Stéphane Boyer | Unitec New Zealand (original) (raw)

Papers by Stéphane Boyer

The lack of understanding of complex food-web interactions has been a major gap in the history of... more The lack of understanding of complex food-web interactions has been a major gap in the history of biological control. In particular, a better understanding of the functioning of pest food-webs and how they vary between native and invaded geographical ranges is of prime interest for biological control research and associated integrated pest management. Technical limitations associated with the deciphering of complex food-webs can now be largely overcome by the use of high throughput DNA sequencing techniques such as Illumina MiSeq. We tested the efficiency of this next generation sequencing technology in a metabarcoding approach, to study aphid food-webs using the cabbage aphid as model. We compared the variations in structure and composition of aphid food-webs in the species' native range (United Kingdom, UK) and in an invaded range (New Zealand, NZ). We showed that Illumina MiSeq is a well suited technology to study complex aphid food-webs from aphid mummies. We found an unexpectedly high top down pressure in the NZ cabbage aphid food-web, which coupled to a large ratio of consumer species / prey ‡, § § | ¶ #, ‡

Background: Deciphering the amount of work provided by different co-authors of a scientific paper... more Background: Deciphering the amount of work provided by different co-authors of a scientific paper has been a recurrent problem in science. Despite the myriad of metrics available, the scientific community still largely relies on the position in the list of authors to evaluate contributions, a metric that attributes subjective and unfounded credit to co-authors. We propose an easy to apply, universally comparable and fair metric to measure and report co-authors contribution in the scientific literature. Methods: The proposed Author Contribution Index (ACI) is based on contribution percentages provided by the authors, preferably at the time of submission. Researchers can use ACI to compare the contributions of different authors, describe the contribution profile of a particular researcher or analyse how contribution changes through time. We provide such an analysis based on contribution percentages provided by 97 scientists from the field of ecology who voluntarily responded to an online anonymous survey.

Important knowledge gaps remain with regards to the ecology and the systematics of New Zealand’s ... more Important knowledge gaps remain with regards to the ecology and the systematics of New Zealand’s native earthworms. With many putative new species yet to be described, often specimens cannot be named, which makes species inventory, monitoring and community comparisons dif cult. Our work aimed to identify new putative taxa of New Zealand native species of earthworms, and describe their distribution in selected human-modi ed ecosystems. A total of 24 earthworm taxa (13 native and 11 exotic) were identi ed using a DNA barcoding approach focusing on 16S rDNA and COI (cytochrome oxidase subunit 1). The combination of morphological and molecular analyses were complementary in elucidating species identity. However, of the 13 native taxa, eight could not be named and are likely to be undescribed species from the genera Octochaetus, Maoridrilus and Deinodrilus. Most native species appeared to have a restricted geographic distribution linked to soil conditions, in particular pH and organic matter.

Attempts to restore native biodiversity into agricultural landscapes in New Zealand appear to be ... more Attempts to restore native biodiversity into agricultural landscapes in New Zealand appear to be compromised both by soil nitrogen enrichment from farming and N-leakage to the wider environment. We investigated whether interactions between native earthworms and a native rhizobium-inoculated leguminous shrub (Sophora microphylla) have a measurable effect on the mobility of nitrogen in an agricultural soil that has been nitrogen-enriched and colonised by exotic earthworms. Plants grew better in the presence of both native and exotic soil-burrowing earthworms. Rates of root nodulation were considerably enhanced in the presence of the native megascolecid anecic earthworm Maoridrilus transalpinus. This species consumed more organic matter in the presence of inoculated plants whilst marginally lowering soil pH and enhancing critical concentrations of nitrate, but also reducing nitrous oxide emissions. Earthworms raised dehydrogenase enzyme activity and microbial activity in soil, but this was not commensurate with rates of nodulation. Our results show that some combination of earthworm-mediated soil aeration, modification of moisture conditions in the rhizosphere and drilosphere, and comminution of organic matter, modify microbial communities and significantly impact the N cycle.

