Pub Date : 2024-09-02DOI: 10.1101/2024.08.30.610510
Margje E. de Jong, Annabel J. Slettenhaar, Rienk W. Fokkema, Marion Leh, Elisabeth Barnreiter, Larry R. Griffin, Maarten J.J.E. Loonen, Eva Millesi, Børge Moe, Isabella B.R. Scheiber
Birds that migrate from temperate areas to the Arctic for breeding lose their strongest Zeitgeber of circadian organization when they cross the Arctic circle in spring — the 24h geophysical light-dark cycle. Under continuous daylight various behavioural and physiological patterns have been detected in both free-ranging and laboratory animals. To better understand the evolution of plasticity in circadian clocks, it is essential to study behavioural and physiological rhythmicity in the context of a species' ecology. Employing a multifaceted approach, which included wildlife cameras, accelerometers, and non-invasive sampling of hormone metabolites, we investigated activity patterns and corticosterone rhythmicity in a migratory herbivore, the Svalbard barnacle goose (Branta leucopsis), during its Arctic breeding season. We detected that females showed a combination of both ultradian and diel rhythmicity in incubation recesses and sleep, respectively. In both parents, rhythms in activity continued over the period, when goslings were present. During moult, many geese aligned activity with the tidal rhythm. Barnacle geese showed weak diel rhythmicity in excreted corticosterone metabolites. This suggests that while Arctic geese may adopt an alternative Zeitgeber during the Arctic summer to keep a diel rhythm, ultradian rhythmicity is crucial and geese are able to tune their rhythms flexibly to environmental conditions.
{"title":"Diel and seasonal rhythmicity in activity and corticosterone in an Arctic migratory herbivore: A multifaceted approach","authors":"Margje E. de Jong, Annabel J. Slettenhaar, Rienk W. Fokkema, Marion Leh, Elisabeth Barnreiter, Larry R. Griffin, Maarten J.J.E. Loonen, Eva Millesi, Børge Moe, Isabella B.R. Scheiber","doi":"10.1101/2024.08.30.610510","DOIUrl":"https://doi.org/10.1101/2024.08.30.610510","url":null,"abstract":"Birds that migrate from temperate areas to the Arctic for breeding lose their strongest <em>Zeitgeber</em> of circadian organization when they cross the Arctic circle in spring — the 24h geophysical light-dark cycle. Under continuous daylight various behavioural and physiological patterns have been detected in both free-ranging and laboratory animals. To better understand the evolution of plasticity in circadian clocks, it is essential to study behavioural and physiological rhythmicity in the context of a species' ecology. Employing a multifaceted approach, which included wildlife cameras, accelerometers, and non-invasive sampling of hormone metabolites, we investigated activity patterns and corticosterone rhythmicity in a migratory herbivore, the Svalbard barnacle goose (<em>Branta leucopsis</em>), during its Arctic breeding season. We detected that females showed a combination of both ultradian and diel rhythmicity in incubation recesses and sleep, respectively. In both parents, rhythms in activity continued over the period, when goslings were present. During moult, many geese aligned activity with the tidal rhythm. Barnacle geese showed weak diel rhythmicity in excreted corticosterone metabolites. This suggests that while Arctic geese may adopt an alternative <em>Zeitgeber</em> during the Arctic summer to keep a diel rhythm, ultradian rhythmicity is crucial and geese are able to tune their rhythms flexibly to environmental conditions.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181038","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 : 2024-09-02DOI: 10.1101/2024.08.31.610621
Tatiana Proboste, Abigail Turnlund, Andrew Bengsen, Matthew Gentle, Cameron Wilson, Lana Harriott, Rich Fuller, Darren Marshall, Ricardo Soares-Magalhaes
Feral pigs are threaten biodiversity in 54 countries worldwide, and cause an estimated $120 billion of damage annually in the US. Feral pigs imperil over 600 native species, and have directly driven 14 species to extinction. Moreover, feral pig populations pose a significant zoonotic disease threat to humans such as Japanese encephalitis, and act as reservoir for endemic pathogens such as Brucella and leptospirosis. Efforts to understand and control disease spread by feral pigs rely on models of social dynamics - how the animals interact with one another. Yet social dynamics are known to vary enormously from place to place, so knowledge generated in one location might not easily transfer. Here we fill a continental gap in our understanding of feral pig social dynamics by developing a proximity-based social network analysis approach to rapidly assess social interactions using animal tracking data. This method, applied to the continent of Australia, included 146 GPS-monitored feral pigs and revealed distinct patterns influenced by sex and season, with females demonstrating higher group cohesion and males acting as crucial connectors between independent groups. Contact rates are very high within groups, indicating rapid intra-group disease spread that contrasts with much slower potential for inter-group disease spread. Seasonal variations further complicate this dynamic, with contact rates being much higher in summer. The results show that, in Australia, targeting adult males in feral pig control programs could enhance efforts to contain disease outbreaks. Concern over the economic and human health impacts of animal diseases is higher than ever before. We urge a rapid global effort to use models of feral pig social interactions to develop efficient control strategies tailored to local conditions.
