Pub Date : 2024-09-13DOI: 10.1101/2024.09.08.611921
Sabrina Haque, Hasinika KAH Gamage, Cecilia Kardum Hjort, Fleur Ponton, Francisco Encinas-Viso, Ian Paulsen, Rachael Y Dudaniec
Many species of social insects introduced to regions beyond their native ranges have become highly invasive. The introduction of the eusocial European buff-tailed bumblebee, Bombus terrestris, to the island of Tasmania (Australia) ~30 years ago is of concern due to its ecological impacts and its potential to spill over pathogens to native bees or commercially important honeybees. The health of B. terrestris is intricately connected with its gut microbiome and diet; however, environmental variables may also interact, particularly during invasion into novel environments. Using landscape-wide sampling and a metabarcoding approach to characterize the gut bacteria (16S rRNA) and diet composition from foraged pollen (ITS2: floristic diversity of pollen baskets), this study investigates how the gut microbiota of B. terrestris workers is affected by nutritional diversity (pollenbiome) and environmental variation across diverse landscapes of its invasive range in Tasmania. Gut bacterial community composition and diversity were significantly predicted by site annual precipitation and percentage of pasture. Further, a positive interaction between site annual precipitation and site annual temperature significantly predicted gut bacterial diversity. The interaction effect of pollen diversity and average summer wind velocity was also significantly and positively related to gut bacterial diversity. Following comparison of Akaike information criterion (AIC) and sum of weights, the percentage of pasture was identified as the most strongly weighted variable, which, along with pollen diversity, had a negative impact on gut bacterial diversity. These insights help to uncover how environmental interactions affect the gut microbiome of B. terrestris in an invaded landscape with novel nutritional resources. This knowledge contributes to understanding the factors that predict the spread and persistence of invasive bumblebees.
{"title":"Landscape-wide metabarcoding of the invasive bumblebee (Bombus terrestris) shows interactions among the gut microbiome and pollenbiome","authors":"Sabrina Haque, Hasinika KAH Gamage, Cecilia Kardum Hjort, Fleur Ponton, Francisco Encinas-Viso, Ian Paulsen, Rachael Y Dudaniec","doi":"10.1101/2024.09.08.611921","DOIUrl":"https://doi.org/10.1101/2024.09.08.611921","url":null,"abstract":"Many species of social insects introduced to regions beyond their native ranges have become highly invasive. The introduction of the eusocial European buff-tailed bumblebee, <em>Bombus terrestris</em>, to the island of Tasmania (Australia) ~30 years ago is of concern due to its ecological impacts and its potential to spill over pathogens to native bees or commercially important honeybees. The health of <em>B. terrestris</em> is intricately connected with its gut microbiome and diet; however, environmental variables may also interact, particularly during invasion into novel environments. Using landscape-wide sampling and a metabarcoding approach to characterize the gut bacteria (16S rRNA) and diet composition from foraged pollen (ITS2: floristic diversity of pollen baskets), this study investigates how the gut microbiota of <em>B. terrestris</em> workers is affected by nutritional diversity (pollenbiome) and environmental variation across diverse landscapes of its invasive range in Tasmania. Gut bacterial community composition and diversity were significantly predicted by site annual precipitation and percentage of pasture. Further, a positive interaction between site annual precipitation and site annual temperature significantly predicted gut bacterial diversity. The interaction effect of pollen diversity and average summer wind velocity was also significantly and positively related to gut bacterial diversity. Following comparison of Akaike information criterion (AIC) and sum of weights, the percentage of pasture was identified as the most strongly weighted variable, which, along with pollen diversity, had a negative impact on gut bacterial diversity. These insights help to uncover how environmental interactions affect the gut microbiome of <em>B. terrestris</em> in an invaded landscape with novel nutritional resources. This knowledge contributes to understanding the factors that predict the spread and persistence of invasive bumblebees.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.05.611395
Lucile Muneret, Benjamin Carbonne, Bruno Chauvel, Alexandre Dosset, Chantal Ducourtieux, Nicolas Henon, Emeline Felten, Emilien Laurent, Annick Matejicek, Sandrine Petit
While many herbicide active substances have been banned and weed infestation is a major threat to crop productivity, it is still unknown to what extent natural weed control provided by seed predators can help farmers manage weed communities. We aim to quantify the contribution of seed predators to crop productivity through weed control and to evaluate whether the magnitude of their influence depends on farming systems such as conservation agriculture. We set up 112 seed predator-exclusion cages in 28 cereal fields in France (14 pairs of conservation and conventional agriculture fields), surveyed weed emergence and biomass, measured crop yield and sampled the main seed predators: carabid beetles and rodents. We found that seed predators activity reduces the yield loss due to weeds by 20%. By extrapolation, it represents an economic gain of 285 euros/ha. However, the yield loss remains at 60% below the maximum crop yield potential reached in the absence of weeds. Moreover, conservation agriculture enhances weed control, but this does not translate into increased crop yield. This study demonstrates the tangible importance of considering seed predators for weed control but highlights the need to combine this approach with weed control practices or to substantially redesign cropping systems to enhance the beneficial effects of biodiversity on crop productivity.