Biosolids can be a valuable fertilizer for agriculture and in ecological restoration, although th... more Biosolids can be a valuable fertilizer for agriculture and in ecological restoration, although there are concerns about contaminants. Earthworm activity, including vermicomposting of biosolids, may influence the efficacy of their use. We investigated how two New Zealand endemic anecic species of Maoridrilus (cf. Eisenia fetida) responded to biosolids amendment and affected the mobility of nutrients and trace elements as well as greenhouse gas emissions in biosolids-amended soil. Earthworms were incubated with mixtures of biosolids-amended soil (0, 6.25, 12.5, 25, and 50% biosolids by volume) for 21 d. All species survived in the soil–biosolids mixtures but not in 100% biosolids. The native earthworms, Maoridrilus transalpinus and Maoridrilus sp.2, increased KCl-extractable NH4+ and NO3− by up to 29%, substantially more than E. fetida. All species significantly increased microbial biomass carbon and Ca(NO3)2–extractable Cu but significantly decreased dehydrogenase enzymes activity in biosolids-amended soil. Concentrations of Ca(NO3)2–extractable Mg, S, Fe, Mn, Cd, Co, and Zn varied between earthworm species and with biosolids addition rates. New Zealand native earthworms exacerbated N2O emissions from soil, whereas E. fetida did not. Eisenia fetida is clearly a preferred species for vermicomposting biosolids and is more tolerant of high concentrations of biosolids. However, New Zealand native earthworms may be more suitable for improving the fertility of soil amended with biosolids.

Rethinking Ecology is a new open access, peer-reviewed journal that aims at fostering both forwar... more Rethinking Ecology is a new open access, peer-reviewed journal that aims at fostering both forward-thinking and the publication of novel ideas in all aspects of ecology, evolution and environmental science. This editorial briefly presents the rationale, unique features and the aspiration of the journal.

a r t i c l e i n f o Available online xxxx This special issue comprises seven papers: one review... more a r t i c l e i n f o Available online xxxx This special issue comprises seven papers: one review, one opinion and five experimental papers. Together, these articles illustrate how molecular tools and isotope analyses are improving our understanding of food-web structure and dynamics in agricultural systems. The papers collated here make use of the PCR-based DNA barcoding approach, protein-marking ELISA and the analysis of isotopic ratios to investigate a wide range of ecological questions. These studies advance our understanding of biodiversity and food-web dynamics in agroecosystems, provide direction on how to improve biological control of pests, detail the movement of energy and nutrient fluxes in soil food webs, and quantify anthropogenic disturbances in agroecosystems.

Land conversion and environmental changes associated with agronomic practices are believed to hav... more Land conversion and environmental changes associated with agronomic practices are believed to have led to the disappearance of New Zealand endemic earthworms from agricultural land. Introduced European earthworms have since largely replaced endemic species in farming systems. We investigated the impact of vegetation restoration on earthworm communities. Recolonization by endemic earthworms increased with time after restoration at two studied sites in the South Island of New Zealand. However, exotic species did not disappear with restoration of native vegetation, even after 30 years. The persistence of exotic species leads to the cohabitation of the two communities and potential for interspecific competition.

Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, w... more Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, where a single plant species is usually grown over vast areas. In these systems, it has historically been assumed that the concept of a food chain can describe the relationships between an insect pest and a single biocontrol agent. In reality, multiple potentially complex ecological interactions are involved, and these comprise food webs. However, identifying, analysing and quantifying the relative strengths of these multi-trophic interactions are very difficult using orthodox methods such as dissection and subsequent visual gut-content identification. An emerging field of study using molecular tools to analyse prey DNA in predators as well as parasitoid DNA within their hosts can now begin to address these impediments and help to better understand multi-trophic dynamics and improve biological control. In this article, we review the scientific literature published between 2000 and 2015 related to the use of molecular tools to analyse trophic interactions in agroecosystems in the context of biological control, using the ISI Web of Science search engine. A total of 213 articles were found and a steady increase in the volume of this literature occurred over the period studied. Based on the analysis of those publications, we propose future avenues in which advanced molecular tools can contribute to a mechanistic understanding of biological control, suggesting how this approach could help design agricultural systems based on agroecological techniques.

The effects of the association between grasses and fungal endophytes on orthopterans are very poo... more The effects of the association between grasses and fungal endophytes on orthopterans are very poorly studied although they are important grassland pests. Here, the endemic New Zealand weta, Hemiandrus sp. 'promontorius', and Festulolium loliaceum infected with Epichloë uncinata, were used to study the effect of endophyte-mediated resistance in grasses on this large orthopteran insect in the laboratory, and the effects of this interaction on the grass. The insect was presented with F. loliaceum with and without E. uncinata infection in no-choice and paired choice experiments. Other controls were Epichloë festucae-infected Festuca rubra and endophyte-free Lolium perenne. In no-choice experiments, persistent attempts by the insect to graze the endophyte-infected grasses (but promptly abandoning them) resulted in a significantly higher number of plants lost due to excision at their stems after the first bite (P = 0.004). The inability of affected grasses to compensate for the lost biomass resulted in a lack of significant difference between the dry biomass of endophyte-infected and endophyte-free controls (P = 0.206). However, in choice experiments, there was a preference for the endophyte-free controls when they were paired with the endophyte-infected grasses (P \ 0.05). The current work shows that endophyte-infected grasses can sustain high plant losses when attacked by an orthopteran insect in the absence of an alternative food source. This contrasts other endophyte/ herbivory experiments in which high herbivory occurs because chemical plant defences are at a low concentration or the endophytes have other non-toxin roles in the plant.

