Batrachochytrium dendrobatidis is a fungus belonging to the Phylum Chytridiomycota, Class Chytridiomycetes, Order Chytridiales, and is the highly infectious aetiological agent responsible for a potentially fatal disease, chytridiomycosis, which is currently decimating many of the world's amphibian populations. The fungus infects 2 amphibian orders (Anura and Caudata), 14 families and at least 200 species and is responsible for at least 1 species extinction. Whilst the origin of the agent and routes of transmission are being debated, it has been recognised that successful management of the disease will require effective sampling regimes and detection assays. We have developed a range of unique sampling protocols together with diagnostic assays for the detection of B. dendrobatidis in both living and deceased tadpoles and adults. Here, we formally present our data and discuss them in respect to assay sensitivity, specificity, repeatability and reproducibility. We suggest that compliance with the recommended protocols will avoid the generation of spurious results, thereby providing the international scientific and regulatory community with a set of validated procedures which will assist in the successful management of chytridiomycosis in the future.

/pdf/diagnostic-assays-and-sampling-protocols-for-the-detection-2gocrwtm5f.pdf

Diagnostic assays and sampling protocols for the detection of Batrachochytrium dendrobatidis

Use of biotic indices in semi-enclosed coastal ecosystems and transitional waters habitats - Implications for the implementation of the European Water Framework Directive

Management actions to protect endangered species and conserve ecosystem function may not always be in precise alignment. Efforts to recover the California Ridgway's Rail (Rallus obsoletus obsoletus; hereafter, California rail), a federally and state- listed species, and restoration of tidal marsh ecosystems in the San Francisco Bay estuary provide a prime example of habitat restoration that has conflicted with species conservation. On the brink of extinction from habitat loss and degradation, and non-native predators in the 1990s, California rail populations responded positively to introduction of a non-native plant, Atlantic cordgrass (Spartina alterniflora). California rail populations were in substantial decline when the non-native Spartina was initially introduced as part of efforts to recover tidal marshes. Subsequent hybridization with the native Pacific cordgrass (Spartina foliosa) boosted California rail populations by providing greater cover and increased habitat area. The hybrid cordgrass (S. alterniflora × S. foliosa) readily invaded tidal mudflats and channels, and both crowded out native tidal marsh plants and increased sediment accretion in the marsh plain. This resulted in modification of tidal marsh geomorphology, hydrology, productivity, and species composition. Our results show that denser California rail populations occur in invasive Spartina than in native Spartina in San Francisco Bay. Herbicide treatment between 2005 and 2012 removed invasive Spartina from open intertidal mud and preserved foraging habitat for shorebirds. However, removal of invasive Spartina caused substantial decreases in California rail populations. Unknown facets of California rail ecology, undesirable interim stages of tidal marsh restoration, and competing management objectives among stakeholders resulted in management planning for endangered species or ecosystem restoration that favored one goal over the other. We have examined this perceived conflict and propose strategies for moderating harmful effects of restoration while meeting the needs of both endangered species and the imperiled native marsh ecosystem.

/pdf/endangered-species-management-and-ecosystem-restoration-1ivq2nxqb5.pdf

Endangered species management and ecosystem restoration: finding the common ground

Whereas it is well known that ecosystem engineers can have a large influence on biodiversity, underlying mechanisms are still not fully clear. We try to enhance insight by comparing biodiversity effects of two neighboring intertidal, clonal, ecosystem engineering plant species that modify the physical environmental parameters in a similar way, but with a different magnitude. Macrobenthic assemblages were compared between meadows of the seagrass Zostera
 noltii, small patches (≤0.5 m O) and large areas (≫5 m O) of the emergent halophyte Spartina anglica and the surrounding bare tidal mudflat (control). Multivariate analyses revealed that the mudflat benthic assemblage and Zostera meadow assemblage showed highest similarities, whereas the Spartina marsh assemblage showed the highest dissimilarity with these two areas. Whereas the descriptive nature of our study limits interpretation of the data, some clear patterns were observed. For all vegetated areas, species diversity was lower compared to the unvegetated mudflat, and we observed a strong shift from endo- towards epibenthic species, suggesting that increased above-ground habitat complexity may be a main driving process in our system. As there were no clear patterns related to feeding types, food availability/productivity appeared to be of minor importance in structuring the benthic assemblages. Nevertheless, animals were in general smaller in vegetated areas. Patchiness had a distinct positive effect on biodiversity.