{"title":"Quantifying Feral Pig Interactions to Inform Disease Transmission Networks","authors":"Tatiana Proboste, Abigail Turnlund, Andrew Bengsen, Matthew Gentle, Cameron Wilson, Lana Harriott, Rich Fuller, Darren Marshall, Ricardo Soares-Magalhaes","doi":"10.1101/2024.08.31.610621","DOIUrl":"https://doi.org/10.1101/2024.08.31.610621","url":null,"abstract":"Feral pigs are threaten biodiversity in 54 countries worldwide, and cause an estimated $120 billion of damage annually in the US. Feral pigs imperil over 600 native species, and have directly driven 14 species to extinction. Moreover, feral pig populations pose a significant zoonotic disease threat to humans such as Japanese encephalitis, and act as reservoir for endemic pathogens such as <em>Brucella</em> and leptospirosis. Efforts to understand and control disease spread by feral pigs rely on models of social dynamics - how the animals interact with one another. Yet social dynamics are known to vary enormously from place to place, so knowledge generated in one location might not easily transfer. Here we fill a continental gap in our understanding of feral pig social dynamics by developing a proximity-based social network analysis approach to rapidly assess social interactions using animal tracking data. This method, applied to the continent of Australia, included 146 GPS-monitored feral pigs and revealed distinct patterns influenced by sex and season, with females demonstrating higher group cohesion and males acting as crucial connectors between independent groups. Contact rates are very high within groups, indicating rapid intra-group disease spread that contrasts with much slower potential for inter-group disease spread. Seasonal variations further complicate this dynamic, with contact rates being much higher in summer. The results show that, in Australia, targeting adult males in feral pig control programs could enhance efforts to contain disease outbreaks. Concern over the economic and human health impacts of animal diseases is higher than ever before. We urge a rapid global effort to use models of feral pig social interactions to develop efficient control strategies tailored to local conditions.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181042","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 : 2024-09-02DOI: 10.1101/2024.08.31.610633
Diego F Lozano-Cortes, Melina Rodriguez Moreno, Fernando A Zapata
Dispersal is a key ecological function in marine populations that are naturally fragmented and sometimes isolated. Pelagic larval duration (PLD) is thought to approximate the dispersal potential of coral reef fishes and may reflect the extent of connectivity in reef fish populations. Inter- and intra-specific variation in PLD of four damselfish species was investigated in the Colombian Pacific at four locations (two on the mainland coast, one at a continental island and one at an oceanic island) at multiple spatial scales (between localities and between sites within a single locality). Two of the species (Stegastes acapulcoensis and S. flavilatus) are broadly distributed on the continental coast while the other two (S. beebei and S. arcifrons) are largely restricted to oceanic islands. Nonetheless, individuals of continental species sporadically colonize oceanic habitats, and vice-versa. The PLD was estimated using counts of otolith growth increments from juveniles collected at all localities. Species with an oceanic distribution had longer PLDs than their congeners with continental distributions. Differences in PLD between the two continental species varied between localities and significant intra-specific spatial variability was observed between localities but not within a single locality. Although the species studied have the necessary PLD to reach all available habitat, there are no apparent colonization events between mainland and oceanic islands suggesting that their distribution is not limited by dispersal but by other processes. We discuss the possible underlying causes of the observed variability, and suggest the need to consider spatial variability in the development of dispersal models and connectivity patterns for better management of coral reef fish populations.