{"title":"Natural weed seed predators reduce crop yield loss due to weeds by 20% in cereal fields","authors":"Lucile Muneret, Benjamin Carbonne, Bruno Chauvel, Alexandre Dosset, Chantal Ducourtieux, Nicolas Henon, Emeline Felten, Emilien Laurent, Annick Matejicek, Sandrine Petit","doi":"10.1101/2024.09.05.611395","DOIUrl":"https://doi.org/10.1101/2024.09.05.611395","url":null,"abstract":"While many herbicide active substances have been banned and weed infestation is a major threat to crop productivity, it is still unknown to what extent natural weed control provided by seed predators can help farmers manage weed communities. We aim to quantify the contribution of seed predators to crop productivity through weed control and to evaluate whether the magnitude of their influence depends on farming systems such as conservation agriculture. We set up 112 seed predator-exclusion cages in 28 cereal fields in France (14 pairs of conservation and conventional agriculture fields), surveyed weed emergence and biomass, measured crop yield and sampled the main seed predators: carabid beetles and rodents. We found that seed predators activity reduces the yield loss due to weeds by 20%. By extrapolation, it represents an economic gain of 285 euros/ha. However, the yield loss remains at 60% below the maximum crop yield potential reached in the absence of weeds. Moreover, conservation agriculture enhances weed control, but this does not translate into increased crop yield. This study demonstrates the tangible importance of considering seed predators for weed control but highlights the need to combine this approach with weed control practices or to substantially redesign cropping systems to enhance the beneficial effects of biodiversity on crop productivity.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-11DOI: 10.1101/2024.09.09.611181
Milaja Nykänen, Marja Niemi, Vincent Biard, Matt I. D. Carter, Enrico Pirotta, Mervi Kunnasranta
Background: Foraging rates directly influence animals' energetic intake and expenditure and are thus linked to body condition and the ability to survive and reproduce. Further, understanding the underlying processes driving a species' behaviour and habitat use is important as changes in behaviour could result from changes in environmental conditions. Methods: In this study, the dives of Saimaa ringed seals (Pusa hispida saimensis) were classified for the first time using hidden Markov models and telemetry data collected on individual dives, and the behavioural states of the diving seals were estimated. In addition, we used generalized additive mixed models on the foraging probability of the seals to identify environmental and temporal drivers of foraging behaviour. Results: We inferred three (in winter) or four (in summer) different dive types: sleeping/resting dives, shallow inactive dives, transiting dives and foraging dives, based on differences in dive metrics logged by or derived from data from telemetry tags. Long and relatively deep sleeping/resting dives were missing entirely in the winter, compensated by an increased proportion of time used for haul-out. We found profound differences in the behaviour of Saimaa ringed seals during the summer open water season compared to the ice-covered winter, with the greatest proportion of time allocated to foraging during the summer months (36%) and the lowest proportion in the winter (21%). The seals' foraging probability peaked in summer (July) and was highest during the daytime during both summer and winter months. Moreover, foraging probability was highest at depths of 7-30 m in the winter and at depths >15 m in the summer. We also found some evidence of sex-specific foraging strategies that are adapted seasonally, with females preferring more sheltered water areas during winter. Conclusions: We suggest that the foraging behaviour of Saimaa ringed seals is largely influenced by diel vertical movements and availability of fish, and that the seals optimize their energy acquisition while conserving energy, especially during the cold winter months. Further, the seals display some flexibility in foraging strategies, a feature that may help this endangered subspecies to cope with ongoing anthropogenic climate change.
