Fabian Carriconde

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. 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. 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. 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.

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits

Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43) for fungi. Using variance partitioning, we showed that the effect of aboveground vegetation was the most significant descriptor for both bacterial and fungal communities. The floristic significant predictors explained 43% of the variation for both the bacterial and fungal community structures, while the edaphic significant predictors explained only 32% and 31% of these variations, respectively. These results confirm the previous hypothesis that the distribution of microorganisms was more structured by the vegetation cover rather than the edaphic characteristics and that microbial diversity is not limited in ultramafic ecosystems.

Environmental and geographical factors structure soil microbial diversity in New Caledonian ultramafic substrates: A metagenomic approach

Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi), mostly in non-rainforest formations, and Planctomycetes phylum (bacteria) in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from multiple interactions between abiotic and biotic factors.

Comparison of two monodominant species in New Caledonia: floristic diversity and ecological strategies of Arillastrum gummiferum (Myrtaceae) and Nothofagus aequilateralis (Nothofagaceae) rainforests

Mechanisms leading to monodominance in rainforests are still commonly discussed within the framework of forest succession. Here, we focused on the comparison of two monodominant species, Arillastrum gummiferum (Myrtaceae) and Nothofagus aequilateralis (Nothofagaceae), to try to better understand the underlying ecological mechanisms. Those two species are known to dominate the upper canopy of some rainforests on ultramafic substrates in New Caledonia. We investigated the structure, diversity and composition of Arillastrum-dominated plots and compared them with adjacent Nothofagus-dominated and mixed rainforest plots. We found that the dominance of Arillastrum was more pronounced in terms of basal area, whereas for Nothofagus the dominance was mainly in terms of stem density. Species richness and diversities in the two dominated forests were not lower than those observed in mixed rainforests, suggesting that monodominance would not lead to a limitation of diversity. Finally, our observations were consistent with a transient dominance for the two species. We suggest that resistance of Arillastrum to some wildfire regimes would allow the species to survive and regenerate, whereas Nothofagus may have a supportive strategy towards their seedlings through mycorrhizal networks. Both competitive advantages would contribute to the maintenance of monodominance.

Linkages between root traits, soil fungi and aggregate stability in tropical plant communities along a successional vegetation gradient

AimsDetermining which abiotic and biotic factors influence soil aggregate stability (MWD) in tropical climates is often confounded by soil type. We aimed to better understand the influence of soil physical and chemical components, vegetation and fungal abundance on MWD of a Ferralsol along a successional gradient of vegetation in New Caledonia.MethodsFive plant communities (sedge dominated, open sclerophyllous shrubland, Arillastrum forest, Nothofagus forest and mixed rainforest) were studied. For each community, MWD, soil texture, soil organic carbon (SOC), iron (Fe) and aluminium (Al) sesquioxides, root length density (RLD), specific root length (SRL), root mass density (RMD) and fungal abundance were measured. Generalized linear models were used to predict MWD from soil and plant trait data.ResultsThe best prediction of MWD combined abiotic and biotic factors. Along the gradient, Fe increased MWD, while root traits, fungal abundance and SOC modified MWD. From the sedge-dominated community to Arillastrum forest, RMD and SOC increased MWD, while between Nothofagus and mixed rainforest, it was likely that floristic composition and fungal communities influenced MWD.ConclusionsPlant community, the intrinsic nature of Ferralsol and fungal abundance all modified MWD. However, the specific effect of microbial communities should be addressed through a metagenomics approach to elucidate microbial interactions with plant communities.

Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia

This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.