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20 Feb 2023
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Best organic farming deployment scenarios for pest control: a modeling approach

Towards model-guided organic farming expansion for crop pest management

Recommended by ORCID_LOGO based on reviews by Julia Astegiano, Lionel Hertzog and Sylvain Bart

Reduce the impact the intensification of human activities has on the environmental is the challenge the humanity faces today, a major challenge that could be compared to climbing Everest without an oxygen supply. Indeed, over-population, pollution, burning fossil fuels, and deforestation are all evils which have had hugely detrimental effects on the environment such as climate change, soil erosion, poor air quality, and scarcity of drinking water to name but a few. In response to the ever-growing consumer demand, agriculture has intensified massively along with a drastic increase in the use of chemicals to ensure an adequate food supply while controlling crop pests. In this context, to address the disastrous effects of the intensive usage of pesticides on both human health and biodiversity, organic farming (OF) revealed as a miracle remedy with multiple benefits. Delattre et al. (2023) present a powerful modelling approach to decipher the crossed effects of the landscape structure and the OF expansion scenario on the pest abundance, both in organic and conventional (CF) crop fields. To this end, the authors ingeniously combined a grid-based landscape model with a spatially explicit predator-pest model. Based on an extensive in silico simulation process, they explore a diversity of landscape structures differing in their amount of semi-natural habitats (SHN) and in their fragmentation, to finally propose a ranking of various expansion scenarios according to the pest control methods in organic farming as well as to the pest and predators’ dissemination capacities. In total, 9 landscape structures (3 proportions of SHN x 3 fragmentation levels) were crossed with 3 expansion scenarios (RD = a random distribution of OF and CF in the grid; IP = isolated CF are converted; GP = CF within aggregates are converted), 4 pest management practices, 3 initial densities and 36 biological parameter combinations driving the predator’ and pest’s population dynamics. This exhaustive exploration of possible combinations of landscape and farming practices highlighted the main drivers of the various OF expansion scenarios, such as increased spillover of predators in isolated OF/CF fields, increased pest management efficiency in large patches of CF and the importance of the distance between OF and CF. In the end, this study brings to light the crucial role that landscape planning plays when OF practices have limited efficiency on pests. It also provides convincing arguments to the fact that converting to organic isolated CF as a priority seems to be the most promising scenario to limit pest densities in CF crops while improving predator to pest ratios (considered as a proxy of conservation biological control) in OF ones without increasing pest densities. Once further completed with model calibration validation based on observed life history traits data for both predators and pests, this work should be very helpful in sustaining policy makers to convince farmers of engaging in organic farming.


Delattre T, Memah M-M, Franck P, Valsesia P, Lavigne C (2023) Best organic farming deployment scenarios for pest control: a modeling approach. bioRxiv, 2022.05.31.494006, ver. 2 peer-reviewed and recommended by Peer Community in Ecology.

Best organic farming deployment scenarios for pest control: a modeling approachThomas Delattre, Mohamed-Mahmoud Memah, Pierre Franck, Pierre Valsesia, Claire Lavigne<p style="text-align: justify;">Organic Farming (OF) has been expanding recently around the world in response to growing consumer demand and as a response to environmental concerns. Its share of agricultural landscapes is expected to increase in t...Agroecology, Biological control, Landscape ecologySandrine Charles2022-06-03 11:41:14 View
31 May 2023
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Conservation networks do not match the ecological requirements of amphibians

Amphibians under scrutiny - When human-dominated landscape mosaics are not in full compliance with their ecological requirements

Recommended by ORCID_LOGO based on reviews by Peter Vermeiren and 1 anonymous reviewer

Among vertebrates, amphibians are one of the most diverse groups with more than 7,000 known species. Amphibians occupy various ecosystems, including forests, wetlands, and freshwater habitats. Amphibians are known to be highly sensitive to changes in their environment, particularly to water quality and habitat degradation, so that monitoring abundance of amphibian populations can provide early warning signs of ecosystem disturbances that may also affect other organisms including humans (Bishop et al., 2012). Accordingly, efforts in habitat preservation and sustainable land and water management are necessary to safeguard amphibian populations.

In this context, Matutini et al. (2023) compared ecological requirements of amphibian species with the quality of agricultural landscape mosaics. Doing so, they identified critical gaps in existing conservation tools that include protected areas, green infrastructures, and inventoried sites. Matutini et al. (2023) focused on nine amphibian species in the Pays-de-la-Loire region where the landscape has been fashioned over the years by human activities. Three of the chosen amphibian species are living in a dense hedgerow mosaic landscape, while five others are more generalists.

Matutini et al. (2023) established multi-species habitat suitability maps, together with their levels of confidence, by combining single species maps with a probabilistic stacking method at 500-m resolution. From these maps, habitats were classified in five categories, from not suitable to highly suitable. Then, the circuit theory was used to map the potential connections between each highly suitable patch at the regional scale. Finally, comparing suitability maps with existing conservation tools, Matutini et al. (2023) were able to assess their coverage and efficiency.

Whatever their species status (endangered or not), Matutini et al. (2023) highlighted some discrepancies between the ecological requirements of amphibians in terms of habitat quality and the conservation tools of the landscape mosaic within which they are evolving. More specifically, Matutini et al. (2023) found that protected areas and inventoried sites covered only a small proportion of highly suitable habitats, while green infrastructures covered around 50% of the potential habitat for amphibian species. Such a lack of coverage and efficiency of protected areas brings to light that geographical sites with amphibian conservation challenges are known but not protected. Regarding the landscape fragmentation, Matutini et al. (2023) found that generalist amphibian species have a more homogeneous distribution of suitable habitats at the regional scale. They also identified two bottlenecks between two areas of suitable habitats, a situation that could prove critical to amphibian movements if amphibians were forced to change habitats to global change.

In conclusion, Matutini et al. (2023) bring convincing arguments in support of land-use species-conservation planning based on a better consideration of human-dominated landscape mosaics in full compliance with ecological requirements of the species that inhabit the regions concerned.