{"title":"Linking ringed seal foraging behaviour to environmental variability","authors":"Milaja Nykänen, Marja Niemi, Vincent Biard, Matt I. D. Carter, Enrico Pirotta, Mervi Kunnasranta","doi":"10.1101/2024.09.09.611181","DOIUrl":"https://doi.org/10.1101/2024.09.09.611181","url":null,"abstract":"Background: Foraging rates directly influence animals' energetic intake and expenditure and are thus linked to body condition and the ability to survive and reproduce. Further, understanding the underlying processes driving a species' behaviour and habitat use is important as changes in behaviour could result from changes in environmental conditions. Methods: In this study, the dives of Saimaa ringed seals (Pusa hispida saimensis) were classified for the first time using hidden Markov models and telemetry data collected on individual dives, and the behavioural states of the diving seals were estimated. In addition, we used generalized additive mixed models on the foraging probability of the seals to identify environmental and temporal drivers of foraging behaviour. Results: We inferred three (in winter) or four (in summer) different dive types: sleeping/resting dives, shallow inactive dives, transiting dives and foraging dives, based on differences in dive metrics logged by or derived from data from telemetry tags. Long and relatively deep sleeping/resting dives were missing entirely in the winter, compensated by an increased proportion of time used for haul-out. We found profound differences in the behaviour of Saimaa ringed seals during the summer open water season compared to the ice-covered winter, with the greatest proportion of time allocated to foraging during the summer months (36%) and the lowest proportion in the winter (21%). The seals' foraging probability peaked in summer (July) and was highest during the daytime during both summer and winter months. Moreover, foraging probability was highest at depths of 7-30 m in the winter and at depths >15 m in the summer. We also found some evidence of sex-specific foraging strategies that are adapted seasonally, with females preferring more sheltered water areas during winter. Conclusions: We suggest that the foraging behaviour of Saimaa ringed seals is largely influenced by diel vertical movements and availability of fish, and that the seals optimize their energy acquisition while conserving energy, especially during the cold winter months. Further, the seals display some flexibility in foraging strategies, a feature that may help this endangered subspecies to cope with ongoing anthropogenic climate change.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.06.611583
Andre W Visser
Quantifying the sequestration potential of biologically driven carbon fluxes in the ocean depends critically on residence times, how long carbon remains stored in reservoirs before being re-exposed to the atmosphere. Simple mass balance provides estimates for many of the major ocean biogenic carbon reservoirs. For vegetated coastal ecosystems (mangroves, sea grass meadows, salt marshes) that globally store 20 to 40 PgC, this is 200 to 500 years, while for the biological carbon pump, a reservoir of about 2000 PgC, it is between 200 to 800 years. Over these time scales respective reservoirs reach equilibrium if left undisturbed. Importantly, near equilibrium of ocean reservoirs during the Holocene can be inferred from the near steady atmospheric concentrations during this period. The degradation of habitats and the over-exploitation of living marine resources particularly in the last 75 years have tipped these natural processes out of balance, to the extent where many are now net emitters of legacy carbon back to the atmosphere. The analysis exposes a conflict between how sequestration is reported in oceanographic literature and how it is understood with regards durable carbon capture and storage. Nature-based solutions can be sought to address parts of the climate crisis, by improving ecosystem health and biodiversity, but are unlikely to provide solutions to carbon management on a scale commensurate with anthropogenic emissions. The best we can do is to limit net emissions by restoring what we can, and to ensure that future practices do not further tip ocean carbon reservoirs out of balance.
