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Dick Roelofs - One of the best experts on this subject based on the ideXlab platform.
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antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the Soil living Invertebrate folsomia candida
Scientific Reports, 2019Co-Authors: Valeria Agamennone, Nico M. Van Straalen, A Brouwer, Dick RoelofsAbstract:The microbiome associated with an animal’s gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about Soil Invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the Soil Invertebrate Folsomia candida, an established model organism in Soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia’s metagenome play a role in the digestion of recalcitrant Soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the Soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
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Mechanisms of phenanthrene toxicity in the Soil Invertebrate, Enchytraeus crypticus
Environmental toxicology and chemistry, 2016Co-Authors: Dick Roelofs, Cornelis A.m. Van Gestel, Rita C. Bicho, Tjalf E. De Boer, Marta P. Castro-ferreira, Kora Montagne-wajer, Amadeu M.v.m. Soares, Nico M. Van Straalen, Mónica J.b. AmorimAbstract:Polycyclic aromatic hydrocarbons (PAHs) continue to cause environmental challenges as a result of their release into the environment by a great variety of anthropogenic activities and their accumulation in Soils. Studies were conducted on the toxicological effect of the model PAH phenanthrene using the Soil Invertebrate model Enchytraeus crypticus at the individual, tissue, and molecular levels. Animals were exposed for 2 d and 21 d to phenanthrene concentrations corresponding to the (previously estimated) 3-wk effective concentration, 10% (EC10) and EC50 for effects on reproduction. Gene expression profiling did not reveal a typical phenanthrene-induced biotransformation signature, as it usually does in arthropods and vertebrates. Instead, after 2 d of exposure, only general metabolic processes were affected, such as translation and adenosine triphosphate synthesis-coupled electron transport. Histological sections of tissues of 2-d exposed animals showed no deviations from control. In contrast, after prolonged exposure of up to 21 d, histopathological effects were found: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among Soil Invertebrate communities, which restricts read-across and extrapolation in the context of Soil ecological risk assessment. Environ Toxicol Chem 2016;35:2713-2720. © 2016 SETAC.
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transcriptional profiling of the Soil Invertebrate folsomia candida in pentachlorophenol contaminated Soil
Environmental Toxicology and Chemistry, 2015Co-Authors: Min Qiao, Dick Roelofs, Nico M. Van Straalen, Guangpeng Wang, Cai Zhang, Yongguan ZhuAbstract:Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on Soil Invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of collembola (Folsomia candida) in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure times, and the majority of them were found to be downregulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially expressed genes. Analyses of gene ontology annotation and enrichment revealed that cell cycle-related transcripts were significantly induced by PCP, indicating that PCP can stimulate cell proliferation in springtail, as has been reported in human breast cancer cells. Enrichment of functional terms related to steroid receptors was observed, particularly in 20 significant differentially expressed genes involved in chitin metabolism in response to PCP exposure. Combined with confirmation by quantitative polymerase chain reaction, the results indicate that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and that molting-associated genes may serve as possible biomarkers for assessing toxicological effects.
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genetic structure of Soil Invertebrate populations collembolans earthworms and isopods
Applied Soil Ecology, 2013Co-Authors: Dalila Costa, Dick Roelofs, Martijn J T N Timmermans, Jose Paulo Sousa, Rui Ribeiro, Nico M. Van StraalenAbstract:a b s t r a c t Soil-living animals such as collembolans, earthworms and isopods are considered to be sedentary animals with only limited dispersal capacities. Therefore, gene flow among populations is expected to be low leading to significant population genetic differentiation due to random drift and local adaptation. We reviewed the literature to test this expectation. Our survey reveals a clear signature in the current pattern of genetic variation due to post-glacial colonization events. It also reveals that habitus can be a misleading predictor of dispersal capacity. In some species relatively high gene flow across considerable distances, most likely through passive dispersal (mediated by wind, water flow or animals), might counteract local genetic adaptation and will prevent loss of genetic variation.
