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Article: Do diversity of plants, soil fungi and bacteria influence aggregate stability on ultramafic Ferralsols? A metagenomic approach in a tropical hotspot of biodiversity

Demenois, Julien / Merino-Martín, Luis / Fernandez Nuñez, Nicolas / Stokes, Alexia / Carriconde, Fabian

Plant and soil. 2020 Mar., v. 448, no. 1-2

2020

Abstract: AIMS: Understanding how soil aggregate stability (MWD) is influenced by microbial diversity and abundance can be crucial for ecological restoration in severely disturbed areas. We investigated the relationships between plant and soil microbial diversity ... ...

Abstract	AIMS: Understanding how soil aggregate stability (MWD) is influenced by microbial diversity and abundance can be crucial for ecological restoration in severely disturbed areas. We investigated the relationships between plant and soil microbial diversity and MWD of an ultramafic Ferralsol along a vegetational succession gradient in New Caledonia, where wildfires and extensive nickel mining have degraded the landscape. METHODS: Five plant communities were studied. For each one, MWD, soil physicochemical parameters (e.g. soil organic carbon (SOC)), plant root traits and fungal abundance were measured. The diversity and structure of plant and microbial communities were respectively assessed via botanical inventories and a metagenomic approach. A generalized linear model (GLM) was used to assess the influence of diversity indexes on MWD. Constrained ordinations (CCA) were performed to assess the influence of communities’ structures on MWD. RESULTS: GLM highlighted the linkage between SOC and MWD but did not identify any significant influence of diversity indexes on MWD. CCA revealed a significant influence of communities’ structures, especially the abundance of saprotrophic fungi, on MWD. CONCLUSIONS: We showed that the structure, but not species richness and diversity of plants, soil fungi and bacteria influence aggregate stability on Ferralsols.
Keywords	Ferralsols ; aggregate stability ; ecological restoration ; landscapes ; linear models ; metagenomics ; nickel ; roots ; saprotrophs ; soil aggregates ; soil organic carbon ; species richness ; New Caledonia
Language	English
Dates of publication	2020-03
Size	p. 213-229.
Publishing place	Springer International Publishing
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	208908-7
ISSN	1573-5036 ; 0032-079X
ISSN (online)	1573-5036
ISSN	0032-079X
DOI	10.1007/s11104-019-04364-8
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Article: Potential of high-throughput eDNA sequencing of soil fungi and bacteria for monitoring ecological restoration in ultramafic substrates: The case study of the New Caledonian biodiversity hotspot

Fernandez Nuñez, Nicolas / Maggia, Laurent / Stenger, Pierre-Louis / Lelievre, Mélanie / Letellier, Kelly / Gigante, Sarah / Manez, Aurore / Mournet, Pierre / Ripoll, Julie / Carriconde, Fabian

Ecological engineering. 2021 Dec., v. 173

2021

Abstract: Due to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, ... ...

Abstract	Due to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and bacterial community diversity, composition, and structure from ultramafic soils in New Caledonia, an archipelago in the southwest Pacific recognized as a priority for conservation and restoration. The emerging approach of high-throughput amplicon sequencing of environmental DNA (eDNA) – metabarcoding of eDNA – was used to compare soil microbial communities from four different native vegetation types, representing different stages of a chronosequence and defined as reference ecosystems, to five distinct post-mining sites revegetated several years ago. Our results clearly revealed changes in soil microbial phyla and functional groups along the reference chronosequence and variable responses at the different revegetated sites, with two of the five sites showing a good trajectory of recovery. We thus propose three ratios as metrics for monitoring the restoration trajectory of soil microorganisms: the Ascomycota:Basidiomycota and Saprotrophic:Ectomycorrhizal ratios for fungi, and the Cyanobacteria:Chloroflexi ratios for bacteria. Our study, combined with recent works undertaken in other geographical areas, underpins the great promise that could represent soil microbial eDNA metabarcoding for monitoring restoration progress and success. With the emergence of these new cost-effective and scalable sequencing technologies, soil microbes could, in the near future, be included in guidelines for restoration operations in complement to more conventional approaches.
Keywords	DNA barcoding ; bacterial communities ; biodiversity ; case studies ; chronosequences ; complement ; cost effectiveness ; environmental DNA ; indigenous species ; land degradation ; land restoration ; soil ; New Caledonia
Language	English
Dates of publication	2021-12
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1127407-4
ISSN	0925-8574
ISSN	0925-8574
DOI	10.1016/j.ecoleng.2021.106416
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Article ; Online: Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions.