{"title":"Residence Times and Legacy of Biogenic Carbon in Ocean Reservoirs","authors":"Andre W Visser","doi":"10.1101/2024.09.06.611583","DOIUrl":"https://doi.org/10.1101/2024.09.06.611583","url":null,"abstract":"Quantifying the sequestration potential of biologically driven carbon fluxes in the ocean depends critically on residence times, how long carbon remains stored in reservoirs before being re-exposed to the atmosphere. Simple mass balance provides estimates for many of the major ocean biogenic carbon reservoirs. For vegetated coastal ecosystems (mangroves, sea grass meadows, salt marshes) that globally store 20 to 40 PgC, this is 200 to 500 years, while for the biological carbon pump, a reservoir of about 2000 PgC, it is between 200 to 800 years. Over these time scales respective reservoirs reach equilibrium if left undisturbed. Importantly, near equilibrium of ocean reservoirs during the Holocene can be inferred from the near steady atmospheric concentrations during this period. The degradation of habitats and the over-exploitation of living marine resources particularly in the last 75 years have tipped these natural processes out of balance, to the extent where many are now net emitters of legacy carbon back to the atmosphere. The analysis exposes a conflict between how sequestration is reported in oceanographic literature and how it is understood with regards durable carbon capture and storage. Nature-based solutions can be sought to address parts of the climate crisis, by improving ecosystem health and biodiversity, but are unlikely to provide solutions to carbon management on a scale commensurate with anthropogenic emissions. The best we can do is to limit net emissions by restoring what we can, and to ensure that future practices do not further tip ocean carbon reservoirs out of balance.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611506
Joshua C. Fowler, Jacob Moutouama, Tom E.X. Miller
Species' distributions and abundances are shifting in response to climate change. Most species harbor microbial symbionts that have the potential to influence these responses. Mutualistic microbial symbionts may provide resilience to environmental change by protecting their hosts from increasing stress. However, environmental change that disrupts these interactions may lead to declines in hosts or symbionts. Microbes preserved within herbarium specimens offer a unique opportunity to quantify changes in microbial symbiosis across broad temporal and spatial scales. We asked how the prevalence of seed-transmitted fungal symbionts of grasses (Epichloe endophytes), which can protect hosts from abiotic stress, have changed over time in response to climate change, and how these changes vary across host species' ranges. Specifically, we analyzed 2,346 herbarium specimens of three grass host species collected over the last two centuries (1824 -- 2019) for the presence or absence of endophyte symbiosis, and evaluated spatial and temporal trends in endophyte prevalence. We found that endophytes increased in prevalence over the last two centuries from ca. 25% prevalence to ca. 75% prevalence, on average, across three host species. We also found that changes in prevalence were associated with observed changes in seasonal climate drivers; notably increasing precipitation corresponding to each host species' peak growing season and changes in off-peak season variability in precipitation. Our analysis performed favorably in an out-of-sample predictive test with contemporary data, however we identified greater local-scale variability in endophyte prevalence in contemporary data compared to historic data, suggesting that model fusion may be an important step moving forward. Our results provide novel evidence for a cryptic biological response to climate change that may contribute to the resilience of host-microbe symbiosis through context-dependent benefits that confer a fitness advantage to symbiotic hosts under environmental change.
