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Mapping small water channels using machine learning
No full textDet boreala landskapet präglas av ett omfattande nätverk av naturliga vattendrag, modifierade vattendrag och diken som tillsammans reglerar hydrologi, näringsflöden och ekosystemfunktioner. Historiskt har vattendrag rätats och rensats för timmerflottning medan diken har grävts för att öka jordbruks- och skogsproduktionen. Trots att nydikning numera är ovanlig påverkar dessa historiska ingrepp fortfarande vattenförvaltning och skogsbruk. Små vattendrag och diken fungerar som landskapets kapillärer men är fortfarande bristfälligt kartlagda, trots deras centrala hydrologiska och ekologiska betydelse. Denna avhandling utvecklar en metod för att kartlägga små vattendrag och diken på nationell skala med högupplösta topografiska data och maskininlärning. Genom att kombinera konvolutionella neurala nätverk, XGBoost-klassificering, osäkerhetsanalys och data på flödesackumulering identifieras geomorfologiska och hydrologiska indicier som skiljer diken från naturliga vattendrag. Den bästa metoden visar att digitala höjdmodeller och terrängindicier kan användas för att effektivt avgränsa vattendrag och diken. Metoden hade hög precision för diken (recall=76%, precision=88%) och mer måttliga resultat för naturliga vattendrag (recall=58%, precision=56%). Osäkerhetskartor visar dessutom var framtida förbättringar av kartläggningen bör riktas. Detta är den första studien som framgångsrikt särskiljer vattendrag och diken för ett helt land. Genom att skapa konsekventa, skalbara kartor över små vattendrag och diken bidrar forskningen till restaureringsprioritering, hållbar skogsförvaltning och nationell miljörapportering inom EU:s och FN:s ramar. Metoden erbjuder även ett reproducerbart sätt att beskriva sammankopplade naturliga och artificiella dräneringssystem i boreala och tempererade regioner
KSGP 3.1: improved taxonomic annotation of Archaea communities using LotuS2, the genome taxonomy database and RNAseq data
No full textTaxonomic annotation is a substantial challenge for Archaea metabarcoding. A limited number of reference sequences are available; a substantial fraction of phylogenetic diversity is not fully characterized; widely used databases do not reflect current archaeal taxonomy and contain mislabelled sequences. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB) combined with the eukaryote PR2 and MIDORI mitochondrial databases. After removing incongruent, chimeric and duplicate SSU sequences, this combination (GTDB+) provides a small improvement in annotation of a set of estuarine Archaea Operational Taxonomic Units (OTUs) compared to SILVA. We add to this a collection of near full length rRNA sequences and the prokaryote SSU sequences in SILVA, creating a new reference database, KSGP (Karst, Silva, GTDB, and PR2). The additional sequences are (re-)annotated using three different approaches. The most conservative, using lowest common ancestor, gives a further small improvement. Annotation using SINTAX increases Class and Order assignments by 2.7 and 4.2 times over SILVA, although this may include some "lumping" of un-named and named clades. Still further improvement can be made using similarity based clustering to group database sequences into putative taxa at all taxonomic levels, assigning 60% and 41% of Archaea OTUs to putative family and genus level taxa respectively. GTDB without cleaning and GreenGenes2 both perform poorly and cannot be recommended for use with Archaea. We make the GTDB+ and KSGP databases available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline their use to annotate Archaea OTUs and metatranscriptomic data
Livestock and poultry production in Sri Lanka: challenges and strategies for climate-resilient food security
No full textLivestock and poultry production is critical to Sri Lanka's food security, providing essential animal-sourced proteins, contributing to economic growth, and supporting rural livelihoods. This review examines the current status, challenges, and opportunities within the livestock and poultry sectors in Sri Lanka. Key performance indicators such as production growth, accessibility, affordability, and disease management are analyzed to assess the industry's resilience. The study highlights the impact of economic fluctuations, feed price volatility, policy constraints, and climate change on the industry. Integrating climate-resilient strategies into Sri Lanka's livestock and poultry sectors is essential to enhance sustainability. Key approaches include breeding heat-tolerant animals, introducing climate-smart feeds and nutritional strategies, improving water conservation, adopting climate-resilient housing systems, implementing sustainable waste management, utilizing renewable energy sources, enhancing farmer capacity through training and policy support, and strengthening disease surveillance and biosecurity measures. Implementing these strategies will improve productivity, reduce environmental impact, and enhance resilience against climate extremes. The review also explores the role of integrated livestock systems, digital technologies, and export potential in further strengthening the sector by guiding policymakers, researchers, and stakeholders in developing sustainable and climate-resilient solutions. Addressing these challenges through data-driven policies, farmer empowerment, and investment in innovation is essential to achieving a resilient and self-sufficient livestock industry in Sri Lanka
An improved and simplified somatic embryogenesis protocol in Chir pine (Pinus roxburghii)
No full textForests are considered to be an important pillar for a country's bioeconomy but unfortunately are being depleted globally. Pinus roxburghii has considerable ecological and economic importance for Pakistan. It is successfully used as a pioneer species in afforestation and reforestation programs in the era of climate change. This paper reports on a significantly improved protocol for P. roxburghii somatic embryogenesis. Successive developmental stages for zygotic as well as somatic embryos were reported first time for this important pine species. Initiation of somatic embryogenesis was affected by the developmental stage of the zygotic embryo. Immature pre-cotyledonary zygotic embryos produced 33% initiation of embryonic masses on LP-889 medium supplemented with 11 mu M Naphthaleneacetic acid (NAA), 2.5 mu M Benzylaminopurine (BAP), 2.5 mu M kinetin and 4 mu M Abscisic acid (ABA). LP-1250 medium provided with 2 mu M BAP, 2 mu M kinetin, 5 mu M 2, 4-Dichlorophenoxyacetic acid (2, 4-D) and 5 mu M ABA was used for the proliferation and maintenance of embryogenic tissue. Polarized immature somatic embryos were clearly visible during the proliferation and maintenance phase. Two media; mLV and LP-1562 were tested as well as several combinations of L-glutamine and ABA for maturation. Maximum number of somatic embryos (310 embryos per g embryogenic tissue) was obtained on LP-1562 medium (containing 450 mg/l of L-glutamine and 20 mu M ABA) as compared to 204 embryos per g embryogenic tissue on mLV medium (containing 900 mg/l L-glutamine and 60 mu M ABA). Mature somatic embryos were formed on maturation medium after 6-8 weeks. Successful conversion of somatic embryos resulted after 12 weeks on LP-397 medium. However, low rooting rates (7% and 3%) were observed for somatic embryos formed on maturation media, i.e. LP-1562 and mLV, respectively and precocious germination of the mature somatic embryos still remains a serious constraint