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gene expression microarray analysis of heat stress in the Soil Invertebrate folsomia candida
Insect Molecular Biology, 2010Co-Authors: Benjamin Nota, Bauke Ylstra, Nico M Van Straalen, Dick RoelofsAbstract:Sudden temperature changes in Soil can induce stress in Soil-dwelling Invertebrates. Hyperthermic conditions have an impact on gene expression as one of the first steps. We use a transcriptomics approach using microarrays to identify expression changes in response to heat in the springtail Folsomia candida. An elevation of temperature (Δ 10 °C) altered the expression of 142 genes (116 up-, 26 down-regulated). Many up-regulated genes encoded heat shock proteins, enzymes involved in ATP synthesis, oxidative stress responsive enzymes and anion-transporting ATPases. Down-regulated were glycoside hydrolases, involved in catalysis of disaccharides. The small number of altered transcripts suggest a mild response to heat in this Soil Invertebrate, but further research is needed to confirm this. This study presents candidate genes for future functional studies concerning thermal stress in Soil-dwelling Invertebrates. © 2010 The Royal Entomological Society.
Mónica J.b. Amorim - One of the best experts on this subject based on the ideXlab platform.
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embryotoxicity of silver nanomaterials ag nm300k in the Soil Invertebrate enchytraeus crypticus functional assay detects ca channels shutdown
NanoImpact, 2021Co-Authors: Rita C. Bicho, Amadeu M.v.m. Soares, Janeck J Scottfordsmand, Augusto Faustino, Fatima Carvalho, Mónica J.b. AmorimAbstract:Abstract Despite that silver (Ag) is among the most studied nanomaterials (NM) in environmental species and Ag’s embryotoxicity is well known, there are no studies on Ag NMs embryotoxicity in Soil Invertebrates. Previous Full Life Cycle (FLC) studies in Enchytraeus crypticus, a standard Soil Invertebrate, showed that Ag materials decreased hatching success, which was confirmed to be a hatching delay effect for silver nitrate (AgNO3) and mortality for Ag NM300K. In the present study, we aimed to investigate if the impact of Ag takes place during the embryonic development, using histology and immunohistochemistry. E. crypticus cocoons were exposed to a range of concentrations of Ag NM300K (0–10–20–60–115 mg Ag/kg) and AgNO3 (0–20–45–60–96 mg Ag/kg) in LUFA 2.2 Soil, in an embryotoxicity test, being sampled at days 1, 2, 3 and 6 (3, 4, 5 and 7 days after cocoon laying). Measured endpoints included the number of embryonic structures, expression of transferrin receptor (TfR) and L type calcium channels (LTCC) through histological and immunohistochemistry analysis, respectively. Results confirmed that Ag materials affected the embryonic development, specifically at the blastula stage (day 3). The expression and localization of TfR in E. crypticus was shown in the teloblasts cells, although this transcytosis mechanism was not activated. Ag affected calcium (Ca) metabolism during embryonic development: for AgNO3, LTCC was initially activated, compensating the impact, for Ag NM300K, LTCC was not activated, hence no Ca balance, with irreversible consequences, i.e. terminated embryonic development. An Adverse Outcome Pathway was drafted, integrating the mechanisms here discovered with previous knowledge.
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multigenerational exposure to wcco nanomaterials epigenetics in the Soil Invertebrate enchytraeus crypticus
Nanomaterials, 2020Co-Authors: Rita C. Bicho, Janeck J Scottfordsmand, Mónica J.b. AmorimAbstract:It has become clear how important it is to assess longer term effects of (nano) materials in the environment given the current evidence showing how epigenetics drives response mechanisms. Here we studied global DNA methylation in standard Soil Invertebrate Enchytraeus crypticus over 224 days when exposed to nanostructured tungsten carbide cobalt (WCCo nanomaterials (NMs)) and to cobalt (CoCl2) in a multigenerational experiment. In order to assess the transgenerational effect, we used a multigenerational (MG) test design consisting of four generations in spiked Soil followed by two generations in clean Soil. Results showed that MG exposure to WCCo NMs caused global DNA methylation to increase, which continued in unexposed generations and was associated with an increase in reproduction (phenotypic effect). In general, WCCo NMs caused more (and more consistent) methylation than CoCl2.