散布是海洋种群的一项关键生态功能，因为海洋种群是自然破碎的，有时甚至是孤立的。浮游幼体持续时间（PLD）被认为是珊瑚礁鱼类扩散潜力的近似值，可以反映珊瑚礁鱼类种群的连接程度。研究人员在哥伦比亚太平洋的四个地点（两个在大陆海岸，一个在大陆岛屿，一个在海洋岛屿），以多种空间尺度（地点之间和同一地点内不同地点之间）调查了四个豆娘物种幼体持续时间的种间和种内差异。其中两个物种（Stegastes acapulcoensis 和 S. flavilatus）广泛分布于大陆海岸，而另外两个物种（S. beebei 和 S. arcifrons）则主要局限于大洋岛屿。不过，大陆物种的个体也会零星地移居到海洋栖息地，反之亦然。利用在所有地点采集的幼鱼耳石生长增量计数来估算PLD。与分布于大陆的同类相比，分布于海洋的物种的 PLD 更长。两个大陆物种的 PLD 在不同地点之间存在差异，在不同地点之间观察到显著的种内空间差异，但在单个地点内则没有。虽然所研究的物种具有到达所有可用栖息地的必要 PLD，但在大陆和海洋岛屿之间没有明显的殖民事件，这表明它们的分布不是受扩散限制，而是受其他过程的限制。我们讨论了观察到的变异性的可能根本原因，并建议在开发散布模型和连接模式时需要考虑空间变异性，以便更好地管理珊瑚礁鱼类种群。
{"title":"Inter- and intra-specific variation in the pelagic larval duration of four Tropical Eastern Pacific damselfishes (Pomacentridae: Stegastes) with contrasting distribution patterns","authors":"Diego F Lozano-Cortes, Melina Rodriguez Moreno, Fernando A Zapata","doi":"10.1101/2024.08.31.610633","DOIUrl":"https://doi.org/10.1101/2024.08.31.610633","url":null,"abstract":"Dispersal is a key ecological function in marine populations that are naturally fragmented and sometimes isolated. Pelagic larval duration (PLD) is thought to approximate the dispersal potential of coral reef fishes and may reflect the extent of connectivity in reef fish populations. Inter- and intra-specific variation in PLD of four damselfish species was investigated in the Colombian Pacific at four locations (two on the mainland coast, one at a continental island and one at an oceanic island) at multiple spatial scales (between localities and between sites within a single locality). Two of the species (Stegastes acapulcoensis and S. flavilatus) are broadly distributed on the continental coast while the other two (S. beebei and S. arcifrons) are largely restricted to oceanic islands. Nonetheless, individuals of continental species sporadically colonize oceanic habitats, and vice-versa. The PLD was estimated using counts of otolith growth increments from juveniles collected at all localities. Species with an oceanic distribution had longer PLDs than their congeners with continental distributions. Differences in PLD between the two continental species varied between localities and significant intra-specific spatial variability was observed between localities but not within a single locality. Although the species studied have the necessary PLD to reach all available habitat, there are no apparent colonization events between mainland and oceanic islands suggesting that their distribution is not limited by dispersal but by other processes. We discuss the possible underlying causes of the observed variability, and suggest the need to consider spatial variability in the development of dispersal models and connectivity patterns for better management of coral reef fish populations.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181037","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 : 2024-09-02DOI: 10.1101/2024.08.30.610551
Jocelyn Lauzon, Jérémie Pelletier, Élanore Favron, Zihui Wang, Steven W Kembel
The phyllosphere - the aerial parts of plants - forms a vast microbial habitat that harbors diverse bacterial communities playing key roles in ecosystem function. The foliar surface is thus a promising study system to investigate biodiversity-ecosystem function relationships. Researchers have found a positive correlation between leaf bacterial diversity and ecosystem productivity, but the causality of this relationship has yet to be demonstrated. To understand how the diversity and composition of phyllosphere bacterial communities could cause variation in the growth of their host plants, we assembled synthetic communities composed of different diversity and compositions of Methylobacterium strains - a plant growth-promoting bacterial genus ubiquitous in the phyllosphere - that we inoculated on Arabidopsis thaliana grown in gnotobiotic conditions. We hypothesized that (1) increasing Methylobacterium diversity should cause an increase in host growth; (2) strains should differ in their impact on host growth; and (3) the relationship between bacterial diversity and plant productivity should be strain-dependent. Our results supported our three hypotheses but revealed unpredicted patterns in how A. thaliana leaf biomass varied