The phylum Chloroflexi and their SAR202 clade dominate the microbiome of two marine sponges living in extreme environmental conditions

The capacity of marine sponges to cope with environmental changes is often attributed to the specific composition of their bacterial communities. In this study, we assessed the bacterial microbiome of two dominant sponges, Rhabdastrella globostellata (Rg) and Hyrtios erectus (He), living in the Bouraké lagoon (New Caledonia), where abiotic conditions daily fluctuate according to the tide. Sponge specimens, sediment and seawater samples were collected at 2–3 m depth. The bacterial communities were assessed using 16S rRNA metabarcoding, and variations between the two sponges were compared using PCA biplots. Chloroflexi was the dominant phyla in both He and Rg with an average relative abundance of 41.2% and 53.2%, respectively, while it was absent in sediment and seawater. Among the phylum Chloroflexi, SAR202 clade was dominant in both sponges, reaching an average relative abundance of 53.2% (He) and 78.7% (Rg). Principal component analysis (PCA) was used to identify the main variables driving the bacterial community structure in both sponges. The results indicated that the bacterial community structure in both sponges was strongly associated with Chloroflexi (70.9% of the phyla variance) and SAR202 clade (86.6% of the clade variance). The high relative abundance of the phylum Chloroflexi and the SAR202 clade observed in this study is the highest reported so far in the literature in marine sponges. Such a high relative abundance of these bacteria could suggest their involvement in the well-being of sponges in the extreme environmental conditions of Bouraké

Evidence of nickel (Ni) efflux in Ni-tolerant ectomycorhizal Pisolithus albus isolated from ultramafic soil

Nickel (Ni)-tolerant ectomycorrhizal Pisolithus albus was isolated from extreme ultramafic soils that are naturally rich in heavy metals. This study aimed to identify the specific molecular mechanisms associated with the response of P. albus to nickel. In presence of high concentration of nickel, P. albus Ni-tolerant isolate showed a low basal accumulation of nickel in its fungal tissues and was able to perform a metal efflux mechanism. Three genes putatively involved in metal efflux were identified from the P. albus transcriptome, and their overexpression was confirmed in the mycelium that was cultivated in vitro in the presence of nickel and in fungal tissues that were sampled in situ. Cloning these genes in yeast provided significant advantages in terms of nickel tolerance (+ 31% Ni EC50) and growth (+ 83% ) compared with controls. Furthermore, nickel efflux was also detected in the transformed yeast cells. Protein sequence analysis indicated that the genes encoded a P-type-ATPase, an ABC transporter and a major facilitator superfamily permease (MFS). This study sheds light on a global mechanism of metal efflux by P. albus cells that supports nickel tolerance. These specific responses to nickel might contribute to the fungal adaptation in ultramafic soil

New insights into the mycorrhizal status of Cyperaceae from ultramafic soils in New Caledonia

In New Caledonia, a hot spot of biodiversity, plants from the Cyperaceae family are mostly endemic and considered pioneers of the nickel-rich natural serpentine ecosystem. The aim of the study was to highlight the mycorrhizal status of these Cyperaceae and to bring new insights into the role of this symbiosis in plant tolerance to ultramafic soils. Nine Cyperaceae species were studied and presented evidence of root colonization by arbuscular mycorrhizas (AMs), with frequencies ranging from 8% to 57%. The highest level of AM colonization was observed in plants from the endemic dominant genus Costularia. Molecular evidence demonstrated the presence of Glomus sp. inside the roots. In a controlled greenhouse assay, AM inoculation of Costularia comosa grown under ultramafic conditions significantly enhanced plant growth, with an increase in biomass by up to 2.4-fold for shoots and 1.2-fold for roots, and also reduced nickel content in roots by 2.5-fold, as compared with the controls. All these data support our hypotheses (i) that a relationship exists between the mycorrhizal status of Cyperaceae and their habitat, and (ii) that AM have a positive role in plant tolerance to ultramafic soils (mineral nutrition and metal tolerance), suggesting the use of these pioneer plants with AM management as potential tools for nickel mine site rehabilitation in New Caledonia

Combinations of different arbuscular mycorrhizal fungi improve fitness and metal tolerance of sorghum in ultramafic soil