Bishop, P.J., Angulo, A., Lewis, J.P., Moore, R.D., Rabb, G.B., Moreno, G., 2012. The Amphibian Extinction Crisis - what will it take to put the action into the Amphibian Conservation Action Plan? Sapiens - Surveys and Perspectives Integrating Environment and Society 5, 1–16.

Matutini, F., Baudry, J., Fortin, M.-J., Pain, G., Pithon, J., 2023. Conservation networks do not match ecological requirements of amphibians. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Conservation networks do not match the ecological requirements of amphibiansMatutini Florence, Jacques Baudry, Marie-Josée Fortin, Guillaume Pain, Joséphine Pithon<p style="text-align: justify;">1. Amphibians are among the most threatened taxa as they are highly sensitive to habitat degradation and fragmentation. They are considered as model species to evaluate habitats quality in agricultural landscapes. I...Biodiversity, Biogeography, Human impact, Landscape ecology, Macroecology, Spatial ecology, Metacommunities & Metapopulations, Species distributions, Terrestrial ecologySandrine Charles2022-09-20 14:40:03 View
23 Mar 2020
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Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascades

Tell me what you’ve eaten, I’ll tell you how much you’ll eat (and be eaten)

Recommended by and based on reviews by Bastien Castagneyrol and 1 anonymous reviewer

Tritrophic interactions have a central role in ecological theory and applications [1-3]. Particularly, systems comprised of plants, herbivores and predators have historically received wide attention given their ubiquity and economic importance [4]. Although ecologists have long aimed to understand the forces that govern alternating ecological effects at successive trophic levels [5], several key open questions remain (at least partially) unanswered [6]. In particular, the analysis of complex food webs has questioned whether ecosystems can be viewed as a series of trophic chains [7,8]. Moreover, whether systems are mostly controlled by top-down (trophic cascades) or bottom-up processes remains an open question [6].
Traditionally, studies have addressed how species diversity at different food chain compartments affect the strength and direction of trophic cascades [9]. For example, many studies have tested whether biological control was more efficient with more than one species of natural enemies [10-12]. Much less attention has been given to the role of within-species variation in shaping trophic cascades [13]. In particular, whereas the impact of trait variation within species of plants or predators on successive trophic levels has been recently addressed [14,15], the impact of intraspecific herbivore variation is in its infancy (but see [16]). This is at odds with the resurgent acknowledgment of the importance of individual variation for several ecological processes operating at higher levels of biological organization [17].
Sources of variation within species can come in many flavours. In herbivores, striking ecological variation can be found among populations occurring on different host plants, which become genetically differentiated, thus forming host races [18,19]. Curiously, the impact of variation across host races on the strength of trophic cascades has, to date, not been explored. This is the gap that the manuscript by Sentis and colleagues [20] fills. They experimentally studied a curious tri-trophic system where the primary consumer, pea aphids, specializes in different plant hosts, creating intraspecific variation across biotypes. Interestingly, there is also ecological variation across lineages from the same biotype. The authors set up experimental food chains, where pea aphids from different lineages and biotypes were placed in their universal legume host (broad bean plants) and then exposed to a voracious but charming predator, ladybugs. The full factorial design of this experiment allowed the authors to measure vertical effects of intraspecific variation in herbivores on both plant productivity (top-down) and predator individual growth (bottom-up).
The results nicely uncover the mechanisms by which intraspecific differences in herbivores precipitates vertical modulation in food chains. Herbivore lineage and host-plant specialization shaped the strength of trophic cascades, but curiously these effects were not modulated by density-dependence. Further, ladybugs consuming pea aphids from different lineages and biotypes grew at distinct rates, revealing bottom-up effects of intraspecific variation in herbivores.
These findings are novel and exciting for several reasons. First, they show how intraspecific variation in intermediate food chain compartments can simultaneously reverberate both top-down and bottom-up effects. Second, they bring an evolutionary facet to the understanding of trophic cascades, providing valuable insights on how genetically differentiated populations play particular ecological roles in food webs. Finally, Sentis and colleagues’ findings [20] have critical implications well beyond their study systems. From an applied perspective, they provide an evident instance on how consumers’ evolutionary specialization matters for their role in ecosystems processes (e.g. plant biomass production, predator conversion rate), which has key consequences for biological control initiatives and invasive species management. From a conceptual standpoint, their results ignite the still neglected value of intraspecific variation (driven by evolution) in modulating the functioning of food webs, which is a promising avenue for future theoretical and empirical studies.