Managing nitrogen fertility and stand density for sustaining Kernza intermediate wheatgrass yields
No full textKernza intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D.R. Dewey] is a promising perennial grain and forage crop, but experiences grain yield decline, potentially due to limited nitrogen (N) and stand overcrowding. We evaluated the effects of N fertilization and stand thinning on grain and forage yield, weed biomass, thousand-kernel weight (TKW), and harvest index (HI). We used a full factorial design with N rates of 0, 75, and 150 kg N ha(-1) and thinning intensities of 0%, 25%, 38%, or 50% stand density reduction via banded herbicide at two locations in Wisconsin over 2 years. Fertilization and thinning did not interact. Grain yields increased with N fertilization except at Madison in Year 2. At Lancaster, grain yield increased from 293 with no N to 497 and 701 kg ha(-1) with 75 and 150 kg N ha(-1), respectively, across years. At Madison, grain yield increased only in Year 1. Forage mass also increased with N at both sites except Madison in Year 2. At Lancaster, forage mass ranged from 4016 to 6500 kg ha(-1) across years and N rates. TKW and HI increased with N at both sites, except at Madison in Year 2. Weed biomass was unaffected by treatments. Thinning had no effect on grain yield at Lancaster in Year 1, but in Year 2, grain yield increased from 368 to 505 kg ha(-1) with 50% thinning. These results suggest that applying 75 kg N ha(-1) is important for maintaining IWG productivity and that thinning can help sustain grain yield in older stands
Medical-grade honey as treatment for udder cleft dermatitis in dairy cows
No full textUdder cleft dermatitis (UCD) is a common inflammatory dermatological condition of the udder skin in dairy cows, localized at the fore udder attachment or between the front udder halves. The severity of the condition can vary from superficial dermatitis to extensive wounds and different classification scales exist. To date, no effective curative treatment has been identified. Honey has been used in wound care for a long time due to its ability to promote healing and antimicrobial and anti-inflammatory properties. Thus, the aim of this pilot study was to investigate whether medical-grade honey could be as effective as zinc ointment in treating UCD. Fourteen cows with severe UCD (large crusts or open wound) were matched into pairs and then randomly assigned to treatment with medical-grade honey (n = 7) or zinc ointment (n = 7). Treatment continued for 8 wk, and UCD was graded at 3 different time points during the study. Treatment with medical-grade honey resulted in a higher improvement rate (42.9%) compared with zinc ointment (14.3%), although the result was not statistically significant. This study indicates that medical-grade honey could be an alternative treatment of severe UCD
Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes
No full textDiverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort
Fireworks and Animals
No full textThe use of fireworks is debated from an animal welfare perspective. However, a comprehensive overview of how fireworks affect the welfare of different animal species and how fireworks legislation influences animal protection is lacking. The Swedish Centre for Animal Welfare (SCAW), Swedish University of Agricultural Sciences (SLU), was therefore commissioned by the Swedish Association for the Protection of Animals (Svenska Djurskyddsföreningen) to review the current scientific literature and legislation in this area. More specifically, this report aims to compile the literature and scientific knowledge regarding the effects of fireworks on the welfare of various animal species; map the legislation on fireworks in Sweden, in selected EU member states, and at EU level; identify potential knowledge gaps and further research; and propose recommendations on the use of fireworks, considering animal welfare and legislation
Pest survey card on Ips typographus
No full textThis document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M-2020-0114) at the request of the European Commission. The full pest survey card for Ips typographus is published and available online in the EFSA Pest Survey Card gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/ips-typographu
Quantification of root biomass in barley variety mixtures using variety-specific genetic markers
No full textBackgroundVariety mixtures combining crop varieties with different root system properties have the potential to improve soil exploration through belowground niche complementarity, which can improve soil resource acquisition and crop productivity. However, there is a lack of appropriate methods to distinguish and quantify roots of different varieties, which limits our ability to elucidate belowground processes that underpin soil exploration and resource uptake by plants in variety mixtures.ResultsIn the present study, we developed a method to quantify root biomass and distribution patterns of different barley varieties grown together in mixtures using DNA extraction and quantitative PCR with variety-specific genetic markers. Two field experiments, one in Sweden and one in Denmark, were conducted that included two barley varieties grown either alone in pure stands or together in the same plot. The genetic markers were highly variety-specific, enabling accurate detection of the roots of each individual variety in the mixture. We found that the contribution of varieties to total root biomass in the mixture differed between the two locations, indicating the effects of the environment on root distribution patterns in variety mixtures.ConclusionsThe method presented here opens new possibilities for rapid quantification of root biomass and can provide new insights into belowground processes underpinning the functioning of mixed variety systems. Ultimately, such understanding is needed to assess the potential to adopt mixed variety systems in practical agriculture