A1 - Meslin, Camille A1 - Montagné, Nicolas A1 - Pak, Nina A1 - Poirié, Marylène A1 - Salvia, Rosanna A1 - Smith, Chris R. A1 - Tagu, Denis A1 - Tares, Sophie A1 - Vogel, Heiko A1 - Schwander, Tanja A1 - Simon, Jean-Christophe A1 - Figueroa, Christian C. A1 - Vorburger, Christoph A1 - Legeai, Fabrice A1 - Gadau, Jürgen T1 - Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum JF - BMC Genomics N2 - Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org. KW - Parasitoid wasp KW - Aphid host KW - Aphidius ervi KW - Lysiphlebus fabarum KW - de novo genome assembly KW - DNA methylation loss KW - Chemosensory genes KW - Venom proteins KW - GC content KW - Toll and Imd pathways Y1 - 2020 U6 - https://doi.org/10.1186/s12864-020-6764-0 SN - 1471-2164 VL - 21 PB - BioMed Central CY - London ER - TY - JOUR A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Henneberger, Kirstin A1 - Fickel, Jörns A1 - Hofreiter, Michael A1 - Foerste, Daniel W. G. T1 - Ancestral mitogenome capture of the Southeast Asian banded linsang JF - PLoS ONE N2 - Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives. KW - Shotgun sequencing KW - Mitochondria KW - Phylogenetics KW - Phylogenetic analysis KW - Paleogenetics KW - Sequence alignment KW - Genomics KW - Museum collections Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0234385 SN - 1932-6203 VL - 15 IS - 6 PB - PLOS CY - San Francisco, California, US ER - TY - JOUR A1 - Bolius, Sarah A1 - Karoline Morling, A1 - Wiedner, Claudia A1 - Weithoff, Guntram T1 - Genetic Identity and Herbivory Drive the Invasion of a Common Aquatic Microbial Invader JF - Frontiers in Microbiology N2 - Despite the increasing number of species invasions, the factors driving invasiveness are still under debate. This is particularly the case for “invisible” invasions by aquatic microbial species. Since in many cases only a few individuals or propagules enter a new habitat, their genetic variation is low and might limit their invasion success, known as the genetic bottleneck. Thus, a key question is, how genetic identity and diversity of invading species influences their invasion success and, subsequently, affect the resident community. We conducted invader-addition experiments using genetically different strains of the globally invasive, aquatic cyanobacterium Raphidiopsis raciborskii (formerly: Cylindrospermopsis raciborskii) to determine the role of invader identity and genetic diversity (strain richness) at four levels of herbivory. We tested the invasion success of solitary single strain invasions against the invader genetic diversity, which was experimentally increased up to ten strains (multi-strain populations). By using amplicon sequencing we determined the strain-specific invasion success in the multi-strain treatments and compared those with the success of these strains in the single-strain treatments. Furthermore, we tested for the invasion success under different herbivore pressures. We showed that high grazing pressure by a generalist herbivore prevented invasion, whereas a specialist herbivore enabled coexistence of consumer and invader. We found a weak effect of diversity on invasion success only under highly competitive conditions. When invasions were successful, the magnitude of this success was strain-specific and consistent among invasions performed with single-strain or multi-strain populations. A strain-specific effect was also observed on the resident phytoplankton community composition, highlighting the strong role of invader genetic identity. Our results point to a strong effect of the genetic identity on the invasion success under low predation pressure. The genetic diversity of the invader population, however, had little effect on invasion success in our study, in contrast to most previous findings. Instead, it is the interaction between the consumer abundance and type together with the strain identity of the invader that defined invasion success. This study underlines the importance of strain choice in invasion research and in ecological studies in general. KW - alien species KW - genotype KW - invasibility KW - cyanobacteria KW - consumptive resistance KW - phytoplankton KW - Raphidiopsis KW - genetic diversity Y1 - 2019 U6 - https://doi.org/10.3389/fmicb.2020.01598 SN - 1664-302X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Gubelit, Yulia I. A1 - Grossart, Hans-Peter T1 - New Methods, New Concepts BT - What Can Be Applied to Freshwater Periphyton? JF - Frontiers in Microbiology N2 - Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the “Black Queen Hypothesis”) derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems. KW - freshwater KW - lake periphyton KW - microbial interactions KW - Black