/pdf/comparing-biodiversity-effects-among-ecosystem-engineers-of-4wgwnirsh2.pdf

Comparing biodiversity effects among ecosystem engineers of contrasting strength: macrofauna diversity in Zostera noltii and Spartina anglica vegetations

Several species of ecosystem engineers inhabiting coastal environments have been reported structuring different kinds of communities. The magnitude of this influence often depends on the habitat complexity introduced by the engineers. It is commonly accepted that an increase in habitat complexity will result in an increase in diversity and/or abundance in the associated fauna. The rocky salt marshes along the coast of Patagonia are dominated by cordgrasses, mussels, and barnacles forming a mosaic of engineered habitats with different complexity. This system allows us to address the following questions: how different is a macroinvertebrate assemblage when dominated by different ecosystem engineers? And, is there a positive relationship between increasing habitat complexity and the species richness, diversity and total density of the assemblages? To address these questions, we compared the three ecological scenarios with decreasing habitat complexity: cordgrass–mussel, mussel, and barnacle-engineered habitats. We found a total of 22 taxa mostly crustaceans and polychaetes common to all scenarios. The three engineered habitats showed different macroinvertebrate assemblages, mainly due to differences in individual abundances of some taxa. The cryptogenic amphipod Orchestia gammarella was found strictly associated with the cordgrass–mussel habitat. Species richness and diversity were positively related with habitat complexity while total density showed the opposite trend. Our study suggests that species vary their relative distribution and abundances in response to different habitat complexity. Nevertheless, the direction (i.e., neutral, positive or negative) and intensity of the community’s response seem to depend on the physiological requirements of the different species and their efficiency to readjust their local spatial distribution in the short term.

/pdf/habitat-complexity-and-community-composition-relationships-3lttz3nrxs.pdf

Habitat complexity and community composition: relationships between different ecosystem engineers and the associated macroinvertebrate assemblages

High coastal erosion rates along the beaches of the Medoc peninsula urge for the study of the Pleistocene and Holocene deposits buried under the modern dune. Those deposits are known to be exceptionally rich in archaeological remains (from the Mesolithic at least). The aggressive predation of these fossil deposits by the sea explains the urgency of exploring their content and their sedimentological history. Within these formations, the “Lede du Gurp” archaeological site located on the shore, on the administrative boundary of Soulac-sur-Mer and Grayan-et-l’Hopital, is of tremendous value for palaeogeographical and palaeoenvironmental reconstructions of the Medoc peninsula. This site has preserved remains of dense anthropic activity but also evidence of the history of the estuary’s migration before our contemporary era (i.e. recent centuries). Here we present results of new sedimentological investigations conducted as part of the LITAQ project on and around the site. Continuous and undisturbed sections several metres thick (up to 3.5 m) have been obtained by sampling (sediment slides) and coring operations in the field and studied for their lithostratigraphy (using classic and X-ray imaging coupled with spectrocolorimetry, X-ray fluorescence and grain-size analyses together with radiocarbon dating) along with simultaneous archaeological investigations. Our study refines the palaeoenvironmental evolution of the site over at least the Neolithic period and supports previous interpretations of the origin of these atypical lithofacies, i.e. the deposition of a thick Holocene sequence of clays and peats in a depression associated with karstification processes. Our new datings and observations suggest the possible occurrence of a thermokarst system during the coldest phases of the last deglaciation.

Holocene palaeoenvironmental evolution of the Médoc peninsula (SW France): insights from the sedimentological study of the “Lède du Gurp” archaeological site

The cordgrass Spartina anglica is an introduced species that tends to invade sheltered sand and mudflats, at the upper low marsh level In Arcachon Bay, a lagoon in South West of France, the cordgrass can also replace Zostera noltii beds The consequence of cordgrass presence on macrobenthic fauna was estimated and compared to adjacent habitats (bare sands, Z noltii sea grass beds) during one year The communities of the three habitats were characterised by low species richness, low abundance and biomass (when Hydrobia ulvae , 90% of abundance, is not considered) and high seasonal stability The infaunal assemblages were particularly homogeneous between habitats without any characteristic species Cordgrass eradication experiments were performed and zoobenthic recolonisation was observed the following year Modifications in benthic fauna were observed on epifauna only These results highlight the limited structuring effect of habitat heterogeneity at high tidal levels and in soft-bottom sediments where desiccation becomes the dominant factor determining infauna community structure

Spartina anglica eradication experiment and in situ monitoring assess structuring strength of habitat complexity on marine macrofauna at high tidal level

https://hal.archives-ouvertes.fr/hal-02991674/document

A high-resolution elemental record of post-glacial lithic sedimentation in Upernavik Trough, western Greenland: History of ice-sheet dynamics and ocean circulation changes over the last 9100 years

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Holocene palaeoenvironmental evolution of the Médoc peninsula (SW France): insights from the sedimentological study of the “Lède du Gurp” archaeological site

Spartina anglica eradication experiment and in situ monitoring assess structuring strength of habitat complexity on marine macrofauna at high tidal level

A high-resolution elemental record of post-glacial lithic sedimentation in Upernavik Trough, western Greenland: History of ice-sheet dynamics and ocean circulation changes over the last 9100 years