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high throughput gene expression in Soil Invertebrate embryos mechanisms of cd toxicity in enchytraeus crypticus
Chemosphere, 2018Co-Authors: Susana I L Gomes, Rita C. Bicho, Amadeu M.v.m. Soares, Janeck J Scottfordsmand, Micael F M Goncalves, Carlos P Roca, Mónica J.b. AmorimAbstract:Abstract Gene expression can vary with the organisms' life stage. It is known that embryos can be more sensitive to toxicant exposure, as previously demonstrated for Enchytraeus crypticus (Oligochaeta) exposed to cadmium (Cd), known to cause embryotoxicity and hatching delay. It was shown that Ca enters embryos via the L-type Ca channels in the cocoon membrane, this being affected in Cd exposed embryos (Cd-Ca competition is well-known). In the present study, the embryotoxic mechanisms of Cd were studied via high-throughput gene expression for E. crypticus. Cocoons (1–2 days old), instead of the adult organism, were exposed in Cd spiked LUFA 2.2 Soil during 1 day. Results showed that Cd affected Ca homeostasis which is implicated in several other molecular processes. Several of the major modulators of Cd toxicity (e.g., impaired gene expression, cell cycle arrest, DNA and mitochondrial damage) were identified in the embryos showing its relevancy as a model in ecotoxicogenomics. The draft Adverse Outcome Pathway was improved. Previously was hypothesized that gene regulation mechanisms were activated to synthesize more Ca channel proteins – this was confirmed here. Further, novel evidences were that, besides the extracellular competition, Cd competes intracellularly which causes a reduction in Ca efflux, and potentiates Cd embryotoxicity.
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Mechanisms of phenanthrene toxicity in the Soil Invertebrate, Enchytraeus crypticus
Environmental toxicology and chemistry, 2016Co-Authors: Dick Roelofs, Cornelis A.m. Van Gestel, Rita C. Bicho, Tjalf E. De Boer, Marta P. Castro-ferreira, Kora Montagne-wajer, Amadeu M.v.m. Soares, Nico M. Van Straalen, Mónica J.b. AmorimAbstract:Polycyclic aromatic hydrocarbons (PAHs) continue to cause environmental challenges as a result of their release into the environment by a great variety of anthropogenic activities and their accumulation in Soils. Studies were conducted on the toxicological effect of the model PAH phenanthrene using the Soil Invertebrate model Enchytraeus crypticus at the individual, tissue, and molecular levels. Animals were exposed for 2 d and 21 d to phenanthrene concentrations corresponding to the (previously estimated) 3-wk effective concentration, 10% (EC10) and EC50 for effects on reproduction. Gene expression profiling did not reveal a typical phenanthrene-induced biotransformation signature, as it usually does in arthropods and vertebrates. Instead, after 2 d of exposure, only general metabolic processes were affected, such as translation and adenosine triphosphate synthesis-coupled electron transport. Histological sections of tissues of 2-d exposed animals showed no deviations from control. In contrast, after prolonged exposure of up to 21 d, histopathological effects were found: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among Soil Invertebrate communities, which restricts read-across and extrapolation in the context of Soil ecological risk assessment. Environ Toxicol Chem 2016;35:2713-2720. © 2016 SETAC.
Nico M. Van Straalen - One of the best experts on this subject based on the ideXlab platform.