Queen Hypothesis KW - OMICs tools Y1 - 2020 U6 - https://doi.org/10.3389/fmicb.2020.01275 SN - 1664-302X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Stiegler, Jonas A1 - von Hoermann, Christian A1 - Müller, Jörg A1 - Benbow, Mark Eric A1 - Heurich, Marco T1 - Carcass provisioning for scavenger conservation in a temperate forest ecosystem JF - Ecosphere N2 - Carrion plays an essential role in shaping the structure and functioning of ecosystems and has far‐reaching implications for biodiversity conservation. The change in availability and type of carcasses throughout ecosystems can involve negative effects for scavenging communities. To address this issue, there have been recent conservation management measures of carrion provision in natural systems. However, the optimal conditions under which exposing carcasses to optimize conservation outcomes are still limited. Here, we used camera traps throughout elevational and vegetational gradients to monitor the consumption of 48 deer carcasses over a study period of six years by evaluating 270,279 photographs resulting out of 15,373 trap nights. We detected 17 species visiting carcass deployments, including five endangered species. Our results show that large carcasses, the winter season, and a heterogeneous surrounding habitat enhanced the frequency of carcass visits and the species richness of scavenger assemblages. Contrary to our expectations, carcass species, condition (fresh/frozen), and provision schedule (continuous vs single exposure) did not influence scavenging frequency or diversity. The carcass visitation frequency increased with carcass mass and lower temperatures. The effect of large carcasses was especially pronounced for mesopredators and the Eurasian lynx (Lynx lynx ). Lynx were not too influenced in its carrion acquisition by the season, but exclusively preferred remote habitats containing higher forest cover. Birds of prey, mesopredators, and top predators were also positively influenced by the visiting rate of ravens (Corvus corax ), whereas no biotic or abiotic preferences were found for wild boars (Sus scrofa ). This study provides evidence that any ungulate species of carrion, either in a fresh or in previously frozen condition, attracts a high diversity of scavengers especially during winter, thereby supporting earlier work that carcass provisions may support scavenger communities and endangered species. KW - anthropogenic food subsidies KW - carrion ecology KW - diversity KW - nature conservation KW - necrobiome KW - vertebrate scavenger KW - wildlife management Y1 - 2020 U6 - https://doi.org/10.1002/ecs2.3063 SN - 2150-8925 VL - 11 IS - 4 PB - ESA CY - Ithaca, NY ER - TY - JOUR A1 - Reeg, Jette A1 - Heine, Simon A1 - Mihan, Christine A1 - McGee, Sean A1 - Preuss, Thomas G. A1 - Jeltsch, Florian T1 - A graphical user interface for the plant community model IBC-grass JF - Plos One N2 - Plants located adjacent to agricultural fields are important for maintaining biodiversity in semi-natural landscapes. To avoid undesired impacts on these plants due to herbicide application on the arable fields, regulatory risk assessments are conducted prior to registration to ensure proposed uses of plant protection products do not present an unacceptable risk. The current risk assessment approach for these non-target terrestrial plants (NTTPs) examines impacts at the individual-level as a surrogate approach for protecting the plant community due to the inherent difficulties of directly assessing population or community level impacts. However, modelling approaches are suitable higher tier tools to upscale individual-level effects to community level. IBC-grass is a sophisticated plant community model, which has already been applied in several studies. However, as it is a console application software, it was not deemed sufficiently user-friendly for risk managers and assessors to be conveniently operated without prior expertise in ecological models. Here, we present a user-friendly and open source graphical user interface (GUI) for the application of IBC-grass in regulatory herbicide risk assessment. It facilitates the use of the plant community model for predicting long-term impacts of herbicide applications on NTTP communities. The GUI offers two options to integrate herbicide impacts: (1) dose responses based on current standard experiments (acc. to testing guidelines) and (2) based on specific effect intensities. Both options represent suitable higher tier options for future risk assessments of NTTPs as well as for research on the ecological relevance of effects. Y1 - 2020 U6 - https://doi.org/10.1371/journal.pone.0230012 SN - 1932-6203 VL - 15 IS - 3 PB - Plos 1 CY - San Francisco ER -