Distinct respiratory responses of soils to complex organic substrate are governed predominantly by soil architecture and its microbial community

Factors governing the turnover of organic matter (OM) added to soils, including substrate quality, climate, environment and biology, are well known, but their relative importance has been difficult to ascertain due to the interconnected nature of the soil system. This has made their inclusion in mechanistic models of OM turnover or nutrient cycling difficult despite the potential power of these models to unravel complex interactions. Using high temporal-resolution respirometery (6 min measurement intervals), we monitored the respiratory response of 67 soils sampled from across England and Wales over a 5 day period following the addition of a complex organic substrate (green barley powder). Four respiratory response archetypes were observed, characterised by different rates of respiration as well as different time-dependent patterns. We also found that it was possible to predict, with 95% accuracy, which type of respiratory behaviour a soil would exhibit based on certain physical and chemical soil properties combined with the size and phenotypic structure of the microbial community. Bulk density, microbial biomass carbon, water holding capacity and microbial community phenotype were identified as the four most important factors in predicting the soils’ respiratory responses using a Bayesian belief network. These results show that the size and constitution of the microbial community are as important as physico-chemical properties of a soil in governing the respiratory response to OM addition. Such a combination suggests that the 'architecture' of the soil, i.e. the integration of the spatial organisation of the environment and the interactions between the communities living and functioning within the pore networks, is fundamentally important in regulating such processes

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.Peer reviewe

The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6

The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.Peer reviewe

Narrow-clawed crayfish in Finland:

The narrow-clawed crayfish (Pontastacus leptodactylus) is an alien species in Finland with only a few populations reported from the southeastern region during the last century. We discovered a productive population in the lake Jängynjärvi, which is upstream from the previously reported wild narrow-clawed crayfish population in that region. Preliminary studies indicated that this population is not infected with Aphanomyces astaci. We collected narrow-clawed crayfish samples from the lake Jängynjärvi population for both infection challenge and genetic studies, in order to investigate possible A. astaci resistance among this Finnish population and to evaluate their phylogenetic position that would enable us to speculate different scenarios of distribution pathways or origin of the population. The infection studies indicated that the narrow-clawed crayfish in this population were more resistant against A. astaci infection (B haplogroup A. astaci) compared to the noble crayfish (Astacus astacus) from the lake Rytky in North Savo, while all crayfish of both species in the B haplogroup A. astaci challenged groups died within 58 days post-infection. Results of the phylogenetic reconstruction indicate that the lake Jängynjärvi narrow-clawed crayfish are closely related to narrow-clawed crayfish from the lake Bolshoye near Krasnoye, located on the White Sea island of Solovestky and also populations from Tyumen region, both in Russia. This could confirm previous speculations about introduction of the narrow-clawed crayfish from Russia into Finland or could indicate previous hydrological connection

Crayfish plague in Japan: A real threat to the endemic Cambaroides japonicus

Global introductions of aquatic species and their associated pathogens are threatening worldwide biodiversity. The introduction of two North American crayfish species, Procambarus clarkii and Pacifastacus leniusculus, into Japan in 1927 seems to have negatively affected native Japanese crayfish populations of Cambaroides japonicus. Several studies have shown the decline of these native populations due to competition, predation and habitat colonization by the two invasive North American crayfish species. Here, we identify an additional factor contributing to this decline. We report the first crayfish plague outbreaks in C. japonicus populations in Japan, which were diagnosed using both histological and molecular approaches (analyses of the internal transcribed spacer region). Subsequent analyses of the mitochondrial ribosomal rnnS and rnnL regions of diseased specimens indicate that these outbreaks originated from a P. clarkii population and identify a novel haplotype of Aphanomyces astaci, d3-haplotype, hosted by P. clarkii. Overall, our findings demonstrate the first two cases of crayfish plague in Japan, and the first case in a non-European native crayfish species, which originated from the red swamp crayfish P. clarkii. This finding is a matter of concern for the conservation of the native freshwater species of Japan and also highlights the risk of introducing crayfish carrier species into biogeographic regions harboring species susceptible to the crayfish plague.This research was partially supported by a grant from the Spanish Ministry of Economy and Competitiveness (CGL2016-80526-R)

Observations of crayfish plague infections in commercially important narrow-clawed crayfish populations in Turkey

We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed crayfish (Astacus leptodactylus) populations by analyzing the prevalence and genotypes of the disease agent A. astaci. The qPCR analyses revealed A. astaci infection in seven of the studied eight populations, with the agent level A2 or higher. The agent levels among the infected populations varied from A0 to A5, i.e., from negative to high level of infection, based on qPCR ranking. Based on the sequencing of the chitinase gene and the mitochondrial ribosomal rnnS and rnnL subunits, we detected both A (As) and B (PsI) haplogroups of A. astaci in our samples, with each of the studied populations being carriers of only one haplotype. The results confirm previous detections of A. astaci in Turkish narrow-clawed crayfish populations and reveal, that both A and B haplogroup A. astaci carriers exist widely in A. leptodactylus populations of Turkey

Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans

180 York Street, New Haven, CT 06511interior, bridge over drafting room, 196

Observations of crayfish plague infections in commercially important narrow-clawed crayfish populations in Turkey

We studied the presence of possible Aphanomyces astaci infections in eight Turkish narrow-clawed crayfish (Astacus leptodactylus) populations by analyzing the prevalence and genotypes of the disease agent A. astaci. The qPCR analyses revealed A. astaci infection in seven of the studied eight populations, with the agent level A2 or higher. The agent levels among the infected populations varied from A0 to A5, i.e., from negative to high level of infection, based on qPCR ranking. Based on the sequencing of the chitinase gene and the mitochondrial ribosomal rnnS and rnnL subunits, we detected both A (As) and B (PsI) haplogroups of A. astaci in our samples, with each of the studied populations being carriers of only one haplotype. The results confirm previous detections of A. astaci in Turkish narrow-clawed crayfish populations and reveal, that both A and B haplogroup A. astaci carriers exist widely in A. leptodactylus populations of Turkey