according to inoculated Methylobacterium strain richness and identity. Increasing bacterial richness induced a higher host leaf biomass, but only after an initial reduction in biomass, suggesting competition alleviation by multispecies interactions. Two Methylobacterium strains showed beneficial effects on A. thaliana growth, and one strain was detrimental for the plant. Community composition shaped the relationship between diversity and productivity, highlighting the importance of community mutualistic and antagonistic interactions. Furthermore, niche complementarity was likely the main ecological mechanism driving the diversity-productivity relationship in our study system. By demonstrating the causal effects of Methylobacterium community diversity and composition on host plant growth, our experiment shed light on the importance of phyllosphere bacteria in terrestrial ecosystem functioning.
{"title":"Richness and composition of phyllosphere Methylobacterium communities cause variation in Arabidopsis thaliana growth","authors":"Jocelyn Lauzon, Jérémie Pelletier, Élanore Favron, Zihui Wang, Steven W Kembel","doi":"10.1101/2024.08.30.610551","DOIUrl":"https://doi.org/10.1101/2024.08.30.610551","url":null,"abstract":"The phyllosphere - the aerial parts of plants - forms a vast microbial habitat that harbors diverse bacterial communities playing key roles in ecosystem function. The foliar surface is thus a promising study system to investigate biodiversity-ecosystem function relationships. Researchers have found a positive correlation between leaf bacterial diversity and ecosystem productivity, but the causality of this relationship has yet to be demonstrated. To understand how the diversity and composition of phyllosphere bacterial communities could cause variation in the growth of their host plants, we assembled synthetic communities composed of different diversity and compositions of Methylobacterium strains - a plant growth-promoting bacterial genus ubiquitous in the phyllosphere - that we inoculated on Arabidopsis thaliana grown in gnotobiotic conditions. We hypothesized that (1) increasing Methylobacterium diversity should cause an increase in host growth; (2) strains should differ in their impact on host growth; and (3) the relationship between bacterial diversity and plant productivity should be strain-dependent. Our results supported our three hypotheses but revealed unpredicted patterns in how A. thaliana leaf biomass varied according to inoculated Methylobacterium strain richness and identity. Increasing bacterial richness induced a higher host leaf biomass, but only after an initial reduction in biomass, suggesting competition alleviation by multispecies interactions. Two Methylobacterium strains showed beneficial effects on A. thaliana growth, and one strain was detrimental for the plant. Community composition shaped the relationship between diversity and productivity, highlighting the importance of community mutualistic and antagonistic interactions. Furthermore, niche complementarity was likely the main ecological mechanism driving the diversity-productivity relationship in our study system. By demonstrating the causal effects of Methylobacterium community diversity and composition on host plant growth, our experiment shed light on the importance of phyllosphere bacteria in terrestrial ecosystem functioning.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181040","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 : 2024-09-02DOI: 10.1101/2024.09.02.610701
Justin Campbell, Aarin Allen, Danielle Sattelberger, Matthew White, James Fourqurean
The first record of Halophila stipulacea is reported for the continental waters of the United States. In August 2024, a small meadow was identified inside Crandon Marina on Key Biscayne, Florida, USA. Following surveys have revealed that H. stipulacea has spread to adjacent areas immediately outside of the marina, often growing either in close proximity to, or interspersed with, the native seagrasses Thalassia testudinum, Syringodium filiforme, and Halodule wrightii. This serves as an initial report and extends the geographic scope of this introduced species in the Western Atlantic basin.