International audienceResearch on arbuscular mycorrhizal fungi (AMF) in ultramafic soils has principally focused on ecological restorationwhereas little attention has been given to agriculture. The present study aims at understanding ifmixtures of different AMF species from a New Caledonian ultramafic soil induced a better plant fitness and lowercontents of potentially toxic metals in aerial parts of a crop plant than single species inoculants. Sorghum vulgareplants were inoculated using six AMF species separately and in different mixtures of these species in a glasshouseexperiment in ultramafic soil. The tested inocula showed very different effects on plant fitness. Results highlightthat, when sorghum is grown in ultramafic soil, AMF mixes were more efficient than single species inoculation inalleviating abiotic stresses by reducing translocation of potentially toxic metals to the aerial part of the plant andthereby improving the fitness of the plants. Our findings point out the utility of arbuscular mycorrhizal biotechnologyfor agricultural ultramafic soils

Ectomycorrhizal Pisolithus albus inoculation of Acacia spirorbis and Eucalyptus globulus grown in ultramafic topsoil enhances plant growth and mineral nutrition while limits metal uptake

Ectomycorrhizal fungi (ECM) isolates of Pisolithus albus (Cooke and Massee) from nickel-rich ultramafic topsoils in New Caledonia were inoculated onto Acacia spirorbis Labill. (an endemic Fabaceae) and Eucalyptus globulus Labill. (used as a Myrtaceae plant host model). The aim of the study was to analyze the growth of symbiotic ECM plants growing on the ultramafic substrate that is characterized by high and toxic metal concentrations i.e. Co, Cr, Fe, Mn and Ni, deficient concentrations of plant essential nutrients such as N, P, K, and that presents an unbalanced Ca/Mg ratio (1/19). ECM inoculation was successful with a plant level of root mycorrhization up to 6.7%. ECM symbiosis enhanced plant growth as indicated by significant increases in shoot and root biomass. Presence of ECM enhanced uptake of major elements that are deficient in ultramafic substrates; in particular P, K and Ca. On the contrary, the ECM symbioses strongly reduced transfer to plants of element in excess in soils; in particular all metals. ECM-inoculated plants released metal complexing molecules as free thiols and oxalic acid mostly at lower concentrations than in controls. Data showed that ECM symbiosis helped plant growth by supplying uptake of deficient elements while acting as a protective barrier to toxic metals, in particular for plants growing on ultramafic substrate with extreme soil conditions. Isolation of indigenous and stress-adapted beneficial ECM fungi could serve as a potential tool for inoculation of ECM endemic plants for the successful restoration of ultramafic ecosystems degraded by mining activities

Tracking nickel-adaptive biomarkers in Pisolithus albus from New Caledonia using a transcriptomic approach

The fungus Pisolithus albus forms ectomycorrhizal (ECM) associations with plants growing on extreme ultramafic soils, which are naturally rich in heavy metals such as nickel. Both nickel-tolerant and nickel-sensitive isolates of P.similar to albus are found in ultramafic soils in New Caledonia, a biodiversity hotspot in the Southwest Pacific. The aim of this work was to monitor the expression of genes involved in the specific molecular response to nickel in a nickel-tolerant P.similar to albus isolate. We used pyrosequencing and quantitative polymerase chain reaction (qPCR) approaches to investigate and compare the transcriptomes of the nickel-tolerant isolate MD06-337 in the presence and absence of nickel. A total of 1 071 375 sequencing reads were assembled to infer expression patterns of 19 518 putative genes. Comparison of expression levels revealed that 30% of the identified genes were modulated by nickel treatment. The genes, for which expression was induced most markedly by nickel, encoded products that were putatively involved in a variety of biological functions, such as the modification of cellular components (53%), regulation of biological processes (27%) and molecular functions (20%). The 10 genes that pyrosequencing analysis indicated were induced the most by nickel were characterized further by qPCR analysis of both nickel-tolerant and nickel-sensitive P.similar to albus isolates. Five of these genes were expressed exclusively in nickel-tolerant isolates as well as in ECM samples in situ, which identified them as potential biomarkers for nickel tolerance in this species. These results clearly suggest a positive transcriptomic response of the fungus to nickel-rich environments. The presence of both nickel-tolerant and nickel-sensitive fungal phenotypes in ultramafic soils might reflect environment-dependent phenotypic responses to variations in the effective concentrations of nickel in heterogeneous ultramafic habitats