Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin.

Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.

Mapping the race between crop phenology and climate risks for wheat in France under climate change.

Climate change threatens food security by affecting the productivity of major cereal crops. To date, agroclimatic risk projections through indicators have focused on expected hazards exposure during the crop's current vulnerable seasons, without considering the non-stationarity of their phenology under evolving climatic conditions. We propose a new method for spatially classifying agroclimatic risks for wheat, combining high-resolution climatic data with a wheat's phenological model. The method is implemented for French wheat involving three GCM-RCM model pairs and two emission scenarios. We found that the precocity of phenological stages allows wheat to avoid periods of water deficit in the near future. Nevertheless, in the coming decades the emergence of heat stress and increasing water deficit will deteriorate wheat cultivation over the French territory. Projections show the appearance of combined risks of heat and water deficit up to 4 years per decade under the RCP 8.5 scenario. The proposed method provides a deep level of information that enables regional adaptation strategies: the nature of the risk, its temporal and spatial occurrence, and its potential combination with other risks. It's a first step towards identifying potential sites for breeding crop varieties to increase the resilience of agricultural systems.

A reduced but stable core microbiome found in seeds of hyperaccumulators.

The seed microbiota is currently of great interest in the scientific community since seed germination is a critical stage in plant life cycle. Some seed endophytic bacteria could be commonly found in seeds of hyperaccumulating plants and may confer them an evolutionary advantage over non-hyperaccumulating plants when confronted to biotic or abiotic stress. This study focuses on the endophytic bacterial diversity of a wide diversity of metal hyperaccumulating and non-hyperaccumulating plants (93 seed samples from Mediterranean regions, Oceania, South-East Asia) to reveal the core endophyte communities specific of hyperaccumulating plants. The rather low richness of the seed bacterial communities found in all seeds suggest that a sub-population of specialized endophytic strains is able to colonize seeds and survive. The factor that shapes the diversity of those bacterial communities was first the botanical family and secondly the hyperaccumulation trait of the host plants. Based on the taxonomic affiliation, we revealed that the Brassicales had 1349 OTUs that were specific to them and the Asterales 204 OTUs, independently of their metal accumulation strategy. Nonetheless, a set of 12 OTUs were shared by the seeds of all the hyperaccumulators independently of the taxonomic order of the plants (among Asterales and Brassicales) and could be considered as a 'stable' core microbiome. Those OTUs identified as Luteibacter, Alphaproteobacteria unclassified, Sphingopyxis, Alishewanella, bacteria unclassified, Heliimonas, Aeromicrobium, Proteobacteria unclassified, Xanthomonadales unclassified and Micromonosporaceae unclassified may constitute an endophytic bacterial core with PGP traits. Further studies are needed to extend our knowledge of the possible role played by those bacteria.

Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes.

Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.

Pioneer trees of Betula pendula at a red gypsum landfill harbour specific structure and composition of root-associated microbial communities.

The study of root-associated microbial communities is important to understand the natural processes involved in plant recolonisation at degraded areas. Root associated bacterial and fungal communities of woody species colonising a red gypsum landfill (a metal-enriched environment) were characterised through metabarcoding. Among trees naturally growing on the landfill, Betula pendula is the only tree species in the centre of the area, whereas companion tree species such as Populus nigra, P. tremula and Salix purpurea were present on the edges. The bacterial community was dominated by Proteobacteria (38%), Actinobacteria (35%) and Bacteroidetes (20%) and the most abundant bacterial OTU belonged to the family Streptomycetaceae. The fungal community was dominated by Ascomycota (60%) and Basidiomycota (30%) and the most abundant family was Pyronemataceae. Analysis of similarities, heatmap and hierarchical cluster analysis showed that B. pendula grown in the centre of the landfill harboured a specific microbial community, which was unique and different, not only from other tree species (Populus or Salix spp.), but also from other B. pendula growing at the edges. Our findings on relevant indicator OTUs associated to the birches located in the centre of the landfill (such as Otu00716 Catellatospora sp. (family Micromonosporaceae, phylum Actinobacteria) or Otu4_35502 Russula sp. (family Russulaceae, phylum Basidiomycota)) may have important implications for the successful revegetation of these harsh environments using microbial-based phytostabilisation approaches.

Poplar rotation coppice at a trace element-contaminated phytomanagement site: A 10-year study revealing biomass production, element export and impact on extractable elements.

Growing lignocellulosic crops on marginal lands could compose a substantial proportion of future energy resources. The potential of poplar was explored, by devising a field trial of two hectares in 2007 in a metal-contaminated site to quantify the genotypic variation in the growth traits of 14 poplar genotypes grown in short-rotation coppice and to assess element transfer and export by individual genotypes. Our data led us to conclusions about the genotypic variations in poplar growth on a moderately contaminated site, with the Vesten genotype being the most productive. This genotype also accumulated the least amounts of trace elements, whereas the Trichobel genotype accumulated up to 170 mg Zn kg-1 DW in the branches, with large variation being exhibited among the genotypes for trace element (TE) accumulation. Soil element depletion occurred for a range of TEs, whereas the soil content of major nutrients and the pH remained unchanged or slightly increased after 10 years of poplar growth. The higher TE content of bark tissues compared with the wood and the higher proportion of bark in branches compared with the wood led us to recommend that only stem wood be harvested, instead of the whole tree, which will enable a reduction in the risks encountered with TE-enriched biomass in the valorization process.

Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria.