{"title":"First record of the seagrass Halophila stipulacea (Forskkal) Ascherson in the waters of the continental United States (Key Biscayne, Florida)","authors":"Justin Campbell, Aarin Allen, Danielle Sattelberger, Matthew White, James Fourqurean","doi":"10.1101/2024.09.02.610701","DOIUrl":"https://doi.org/10.1101/2024.09.02.610701","url":null,"abstract":"The first record of Halophila stipulacea is reported for the continental waters of the United States. In August 2024, a small meadow was identified inside Crandon Marina on Key Biscayne, Florida, USA. Following surveys have revealed that H. stipulacea has spread to adjacent areas immediately outside of the marina, often growing either in close proximity to, or interspersed with, the native seagrasses Thalassia testudinum, Syringodium filiforme, and Halodule wrightii. This serves as an initial report and extends the geographic scope of this introduced species in the Western Atlantic basin.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181036","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 : 2024-09-02DOI: 10.1101/2024.08.30.610482
Xiaowei Lin, Jialu Wan, Qingyi Luo, Qinghua Cai, Ming-Chih Chiu, Vincent H. Resh
Climate fluctuations exhibit spatial heterogeneity in influencing ecological processes and community dynamics. However, the mechanisms underlying these impacts on biodiversity remain largely unexplored. This study investigates how spatial variations in climate fluctuations affect the relative significance of ecological processes shaping invertebrate community dynamics across 15 rivers in the European Iberian Peninsula over 21 years. Spatial shifts in community dynamics were driven by a combination of deterministic (climatic filtering) and stochastic (temporal variability) processes. Notably, the dominance of deterministic versus stochastic processes showed an elevation-dependent pattern characterized by a single peak. Analyzing community dynamics across different elevations provides a foundational basis for predicting and mitigating the biodiversity impacts of climate change, guiding effective conservation strategies.
{"title":"Spatial Heterogeneity of Climate Fluctuations Shapes Ecological Processes and Community Dynamics in Riverine Invertebrates Across a Landscape","authors":"Xiaowei Lin, Jialu Wan, Qingyi Luo, Qinghua Cai, Ming-Chih Chiu, Vincent H. Resh","doi":"10.1101/2024.08.30.610482","DOIUrl":"https://doi.org/10.1101/2024.08.30.610482","url":null,"abstract":"Climate fluctuations exhibit spatial heterogeneity in influencing ecological processes and community dynamics. However, the mechanisms underlying these impacts on biodiversity remain largely unexplored. This study investigates how spatial variations in climate fluctuations affect the relative significance of ecological processes shaping invertebrate community dynamics across 15 rivers in the European Iberian Peninsula over 21 years. Spatial shifts in community dynamics were driven by a combination of deterministic (climatic filtering) and stochastic (temporal variability) processes. Notably, the dominance of deterministic versus stochastic processes showed an elevation-dependent pattern characterized by a single peak. Analyzing community dynamics across different elevations provides a foundational basis for predicting and mitigating the biodiversity impacts of climate change, guiding effective conservation strategies.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142181043","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 : 2024-09-02DOI: 10.1101/2024.08.30.610541
Na Wei, Madelynn Nakaji-Conley
Background and aims: Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the plant rhizosphere remains limited. Methods: By leveraging a 'natural' experiment in urban farming with fields of different ages and multiple plant genotypes, we tracked the relative abundance, richness, and microbial networks of plant pathogens, mycorrhizal fungi, and saprotrophic fungi across fields over two years. Results: We observed an increase in the relative abundance of plant pathogens in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. Unlike plant pathogens and mycorrhizal fungi, the relative abundance of saprotrophic fungi remained similar among fields. While the richness of plant pathogens and saprotrophic fungi were similar across fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogens remained similar across fields. Conclusion: Our study reveals contrasting dynamics of essential soil fungal functional groups in the plant rhizosphere, and provides a predictive insight into the potential shifts in soil function and their impact on plant productivity.