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antimicrobial activity and carbohydrate metabolism in the bacterial metagenome of the Soil living Invertebrate folsomia candida
Scientific Reports, 2019Co-Authors: Valeria Agamennone, Nico M. Van Straalen, A Brouwer, Dick RoelofsAbstract:The microbiome associated with an animal’s gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about Soil Invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the Soil Invertebrate Folsomia candida, an established model organism in Soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia’s metagenome play a role in the digestion of recalcitrant Soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the Soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
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Mechanisms of phenanthrene toxicity in the Soil Invertebrate, Enchytraeus crypticus
Environmental toxicology and chemistry, 2016Co-Authors: Dick Roelofs, Cornelis A.m. Van Gestel, Rita C. Bicho, Tjalf E. De Boer, Marta P. Castro-ferreira, Kora Montagne-wajer, Amadeu M.v.m. Soares, Nico M. Van Straalen, Mónica J.b. AmorimAbstract:Polycyclic aromatic hydrocarbons (PAHs) continue to cause environmental challenges as a result of their release into the environment by a great variety of anthropogenic activities and their accumulation in Soils. Studies were conducted on the toxicological effect of the model PAH phenanthrene using the Soil Invertebrate model Enchytraeus crypticus at the individual, tissue, and molecular levels. Animals were exposed for 2 d and 21 d to phenanthrene concentrations corresponding to the (previously estimated) 3-wk effective concentration, 10% (EC10) and EC50 for effects on reproduction. Gene expression profiling did not reveal a typical phenanthrene-induced biotransformation signature, as it usually does in arthropods and vertebrates. Instead, after 2 d of exposure, only general metabolic processes were affected, such as translation and adenosine triphosphate synthesis-coupled electron transport. Histological sections of tissues of 2-d exposed animals showed no deviations from control. In contrast, after prolonged exposure of up to 21 d, histopathological effects were found: chloragogenous cells were highly vacuolated and hypertrophic. This was corroborated by differential expression of genes related to immune response and oxidative stress at the transcriptomic level. The data exemplify the complexity and species-specific features of PAH toxicity among Soil Invertebrate communities, which restricts read-across and extrapolation in the context of Soil ecological risk assessment. Environ Toxicol Chem 2016;35:2713-2720. © 2016 SETAC.
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transcriptional profiling of the Soil Invertebrate folsomia candida in pentachlorophenol contaminated Soil
Environmental Toxicology and Chemistry, 2015Co-Authors: Min Qiao, Dick Roelofs, Nico M. Van Straalen, Guangpeng Wang, Cai Zhang, Yongguan ZhuAbstract:Pentachlorophenol (PCP), a widely used pesticide, is considered to be an endocrine disruptor. The molecular effects of chemicals with endocrine-disrupting potential on Soil Invertebrates are largely unknown. In the present study, the authors explored the transcriptional expression changes of collembola (Folsomia candida) in response to PCP contamination. A total of 92 genes were significantly differentially expressed at all exposure times, and the majority of them were found to be downregulated. In addition to the transcripts encoding cytochrome P450s and transferase enzymes, chitin-binding protein was also identified in the list of common differentially expressed genes. Analyses of gene ontology annotation and enrichment revealed that cell cycle-related transcripts were significantly induced by PCP, indicating that PCP can stimulate cell proliferation in springtail, as has been reported in human breast cancer cells. Enrichment of functional terms related to steroid receptors was observed, particularly in 20 significant differentially expressed genes involved in chitin metabolism in response to PCP exposure. Combined with confirmation by quantitative polymerase chain reaction, the results indicate that the adverse effects on reproduction of springtails after exposure to PCP can be attributed to a chemical-induced delay in the molting cycle and that molting-associated genes may serve as possible biomarkers for assessing toxicological effects.
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genetic structure of Soil Invertebrate populations collembolans earthworms and isopods
Applied Soil Ecology, 2013Co-Authors: Dalila Costa, Dick Roelofs, Martijn J T N Timmermans, Jose Paulo Sousa, Rui Ribeiro, Nico M. Van StraalenAbstract:a b s t r a c t Soil-living animals such as collembolans, earthworms and isopods are considered to be sedentary animals with only limited dispersal capacities. Therefore, gene flow among populations is expected to be low leading to significant population genetic differentiation due to random drift and local adaptation. We reviewed the literature to test this expectation. Our survey reveals a clear signature in the current pattern of genetic variation due to post-glacial colonization events. It also reveals that habitus can be a misleading predictor of dispersal capacity. In some species relatively high gene flow across considerable distances, most likely through passive dispersal (mediated by wind, water flow or animals), might counteract local genetic adaptation and will prevent loss of genetic variation.
Apolline Auclerc - One of the best experts on this subject based on the ideXlab platform.