[1] Price, P. W., Bouton, C. E., Gross, P., McPheron, B. A., Thompson, J. N., & Weis, A. E. (1980). Interactions among three trophic levels: influence of plants on interactions between insect herbivores and natural enemies. Annual review of Ecology and Systematics, 11(1), 41-65. doi: 10.1146/
[2] Olff, H., Brown, V.K. & Drent, R.H. (1999). Herbivores: between plants and predators. Blackwell Science, Oxford.
[3] Tscharntke, T. & Hawkins, B.A. (2002). Multitrophic level interactions. Cambridge University Press. doi: 10.1017/CBO9780511542190
[4] Agrawal, A. A. (2000). Mechanisms, ecological consequences and agricultural implications of tri-trophic interactions. Current opinion in plant biology, 3(4), 329-335. doi: 10.1016/S1369-5266(00)00089-3
[5] Pace, M. L., Cole, J. J., Carpenter, S. R., & Kitchell, J. F. (1999). Trophic cascades revealed in diverse ecosystems. Trends in ecology & evolution, 14(12), 483-488. doi: 10.1016/S0169-5347(99)01723-1
[6] Abdala‐Roberts, L., Puentes, A., Finke, D. L., Marquis, R. J., Montserrat, M., Poelman, E. H., ... & Mooney, K. (2019). Tri‐trophic interactions: bridging species, communities and ecosystems. Ecology letters, 22(12), 2151-2167. doi: 10.1111/ele.13392
[7] Polis, G.A. & Winemiller, K.O. (1996). Food webs. Integration of patterns and dynamics. Chapmann & Hall, New York. doi: 10.1007/978-1-4615-7007-3
[8] Torres‐Campos, I., Magalhães, S., Moya‐Laraño, J., & Montserrat, M. (2020). The return of the trophic chain: Fundamental vs. realized interactions in a simple arthropod food web. Functional Ecology, 34(2), 521-533. doi: 10.1111/1365-2435.13470
[9] Polis, G. A., Sears, A. L., Huxel, G. R., Strong, D. R., & Maron, J. (2000). When is a trophic cascade a trophic cascade?. Trends in Ecology & Evolution, 15(11), 473-475. doi: 10.1016/S0169-5347(00)01971-6
[10] Sih, A., Englund, G., & Wooster, D. (1998). Emergent impacts of multiple predators on prey. Trends in ecology & evolution, 13(9), 350-355. doi: 10.1016/S0169-5347(98)01437-2
[11] Diehl, E., Sereda, E., Wolters, V., & Birkhofer, K. (2013). Effects of predator specialization, host plant and climate on biological control of aphids by natural enemies: a meta‐analysis. Journal of Applied Ecology, 50(1), 262-270. doi: 10.1111/1365-2664.12032
[12] Snyder, W. E. (2019). Give predators a complement: conserving natural enemy biodiversity to improve biocontrol. Biological control, 135, 73-82. doi: 10.1016/j.biocontrol.2019.04.017
[13] Des Roches, S., Post, D. M., Turley, N. E., Bailey, J. K., Hendry, A. P., Kinnison, M. T., ... & Palkovacs, E. P. (2018). The ecological importance of intraspecific variation. Nature Ecology & Evolution, 2(1), 57-64. doi: 10.1038/s41559-017-0402-5
[14] Bustos‐Segura, C., Poelman, E. H., Reichelt, M., Gershenzon, J., & Gols, R. (2017). Intraspecific chemical diversity among neighbouring plants correlates positively with plant size and herbivore load but negatively with herbivore damage. Ecology Letters, 20(1), 87-97. doi: 10.1111/ele.12713
[15] Start, D., & Gilbert, B. (2017). Predator personality structures prey communities and trophic cascades. Ecology letters, 20(3), 366-374. doi: 10.1111/ele.12735
[16] Turcotte, M. M., Reznick, D. N., & Daniel Hare, J. (2013). Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid. The American Naturalist, 181(S1), S46-S57. doi: 10.1086/668078
[17] Bolnick, D. I., Amarasekare, P., Araújo, M. S., Bürger, R., Levine, J. M., Novak, M., ... & Vasseur, D. A. (2011). Why intraspecific trait variation matters in community ecology. Trends in ecology & evolution, 26(4), 183-192. doi: 10.1016/j.tree.2011.01.009
[18] Drès, M., & Mallet, J. (2002). Host races in plant–feeding insects and their importance in sympatric speciation. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 357(1420), 471-492. doi: 10.1098/rstb.2002.1059
[19] Magalhães, S., Forbes, M. R., Skoracka, A., Osakabe, M., Chevillon, C., & McCoy, K. D. (2007). Host race formation in the Acari. Experimental and Applied Acarology, 42(4), 225-238. doi: 10.1007/s10493-007-9091-0
[20] Sentis, A., Bertram, R., Dardenne, N., Simon, J.-C., Magro, A., Pujol, B., Danchin, E. and J.-L. Hemptinne (2020) Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascades. bioRxiv, 722140, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/722140

Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascadesArnaud Sentis, Raphaël Bertram, Nathalie Dardenne, Jean-Christophe Simon, Alexandra Magro, Benoit Pujol, Etienne Danchin and Jean-Louis Hemptinne<p>Trophic cascades, the indirect effect of predators on non-adjacent lower trophic levels, are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on the strength of t...Community ecology, Eco-evolutionary dynamics, Food webs, Population ecologySara Magalhães2019-08-02 09:11:03 View
22 Mar 2021
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Host-mediated, cross-generational intraspecific competition in a herbivore species

Plants preserve the ghost of competition past for herbivores, but mothers don’t care

Recommended by based on reviews by Inês Fragata and Raul Costa-Pereira

Some biological hypotheses are widely popular, so much so that we tend to forget their original lack of success. This is particularly true for hypotheses with catchy names. The ‘Ghost of competition past’ is part of the title of a paper by the great ecologist, JH Connell, one of the many losses of 2020 (Connell 1980). The hypothesis states that, even though we may not detect competition in current populations, their traits and distributions may be shaped by past competition events. Although this hypothesis has known a great success in the ecological literature, the original paper actually ends with “I will no longer be persuaded by such invoking of "the Ghost of Competition Past"”. Similarly, the hypothesis that mothers of herbivores choose host plants where their offspring will have a higher fitness was proposed by John Jaenike in 1978 (Jaenike 1978), and later coined the ‘mother knows best’ hypothesis. The hypothesis was readily questioned or dismissed: “Mother doesn't know best” (Courtney and Kibota 1990), or “Does mother know best?” (Valladares and Lawton 1991), but remains widely popular. It thus seems that catchy names (and the intuitive ideas behind them) have a heuristic value that is independent from the original persuasion in these ideas and the accumulation of evidence that followed it.

The paper by Castagneryol et al. (2021) analyses the preference-performance relationship in the box tree moth (BTM) Cydalima perspectalis, after defoliation of their host plant, the box tree, by conspecifics. It thus has bearings on the two previously mentioned hypotheses. Specifically, they created an artificial population of potted box trees in a greenhouse, in which 60 trees were infested with BTM third instar larvae, whereas 61 were left uninfested. One week later, these larvae were removed and another three weeks later, they released adult BTM females and recorded their host choice by counting egg clutches laid by these females on the plants. Finally, they evaluated the effect of previously infested vs uninfested plants on BTM performance by measuring the weight of third instar larvae that had emerged from those eggs.  

