Virome release of an invasive exotic plant species in southern France.

The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.

Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8-35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.

High Stocking Density Controls Phillyrea Angustifolia in Mediterranean Grasslands.

Extensive grazing applied in the form of low instantaneous pressure over a long period is a widespread management practice in protected areas. However this kind of stocking method does not always achieve the expected results, in particular because it fails to limit colonization by woody plants.This is the case in the relict xero-halophytic grasslands of the northern Mediterranean coastal region, subjected to widespread colonization by the shrub Phillyrea angustifolia despite the presence of extensive grazing. In this study, we investigated, for an equal annual stocking rate, the respective impact of high stocking density applied over a short period (mob grazing) and low stocking density applied over a long period on both P. angustifolia and herbaceous cover, using an in situ experimental design run for 7 years. Only mob grazing was effective both in controlling the establishment and increasing the mortality of P. angustifolia individuals. We did not find any difference after the 7 years of experimentation between the two stocking methods with regard to the herbaceous community parameters tested: species richness, diversity, evenness, contribution of annual characteristic species. By contrast, the exclusion of domestic grazing led to a strong reduction of these values.The use of mob grazing may be well suited for meeting conservation goals such as maintaining open habitats in these grasslands.

Using Different Grazing Practices for Increasing Plant Biodiversity in the Dykes and Embankments Along the Rhône River (Southern France).

Extensive grazing by domestic herbivores is a widespread management practice used since the 80s in many European agro-ecosystems such as semi-natural grasslands to maintain open habitats and to enhance biodiversity. Such grazing systems have principally been tested in cultural ecosystems of high nature value threatened by grazing abandonment. However, there have been few case studies of grazing management in very anthropized ecosystems, such as the new ecosystems created by urban or industrial conversions. In Southern France, the Rhône channeling for navigation and electricity production generated in the 1950s the construction of thousands of hectares of dams and dykes which were colonized naturally by diverse plant communities. Yet shrub encroachment and the consequent recourse to mechanical cutting to facilitate control and maintenance, raise the question of how best to maintain and manage these new habitats. Consequently, since 1999, different low-intensity grazing management systems using rustic breeds of cattle, horses and goats have been tested on a protected reserve of 1454 ha located in the lower part of the Rhône river. Extensive grazing, more than cutting or no management, positively modified vegetation heterogeneity (beta-diversity), the target open grassland species, but not plant species richness (alpha-diversity). However, the current monitoring shows that these benefits of grazing will be confirmed only if low-intensity grazing systems are sustained and if new adaptations can be also made, such as the use of mixed stocking and the establishment of multiyear contracts with breeders.

Impact of the insecticide Alphacypermetrine and herbicide Oxadiazon, used singly or in combination, on the most abundant frog in French rice fields, Pelophylax perezi.

The potential impact of agricultural pesticides is a major concern with regard to biodiversity conservation. Pesticides are considered as one of the main causes of the worldwide decline of Amphibians. They are rarely used singly, but their cumulative impact and interaction are often neglected, as is the importance of the age or stage of the animal on which the impact of the molecules is assessed. We therefore tested the potential cumulative impact of the only authorized insecticide (Alphacypermetrine) and the main herbicide (Oxadiazon) used in French rice fields on four replicates of 25 eggs, young larvae and prometamorphosis tadpoles of the most abundant frog in paddies (Pelophylax perezi). We found no significant effect of the insecticide and herbicide, used singly or in combination, on hatching and young tadpoles. However, we found a strong impact of insecticide and herbicide used singly and a highly deleterious impact of their combined use on prometamorphosis tadpoles. Among the four replicates, only one of the prometamorphosis tadpoles did not reach this adult stage in the control against 9, 9, 6, 4 and 13, 9, 8, 7 with the herbicide and insecticide, respectively. But when the two pesticides were used in combination, only two prometamorphosis tapdoles reached the adult stage. Our results emphasize the potential impact on amphibians of pesticides used in agriculture and highlight the necessity of testing their role as cocktails. They also stress the importance of the age and/or stage of the target organism, the choice of which can lead to contrasting conclusions. Finally, our results suggest a possible underestimation of the impact of pesticides on non-targeted fauna in the rice fields in particular, and on living organisms in general.

Competition Is a Strong Driving Factor in Wetlands, Peaking during Drying Out Periods.

The aim of the study is to investigate the relative importance of plant-plant interactions with regard to flooding and drought effect on perennial plant performances in wetlands. Flooding is expected to be the major driver and, accordingly, the importance of drought is hardly if ever taken into account. Focusing on five widespread species, the growth, the survival and the competitive ability of plants were monitored on permanent plots spread along two elevation gradients. Flooding duration and drought intensity were found to vary substantially along the ~ 0.5 meter range elevation gradient. Flooding and drought alternate over the hydrological year and the pin-point surveys were thus conducted over the course of one year. The data were modeled taking into account survival, recruitment and competitive growth throughout flooding and drying out periods. Flooding and drought both directly impacted the plant performances and their competitive effect, with the effect of drought being much more general among species and of higher magnitude than flooding. The importance of competition was found to be high for all species, particularly during the drying out period. It varied more along the flooding gradient than along the drought gradient. The higher flooding tolerance shown by the studied species compared to drought may be related to species specific growth timing together with efficient response traits. These results offer new insights into the filters operating over the species pools. This suggests that the drying out period and drought conditions may be even more important for species' relative success and the importance of competition than the flooding pattern. The general applicability of this result, obtained in mild Atlantic climate and fertile wetlands, remains to be studied.

Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus.