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Decadal post-fire succession of Soil Invertebrate communities is dependent on the Soil surface properties in a northern temperate forest
Science of the Total Environment, 2019Co-Authors: Apolline Auclerc, James M Le Moine, Pierre-joseph Hatton, Jeffrey A Bird, Knute J NadelhofferAbstract:Although fires are common disturbances in North American forests, the extent to which Soil Invertebrate assemblages recover from burning remains unclear. Here, we examine long-term (14- to 101-yr) recoveries of Soil Invertebrate communities from common cut and burn treatments conducted at 6 to 26-yr intervals since 1911 in a deciduous forest in the upper Great Lakes region (USA). We characterize Soil surface macro-Invertebrate communities during both fall and spring across a long-term, experimental fire chronosequence to characterize Invertebrate community recovery at decadal time-scales and community changes between seasons. We posited that changes in Invertebrate community structure might, in turn, impact decomposition process. We sampled active organisms at the Soil surface using pitfall traps. We described understory vegetation, measured Soil properties, and conducted a 4-year litter bag study with big-toothed aspen leaves (Populus grandidentata). Invertebrate community responses followed a habitat accommodation model of succession showing that Invertebrate succession is dependent on the Soil surface properties. The fall and spring measures revealed that the densities of active Invertebrates were highest 101 years after fire. For a given pair of stands, a pattern of sharing higher percentage of taxa was denoted when stands were of similar age. Some species such as the beetle Stelidota octomaculata appeared to be indicator of the chronosequence succession stage because it tracks the successional increase of Quercus and acorn production at the study site. We also found a significant positive correlation between leaf decomposition of Soil macrofaunal accessible leaves and millipedes density across the chronosequence. We show that vegetation cover changes and related shifts in habitat structure occurring during post-fire succession are important in shaping communities assemblages. This finding highlights the importance of simultaneously considering abiotic-biotic factors together with above- and belowground measurements to better characterize controls on successional community dynamics after disturbance.
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A Thesaurus for Soil Invertebrate Trait-Based Approaches
PloS one, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Marie-angélique Laporte, Johanne Nahmani, Apolline Auclerc, Gaël Caro, Florence DubsAbstract:Soil Invertebrates are known to be much involved in Soil behaviour and therefore in the provision of ecosystem services. Functional trait-based approaches are methodologies which can be used to understand Soil Invertebrates' responses to their environment. They (i) improve the predictions and (ii) are less dependent on space and time. The way traits have been used recently has led to misunderstandings in the integration and interpretation of data. Trait semantics are especially concerned. The aim of this paper is to propose a thesaurus for Soil Invertebrate trait-based approaches. T-SITA, an Internet platform, is the first initiative to deal with the semantics of traits and ecological preferences for Soil Invertebrates. It reflects the agreement of a scientific expert community to fix semantic properties (e.g. definition) of approximately 100 traits and ecological preferences. In addition, T-SITA has been successfully linked with a fully operational database of Soil Invertebrate traits. Such a link enhances data integration and improves the scientific integrity of data.
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Current use of and future needs for Soil Invertebrate functional traits in community ecology
Basic and Applied Ecology, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Louis Deharveng, Florence Dubs, Johanne Nahmani, Apolline Auclerc, Sophie JoimelAbstract:Soil Invertebrates are assumed to play a major role in ecosystem dynamics, since they are involved in Soil functioning. Functional traits represent one of the main opportunities to bring new insights into the understanding of Soil Invertebrate responses to environmental changes. They are properties of individuals which govern their responses to their environment. As no clear conceptual overview of Soil Invertebrate trait definitions is available, we first stress that previously-described concepts of trait are applicable to Soil Invertebrate ecology after minor modification, as for instance the inclusion of behavioural traits. A decade of literature on the use of traits for assessing the effects of the environment on Soil Invertebrates is then reviewed. Trait-based approaches may improve the understanding of Soil Invertebrate responses to environmental changes as they help to establish relationships between environmental changes and Soil Invertebrates. Very many of the articles are dedicated to the effect of one kind of stress at limited spatial scales. Underlying mechanisms of assembly rules were sometimes assessed. The patterns described seemed to be similar to those described for other research fields (e.g. plants). The literature suggests that trait-based approaches have not been reliable over eco-regions. Nevertheless, current work gives some insights into which traits might be more useful than others to respond to a particular kind of environmental change. This review also highlights methodological advantages and drawbacks. First, trait-based approaches provide complementary information to taxonomic ones. However the literature does not allow us to differentiate between trait-based approaches and the use of a priori functional groups. It also reveals methodological shortcomings. For instance, the ambiguity of the trait names can impede data gathering, or the use of traits at a species level, which can hinder scientific interpretation as intra-specific variability is not taken into account and may lead to some biases. To overcome these shortcomings, the last part aims at proposing some solutions and prospects. It concerns notably the development of a trait database and a thesaurus to improve data management.