This experimental design was adopted because BTM is a multivoltine species. When the second generation of BTM arrives, plants have been defoliated by the first generation and did not fully recover. Indeed, Castagneryol et al. (2021) found that larvae that developed on previously infested plants were much smaller than those developing on uninfested plants, and the same was true for the chrysalis that emerged from those larvae. This provides unequivocal evidence for the existence of a ghost of competition past in this system. However, the existence of this ghost still does not result in a change in the distribution of BTM, precisely because mothers do not know best: they lay as many eggs on plants previously infested than on uninfested plants. 

The demonstration that the previous presence of a competitor affects the performance of this herbivore species confirms that ghosts exist. However, whether this entails that previous (interspecific) competition shapes species distributions, as originally meant, remains an open question. Species phenology may play an important role in exposing organisms to the ghost, as this time-lagged competition may have been often overlooked. It is also relevant to try to understand why mothers don’t care in this, and other systems. One possibility is that they will have few opportunities to effectively choose in the real world, due to limited dispersal or to all plants being previously infested. 


Castagneyrol, B., Halder, I. van, Kadiri, Y., Schillé, L. and Jactel, H. (2021) Host-mediated, cross-generational intraspecific competition in a herbivore species. bioRxiv, 2020.07.30.228544, ver. 5 peer-reviewed and recommended by PCI Ecology. doi:

Connell, J. H. (1980). Diversity and the coevolution of competitors, or the ghost of competition past. Oikos, 131-138. doi:

Courtney, S. P. and Kibota, T. T. (1990) in Insect-plant interactions (ed. Bernays, E.A.) 285-330.

Jaenike, J. (1978). On optimal oviposition behavior in phytophagous insects. Theoretical population biology, 14(3), 350-356. doi:

Valladares, G., and Lawton, J. H. (1991). Host-plant selection in the holly leaf-miner: does mother know best?. The Journal of Animal Ecology, 227-240. doi:


Host-mediated, cross-generational intraspecific competition in a herbivore speciesBastien Castagneyrol, Inge van Halder, Yasmine Kadiri, Laura Schillé, Hervé Jactel<p>Conspecific insect herbivores co-occurring on the same host plant interact both directly through interference competition and indirectly through exploitative competition, plant-mediated interactions and enemy-mediated interactions. However, the...Competition, Herbivory, ZoologySara Magalhães2020-08-03 15:50:23 View
08 Jan 2020
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Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits

Nitrate or not nitrate. That is the question

Recommended by based on reviews by Vincent Maire and 1 anonymous reviewer

The article by Legay et al. [1] addresses two main issues: the links between belowground and aboveground plant traits and the links between plant strategies (as defined by these traits) and the capacity to absorb nitrate and ammonium. I recommend this work because these are important and current issues. The literature on plant traits is extremely rich and the existence of a leaf economic spectrum linked to a gradient between conservative and acquisitive plants is now extremely well established [2-3]. Many teams are now working on belowground traits and possible links with the aboveground gradients [4-5]. It seems indeed that there is a root economic spectrum but this spectrum is apparently less pronounced than the leaf economic spectrum. The existence of links between the two spectrums are still controversial and are likely not universal as suggested by discrepant results and after all a plant could have a conservative strategy aboveground and an acquisitive strategy belowground (or vice-versa) because, indeed, constraints are different belowground and aboveground (for example because in given ecosystem/vegetation type light may be abundant but not water or mineral nutrients). The various results obtained also suggest that we do not full understand the diversity of belowground strategies, what is at stake with these strategies, and the links with root characteristics.
Each time I give a conference on the work we are carrying out on African grasses that likely absorb ammonium preferentially because they inhibit nitrification [6-7], somebody asks me a question about the fact that plant essentially absorb nitrate because ammonium is toxic and nitrate more available in the soil. The present article confirms that this is not the case and that, though there are currently some teams working on the subject, we do not really know for the moment whether plants absorb nitrate or ammonium, in which proportion, how plastic this proportion is within individuals and within species. This subject seems to me crucial because it is linked to (1) the capacity of ecosystems to conserve nitrogen [8], because nitrate, much more than ammonium, goes out of ecosystems through leaching and denitrification, (2) to carbon cycling and plant energy budget because absorbing nitrate requires spending mucho more energy than absorbing ammonium because nitrate must be reduced before being incorporated in plant biomass, which is very energy costly. These two issues are naturally very relevant to develop efficient cropping systems in terms of carbon and nitrogen.
Interestingly, the present article, comparing three grass species in different sites, suggests that there is no trade-off between the absorption of nitrate and ammonium: more acquisitive individuals tend to absorb more ammonium and nitrate. This is contrary to hypotheses we made to predict the outcome of competition between plants absorbing nitrate and ammonium in different proportions [9] but should be tested in the future comparing many different types of plants. The results also suggest that more conservative plants absorb relatively more ammonium, which makes sense because this allows them to spare the energy necessary to reduce nitrate. This leads to the question of the effect of these strategies on nitrogen retention within the ecosystem. If nitrification is high (low), absorbing ammonium is not efficient and likely leads to high (low) nitrogen losses. This should be tested in the future. Moreover, the authors have measured the absorption of nitrate and ammonium through measurements at the root scale on cut roots. This should be complemented by measurements at the whole plant scale.