Ecosystem services (ES) such as pollination are vital for the continuous supply of food to a grow... more Ecosystem services (ES) such as pollination are vital for the continuous supply of food to a growing human population, but the decline in populations of insect pollinators worldwide poses a threat to food and nutritional security. Using a pollinator (honeybee) exclusion approach, we evaluated the impact of pollinator scarcity on production in four brassica fields, two producing hybrid seeds and two producing open-pollinated ones. There was a clear reduction in seed yield as pollination rates declined. Open-pollinated crops produced significantly higher yields than did the hybrid ones at all pollination rates. The hybrid crops required at least 0.50 of background pollination rates to achieve maximum yield, whereas in open-pollinated crops, 0.25 pollination rates were necessary for maximum yield. The total estimated economic value of pollination services provided by honeybees to the agricultural industry in New Zealand is NZD 1.96billionannually.ThisstudyindicatesthatlossofpollinationservicescanresultinsignificantdeclinesinproductionandhaveseriousimplicationsforthemarketeconomyinNewZealand.Dependingontheextentofhoneybeepopulationdecline,andassumingthatresultsindecliningpollinationservices,theestimatedeconomiclosstoNewZealandagriculturecouldbeintherangeofNZD1.96 billion annually. This study indicates that loss of pollination services can result in significant declines in production and have serious implications for the market economy in New Zealand. Depending on the extent of honeybee population decline, and assuming that results in declining pollination services, the estimated economic loss to New Zealand agriculture could be in the range of NZD 1.96billionannually.ThisstudyindicatesthatlossofpollinationservicescanresultinsignificantdeclinesinproductionandhaveseriousimplicationsforthemarketeconomyinNewZealand.Dependingontheextentofhoneybeepopulationdecline,andassumingthatresultsindecliningpollinationservices,theestimatedeconomiclosstoNewZealandagriculturecouldbeintherangeofNZD295-728 million annually.

Specimens of a previously unrecorded collembolan species were found in a field margin of a commer... more Specimens of a previously unrecorded collembolan species were found in a field margin of a commercial dairy farm near Christchurch, New Zealand. They were consistently observed apparently feeding on egg batches of the light brown apple moth Epiphyas postvittana, which were being used as bait to assess predation rate by potential biocontrol agents. The collembolan specimens were identified as the European species Dicyrtoma fusca based on published morphological descriptions of this species. DNA sequence data of the New Zealand specimens clustered with sequence data from GenBank of this species from Norway and England, confirming that D. fusca populations in New Zealand originated from Europe. A GenBank sequence had previously identified a collembolan species from Estonia as this species, but its position in the phylogeny indicates that it is a different species. Some morphological variations observed in arrangement of macrochaetae on the head were shown by sequence data to be intraspecific differences only.

[ Research paper thumbnail of Can ecosystem-scale translocations mitigate the impact of climate change on terrestrial biodiversity? Promises, pitfalls, and possibilities [version 1; referees: 2 approved](https://attachments.academia-assets.com/45605697/thumbnails/1.jpg)

Because ecological interactions are the first components of the ecosystem to be impacted by clima... more Because ecological interactions are the first components of the ecosystem to be impacted by climate change, future forms of threatened-species and ecosystem management should aim at conserving complete, functioning communities rather than single charismatic species. A possible way forward is the deployment of ecosystem-scale translocation (EST), where above-and below-ground elements of a functioning terrestrial ecosystem (including vegetation and topsoil) are carefully collected and moved together. Small-scale attempts at such practice have been made for the purpose of ecological restoration. By moving larger subsets of functioning ecosystems from climatically unstable regions to more stable ones, EST could provide a practical means to conserve mature and complex ecosystems threatened by climate change. However, there are a number of challenges associated with EST in the context of climate change mitigation, in particular the choice of donor and receptor sites. With the aim of fostering discussion and debate about the EST concept, we 1) outline the possible promises and pitfalls of EST in mitigating the impact of climate change on terrestrial biodiversity and 2) use a GIS-based approach to illustrate how potential source and receptor sites, where EST could be trialed and evaluated globally, could be identified.