{"title":"Increasing prevalence of plant-fungal symbiosis across two centuries of environmental change","authors":"Joshua C. Fowler, Jacob Moutouama, Tom E.X. Miller","doi":"10.1101/2024.09.05.611506","DOIUrl":"https://doi.org/10.1101/2024.09.05.611506","url":null,"abstract":"Species' distributions and abundances are shifting in response to climate change. Most species harbor microbial symbionts that have the potential to influence these responses. Mutualistic microbial symbionts may provide resilience to environmental change by protecting their hosts from increasing stress. However, environmental change that disrupts these interactions may lead to declines in hosts or symbionts. Microbes preserved within herbarium specimens offer a unique opportunity to quantify changes in microbial symbiosis across broad temporal and spatial scales. We asked how the prevalence of seed-transmitted fungal symbionts of grasses (Epichloe endophytes), which can protect hosts from abiotic stress, have changed over time in response to climate change, and how these changes vary across host species' ranges. Specifically, we analyzed 2,346 herbarium specimens of three grass host species collected over the last two centuries (1824 -- 2019) for the presence or absence of endophyte symbiosis, and evaluated spatial and temporal trends in endophyte prevalence. We found that endophytes increased in prevalence over the last two centuries from ca. 25% prevalence to ca. 75% prevalence, on average, across three host species. We also found that changes in prevalence were associated with observed changes in seasonal climate drivers; notably increasing precipitation corresponding to each host species' peak growing season and changes in off-peak season variability in precipitation. Our analysis performed favorably in an out-of-sample predictive test with contemporary data, however we identified greater local-scale variability in endophyte prevalence in contemporary data compared to historic data, suggesting that model fusion may be an important step moving forward. Our results provide novel evidence for a cryptic biological response to climate change that may contribute to the resilience of host-microbe symbiosis through context-dependent benefits that confer a fitness advantage to symbiotic hosts under environmental change.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Birds and their habitats are threatened with extinction around the world. Regional assessments of the 'State of Birds' are a vital means to prioritize data-driven conservation action by informing national and global policy. Such evaluations have traditionally relied on data derived from extensive, long-term, systematic surveys that require significant resources, limiting their feasibility to a few regions in the world. In the absence of such 'structured' long-term datasets, 'semi-structured' datasets have recently emerged as a promising alternative in other regions around the world. Semi-structured data are generated and uploaded by birdwatchers to citizen science platforms like eBird. Such data contain inherent biases because birdwatchers are not required to adhere to a fixed protocol. An evaluation of the status of birds from semi-structured data is therefore a difficult task that requires careful curation of data and the use of robust statistical methods to reduce errors and biases. In this paper, we present a methodology that was developed for this purpose, and was applied to produce the comprehensive State of India's Birds (SoIB) 2023 report. SoIB 2023 assessed the status of 942 bird species in India by evaluating each species based on three metrics: 1) long-term change: change in abundance between the year 2022 and the year-interval pre-2000; 2) current annual trend: mean annual change in abundance from 2015 to 2022; and 3) distribution range size. We found evidence that 204 species have declined in the long term, and 142 species are currently declining. We present and discuss important insights about India's birds that can guide research and conservation action in the region. We hope that the detailed methodology described here can act as a blueprint to produce State of Birds assessments from semi-structured citizen science datasets and springboard conservation action in many other regions where structured data is lacking but strong communities of birders exist.
{"title":"State of India's Birds 2023: A framework to leverage semi-structured citizen science for bird conservation","authors":"Ashwin Viswanathan, Karthik Thrikkadeeri, Pradeep Koulgi, Praveen J, Arpit Deomurari, Ashish Jha, Ashwin Warudkar, Kulbhushansingh Suryawanshi, MD Madhusudan, Monica Kaushik, Naman Goyal, Priti bangal, Rajah Jayapal, Suhel Quader, Sutirtha Dutta, Tarun Menon, Vivek Ramachandran","doi":"10.1101/2024.09.05.611348","DOIUrl":"https://doi.org/10.1101/2024.09.05.611348","url":null,"abstract":"Birds and their habitats are threatened with extinction around the world. Regional assessments of the 'State of Birds' are a vital means to prioritize data-driven conservation action by informing national and global policy. Such evaluations have traditionally relied on data derived from extensive, long-term, systematic surveys that require significant resources, limiting their feasibility to a few regions in the world. In the absence of such 'structured' long-term datasets, 'semi-structured' datasets have recently emerged as a promising alternative in other regions around the world. Semi-structured data are generated and uploaded by birdwatchers to citizen science platforms like eBird. Such data contain inherent biases because birdwatchers are not required to adhere to a fixed protocol. An evaluation of the status of birds from semi-structured data is therefore a difficult task that requires careful curation of data and the use of robust statistical methods to reduce errors and