[1] Legay, N., Grassein, F., Arnoldi, C., Segura, R., Laîné, P., Lavorel, S. and Clément, J.-C. (2020). Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits. bioRxiv, 372235, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/372235
[2] Shipley, B., Lechowicz, M.J., Wright, I. & Reich, P.B. (2006) Fundamental trade-offs generating the worldwide leaf economics spectrum. Ecology, 87, 535-541. doi: 10.1890/05-1051
[3] Reich, P.B. (2014) The world-wide ‘fast-slow’ plant economics spectrum: a traits manifesto. J. Ecol., 102, 275-301. doi: 10.1111/1365-2745.12211
[4] Maire, V., Gross, N., Pontes, L.D.S., Picon-Cochard, C. & Soussana, J.F. (2009) Trade-off between root nitrogen acquisition and shoot nitrogen utilization across 13 co-occurring pasture grass species. Func. Ecol., 23, 668-679. doi: 10.1111/j.1365-2435.2009.01557.x
[5] Roumet, C., Birouste, M., Picon-Cochard, C., Ghestem, M., Osman, N., Vrignon-Brenas, S., Cao, K.F. & Stokes, A. (2016) Root structure-function relationships in 74 species: evidence of a root economics spectrum related to carbon economy. New. Phytol., 210, 815-826. doi: 10.1111/nph.13828
[6] Lata, J.-C., Degrange, V., Raynaud, X., Maron, P.-A., Lensi, R. & Abbadie, L. (2004) Grass populations control nitrification in savanna soils. Funct. Ecol., 18, 605-611. doi: 10.1111/j.0269-8463.2004.00880.x
[7] Srikanthasamy, T., Leloup, J., N’Dri, A.B., Barot, S., Gervaix, J., Koné, A.W., Koffi, K.F., Le Roux, X., Raynaud, X. & Lata, J.-C. (2018) Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna. Soil Biol. Biochem., 117, 153-163. doi: 10.1016/j.soilbio.2017.11.016
[8] Boudsocq, S., Lata, J.C., Mathieu, J., Abbadie, L. & Barot, S. (2009) Modelling approach to analyze the effects of nitrification inhibition on primary production. Func. Ecol., 23, 220-230. doi: 10.1111/j.1365-2435.2008.01476.x
[9] Boudsocq, S., Niboyet, A., Lata, J.-C., Raynaud, X., Loeuille, N., Mathieu, J., Blouin, M., Abbadie, L. & Barot, S. (2012) Plant preference for ammonium versus nitrate: a neglected determinant of ecosystem functioning? Am. Nat., 180, 60-69. doi: 10.1086/665997

Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traitsLegay Nicolas, Grassein Fabrice, Arnoldi Cindy, Segura Raphaël, Laîné Philippe, Lavorel Sandra, Clément Jean-Christophe<p>The leaf economics spectrum (LES) is based on a suite of leaf traits related to plant functioning and ranges from resource-conservative to resource-acquisitive strategies. However, the relationships with root traits, and the associated belowgro...Community ecology, Physiology, Terrestrial ecologySébastien Barot2018-07-19 14:22:28 View
07 Oct 2019
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Deer slow down litter decomposition by reducing litter quality in a temperate forest

Disentangling effects of large herbivores on litter decomposition

Recommended by based on reviews by 2 anonymous reviewers

Aboveground – belowground interactions is a fascinating field that has developed in ecology since about 20 years [1]. This field has been very fruitful as measured by the numerous articles published but also by the particular role it has played in the development of soil ecology. While soil ecology has for a long time developed partially independently from “general ecology” [2], the field of aboveground – belowground interactions has shown that all ecological interactions occurring within the soil are likely to impact plant growth and plant physiology because they have their roots within the soil. In turns, this should impact the aerial system of plants (higher or lower biomasses, changes in leaf quality…), which should cascade on the aboveground food web. Conversely, all ecological interactions occurring aboveground likely impact plant growth, which should cascade to their root systems, and thus to the soil functioning and the soil food web (through changes in the emission of exudates or inputs of dead roots…). Basically, plants are linking the belowground and aboveground worlds because, as terrestrial primary producers, they need to have (1) leaves to capture CO2 and exploit light and (2) roots to absorb water and mineral nutrients. The article I presently recommend [3] tackles this general issue through the prism of the impact of large herbivores on the decomposition of leaf litter.
This issue is a relatively old one [4, 5] but still deserves efforts because there have been relatively few studies on the subject and because the issue is relatively complex due to the diversity of mechanisms involved and the difficulty to disentangle them. I recommend this article because the authors have cleverly taken advantage of a ‘‘natural’’ long-term experiment, i.e. three islands with contrasted deer densities, to test whether these large mammals are able to impact leaf litter decomposition and whether they are able to do so through changes in litter quality (because they browse the vegetation) or through changes in soil characteristics (either physical or chemical characteristics or the composition of the decomposer community). They have found that deer decrease litter decomposition, mainly through a decrease in litter quality (increase in its C:N ratio). I particularly appreciate the combination of statistics achieved to test the different hypotheses and the fair and in-depth discussion of the results.
I have to confess that I have two small regrets with this work. First, all replications are implemented within the same three islands, so that it cannot be fully excluded that measured effects should not be attributed to any other possible difference between the three islands. I am fairly sure this is not the case (at least because the three islands have the same environments) but I hope that future studies or meta-analyses will be able analyse independent deer density treatments. Second, as a soil ecologist, I am eager to see results on the decomposer communities, both microorganisms and macrofauna, of the three islands.


[1] Hooper, D. U., Bignell, D. E., Brown, V. K., Brussard, L., Dangerfield, J. M., Wall, D. H. and Wolters, V. (2000). Interactions between Aboveground and Belowground Biodiversity in Terrestrial Ecosystems: Patterns, Mechanisms, and Feedbacks. BioScience, 50(12), 1049-1061. doi: 10.1641/0006-3568(2000)050[1049:ibaabb];2
[2] Barot, S., Blouin, M., Fontaine, S., Jouquet, P., Lata, J.-C., and Mathieu, J. (2007). A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System. PLOS ONE, 2(11), e1248. doi: 10.1371/journal.pone.0001248
[3] Chollet S., Maillard M., Schörghuber J., Grayston S. and Martin J.-L. (2019). Deer slow down litter decomposition by reducing litter quality in a temperate forest. bioRxiv, 690032, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/690032
[4] Wardle, D. A., Barker, G. M., Yeates, G. W., Bonner, K. I., and Ghani, A. (2001). Introduced browsing mammals in New Zealand natural forests: aboveground and belowground consequences. Ecological Monographs, 71(4), 587-614. doi: 10.1890/0012-9615(2001)071[0587:ibminz];2
[5] Bardgett, R. D., and Wardle, D. A. (2003). Herbivore-mediated linkages between aboveground and belowground communities. Ecology, 84(9), 2258-2268. doi: 10.1890/02-0274