To advance our restricted knowledge on mosquito biodiversity and distribution in Belgium, a natio... more To advance our restricted knowledge on mosquito biodiversity and distribution in Belgium, a national inventory started in 2007 (MODIRISK) based on a random selection of 936 collection points in three main environmental types: urban, rural and natural areas. Additionally, 64 sites were selected because of the risk of importing a vector or pathogen in these sites. Each site was sampled once between May and October 2007 and once in 2008 using Mosquito Magnet Liberty Plus traps. Diversity in pre-defined habitat types was calculated using three indices. The association between species and environmental types was assessed using a correspondence analysis. Twenty-three mosquito species belonging to traditionally recognized genera were found, including 21 indigenous and two exotic species. Highest species diversity (Simpson 0.765) and species richness (20 species) was observed in natural areas, although urban sites scored also well (Simpson 0.476, 16 species). Four clusters could be distinguished based on the correspondence analysis. The first one is related to human modified landscapes (such as urban, rural and industrial sites). A second is composed of species not associated with a specific habitat type, including the now widely distributed Anopheles plumbeus. A third group includes species commonly found in restored natural or bird migration areas, and a fourth cluster is composed of forest species. Outcomes of this study demonstrate the effectiveness of the designed sampling scheme and support the choice of the trap type. Obtained results of this first country-wide inventory of the Culicidae in Belgium may serve as a basis for risk assessment of emerging mosquito-borne diseases.

Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, w... more Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, where a single plant species is usually grown over vast areas. In these systems, it has historically been assumed that the concept of a food chain can describe the relationships between an insect pest and a single biocontrol agent. In reality, multiple potentially complex ecological interactions are involved, and these comprise food webs. However, identifying, analysing and quantifying the relative strengths of these multi- trophic interactions are very difficult using orthodox methods such as dissection and subsequent visual gut-content identification. An emerging field of study using molecular tools to analyse prey DNA in predators as well as parasitoid DNA within their hosts can now begin to address these impediments and help to better understand multi-trophic dynamics and improve biological control. In this article, we review the scientific literature published between 2000 and 2015 related to the use of molecular tools to analyse trophic interactions in agroecosystems in the context of biological control, using the ISI Web of Science search engine. A total of 213 articles were found and a steady increase in the volume of this literature occurred over the period studied. Based on the analysis of those publications, we propose future avenues in which advanced molecular tools can contribute to a mechanistic understanding of biological control, suggesting how this approach could help design agricultural systems based on agroecological techniques.

A B S T R A C T Native and exotic earthworms and plants co-exist on the margins of agricultural l... more A B S T R A C T Native and exotic earthworms and plants co-exist on the margins of agricultural land in New Zealand. Remnants of native vegetation support mixed assemblages of depleted populations of native Megascolecid earthworms together with apparently increasing invasive populations of introduced Lumbricidae. We question whether the survival and viability of these earthworm populations is a function of soil preference and whether there are significant differences in terms of how the two groups are influenced by and modify soil properties and plant growth. Choice chamber and mesocosm experiments, with and without plant rhizospheres, were used to study five species of native earthworms, two of which could be identified only by DNA barcoding, and four introduced exotic species. Both natives and exotics preferred agricultural soils to a plantation forest and a native forest soil. Earthworms also modified the physico-chemistry of soils and greenhouse gas emissions, with a marked interaction with root morphology of two native species of tea tree. Lesser differences were found between native and exotic earthworms than between functional groups. It is concluded that New Zealand's production landscapes provide novel habitats with clear benefits both to threatened species conservation and to soil ecosystem services.

Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, w... more Modern monocultural agro-ecosystems can be perceived as a simplification of natural ecosystems, where a single plant species is usually grown over vast areas. In these systems, it has historically been assumed that the concept of a food chain can describe the relationships between an insect pest and a single biocontrol agent. In reality, multiple potentially complex ecological interactions are involved, and these comprise food webs. However, identifying, analysing and quantifying the relative strengths of these multi- trophic interactions are very difficult using orthodox methods such as dissection and subsequent visual gut-content identification. An emerging field of study using molecular tools to analyse prey DNA in predators as well as parasitoid DNA within their hosts can now begin to address these impediments and help to better understand multi-trophic dynamics and improve biological control. In this article, we review the scientific literature published between 2000 and 2015 related to the use of molecular tools to analyse trophic interactions in agroecosystems in the context of biological control, using the ISI Web of Science search engine. A total of 213 articles were found and a steady increase in the volume of this literature occurred over the period studied. Based on the analysis of those publications, we propose future avenues in which advanced molecular tools can contribute to a mechanistic understanding of biological control, suggesting how this approach could help design agricultural systems based on agroecological techniques.