Fournier, Bertrand

2016-3-1, Seppey, Christophe, Fournier, Bertrand, Szelecz, Ildikò, Singer, David, Mitchell, Edward, Lara, Enrique

Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro- environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.

2013, Qin, Yangmin, Fournier, Bertrand, Lara, Enrique, Gu, Yansheng, Wang, Hongmei, Cui, Yongde, Zhang, Xiaoke, Mitchell, Edward

The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes in this area have suffered from eutrophication and serious environmental pollution during recent decades. The aquatic biodiversity in the lakes of the area is thus currently under significant threat from continuous human activities. Testate amoebae (TA) are benthic (rarely planktonic) microorganisms characterized by an agglutinated or autogenous shell. Owing to their high abundance, preservation potential in lacustrine sediments, and distinct response to environmental stress, they are increasingly used as indicators for monitoring water quality and reconstructing palaeoenvironmental changes. However this approach has not yet been developed in China. This study presents an initial assessment of benthic TA assemblages in eight lakes of Lake Donghu in the region of Wuhan, China. Testate amoeba community structure was most strongly correlated to water pH. In more alkaline conditions, communities were dominated by Centropyxis aculeata, Difflugia oblonga, Pontigulasia compressa, Pon. elisa and Lesquereusia modesta. These results are consistent with previous studies and show that TA could be useful for reconstructing past water pH fluctuations in China. To achieve this, the next step will be to expand the database and build transfer function models.

2014, Szelecz, Ildikò, Fournier, Bertrand, Seppey, Christophe, Amendt, Jens, Mitchell, Edward

Estimation of the post-mortem interval (PMI, the time interval between death and recovery of a body) can be crucial in solving criminal cases. Today minimum PMI calculations rely mainly on medical and entomological evidence. However, beyond 4-6 weeks even entomological methods become less accurate. Thus additional tools are needed. Cadaveric fluids released by decomposing cadavers modify the soil environment and thus impact soil organisms, which may thus be used to estimate the PMI. Although the response of bacteria or fungi to the presence of a corpse has been studied, to the best of our knowledge nothing is known about other soil organisms. Testate amoebae, a group of shelled protozoa, are sensitive bioindicators of soil physico-chemical and micro-climatic conditions and are therefore good potential PMI indicators. We investigated the response of testate amoebae to three decomposing pig cadavers, and compared the pattern to two controls each, bare soils and fake cadavers, in a beach-oak forest near Neuchatel, Switzerland. Forest litter samples collected in the three treatments over 10 months were analysed by microscopy. The pig treatment significantly impacted the testate amoeba community: after 22 and 33 days no living amoeba remained underneath the pig cadavers. Communities subsequently recovered but 10 months after the beginning of the experiment recovery was not complete. The fake cadavers also influenced the testate amoeba communities by altering the soil microclimate during a dry hot period, but less than the cadavers. These results confirm the sensitivity of soil testate amoebae to micro-climatic conditions and show that they respond fast to the presence of cadavers -and that this effect although decreasing over time lasts for months, possibly several years. This study therefore confirms that soil protozoa could potentially be useful as forensic indicators, especially in cases with a longer PMI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

2013, Fournier, Bertrand, Guenat, C., Bullinger-Weber, G., Mitchell, Edward

Floodplains have been intensively altered in industrialized countries, but are now increasingly being restored. It is therefore important to assess the effect of these restoration projects on the aquatic and terrestrial components of ecosystems. However, despite being functionally crucial components of terrestrial ecosystems, soils are generally overlooked in floodplain restoration assessments. We studied the spatio-temporal heterogeneity of soil morphology in a restored (riverbed widening) river reach along the River Thur (Switzerland) using three criteria (soil diversity, dynamism and typicality) and their associated indicators. We hypothesized that these criteria would correctly discriminate the post-restoration changes in soil morphology, and that these changes correspond to patterns of vascular plant diversity. Soil diversity and dynamism increased 5 yr after the restoration, but some typical soils of braided rivers were still missing. Soil typicality and dynamism were correlated to vegetation changes. These results suggest a limited success of the project, in agreement with evaluations carried out at the same site using other, more resource-demanding, methods (e.g., soil fauna, fish diversity, ecosystem functioning). Soil morphology provides structural and functional information on floodplain ecosystems. The spatio-temporal heterogeneity of soil morphology represents a cost-efficient ecological indicator that could easily be integrated into rapid assessment protocols of floodplain and river restoration projects. The follow-up assessment after several major floods (>= HQ20) should take place to allow for testing the longerterm validity of our conclusion for the River Thur site. More generally, it would be useful to apply the soil morphology indicator approach in different settings to test its broader applicability.