Deer slow down litter decomposition by reducing litter quality in a temperate forest Simon Chollet, Morgane Maillard, Juliane Schorghuber, Sue Grayston, Jean-Louis Martin<p>In temperate forest ecosystems, the role of deer in litter decomposition, a key nutrient cycling process, remains debated. Deer may modify the decomposition process by affecting plant cover and thus modifying litter abundance. They can also alt...Community ecology, Ecosystem functioning, Herbivory, Soil ecologySébastien Barot2019-07-04 14:30:19 View
14 Dec 2022
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The contrasted impacts of grasshoppers on soil microbial activities in function of primary production and herbivore diet

Complex interactions between ecosystem productivity and herbivore diets lead to non-predicted effects on nutrient cycling

Recommended by based on reviews by Manuel Blouin and Tord Ranheim Sveen

The authors present a study typical of the field of belowground-aboveground interactions [1]. This framework has been extremely fruitful since the beginning of 2000s [2]. It has also contributed to bridge the gap between soil ecology and the rest of ecology [3]. The study also pertains to the rich field on the impacts of herbivores on soil functioning [4].

The study more precisely tested during two years the effect on nutrient cycling of the interaction between the type of grassland (along a gradient of biomass productivity) and the diet of the community of insect herbivores (5 treatments manipulating the grasshopper community on 1 m2 plots, with a gradient from no grasshopper to grasshoppers either specialized on forbs or grasses). What seems extremely interesting is that the study is based on a rigorous hypothesis-testing approach. They compare the predictions of two frameworks: (1) The “productivity model” predicts that in productive ecosystems herbivores consume a high percentage of the net primary production thus accelerating nutrient cycling. (2) The “diet model” distinguishes herbivores consuming exploitative plants from those eating conservative plants. The former (later) type of herbivores favours conservative (exploitative) plants therefore decelerating (accelerating) nutrient cycling. Interestingly, the two frameworks have similar predictions (and symmetrically opposite predictions) in two cases out of four combinations between ecosystem productivities and types of diet (see Table 1). An other merit of the study is to combine in a rather comprehensive way all the necessary measurements to test these frameworks in combination: grasshopper diet, soil properties, characteristics of the soil microbial community, plant traits, vegetation survey and plant biomass.

The results were in contradiction with the ‘‘diet model’’: microbial properties and nitrogen cycling did not depend on grasshopper diet. The productivity of the grasslands did impact nutrient cycling but not in the direction predicted by the “productivity model”: productive grasslands hosted exploitative plants that depleted N resources in the soil and microbes producing few extracellular enzymes, which led to a lower potential N mineralization and a deceleration of nutrient cycling. Because, the authors stuck to their original hypotheses (that were not confirmed), they were able to discuss in a very relevant way their results and to propose some interpretations, at least partially based on the time scales involved by the productivity and diet models.

Beyond all the merits of this article, I think that two issues remain largely open in relation with the dynamics of the studied systems, and would deserve future research efforts. First, on the ‘‘short’’ term (up to several decades), can we predict how the communities of plants, soil microbes, and herbivores interact to drive the dynamics of the ecosystems? Second, at the evolutionary time scale, can we understand and predict the interactions between the evolution of plant, microbe and herbivore strategies and the consequences for the functioning of the grasslands? The two issues are difficult because of the multiple feedbacks involved. One way to go further would be to complement the empirical approach with models along existing research avenues [5, 6]. 


[1] Ibanez S, Foulquier A, Brun C, Colace M-P, Piton G, Bernard L, Gallet C, Clément J-C (2022) The contrasted impacts of grasshoppers on soil microbial activities in function of primary production and herbivore diet. bioRxiv, 2022.07.04.497718, ver. 2 peer-reviewed and recommended by Peer Community in Ecology.

[2] Hooper, D. U., Bignell, D. E., Brown, V. K., Brussaard, L., Dangerfield, J. M., Wall, D. H., Wardle, D. A., Coleman, D. C., Giller, K. E., Lavelle, P., Van der Putten, W. H., De Ruiter, P. C., et al. 2000. Interactions between aboveground and belowground biodiversity in terretrial ecosystems: patterns, mechanisms, and feedbacks. BioScience, 50, 1049-1061.[1049:IBAABB]2.0.CO;2

[3] Barot, S., Blouin, M., Fontaine, S., Jouquet, P., Lata, J.-C., and Mathieu, J. 2007. A tale of four stories: soil ecology, theory, evolution and the publication system. PLoS ONE, 2, e1248.

[4] Bardgett, R. D., and Wardle, D. A. 2003. Herbivore-mediated linkages between aboveground and belowground communities. Ecology, 84, 2258-2268.

[5] Barot, S., Bornhofen, S., Loeuille, N., Perveen, N., Shahzad, T., and Fontaine, S. 2014. Nutrient enrichment and local competition influence the evolution of plant mineralization strategy, a modelling approach. J. Ecol., 102, 357-366.

[6] Schweitzer, J. A., Juric, I., van de Voorde, T. F. J., Clay, K., van der Putten, W. H., Bailey, J. K., and Fox, C. 2014. Are there evolutionary consequences of plant-soil feedbacks along soil gradients? Func. Ecol., 28, 55-64.


The contrasted impacts of grasshoppers on soil microbial activities in function of primary production and herbivore dietSébastien Ibanez, Arnaud Foulquier, Charles Brun, Marie-Pascale Colace, Gabin Piton, Lionel Bernard, Christiane Gallet, Jean-Christophe Clément<p style="text-align: justify;">Herbivory can have contrasted impacts on soil microbes and nutrient cycling, which has stimulated the development of conceptual frameworks exploring the links between below- and aboveground processes. The "productiv...Ecosystem functioning, Herbivory, Soil ecology, Terrestrial ecologySébastien Barot2022-07-14 09:06:13 View
06 Mar 2020
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The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies

The importance of spatio-temporal dynamics on MPA's design

Recommended by based on reviews by Ana S. L. Rodrigues and 1 anonymous reviewer

Marine protected areas (MPA) have arisen as the main approach for conservation of marine species. Fishes, marine mammals and birds can be conservation targets that justify the implementation of these areas. However, MPAs undergo many of the problems faced by their terrestrial equivalent. One of the major concerns is that these conservation areas are spatially constrained, by logistic reasons, and many times these constraints caused that key areas for the species (reproductive sites, refugees, migration) fall outside the limits, making conservation efforts even more difficult. Lambert et al. [1] evaluate at what point the Bay of Biscay MPA contains key ecological areas for several emblematic species. The evaluation incorporated a spatio-temporal dimension. To evaluate these ideas, authors evaluate two population descriptors: aggregation and persistence of several species of cetaceans and seabirds.
The authors determined that despite the MPA contains key areas for some species, for many others the key areas fall outside the MPA (aggregation sites) or observed aggregation sites are poorly persistent in time. They found that aggregation and persistence behave as two uncorrelated descriptors of the spatio-temporal distribution of populations. Variability of both characteristics was species-specific, but in all cases the message is clear: both features must be taken into account to evaluate the effectiveness of MPAs. Both conclusions pointed out to the difficulties that a strategy based on MPAs could face when the target are those species with low aggregation or those where key sites show low persistence in time.
Conceptually, the manuscript and its conclusions are very interesting, specially its recommendation of including temporal variability of species abundances and aggregation in the design of MPAs. However, despite the clear biological importance of persistence and aggregation of the conservation targets for the design of a MPA, its implementation will still be an extremely complex task. A first constraint is that important areas for one species could not be relevant for others, making the design of the MPA difficult because the more target species we include the larger the area needed for the MPA. As a consequence, the management of the MPA turns difficult and expensive as the area increases. These increased costs could be a key point for accepting/rejecting the implementation of these MPAs for governments. Also larger areas could imply highest level of conflict with local communities or stakeholders. In many the inclusion inside MPAs of areas with traditional social or economic use will be a major source of conflict with the people.
Despite these difficulties, the results of Lambert et al. [1] give us a key message for improving MPA’s design. The best strategy for including their conclusions in the effective implementation of these areas will be the next target in conservation research.


[1] Lambert, C., Dorémus, G. and V. Ridoux (2020) The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategies. bioRxiv, 790634, ver. 3 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/790634

The persistence in time of distributional patterns in marine megafauna impacts zonal conservation strategiesCharlotte Lambert, Ghislain Dorémus, Vincent Ridoux<p>The main type of zonal conservation approaches corresponds to Marine Protected Areas (MPAs), which are spatially defined and generally static entities aiming at the protection of some target populations by the implementation of a management pla...Conservation biology, Habitat selection, Species distributionsSergio Estay2019-10-03 08:47:17 View
24 Jan 2023
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Four decades of phenology in an alpine amphibian: trends, stasis, and climatic drivers

Alpine ecology and their dynamics under climate change

Recommended by based on reviews by Nigel Yoccoz and 1 anonymous reviewer

​​Research about the effects of climate change on ecological communities has been abundant in the last decades. In particular, studies about the effects of climate change on mountain ecosystems have been key for understanding and communicating the consequences of this global phenomenon. Alpine regions show higher increases in warming in comparison to low-altitude ecosystems and this trend is likely to continue. This warming has caused reduced snowfall and/or changes in the duration of snow cover. For example, Notarnicola (2020) reported that 78% of the world’s mountain areas have experienced a snow cover decline since 2000. In the same vein, snow cover has decreased by 10% compared with snow coverage in the late 1960s (Walther et al., 2002) and snow cover duration has decreased at a rate of 5 days/decade (Choi et al., 2010). These changes have impacted the dynamics of high-altitude plant and animal populations. Some impacts are changes in the hibernation of animals, the length of the growing season for plants and the soil microbial composition (Chávez et al. 2021).

Lenzi et al. (2023), give us an excellent study using long-term data on alpine amphibian populations. Authors show how climate change has impacted the reproductive phenology of Bufo bufo, especially the breeding season starts 30 days earlier than ~40 years ago. This earlier breeding is associated with the increasing temperatures and reduced snow cover in these alpine ecosystems. However, these changes did not occur in a linear trend but a marked acceleration was observed until mid-1990s with a later stabilization. Authors associated these nonlinear changes with complex interactions between the global trend of seasonal temperatures and site-specific conditions. 

Beyond the earlier breeding season, changes in phenology can have important impacts on the long-term viability of alpine populations. Complex interactions could involve positive and negative effects like harder environmental conditions for propagules, faster development of juveniles, or changes in predation pressure. This study opens new research opportunities and questions like the urgent assessment of the global impact of climate change on animal fitness. This study provides key information for the conservation of these populations.


Chávez RO, Briceño VF, Lastra JA, Harris-Pascal D, Estay SA (2021) Snow Cover and Snow Persistence Changes in the Mocho-Choshuenco Volcano (Southern Chile) Derived From 35 Years of Landsat Satellite Images. Frontiers in Ecology and Evolution, 9.

Choi G, Robinson DA, Kang S (2010) Changing Northern Hemisphere Snow Seasons. Journal of Climate, 23, 5305–5310.

Lenzi O, Grossenbacher K, Zumbach S, Lüscher B, Althaus S, Schmocker D, Recher H, Thoma M, Ozgul A, Schmidt BR (2022) Four decades of phenology in an alpine amphibian: trends, stasis, and climatic drivers.bioRxiv, 2022.08.16.503739, ver. 3 peer-reviewed and recommended by Peer Community in Ecology.

Notarnicola C (2020) Hotspots of snow cover changes in global mountain regions over 2000–2018. Remote Sensing of Environment, 243, 111781.

Four decades of phenology in an alpine amphibian: trends, stasis, and climatic driversOmar Lenzi, Kurt Grossenbacher, Silvia Zumbach, Beatrice Luescher, Sarah Althaus, Daniela Schmocker, Helmut Recher, Marco Thoma, Arpat Ozgul, Benedikt R. Schmidt<p style="text-align: justify;">Strong phenological shifts in response to changes in climatic conditions have been reported for many species, including amphibians, which are expected to breed earlier. Phenological shifts in breeding are observed i...Climate change, Population ecology, ZoologySergio EstayAnonymous, Nigel Yoccoz2022-08-18 08:25:21 View
20 Feb 2019
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Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal

Are all the roads leading to Rome?