{"title":"Contrasting dynamics of soil fungal functional groups in the plant rhizosphere","authors":"Na Wei, Madelynn Nakaji-Conley","doi":"10.1101/2024.08.30.610541","DOIUrl":"https://doi.org/10.1101/2024.08.30.610541","url":null,"abstract":"Background and aims: Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the plant rhizosphere remains limited. Methods: By leveraging a 'natural' experiment in urban farming with fields of different ages and multiple plant genotypes, we tracked the relative abundance, richness, and microbial networks of plant pathogens, mycorrhizal fungi, and saprotrophic fungi across fields over two years. Results: We observed an increase in the relative abundance of plant pathogens in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. Unlike plant pathogens and mycorrhizal fungi, the relative abundance of saprotrophic fungi remained similar among fields. While the richness of plant pathogens and saprotrophic fungi were similar across fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogens remained similar across fields. Conclusion: Our study reveals contrasting dynamics of essential soil fungal functional groups in the plant rhizosphere, and provides a predictive insight into the potential shifts in soil function and their impact on plant productivity.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223719","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 : 2024-08-12DOI: 10.1101/2024.08.06.606794
Christian Damgaard
To understand and estimate the effects of environmental drivers on wet heathland vegetation, pin-point cover data from 42 sites sampled during a 15-year period was regressed onto environmental variables (nitrogen deposition, soil pH, soil C-N ratio, soil type, precipitation and grazing) in a spatio-temporal structural equation model using a Bayesian hierarchical model structure with latent variables to model the effect of measurement and sampling uncertainties. The results suggest that the modelled environmental variables have various regulating effects on the large-scale spatial variation as well as plant community dynamics in wet heathlands. Most noticeably, nitrogen deposition and yearly precipitation had relatively large and opposite effects on the characteristic species Erica tetralix and Molinia caerulea, where nitrogen deposition had negative effects on E. tetralix and positive effects on M. caerulea. The results of this study differed in important qualitative aspects from the findings of an earlier study where comparable data from a shorter time-series (7 years instead of 15 years) were analyzed with a similar model, which suggests that relatively long time-series are needed for studying ecosystem dynamics. Furthermore, it was concluded that the effect of nitrogen deposition on plant community dynamics mainly was through direct effects, whereas the effect of soil type on plant community dynamics was both direct and indirect mediated by the effect of soil type on soil pH. It was concluded that the modeled environmental variables are sufficient for predicting the average plant community dynamics of wet heathlands. However, caution and humbleness are required if the fitted model is used for generating local ecological predictions as input to a process of generating adaptive management plans for specific wet heathland sites. Moreover, the results suggest that the ratio between the two species E. tetralix and M. caerulea may be used as an indicator for the conservation status of wet heathlands.
