Predator-driven behavioural shifts in a common lizard shape resource-flow from marine to terrestrial ecosystems

Foraging decisions shape the structure of food webs. Therefore, a behavioural shift in a single species can potentially modify resource-flow dynamics of entire ecosystems. To examine this, we conducted a field experiment to assess foraging niche dynamics of semi-arboreal brown anole lizards in the presence/absence of predatory ground-dwelling curly-tailed lizards in a replicated set of island ecosystems. One year after experimental translocation, brown anoles exposed to these predators had drastically increased perch height and reduced consumption of marine-derived food resources. This foraging niche shift altered marine-to-terrestrial resource-flow dynamics and persisted in the diets of the first-generation offspring. Furthermore, female lizards that displayed more risk-taking behaviours consumed more marine prey on islands with predators present. Our results show how predator-driven rapid behavioural shifts can alter food-web connectivity between oceanic and terrestrial ecosystems and underscore the importance of studying behaviour-mediated niche shifts to understand ecosystem functioning in rapidly changing environments.

Microbial mats as model to decipher climate change effect on microbial communities through a mesocosm study

Marine environments are expected to be one of the most affected ecosystems by climate change, notably with increasing ocean temperature and ocean acidification. In marine environments, microbial communities provide important ecosystem services ensuring biogeochemical cycles. They are threatened by the modification of environmental parameters induced by climate change that, in turn, affect their activities. Microbial mats, ensuring important ecosystem services in coastal areas, are well-organized communities of diverse microorganisms representing accurate microbial models. It is hypothesized that their microbial diversity and metabolic versatility will reveal various adaptation strategies in response to climate change. Thus, understanding how climate change affects microbial mats will provide valuable information on microbial behaviour and functioning in changed environment. Experimental ecology, based on mesocosm approaches, provides the opportunity to control physical-chemical parameters, as close as possible to those observed in the environment. The exposure of microbial mats to physical-chemical conditions mimicking the climate change predictions will help to decipher the modification of the microbial community structure and function in response to it. Here, we present how to expose microbial mats, following a mesocosm approach, to study the impact of climate change on microbial community.

Convergence or Redundancy: Alternative Views about the Evolutionary Genomics of Character Displacement

An evolutionary debate contrasts the importance of genetic convergence versus genetic redundancy. In genetic convergence, the same adaptive trait evolves because of similar genetic changes. In genetic redundancy, the adaptive trait evolves using different genetic combinations, and populations might not share the same genetic changes. Here we address this debate by examining single nucleotide polymorphisms (SNPs) associated with rapid evolution of character displacement in Anolis carolinensis populations inhabiting replicate islands with and without a competitor species (1Spp and 2Spp islands, respectively). We identify 215-outliers SNPs that have improbably large FST values, low nucleotide variation, greater linkage than expected and that are enriched for genes underlying animal movement. The pattern of SNP divergence between 1Spp and 2Spp populations supports both genetic convergence and genetic redundancy for character displacement. In support of genetic convergence: all 215-outliers SNPs are shared among at least three of the five 2Spp island populations, and 23% of outlier SNPS are shared among all five 2Spp island populations. In contrast, in support of genetic redundancy: many outlier SNPs only have meaningful allele frequency differences between 1Spp and 2Spp islands on a few 2Spp islands. That is, on at least one of the 2Spp islands, 77% of outlier SNPs have allele frequencies more similar to those on 1Spp islands than to those on 2Spp islands. Focusing on genetic convergence is scientifically rigorous because it relies on replication. Yet, this focus distracts from the possibility that there are multiple, redundant genetic solutions that enhance the rate and stability of adaptive change.

Antipredator behaviors in urban settings: Ecological experimentation powered by citizen science

Animal behaviors are often modified in urban settings due to changes in species assemblages and interactions. The ability of prey to respond to a predator is a critical behavior, but urban populations may experience altered predation pressure, food supplementation, and other human‐mediated disturbances that modify their responsiveness to predation risk and promote habituation.