Recommended by based on reviews by Nadia Aubin-Horth and 1 anonymous reviewer

Identifying the factors which favour the establishment and spread of non-native species in novel environments is one of the keys to predict - and hence prevent or control - biological invasions. This includes biological factors (i.e. factors associated with the invasive species themselves), and one of the prevailing hypotheses is that some species traits may explain their impressive success to establish and spread in novel environments [1]. In animals, most research studies have focused on traits associated with fecundity, age at maturity, level of affiliation to humans or dispersal ability for instance. The “composite picture” of the perfect (i.e. successful) invader that has gradually emerged is a small-bodied animal strongly affiliated to human activities with high fecundity, high dispersal ability and a super high level of plasticity. Of course, the story is not that simple, and actually a perfect invader sometimes – if not often- takes another form… Carrying on to identify what makes a species a successful invader or not is hence still an important research axis with major implications.
In this manuscript, Charbonnel and collaborators [2] provide an interesting opportunity to gain novel insights into our understanding of (the) traits underlying invasion success. They nicely combine the power of Next-Generation Sequencing (NGS) with a clever comparative approach of two closely-related invasive rodents (the house mouse Mus musculus and the black rat Rattus rattus) in a common environment. They use this experimental design to test the appealing hypothesis that pathogens may be actors of the story, and may indirectly explain why some non-native species are so successful in invading novel habitats.
It is generally assumed that the community of pathogens encountered by non-native species in novel environments is different from that of their native area. On the one hand (the enemy-release hypothesis), it can be hypothesized that non-native species, when they arrive into a novel environment, will be relaxed from the pressure imposed by their native pathogens because local pathogens are not adapted (and hence do not infect) to this novel host. Because immune defence against pathogens is highly costly, non-native species establishing into a novel environment could hence reallocate these costs to other functions such as fecundity or dispersal apparatus. This scenario has been termed the “evolution of increased competitive ability” (EICA) hypothesis [3]. On the other hand (the EICA-refined hypothesis [4]), one can assume that invaders will encounter new pathogens in newly established areas, and will allocate energy toward cost-effective immune pathways to permit allocating a non-negligible amount of energy toward other functions. Finally, a last hypothesis (the “immune protection” hypothesis) assumes major changes in pathogen composition between native and invaded areas, which should lead to an overall increase in immune investment by the native species to successfully invade novel environments [4]. This last hypothesis suggests that only non-native species being able to take up the associated costs of immunity will be successful invaders.
The role of immunity in invasion success has yet been poorly investigated, mainly because of the difficulty to simultaneously analyse multiple immune pathways [4]. Charbonnel and collaborators [2] overpass this difficulty by screening all genes expressed (using a whole RNA sequencing approach) in an immune tissue: the spleen. They do so along the invasion routes of two sympatric invasive rodents in Africa and compare anciently and newly invaded areas (respectively). For one of the two species (the house mouse), they found a high number of immune-related genes to be up-regulated in newly invaded areas compared to anciently invaded areas. All categories of immune pathways (costly and cost-effective) were up-regulated, suggesting an overall increase in immune investment in the mouse, which corroborates the “immune protection” hypothesis. For the black rat, patterns of gene expression were somewhat different, with much less pronounced differentiation in gene expression between newly and anciently invaded areas. Among the few differentiated genes, a few were associated to immune responses and some of theses genes were even down-regulated in the newly invaded areas. This pattern may actually corroborate the EICA hypothesis, although it could alternatively suggest that stochastic processes (drift) associated to recent decrease in population size (which is expected during a colonisation event) are more important than selection imposed by pathogens in shaping patterns of immune gene expression.
Overall, this study [2] suggests (i) that immune-related traits are important in predicting invasion success and (ii) that two successful species with a similar invasion history and living in similar environments can use different life-history strategies to reach the same success. This later finding is particularly relevant and intriguing as it suggests that the traits and strategies deployed by species to colonise new habitats might actually be idiosyncratic, and that, if general trends actually emerge in regards of traits predicting the success of invaders, the devil might actually be into the details. Comparative studies are extremely important to identify the general rules and the specificities sustaining actual patterns, but these approaches are yet poorly used in biological invasions (at least empirically). The work presented by Charbonnel and colleagues [2] calls for future comparative studies performed at multiple spatial scales (native vs. non-native areas, anciently vs. recently invaded areas), multiple taxonomic resolutions and across multiple traits (to search for trade-offs), so that the success of invasive species can be properly understood and predicted.


[1] Jeschke, J. M., & Strayer, D. L. (2006). Determinants of vertebrate invasion success in Europe and North America. Global Change Biology, 12(9), 1608-1619. doi: 10.1111/j.1365-2486.2006.01213.x
[2] Blossey, B., & Notzold, R. (1995). Evolution of increased competitive ability in invasive nonindigenous plants: a hypothesis. Journal of Ecology, 83(5), 887-889. doi: 10.2307/2261425
[3] Charbonnel, N., Galan, M., Tatard, C., Loiseau, A., Diagne, C. A., Dalecky, A., Parrinello, H., Rialle, S., Severac, D., & Brouat, C. (2019). Differential immune gene expression associated with contemporary range expansion of two invasive rodents in Senegal. bioRxiv, 442160, ver. 5 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/442160
[4] Lee, K. A., & Klasing, K. C. (2004). A role for immunology in invasion biology. Trends in Ecology & Evolution, 19(10), 523-529. doi: 10.1016/j.tree.2004.07.012

Differential immune gene expression associated with contemporary range expansion of two invasive rodents in SenegalNathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stephanie Rialle, Dany Severac and Carine Brouat<p>Background: Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. What determines the successful establishment of introduced populations still remains unsolved. Here we explore the appealing as...Biological invasions, Eco-immunology & Immunity, Population ecologySimon Blanchet2018-10-14 12:21:52 View