Industrial waste dumps are rarely colonized by vegetation after they have been abandoned, indicating biological infertility. Revegetation of industrial tailings dumps is thus necessary to prevent wind erosion, metal leaching and has been shown to restore soil functions and ecosystem services. However, little is known about the microbial colonization and community structure of vegetated tailings following the application of restoration technologies. In this study, we investigated the rhizosphere and phyllosphere bacterial communities of a poplar tree plantation within a phytomanagement-based restoration program of a Hg-contaminated site. We used Illumina-based sequencing combined with culture-dependent approaches to describe plant-associated bacterial communities and to isolate growth-promoting bacteria (PGPB) and Hg-resistant bacteria. The genus Streptomyces was highly specific to the root community, accounting for 24.4% of the relative abundance but only representing 0.8% of the soil community, whereas OTUs from the Chloroflexi phylum were essentially detected in the soil community. Aboveground habitats were dominated by bacteria from the Deinococcus-Thermus phylum, which were not detected in belowground habitats. Leaf and stem habitats were characterized by several dominant OTUs, such as those from the phylum Firmicutes in the stems or from the genera Methylobacterium, Kineococcus, Sphingomonas and Hymenobacter in the leaves. Belowground habitats hosted more cultivable Hg-resistant bacteria than aboveground habitats and more Hg-resistant bacteria were found on the episphere than in endospheric habitats. Hg-resistant isolates exhibiting plant growth-promoting (PGP) traits, when used as inoculants of Capsicum annuum, were shown to increase its root dry biomass but not Hg concentration. The N2-fixing and Hg-resistant species Pseudomonas graminis, observed in the poplar phyllosphere, may be a key microorganism for the restoration of industrial tailings dumps.

Enhanced surveillance for the Third United Nations Conference on Small Island Developing States, Apia, Samoa, September 2014.

The Ministry of Health in Samoa, in partnership with the Pacific Community, successfully implemented enhanced surveillance for the high-profile Third United Nations Conference on Small Island Developing States held concurrently with the popular local Teuila festival during a widespread chikungunya outbreak in September 2014. Samoa's weekly syndromic surveillance system was expanded to 12 syndromes and 10 sentinel sites from four syndromes and seven sentinel sites; sites included the national hospital, four private health clinics and three national health service clinics. Daily situation reports were produced and were disseminated through PacNet (the e-mail alert and communication tool of the Pacific Public Health Surveillance Network) together with daily prioritized line lists of syndrome activity to facilitate rapid response and investigation by the Samoan EpiNet team. Standard operating procedures for surveillance and response were introduced, together with a sustainability plan, including a monitoring and evaluation framework, to facilitate the transition of the mass gathering surveillance improvements to routine surveillance. The enhanced surveillance performed well, providing vital disease early warning and health security assurance. A total of 2386 encounters and 708 syndrome cases were reported. Influenza-like illness was the most frequently seen syndrome (17%). No new infectious disease outbreaks were recorded. The experience emphasized: (1) the need for a long lead time to pilot the surveillance enhancements and to maximize their sustainability; (2) the importance of good communication between key stakeholders; and (3) having sufficient staff dedicated to both surveillance and response.

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site.

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.

Impact of poplar-based phytomanagement on soil properties and microbial communities in a metal-contaminated site.

Despite a long history of use in phytomanagement strategies, the impacts of poplar trees on the structure and function of microbial communities that live in the soil remain largely unknown. The current study combined fungal and bacterial community analyses from different management regimes using Illumina-based sequencing with soil analysis. The poplar phytomanagement regimes led to a significant increase in soil fertility and a decreased bioavailability of Zn and Cd, in concert with changes in the microbial communities. The most notable changes in the relative abundance of taxa and operational taxonomic units unsurprisingly indicated that root and soil constitute distinct ecological microbial habitats, as exemplified by the dominance of Laccaria in root samples. The poplar cultivar was also an important driver, explaining 12% and 6% of the variance in the fungal and bacterial data sets, respectively. The overall dominance of saprophytic fungi, e.g. Penicillium canescens, might be related to the decomposition activities needed at the experimental site. Our data further highlighted that the mycorrhizal colonization of poplar cultivars varies greatly between the species and genotypes, which is exemplified by the dominance of Scleroderma under Vesten samples. Further interactions between fungal and bacterial functional groups stressed the potential of high-throughput sequencing technologies in uncovering the microbial ecology of disturbed environments.

Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites.

The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and ß-diversity measures illustrated that the root microbial communities were well separated from the soil microbial communities at both sites. A detailed study of the fungal composition showed that Ascomycota dominated the overall fungal communities on poplar soil, the root samples at Pierrelaye, and the unplanted soil at the experimental sites. Conversely, Basidiomycota accounted for a much higher percentage of the fungal community in poplar root samples from the Leforest site. The root bacterial communities were dominated by Alphaproteobacteria and Actinobacteria, and the soil samples were dominated by Alphaproteobacteria and Acidobacteria. The occurrence and dominance of the ectomycorrhizal community at Leforest but not at Pierrelaye is the major feature of our data set. Overall, ectomycorrhizal root symbionts appeared to be highly constrained by soil characteristics at the phytomanagement sites. Our data support the view that mycorrhizal inoculation is needed in highly stressed and nutrient-poor environments.

Adapting to the health impacts of climate change in a sustainable manner.

The climate is changing and this poses significant threats to human health. Climate change is one of the greatest challenges facing Pacific Island countries and territories due to their unique geophysical features, and their social, economic and cultural characteristics. The Pacific region also faces challenges with widely dispersed populations, limited resources and fragmented health systems. Over the past few years, there has been a substantial increase in international aid for health activities aimed at adapting to the threats of climate change. This funding needs to be used strategically to ensure an effective approach to reducing the health risk from climate change. Respecting the principles of development effectiveness will result in more effective and sustainable adaptation, in particular, 1) processes should be owned and driven by local communities, 2) investments should be aligned with existing national priorities and policies, and 3) existing systems must not be ignored, but rather expanded upon and reinforced.