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Additional file 7: Table S6. List of genes differentially expressed and relative Fold Changes identify by kallisto-sleuth pipeline.

This dataset contains key characteristics about the data described in the Data Descriptor A global database of Holocene paleotemperature records. Contents: 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format

Additional file 1: Table S1. Sponge species with known relations to microorganisms during development and corresponding characteristics. Table S2. Sponge developmental stages microbiome sampled used in meta-analysis. Table S3. Alpha diversity measures for each sponge developmental stages. Table S4. Relative abundance of bacterial phyla for all species of sponge developmental stages. Table S5. Summary of statistical tests for alpha diversity between HMA and LMA sponges. Table S6. Sponge species with profiled bacterial communities and known as an LMA or HMA. Table S7. Summary of PERMANOVA results for compositional comparisons between sponge species and symbiont life-style. Table S8. GenBank accession numbers for 18S rRNS sequences used in gene tree as part of phylosymbiosis. Table S9. Statistical tables for testing phylosymbiosis across geminate species pairs. Table S10. Average alpha rarefaction values for each species based on observed ASVs and phylogenetic diversity [232–267].

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.

Figures showing further hatchling drift scenarios, adult turtle migrations, and associated satellite tracking references.

ABSTRACT: This study sought to evaluate the number of bruises on bovine carcasses and their relationship with loading rates in different truck models. Bruising percentages in the hindquarter, forequarter and short rib regions were evaluated. The space occupied on the truck by each animal in m² was defined as the Practiced area, obtained by dividing the body area by the number of males and females transported in straight trucks (10.60 x 2.40 m) and livestock trailers (14.80 x 2.60 m), 240 and 168, and 120 and 93, respectively, and 80 males in a straight truck with trailer configuration (17.50 x 2.60 m). The minimum area occupied by the animals was assessed according to the Farm Animal Welfare Council (FAWC) and Animal Welfare Advisory Committee (AWAC). The data was analyzed in a completely randomized design and included two sex classes, three carcass regions and three truck types. For males, the minimum areas (m²) calculated by the FAWC and AWAC were smaller (1.37 and 1.29 m², respectively) for the straight truck. The straight truck with trailer configuration had the lowest (P=0.0025) bruising index in the forequarter region (15.1%) and the highest (P=0.047) in the short rib region (30.5%). Females transported in the livestock trailer had a higher (P<0.001) percentage of bruises in the forequarter region (51.7%). There was a relationship between the high bruising rates and the loading rate Practiced for the males. Estimations made by the AWAC are close to those practiced in the upper Pantanal region of Mato Grosso do Sul, Brazil.

The main petroleum product transported through pipelines in Canada is diluted bitumen (dilbit), a semi-liquid form of heavy crude oil mixed with natural gas condensates to facilitate transport. The weathering, fate, behaviour, and environmental effects of dilbit are crucial to consider when responding to a spill, however few environmental studies on dilbit have been completed. Here we report on 11-day long experimental spills of dilbit (Cold Lake Winter Blend) in outdoor micro-cosms meant to simulate a low-energy aquatic system containing natural lake water and sedi-ments treated with a low (1:8,000 oil:water) and high (1:800 oil:water) volume of dilbit. In the first 24 hours of the experiment, volatile hydrocarbons quickly evaporated from the dilbit, result-ing in increased dilbit density and viscosity. These changes in dilbit’s physical and chemical properties ultimately led to its submergence after 8 days. We also detected rapid accumulation of polycyclic aromatic compounds in the water column of the treated-microcosms following the spills. Our study provides new information on the environmental fate and behaviour of dilbit in a freshwater environment that will be critical to environmental risk assessments of proposed pipe-line projects. In particular, our study demonstrates the propensity for dilbit to sink under ambient environmental conditions in fresh waters typical of many boreal lakes.

Abstract: This article estimates economic losses associated with urban mobility problems in Brazil by calculating the average production loss due to commuting time to work, using data from the 2010 Demographic Census. The results are presented in absolute and relative values (% of GDP) for States, Metropolitan Regions (RMs) and municipalities in Brazil, with emphasis on the difference in time spent in RMs and municipalities and the interior of each state. The results were significant, and the total estimated loss is 1.8% of GDP. If the commuting time in the RMs were equal to those of municipalities in the interior, there would be a reduction of 27.6% (R$ 26.7 billion) of total losses, suggesting that improvements in urban mobility can bring great social returns.

Additional file 4: Table S3. List of genes differentially expressed and relative Fold Changes identify by TopHat2-Cufflinks-cummeRbund pipeline.

Additional file 5: Table S4. List of genes differentially expressed and relative Fold Changes identify by HISAT2-featureCounts-DESeq2 pipeline.