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Current use of and future needs for Soil Invertebrate functional traits in community ecology
Basic and Applied Ecology, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Louis Deharveng, Florence Dubs, Johanne Nahmani, Apolline Auclerc, Sophie JoimelAbstract:Soil Invertebrates are assumed to play a major role in ecosystem dynamics, since they are involved in Soil functioning. Functional traits represent one of the main opportunities to bring new insights into the understanding of Soil Invertebrate responses to environmental changes. They are properties of individuals which govern their responses to their environment. As no clear conceptual overview of Soil Invertebrate trait definitions is available, we first stress that previously-described concepts of trait are applicable to Soil Invertebrate ecology after minor modification, as for instance the inclusion of behavioural traits. A decade of literature on the use of traits for assessing the effects of the environment on Soil Invertebrates is then reviewed. Trait-based approaches may improve the understanding of Soil Invertebrate responses to environmental changes as they help to establish relationships between environmental changes and Soil Invertebrates. Very many of the articles are dedicated to the effect of one kind of stress at limited spatial scales. Underlying mechanisms of assembly rules were sometimes assessed. The patterns described seemed to be similar to those described for other research fields (e.g. plants). The literature suggests that trait-based approaches have not been reliable over eco-regions. Nevertheless, current work gives some insights into which traits might be more useful than others to respond to a particular kind of environmental change. This paper also highlights methodological advantages and drawbacks. First, trait-based approaches provide complementary information to taxonomic ones. However the literature does not allow us to differentiate between trait-based approaches and the use of a priori functional groups. It also reveals methodological shortcomings. For instance, the ambiguity of the trait names can impede data gathering, or the use of traits at a species level, which can hinder scientific interpretation as intra-specific variability is not taken into account and may lead to some biases. To overcome these shortcomings, the last part aims at proposing some solutions and prospects. It concerns notably the development of a trait database and a thesaurus to improve data management.
Florence Dubs - One of the best experts on this subject based on the ideXlab platform.
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A Thesaurus for Soil Invertebrate Trait-Based Approaches
PloS one, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Marie-angélique Laporte, Johanne Nahmani, Apolline Auclerc, Gaël Caro, Florence DubsAbstract:Soil Invertebrates are known to be much involved in Soil behaviour and therefore in the provision of ecosystem services. Functional trait-based approaches are methodologies which can be used to understand Soil Invertebrates' responses to their environment. They (i) improve the predictions and (ii) are less dependent on space and time. The way traits have been used recently has led to misunderstandings in the integration and interpretation of data. Trait semantics are especially concerned. The aim of this paper is to propose a thesaurus for Soil Invertebrate trait-based approaches. T-SITA, an Internet platform, is the first initiative to deal with the semantics of traits and ecological preferences for Soil Invertebrates. It reflects the agreement of a scientific expert community to fix semantic properties (e.g. definition) of approximately 100 traits and ecological preferences. In addition, T-SITA has been successfully linked with a fully operational database of Soil Invertebrate traits. Such a link enhances data integration and improves the scientific integrity of data.
