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Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia
Get PDFBackground Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia. Methods Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis. Results The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses. Conclusions To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses
Border carbon adjustments in agri-food markets: Not as effective as one might think
Get PDFUsing the EU as case study, we simulate the impact of border carbon adjustments on agri-food markets. While border carbon adjustments alleviate adverse carbon price impacts on EU agricultural competitiveness and emission leakage, our simulation results also reveal that (i) border carbon adjustments may diminish domestic mitigation efforts, thereby partly offsetting benefits from reduced emission leakage, and (ii) trade diversion further undermines global emission reduction. The results indicate that border carbon adjustments on agri-food products in major exporting countries with emission-efficient production systems may not reduce global emissions as effectively as commonly assumed, highlighting the importance of emission efficiency improvements especially in developing and emerging countries
Reluctance of farmed Atlantic salmon to feed in cold water revealed during automated hydroacoustic feeding control
Get PDFWaste feed remains a major issue in open sea-cage Atlantic salmon aquaculture. "Echofeeding" is an appetite-led feeding method that stops meals based on fish biomass detected by an echo sounder. The method reduced waste feed and upheld fish growth in a relatively vertically unstratified coastal farming environment. Here, we tested echofeeding at a commercially relevant scale over an 8-month period in a fjord environment with seasonal vertical temperature and salinity gradients. We compared fish behaviour and growth between echofed fish, fed at high intensity and near surface, and control fish, with feeding regulated by pellet detection without surface feeding restriction (conventional practice). Growth (SGR>1.81) and FCR (<0.87) were excellent and similar for three months after sea-transfer in August. However, a strong halocline in late November (<5 degrees C surface water) led echofed fish to avoid surface feeding, resulting in underfeeding. Following the setting of a deeper depth interval for triggering feeding, the echofed fish fed more, and fed at similar levels to control fish when feeding intensity was reduced. Echofeeding underperformed in early spring as rising surface temperatures attracted salmon, making it difficult for the system to distinguish between feeding and routine behaviours. Both groups contracted salmonid alphavirus during winter, reducing appetite and promoting early harvest. Results highlight the need for echofeeding to take environmental changes into account. Further, as fish grew, a gradual decline in the echo signal measured during feeding suggests a method for refining meal termination threshold to minimize waste feed while maintaining good fish growth
Hydrochoric Seed Dispersal of Riparian Plants Follows Hydrological Patterns Closer Than Geomorphic Variation
Get PDFWater is an important dispersal vector for seeds of riparian plants, but little is known on how this form of dispersal, called hydrochory, varies throughout seasons and through geomorphically different areas. Therefore, we trapped seeds in 25 x 25 Astroturf mats along a free-flowing boreal river for an entire year. Sites mirrored the full range of geomorphic variation in the area and traps were emptied before and after the annual peak flow. The traps collected 2,062 seeds before the spring flood and 16,157 during the spring flood. While most of the seeds were deposited in the summer-low water traps (from now on "water edge") before the spring flood, they were distributed more equally in the riparian traps (defined as the level 40 cm above the water edge; from now on "riparian zone") during the spring flood. We found 77 species in total, of which 71 were at least recorded during the spring flood. Species numbers were higher at the water edge than at the riparian zone before and during the spring flood. Only 6.6% of the seeds, from 26 species, were viable. Most viable seeds were found in the water edge traps and, during the spring flood, in the riparian zone traps. While species that are primarily dispersed by water were not the most abundant among the viable seeds, they were the most species-rich group. This means that hydrochory is an important dispersal mechanism for riparian vegetation and an important contributor to riparian plant diversity in free-flowing rivers, and that changes in flow regimes, such as by flow regulation, can affect riparian vegetation composition
A global dataset of nitrogen fixation rates across inland and coastal waters
Get PDFBiological nitrogen fixation is the conversion of dinitrogen (N2) gas into bioavailable nitrogen by microorganisms with consequences for primary production, ecosystem function, and global climate. Here we present a compiled dataset of 4793 nitrogen fixation (N2-fixation) rates measured in the water column and benthos of inland and coastal systems via the acetylene reduction assay, 15N2 labeling, or N2/Ar technique. While the data are distributed across seven continents, most observations (88%) are from the northern hemisphere. 15N2 labeling accounted for 67% of water column measurements, while the acetylene reduction assay accounted for 81% of benthic N2-fixation observations. Dataset median area-, volume-, and mass-normalized N2-fixation rates are 7.1 mu mol N2-N m-2 h-1, 2.3 x 10-4 mu mol N2-N L-1 h-1, and 4.8 x 10-4 mu mol N2-N g-1 h-1, respectively. This dataset will facilitate future efforts to study and scale N2-fixation contributions across inland and coastal aquatic environments
ATG8ylation of vacuolar membrane protects plants against cell wall damage