biases. In this paper, we present a methodology that was developed for this purpose, and was applied to produce the comprehensive State of India's Birds (SoIB) 2023 report. SoIB 2023 assessed the status of 942 bird species in India by evaluating each species based on three metrics: 1) long-term change: change in abundance between the year 2022 and the year-interval pre-2000; 2) current annual trend: mean annual change in abundance from 2015 to 2022; and 3) distribution range size. We found evidence that 204 species have declined in the long term, and 142 species are currently declining. We present and discuss important insights about India's birds that can guide research and conservation action in the region. We hope that the detailed methodology described here can act as a blueprint to produce State of Birds assessments from semi-structured citizen science datasets and springboard conservation action in many other regions where structured data is lacking but strong communities of birders exist.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611339
Natsufumi Takenaka, Kimiko Hong Mitsui, Kazuhiro Kunimasa, Kotaro Kawajiri, Chihiro Kayo, Naoki Yoshikawa
Cultivated meat is an alternative meat produced via cell culture. The culture medium accounts for most of the environmental impact of cultivated meat production. This study quantitatively evaluated and analyzed the environmental impact of serum-free food-grade and complex culture medium production for cultivated meat by performing a life cycle assessment (LCA) based on activity data at the laboratory scale. In addition, specific measures were proposed to reduce the environmental impact further. LCAs were performed at current and future production scales. This study also evaluated the impact of multiple electricity sources on the environmental impact of culture-medium production. Expendables at the current scale, as well as electricity and animal-derived materials at both scales, are hotspots in the environmental impact of this culture-medium production. Among these components, the production of serum substitutes accounts for most of the environmental impact. As the scale shifts, the environmental impacts are expected to decrease by 11.3%-93.2% in all impact categories. As the composition of electricity sources changed, the impact on certain categories decreased. However, as the share of renewable energy increased, the impact on land use also increased significantly. This study promotes the practical application of new culture media for low-cost and low-environment-impact cultivated meat.
{"title":"Environmental Impacts of Serum-free Food-grade and Complex Culture Medium Production for Cultivated Meat","authors":"Natsufumi Takenaka, Kimiko Hong Mitsui, Kazuhiro Kunimasa, Kotaro Kawajiri, Chihiro Kayo, Naoki Yoshikawa","doi":"10.1101/2024.09.05.611339","DOIUrl":"https://doi.org/10.1101/2024.09.05.611339","url":null,"abstract":"Cultivated meat is an alternative meat produced via cell culture. The culture medium accounts for most of the environmental impact of cultivated meat production. This study quantitatively evaluated and analyzed the environmental impact of serum-free food-grade and complex culture medium production for cultivated meat by performing a life cycle assessment (LCA) based on activity data at the laboratory scale. In addition, specific measures were proposed to reduce the environmental impact further. LCAs were performed at current and future production scales. This study also evaluated the impact of multiple electricity sources on the environmental impact of culture-medium production. Expendables at the current scale, as well as electricity and animal-derived materials at both scales, are hotspots in the environmental impact of this culture-medium production. Among these components, the production of serum substitutes accounts for most of the environmental impact. As the scale shifts, the environmental impacts are expected to decrease by 11.3%-93.2% in all impact categories. As the composition of electricity sources changed, the impact on certain categories decreased. However, as the share of renewable energy increased, the impact on land use also increased significantly. This study promotes the practical application of new culture media for low-cost and low-environment-impact cultivated meat.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611483
Hailey Robertson, Barbara A Han, Adrian A. Castellanos, David Rosado, Guppy Stott, Ryan Zimmerman, John M. Drake, Ellie Graeden
Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully applied to organize heterogeneous data systematically and to predict new linkages representing unobserved relationships in complex systems. Though not previously applied broadly in ecology, knowledge graphs have much to offer in an era of global change when system dynamics are responding to rapid changes across multiple scales simultaneously. We developed a knowledge graph to demonstrate the method's utility for ecological problems focused on highly pathogenic avian influenza (HPAI), a highly transmissible virus with a broad animal host range, wide geographic distribution, and rapid evolution with pandemic potential. We describe the development of a graph to include a wide range of data related to HPAI including pathogen-host associations, animal species distributions, and human population demographics, using a semantic ontology that defines relationships within the data and between datasets. We use the graph to perform a set of proof-of concept analyses validating the method and identifying new relationships and features of HPAI ecology, underscoring the generalizable value of knowledge graphs to ecology including their utility in revealing previously known relationships between entities and generating testable hypotheses in support of a deeper mechanistic understanding of ecological systems.