{"title":"Ecosystem dynamics in wet heathlands: spatial and temporal effects of environmental drivers on the vegetation","authors":"Christian Damgaard","doi":"10.1101/2024.08.06.606794","DOIUrl":"https://doi.org/10.1101/2024.08.06.606794","url":null,"abstract":"To understand and estimate the effects of environmental drivers on wet heathland vegetation, pin-point cover data from 42 sites sampled during a 15-year period was regressed onto environmental variables (nitrogen deposition, soil pH, soil C-N ratio, soil type, precipitation and grazing) in a spatio-temporal structural equation model using a Bayesian hierarchical model structure with latent variables to model the effect of measurement and sampling uncertainties. The results suggest that the modelled environmental variables have various regulating effects on the large-scale spatial variation as well as plant community dynamics in wet heathlands. Most noticeably, nitrogen deposition and yearly precipitation had relatively large and opposite effects on the characteristic species Erica tetralix and Molinia caerulea, where nitrogen deposition had negative effects on E. tetralix and positive effects on M. caerulea. The results of this study differed in important qualitative aspects from the findings of an earlier study where comparable data from a shorter time-series (7 years instead of 15 years) were analyzed with a similar model, which suggests that relatively long time-series are needed for studying ecosystem dynamics. Furthermore, it was concluded that the effect of nitrogen deposition on plant community dynamics mainly was through direct effects, whereas the effect of soil type on plant community dynamics was both direct and indirect mediated by the effect of soil type on soil pH. It was concluded that the modeled environmental variables are sufficient for predicting the average plant community dynamics of wet heathlands. However, caution and humbleness are required if the fitted model is used for generating local ecological predictions as input to a process of generating adaptive management plans for specific wet heathland sites. Moreover, the results suggest that the ratio between the two species E. tetralix and M. caerulea may be used as an indicator for the conservation status of wet heathlands.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930765","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 : 2024-08-11DOI: 10.1101/2024.08.11.607477
Takumaru Miwa, Naoya Miyashita, Chisato Numa, Hideyuki Doi
Forest canopies, known for their high biodiversity, are essential for understanding forest ecosystems. Traditional methods for canopy surveys, such as tree climbing and canopy walkways, face challenges related to safety, cost, and time constraints. Environmental DNA (eDNA) analysis, which involves examining DNA from environmental samples, offers a promising alternative for these surveys. This study investigates the feasibility of using rainwater to collect eDNA from forest canopies, utilizing rain's natural ability to wash away DNA from hard-to-reach areas. By comparing DNA analysis results from rainwater with conventional records obtained through visual and capture surveys, this research aims to validate the effectiveness and reliability of this method. Preliminary findings suggest that eDNA analysis from rainwater could provide an efficient approach to canopy biodiversity surveys, though further validation is required. This study marks an important first step towards developing eDNA analysis as a complementary tool for forest canopy research.