Get PDFVacuoles are essential for cellular metabolism and growth and the maintenance of internal turgor pressure. They sequester lytic enzymes, ions and secondary metabolites that, if leaked into the cytosol, could lead to cell death. Despite their pivotal roles, quality control pathways that safeguard vacuolar integrity have remained elusive in plants. Here we describe a conserved vacuolar quality control pathway that is activated upon cell wall damage in a turgor-pressure-dependent manner. Cell wall perturbations induce a distinct modification-ATG8ylation-on the vacuolar membrane (tonoplast) that is regulated by the V-ATPase and ATG8 conjugation machinery. Genetic disruption of tonoplast ATG8ylation impairs vacuolar integrity, leading to cell death. Together, our findings reveal a homeostatic pathway that preserves vacuolar integrity upon cell wall damage
Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar
Get PDFWe present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes
Characterization of imogolite-type nanoparticles in Podzols: morphology and association with iron
Get PDFImogolite-type nanoparticles (ITN) are among the most extensively studied particles present in the Bs horizons of Podzols, as they are strongly associated with the adsorption processes of different anions in soils, including phosphate. The aim of this study was to assess the properties of ITN in soil, in order to increase the current knowledge of ITN regarding adsorption models. ITN were isolated from the B horizons of three Swedish Podzols and characterised in terms of size distribution, morphology, elemental composition, and association with iron. Appreciable amounts of ITN were found in two of the three soil samples studied, reaching up to 14 % ITN by mass if all oxalate-extractable Si is assigned to ITN. Furthermore, substantial amounts of Fe were also present in the selected soil samples. Proto-imogolite (PIM) was the predominant form of ITN, suggesting that tubular imogolite have a lower contribution for ion adsorption reactions in Podzols. Three types of PIM morphology were identified: structureless amorphous clusters, fragmented nanotubes, and globular aggregates. The studied PIM, which exhibited a particle size around 50 nm, contained up to 19 % Fe, while no detectable amounts of Fe were found in tubular imogolite. Regarding PIM, Fe atoms were evenly distributed in the structure, providing evidence for the presence of a substituted and/or surface-adsorbed Fe phase, rather than large ferrihydrite clusters. The present study provides novel insights into the properties of ITN and its association with Fe, which will aid in the development of models predicting the fate of oxyanions in Podzols and other ITN-containing soils
Lokal åtgärdssamordning av vattenvårdsåtgärder
Get PDFDen här rapporten bygger på en enkät- och intervjustudie riktad till personer som arbetar med åtgärdssamordning av vattenvårdsåtgärder lokalt i Sverige. Syftet har varit att belysa åtgärdssamordnarnas erfarenheter, utmaningar och behov, samt att identifiera förbättringsförslag för framtida organisering, finansiering och stödstrukturer.Enkäten besvarades av 48 personer med olika organisatorisk tillhörighet, varav hälften var kommunalt anställda. Resultaten visade att rollen som åtgärdssamordnare ofta är bred och komplex, samtidigt som oftast endast en person inom organisationen arbetar med denna typ av uppdrag. Behovet av kollegialt lärande och nationell samordning lyftes som centralt. Ett genomgående hinder i arbetet var bristen på långsiktig finansiering, både för anställningar och för genomförandet av större åtgärder. Även kravet på medfinansiering beskrevs som ett oproportionerligt administrativt hinder. Samtidigt beskrev respondenterna att långa handläggningstider för anmälan om vattenverksamhet och variationer mellan län i bemötande från Länsstyrelsen påverkar effektiviteten i åtgärdsarbetet.Intervjuerna med sex personer med gedigen kunskap och erfarenhet av åtgärdssamordning och vattenvård bekräftade och fördjupade enkätens resultat. De understrykte behovet av samordning och stabila strukturer som möjliggör kontinuitet och kompetensöverföring, och visade på att arbetet fungerar bäst där det finns ett team av personer med kompletterande kunskaper. Tydliga mallar, utbildningar och en samlad plattform för resurser och erfarenhetsutbyte efterfrågades. Flera lyfte behovet av en samverkansplattform som kan fungera som stödstruktur och kunskapsnod.Resultaten pekar på att det finns ett starkt engagemang och praktiskt kunnande bland Sveriges åtgärdssamordnare, men att det nu krävs strukturella förbättringar för att denna kraft ska tas tillvara på fullt ut
Invited review: Future directions for cow-calf contact research and sustainable on-farm applications
Get PDFProlonged cow-calf contact (CCC) is of growing importance to the dairy sector due to increasing societal interest, implementation of CCC on farms, and research efforts. Incorporating CCC into dairy systems may be a polarizing change for academics and farmers. However, by considering the challenges with curiosity, including those mutual to CCC and non-CCC systems, there may be an opportunity to collectively improve the management of dairy animals. The aim of this review was to describe current issues and constraints in CCC, propose opportunities to advance knowledge of CCC, and inspire forward-thinking questions for dairy systems. There are known challenges for CCC implementation, such as research reproducibility (e.g., suitable controls, validity types) and on-farm application (e.g., farmer perspectives, policies, and corporate standards). To facilitate practical solutions for farmers wanting to adopt CCC we need research describing the effects of CCC systems on animal health and behavior. Already researchers have begun to explore cow and calf performance and health, methods for decreasing stress at weaning and separation (e.g., duration of contact, gradual weaning), foster cows, and opportunities for positive animal welfare in CCC systems (e.g., affiliative and play behavior). However, because dairying takes place in a complex system, changes may affect different facets of the system's sustainability. We suggest that the development of CCC systems should happen in dialog with stakeholders. Cow-calf contact is an uncommon practice in dairy systems and exists in different contexts; thus, there are many questions to address before advice can be given to interested dairy stakeholders. Perhaps, these CCC-related questions are an invitation to contemplate how we want dairy systems to look like in 30 years