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Current use of and future needs for Soil Invertebrate functional traits in community ecology
Basic and Applied Ecology, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Louis Deharveng, Florence Dubs, Johanne Nahmani, Apolline Auclerc, Sophie JoimelAbstract:Soil Invertebrates are assumed to play a major role in ecosystem dynamics, since they are involved in Soil functioning. Functional traits represent one of the main opportunities to bring new insights into the understanding of Soil Invertebrate responses to environmental changes. They are properties of individuals which govern their responses to their environment. As no clear conceptual overview of Soil Invertebrate trait definitions is available, we first stress that previously-described concepts of trait are applicable to Soil Invertebrate ecology after minor modification, as for instance the inclusion of behavioural traits. A decade of literature on the use of traits for assessing the effects of the environment on Soil Invertebrates is then reviewed. Trait-based approaches may improve the understanding of Soil Invertebrate responses to environmental changes as they help to establish relationships between environmental changes and Soil Invertebrates. Very many of the articles are dedicated to the effect of one kind of stress at limited spatial scales. Underlying mechanisms of assembly rules were sometimes assessed. The patterns described seemed to be similar to those described for other research fields (e.g. plants). The literature suggests that trait-based approaches have not been reliable over eco-regions. Nevertheless, current work gives some insights into which traits might be more useful than others to respond to a particular kind of environmental change. This review also highlights methodological advantages and drawbacks. First, trait-based approaches provide complementary information to taxonomic ones. However the literature does not allow us to differentiate between trait-based approaches and the use of a priori functional groups. It also reveals methodological shortcomings. For instance, the ambiguity of the trait names can impede data gathering, or the use of traits at a species level, which can hinder scientific interpretation as intra-specific variability is not taken into account and may lead to some biases. To overcome these shortcomings, the last part aims at proposing some solutions and prospects. It concerns notably the development of a trait database and a thesaurus to improve data management.
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Current use of and future needs for Soil Invertebrate functional traits in community ecology
Basic and Applied Ecology, 2014Co-Authors: Benjamin Pey, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Louis Deharveng, Florence Dubs, Johanne Nahmani, Apolline Auclerc, Sophie JoimelAbstract:Soil Invertebrates are assumed to play a major role in ecosystem dynamics, since they are involved in Soil functioning. Functional traits represent one of the main opportunities to bring new insights into the understanding of Soil Invertebrate responses to environmental changes. They are properties of individuals which govern their responses to their environment. As no clear conceptual overview of Soil Invertebrate trait definitions is available, we first stress that previously-described concepts of trait are applicable to Soil Invertebrate ecology after minor modification, as for instance the inclusion of behavioural traits. A decade of literature on the use of traits for assessing the effects of the environment on Soil Invertebrates is then reviewed. Trait-based approaches may improve the understanding of Soil Invertebrate responses to environmental changes as they help to establish relationships between environmental changes and Soil Invertebrates. Very many of the articles are dedicated to the effect of one kind of stress at limited spatial scales. Underlying mechanisms of assembly rules were sometimes assessed. The patterns described seemed to be similar to those described for other research fields (e.g. plants). The literature suggests that trait-based approaches have not been reliable over eco-regions. Nevertheless, current work gives some insights into which traits might be more useful than others to respond to a particular kind of environmental change. This paper also highlights methodological advantages and drawbacks. First, trait-based approaches provide complementary information to taxonomic ones. However the literature does not allow us to differentiate between trait-based approaches and the use of a priori functional groups. It also reveals methodological shortcomings. For instance, the ambiguity of the trait names can impede data gathering, or the use of traits at a species level, which can hinder scientific interpretation as intra-specific variability is not taken into account and may lead to some biases. To overcome these shortcomings, the last part aims at proposing some solutions and prospects. It concerns notably the development of a trait database and a thesaurus to improve data management.
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BETSI, a complete framework for studying Soil Invertebrate functional traits
2012Co-Authors: Mickaël Hedde, Benjamin Pey, Appoline Auclerc, Yvan Capowiez, Daniel Cluzeau, Jérôme Cortet, Thibaud Decaëns, Louis Deharveng, Florence Dubs, Fabien GrumiauxAbstract:BETSI, a complete framework for studying Soil Invertebrate functional traits. XVI ICSZ - International Colloquium on Soil Zoology