{"title":"Understanding Ecological Systems Using Knowledge Graphs: An Application to Highly Pathogenic Avian Influenza","authors":"Hailey Robertson, Barbara A Han, Adrian A. Castellanos, David Rosado, Guppy Stott, Ryan Zimmerman, John M. Drake, Ellie Graeden","doi":"10.1101/2024.09.05.611483","DOIUrl":"https://doi.org/10.1101/2024.09.05.611483","url":null,"abstract":"Ecological systems are complex. Representing heterogeneous knowledge about ecological systems is a pervasive challenge because data are generated from many subdisciplines, exist in disparate sources, and only capture a subset of important interactions underpinning system structure, resilience, and dynamics. Knowledge graphs have been successfully applied to organize heterogeneous data systematically and to predict new linkages representing unobserved relationships in complex systems. Though not previously applied broadly in ecology, knowledge graphs have much to offer in an era of global change when system dynamics are responding to rapid changes across multiple scales simultaneously. We developed a knowledge graph to demonstrate the method's utility for ecological problems focused on highly pathogenic avian influenza (HPAI), a highly transmissible virus with a broad animal host range, wide geographic distribution, and rapid evolution with pandemic potential. We describe the development of a graph to include a wide range of data related to HPAI including pathogen-host associations, animal species distributions, and human population demographics, using a semantic ontology that defines relationships within the data and between datasets. We use the graph to perform a set of proof-of concept analyses validating the method and identifying new relationships and features of HPAI ecology, underscoring the generalizable value of knowledge graphs to ecology including their utility in revealing previously known relationships between entities and generating testable hypotheses in support of a deeper mechanistic understanding of ecological systems.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.08.611906
Gerhard Christoph Marais, Isabelle Celeste Stratton, Jiri Hulcr, Andrew J Johnson
This study presents a tool for the identification of bark beetles. These pests are known for their potential to cause extensive damage to forests globally, as well as for uniform and homoplastic morphology which poses identification challenges. Utilizing a MaxViT-based deep learning model is an innovative approach to classify bark beetles down to the species level from images containing multiple beetles. The methodology involves a comprehensive process of data collection, preparation, and model training, leveraging pre-classified beetle species to ensure accuracy and reliability. The model's high F1 score estimates of 0.99 indicates its exceptional performance, demonstrating a strong ability to accurately classify species, including those previously unknown to the model. This makes it a valuable tool for applications in forest management and ecological research. Despite the controlled conditions of image collection and potential challenges in real-world application, this study provides the first model capable of identifying the bark beetle species, and by far the largest training set of images for any comparable insect group. We also designed a function that reports if a species appears to be unknown. Further research is suggested to enhance the model's generalization capabilities and scalability, emphasizing the integration of advanced machine learning techniques for improved species classification and the detection of invasive or undescribed species.