The family Geminiviridae comprises seven genera differentiated by genome organization, sequence similarity, and insect vector. Capulavirus, an eighth genus, has been proposed to accommodate two newly discovered highly divergent geminiviruses that presently have no known vector. Alfalfa leaf curl virus, identified here as a third capulavirus, is shown to be transmitted by Aphis craccivora. This is the first report of an aphid-transmitted geminivirus.

Using Shrub Clearing, Draining, and Herbivory to Control Bramble Invasion in Mediterranean Dry Grasslands.

For centuries, the dry grassland of the plain of La Crau (south-eastern France) has been subjected to numerous disturbances resulting in the destruction and the fragmentation of this emblematic rangeland ecosystem of the Mediterranean. Today, this ecosystem is facing a new threat from a proliferating native species, the bramble (Rubus ulmifolius Schott), which preferentially colonizes areas that were formerly cultivated and/or exposed to water infiltration. To identify a strategy for effective control of this colonization, in situ experiments testing disturbance regimes (shrub clearing and/or mixed grazing by sheep and goats) combined with the control of access to water resources (with or without drainage trenches) were undertaken between 2010 and 2013. Only clearing and grazing combined over 3 years led to significant changes in vegetation height and bramble cover as well as modifications in the floristic composition, diversity, similarity, and richness of the plant community. Neither a clearing operation carried out in 2010 alone, nor grazing alone, reduced bramble cover, and neither treatment increased the species richness of the plant community. Similarly, digging drainage trenches had no significant impact either on the plant community or on bramble cover. Our study suggests that only annual mechanical clearing coupled with sheep and goats grazing can significantly reduce bramble cover. This combined restoration treatment needs to be applied for at least 3 consecutive years to induce significant changes and enable this ecosystem to return to the dry grassland succession.

Identification of novel Bromus- and Trifolium-associated circular DNA viruses.

The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.

Impact of grazing on the species richness of plant communities in Mediterranean temporary pools (western Morocco).

The impact of grazing on the vegetation of Moroccan temporary pools has been studied at 2 scales: regional (inter-pools) and local (intra-pools). Half of the 16 forest pools studied is located in a reserve and ungrazed. The other half, located within public forest, is grazed. Vegetation relevés coupled to water-depths measurements were carried out in each pool. The results showed a significant effect of grazing on both scales of analysis. This effect was found in the species composition of the vegetation, which differed between the 2 types of pools, and in the lower species richness and abundance of plant species in the grazed pools. These differences are interpreted as resulting from the selection by herbivores and the differential tolerance of species to disturbance. These impacts are likely to expose certain species to local extinction by reducing their populations.

Size-related consumption of Scirpus maritimus tubers by greylag geese Anser anser explained by their functional response.

To explain the preference of wintering greylag geese Anser anser for small Scirpus maritimus tubers (<10mm) over larger ones, our hypothesis was that the former would provide higher intake rates. This 'consumption rate hypothesis' was tested experimentally by deriving the functional responses of geese feeding on tubers of three contrasting sizes. Goose consumption rates were measured as: (i) feeding rate (tubers/min) and (ii) instantaneous intake rate (g fresh weight/min) on various tuber densities (5-200 tubers/tray). Geese had linear functional responses over the range of tuber densities offered, and tuber size affected their consumption rate. The results were then used to re-examine intake rates according to relative biomass of tubers found in the wild. In support of our hypothesis, the larger tubers allowed the lower intake rates. Foraging mechanisms that possibly control the tuber ingestion rate of geese were explored. After controlling (through chemical analyses) that nutritional components of tubers do not differ between sizes, it was concluded that geese preference is mainly due to size-related constraints (i.e. handling time) on their ingestion rates. Additional limiting factors (tuber extraction, digestion capacity) which are likely to constrain food intake of wild geese are also discussed.

Uselessness and indirect negative effects of an insecticide on rice field invertebrates.

Macro-invertebrate assemblages on organic and conventional rice fields were quantitatively compared in the Camargue (Rhone delta, France). There was no major difference in family richness, but significant differences as regard to abundance. Fipronil, the insecticide used to control chironomid larvae, was one of the main factors explaining those differences. Its negative impact on predatory invertebrates appears to explain the paradoxical lack of difference in chironomid abundance between organic and conventional fields, observed during the study. Macro-invertebrate biomass estimation showed that, for some birds such as herons, conventional rice fields offered a lower value as foraging habitats than organic ones.

Competition between an introduced and an indigenous species: the case of Paspalum paspalodes (Michx) Schribner and Aeluropus littoralis (Gouan) in the Camargue (southern France).

Paspalum paspalodes, an introduced grass species, and Aeluropus littoralis, an indigenous species, develop abundantly in seasonally-flooded marshes in the Camargue (Rhône Delta, France). Although they occur together in many multispecies communities, neither species occurs when the other is dominat. The cultivation of cuttings of P. paspalodes and A. littoralis in a replacement series in a combination of five proportions (0/100, 25/75, 50/50, 75/25 and 100/0) and four salinities (0,2 4, and 6 g Cl- · 1-1) gave contrasting results for the two species: (1) strong asymmetrical competition in favour of P. paspalodes at 0 g Cl- · 1-1, (2) no significant effect of salinity on the mean above-ground and underground yields per plant for A. littoralis over the range tested, (3) a major decrease in the mean above-ground and belowground yields per plant for P. paspalodes with increasing salinity, (4) a reversal of the competitive balance between the species with increasing salinity. The cultivation of cuttings at high temperatures in a greenhouse in a combination of the same five proportions at two salinities (0 and 4 g Cl- · 1-1) refuted the hypothesis that the introduced species is better adapted to summer temperatures. Because it is not salt-tolerant, P. paspalodes cannot be considered as a potentially invasive species in the Camargue. Its abundance depends on newly created and artificially maintained habitats.