森林树冠以其高度的生物多样性而闻名，对于了解森林生态系统至关重要。传统的树冠调查方法，如爬树和树冠走道，面临着安全、成本和时间限制等方面的挑战。环境 DNA（eDNA）分析涉及检测环境样本中的 DNA，为这些调查提供了一种很有前景的替代方法。本研究调查了利用雨水从森林树冠收集 eDNA 的可行性，利用雨水冲刷难以到达区域 DNA 的自然能力。通过将雨水中的 DNA 分析结果与通过目测和捕捉调查获得的传统记录进行比较，本研究旨在验证这种方法的有效性和可靠性。初步研究结果表明，从雨水中分析 eDNA 可以为树冠生物多样性调查提供一种有效的方法，但还需要进一步验证。这项研究迈出了重要的第一步，将 eDNA 分析发展成为森林冠层研究的补充工具。
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Pub Date : 2024-08-10DOI: 10.1101/2024.08.05.606345
Andrea Zampetti, Davide Mirante, Pablo Palencia, Luca Santini
Camera-traps are valuable tools for estimating wildlife population density, and recently developed models enable density estimation without the need for individual recognition. Still, processing and analysis of camera-trap data are extremely time-consuming. While algorithms for automated species classification are becoming more common, they have only served as supporting tools, limiting their true potential in being implemented in ecological analyses without human supervision. Here, we assessed the capability of two camera-trap based models to provide robust density estimates when image classification is carried out by machine learning algorithms. We simulated density estimation with Camera-Traps Distance Sampling (CT-DS) and Random Encounter Model (REM) under different scenarios of automated image classification. We then applied the two models to obtain density estimates of three focal species (roe deer Capreolus capreolus, red fox Vulpes vulpes, and Eurasian badger Meles meles) in a reserve in central Italy. Species detection and classification was carried out both by the user and machine learning algorithms (respectively, MegaDetector and Wildlife Insights), and all outputs were used to estimate density and ultimately compared. Simulation results suggested that the CT-DS model could provide robust density estimates even at poor algorithm performances (down to 50% of correctly classified images), while the REM model is more unpredictable and depends on multiple factors. Density estimates obtained from the MegaDetector output were highly consistent for both models with the manually labelled images. While Wildlife Insights performance differed greatly between species (recall: badger = 0.15; roe deer = 0.56; fox = 0.75), CT-DS estimates did not vary significantly; on the contrary, REM systematically overestimated density, with little overlap in standard errors. We conclude that CT-DS and REM models can be robust to the loss of images when machine learning algorithms are used to identify animals, with the CT-DS being an ideal candidate for applications in a fully unsupervised framework. We propose guidelines to evaluate when and how to integrate machine learning in the analysis of camera-trap data for density estimation, further strengthening the applicability of camera traps as a cost-effective method for density estimation in (spatially and temporally) extensive multi-species monitoring programs.
{"title":"Towards an automated protocol for wildlife density estimation using camera-traps","authors":"Andrea Zampetti, Davide Mirante, Pablo Palencia, Luca Santini","doi":"10.1101/2024.08.05.606345","DOIUrl":"https://doi.org/10.1101/2024.08.05.606345","url":null,"abstract":"Camera-traps are valuable tools for estimating wildlife population density, and recently developed models enable density estimation without the need for individual recognition. Still, processing and analysis of camera-trap data are extremely time-consuming. While algorithms for automated species classification are becoming more common, they have only served as supporting tools, limiting their true potential in being implemented in ecological analyses without human supervision. Here, we assessed the capability of two camera-trap based models to provide robust density estimates when image classification is carried out by machine learning algorithms. We simulated density estimation with Camera-Traps Distance Sampling (CT-DS) and Random Encounter Model (REM) under different scenarios of automated image classification. We then applied the two models to obtain density estimates of three focal species (roe deer Capreolus capreolus, red fox Vulpes vulpes, and Eurasian badger Meles meles) in a reserve in central Italy. Species detection and classification was carried out both by the user and machine learning algorithms (respectively, MegaDetector and Wildlife Insights), and all outputs were used to estimate density and ultimately compared. Simulation results suggested that the CT-DS model could provide robust density estimates even at poor algorithm performances (down to 50% of correctly classified images), while the REM model is more unpredictable and depends on multiple factors. Density estimates obtained from the MegaDetector output were highly consistent for both models with the manually labelled images. While Wildlife Insights performance differed greatly between species (recall: badger = 0.15; roe deer = 0.56; fox = 0.75), CT-DS estimates did not vary significantly; on the contrary, REM systematically overestimated density, with little overlap in standard errors. We conclude that CT-DS and REM models can be robust to the loss of images when machine learning algorithms are used to identify animals, with the CT-DS being an ideal candidate for applications in a fully unsupervised framework. We propose guidelines to evaluate when and how to integrate machine learning in the analysis of camera-trap data for density estimation, further strengthening the applicability of camera traps as a cost-effective method for density estimation in (spatially and temporally) extensive multi-species monitoring programs.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141930767","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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