这项研究提供了一种识别树皮甲虫的工具。众所周知，这些害虫可能会对全球森林造成广泛破坏，而且它们的形态均匀一致，给识别工作带来了挑战。利用基于 MaxViT 的深度学习模型是一种创新方法，可从包含多种甲虫的图像中将树皮甲虫分类到物种级别。该方法涉及数据收集、准备和模型训练的综合过程，利用预先分类的甲虫物种来确保准确性和可靠性。该模型的 F1 分数估计值高达 0.99，这表明它具有卓越的性能，能够准确地对物种进行分类，包括模型以前未知的物种。这使其成为森林管理和生态研究领域的重要应用工具。尽管图像采集条件受控，在实际应用中也存在潜在挑战，但这项研究提供了第一个能够识别树皮甲虫物种的模型，也是迄今为止同类昆虫中最大的图像训练集。我们还设计了一个功能，用于报告未知物种。我们建议开展进一步的研究，以提高模型的泛化能力和可扩展性，重点是整合先进的机器学习技术，以改进物种分类和检测入侵或未描述的物种。
{"title":"Progress in Developing a Bark Beetle Identification Tool","authors":"Gerhard Christoph Marais, Isabelle Celeste Stratton, Jiri Hulcr, Andrew J Johnson","doi":"10.1101/2024.09.08.611906","DOIUrl":"https://doi.org/10.1101/2024.09.08.611906","url":null,"abstract":"This study presents a tool for the identification of bark beetles. These pests are known for their potential to cause extensive damage to forests globally, as well as for uniform and homoplastic morphology which poses identification challenges. Utilizing a MaxViT-based deep learning model is an innovative approach to classify bark beetles down to the species level from images containing multiple beetles. The methodology involves a comprehensive process of data collection, preparation, and model training, leveraging pre-classified beetle species to ensure accuracy and reliability. The model's high F1 score estimates of 0.99 indicates its exceptional performance, demonstrating a strong ability to accurately classify species, including those previously unknown to the model. This makes it a valuable tool for applications in forest management and ecological research. Despite the controlled conditions of image collection and potential challenges in real-world application, this study provides the first model capable of identifying the bark beetle species, and by far the largest training set of images for any comparable insect group. We also designed a function that reports if a species appears to be unknown. Further research is suggested to enhance the model's generalization capabilities and scalability, emphasizing the integration of advanced machine learning techniques for improved species classification and the detection of invasive or undescribed species.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BACKGROUND: Reproductive interference (i.e., sexual interaction between males of one species and females of another species that reduce the fitness of one or both the interacting individuals) is an important species interaction significantly affecting population dynamics and persistence. However, its exploitation in pest control remains overlooked. Here, we investigated the possible integration of reproductive interference into the Sterile Insect Technique (SIT) to develop a cross-species SIT. At this aim, we focused on the invasive pest species Drosophila suzukii and used D. melanogaster as the control species. First, we investigated the effect of irradiation on D. melanogaster male sterility and longevity Then, we tested the mating performance of irradiated males and their ability to reduce the D. suzukii fitness. RESULTS: We found by microcosm experiments that: i) irradiation induced high levels of D. melanogaster male sterility without reducing longevity; ii) irradiated D. melanogaster males court D. suzukii females as much as D. suzukii males and they couple, mate and fecund heterospecific females; iii) irradiated D. melanogaster males significantly reduce the offspring of D. suzukii females under different species ratios. CONCLUSIONS: Our results provide the first foundation to develop cross-species Sterile Insect Technique against D. suzukii and fuel to test this approach against other groups of pest species.
{"title":"Can reproductive interference be integrated into the Sterile Insect Technique for pest control? Insights from the spotted wing fly Drosophila suzukii","authors":"Flavia Cerasti, Massimo Cristofaro, Valentina Mastrantonio, Jessica Scifo, Adriano Verna, Daniele Canestrelli, Daniele Porretta","doi":"10.1101/2024.09.05.611447","DOIUrl":"https://doi.org/10.1101/2024.09.05.611447","url":null,"abstract":"BACKGROUND: Reproductive interference (i.e., sexual interaction between males of one species and females of another species that reduce the fitness of one or both the interacting individuals) is an important species interaction significantly affecting population dynamics and persistence. However, its exploitation in pest control remains overlooked. Here, we investigated the possible integration of reproductive interference into the Sterile Insect Technique (SIT) to develop a cross-species SIT. At this aim, we focused on the invasive pest species Drosophila suzukii and used D. melanogaster as the control species. First, we investigated the effect of irradiation on D. melanogaster male sterility and longevity Then, we tested the mating performance of irradiated males and their ability to reduce the D. suzukii fitness. RESULTS: We found by microcosm experiments that: i) irradiation induced high levels of D. melanogaster male sterility without reducing longevity; ii) irradiated D. melanogaster males court D. suzukii females as much as D. suzukii males and they couple, mate and fecund heterospecific females; iii) irradiated D. melanogaster males significantly reduce the offspring of D. suzukii females under different species ratios. CONCLUSIONS: Our results provide the first foundation to develop cross-species Sterile Insect Technique against D. suzukii and fuel to test this approach against other groups of pest species.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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