Citizen‐science programs generally focus on the collection and analysis of observational data (e.g., bird checklists), but there has been increasing interest in the engagement of citizen scientists for ecological experimentation.

Our goal was to implement a behavioral experiment in which citizen scientists recorded antipredator behaviors in wild birds occupying urban areas. In North America, increasing populations of Accipiter hawks have colonized suburban and urban areas and regularly prey upon birds that frequent backyard bird feeders. This scenario, of an increasingly common avian predator hunting birds near human dwellings, offers a unique opportunity to characterize antipredator behaviors within urban passerines.

For two winters, we engaged citizen scientists in Chicago, IL, USA to deploy a playback experiment and record antipredator behaviors in backyard birds. If backyard birds maintained their antipredator behaviors, we hypothesized that birds would decrease foraging behaviors and increase vigilance in response to a predator cue (hawk playback) but that these responses would be mediated by flock size, presence of sentinel species, body size, tree cover, and amount of surrounding urban area.

Using a randomized control–treatment design, citizen scientists at 15 sites recorded behaviors from 3891 individual birds representing 22 species. Birds were more vigilant and foraged less during the playback of a hawk call, and these responses were strongest for individuals within larger flocks and weakest in larger‐bodied birds. We did not find effects of sentinel species, tree cover, or urbanization.

By deploying a behavioral experiment, we found that backyard birds inhabiting urban landscapes largely maintained antipredator behaviors of increased vigilance and decreased foraging in response to predator cues. Experimentation in citizen science poses challenges (e.g., observation bias, sample size limitations, and reduced complexity in protocol design), but unlike programs focused solely on observational data, experimentation allows researchers to disentangle the complex factors underlying animal behavior and species interactions.

Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction

Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities

The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].

Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes

Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.

Variable survival across low pH gradients in freshwater fish species

A series of 14 day experiments was conducted on five common New Zealand fish species (redfin bully Gobiomorphus huttoni, inanga Galaxias maculatus, brown trout Salmo trutta, longfin eel Anguilla dieffenbachii and koaro Galaxias brevipinnis) to assess the effect of pH on survival and changes in body mass. No species survived in water of pH <4 although there was 100% survival of all adults at pH 4.5, G. maculatus larvae were also tested and had high mortality at this pH. Results suggest that adults are tolerant of low-pH waters; however, successful remediation of anthropogenically acidified streams will require an understanding of the susceptibility to low pH on different life cycle stages.

Antibiotics promote aggregation within aquatic bacterial communities

The release of antibiotics (AB) into the environment poses several threats for human health due to potential development of AB-resistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance) in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold. These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of the effects of AB in aquatic ecosystems.

Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics'era

Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field.

Stabilization of yield in plant genotype mixtures through compensation rather than complementation

BACKGROUND AND AIMS

Plant genotypic mixtures have the potential to increase yield stability in variable, often unpredictable environments, yet knowledge of the specific mechanisms underlying enhanced yield stability remains limited. Field studies are constrained by environmental conditions which cannot be fully controlled and thus reproduced. A suitable model system would allow reproducible experiments on processes operating within crop genetic mixtures.

METHODS

Phenotypically dissimilar genotypes of Arabidopsis thaliana were grown in monocultures and mixtures under high levels of competition for abiotic resources. Seed production, flowering time and rosette size were recorded.

KEY RESULTS

Mixtures achieved high yield stability across environments through compensatory interactions. Compensation was greatest when plants were under high levels of heat and nutrient stress. Competitive ability and mixture performance were predictable from above-ground phenotypic traits even though below-ground competition appeared to be more intense.

CONCLUSIONS

This study indicates that the mixing ability of plant genotypes can be predicted from their phenotypes expressed in a range of relevant environments, and implies that a phenotypic screen of genotypes could improve the selection of suitable components of genotypic mixtures in agriculture intended to be resilient to environmental stress.