Hackel, Jan / Henkel, Terry W / Moreau, Pierre-Arthur / De Crop, Eske / Verbeken, Annemieke / Sà, Mariana / Buyck, Bart / Neves, Maria-Alice / Vasco-Palacios, Aída / Wartchow, Felipe / Schimann, Heidy / Carriconde, Fabian / Garnica, Sigisfredo / Courtecuisse, Régis / Gardes, Monique / Manzi, Sophie / Louisanna, Eliane / Roy, Mélanie

The New phytologist

2022 Volume 236, Issue 2, Page(s) 698–713

Abstract: The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred ...

Abstract	The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia. The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid-Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north-temperate origins and are associated with North Andean uplift and the general north-south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas. Neotropical Russulaceae have multiple biogeographic origins since the mid-Eocene involving dispersal and co-migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.
MeSH term(s)	Basidiomycota ; Mycorrhizae/genetics ; Phylogeny ; Phylogeography ; South America
Language	English
Publishing date	2022-07-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18365
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Article: Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii)

Soewarto, Julia / Hamelin, Chantal / Bocs, Stéphanie / Mournet, Pierre / Vignes, Hélène / Berger, Angélique / Armero, Alix / Martin, Guillaume / Dereeper, Alexis / Sarah, Gautier / Carriconde, Fabian / Maggia, Laurent

Data in Brief. 2019 Feb., v. 22

2019

Abstract: The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where ... ...

Abstract	The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level.The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.
Keywords	Eucalyptus grandis ; Myrtus communis ; Syzygium ; biodiversity ; bioinformatics ; cost effectiveness ; fungi ; gene expression regulation ; genome ; genomics ; hosts ; pathogens ; rust diseases ; transcriptome ; transcriptomics ; New Caledonia
Language	English
Dates of publication	2019-02
Size	p. 794-811.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.12.080
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Article: Host effects in high ectomycorrhizal diversity tropical rainforests on ultramafic soils in New Caledonia

Carriconde, Fabian / Gardes, Monique / Bellanger, Jean-Michel / Letellier, Kelly / Gigante, Sarah / Gourmelon, Véronique / Ibanez, Thomas / McCoy, Stéphane / Goxe, Julie / Read, Jennifer / Maggia, Laurent

Fungal ecology. 2019 June, v. 39

2019

Abstract: Tropical rainforests have been thought to have low prevalence and diversity of ectomycorrhizal symbioses. However, to date, tropical regions have been poorly sampled for ectomycorrhizal fungi. Here, we investigated ectomycorrhizal fungal community ... ...

Abstract	Tropical rainforests have been thought to have low prevalence and diversity of ectomycorrhizal symbioses. However, to date, tropical regions have been poorly sampled for ectomycorrhizal fungi. Here, we investigated ectomycorrhizal fungal community diversity and the role of host plants in shaping this diversity in three main ultramafic rainforests in New Caledonia, an archipelago renowned for its exceptional plant diversity and recognized as a biodiversity hotspot. Sampling of ectomycorrhizal root tips and fruit bodies in Nothofagus aequilateralis-dominated, Arillastrum gummiferum-dominated and mixed rainforests showed high fungal diversity with, in total, 28 lineages and 311 operational taxonomic units (OTUs), of which 95% might be endemic. We also found that host preference and host density influenced ectomycorrhizal community composition and contributed to the high fungal diversity of New Caledonian rainforests. Finally, the /cortinarius lineage dominated the below- and above-ground communities, which suggests that this lineage plays a central role in ultramafic ecosystems functioning.
Keywords	Cortinarius ; Nothofagus ; community structure ; ectomycorrhizae ; fruiting bodies ; fungal communities ; host plants ; host preferences ; mycorrhizal fungi ; root tips ; soil ; species diversity ; tropical rain forests ; tropics ; New Caledonia
Language	English
Dates of publication	2019-06
Size	p. 201-212.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	1754-5048
DOI	10.1016/j.funeco.2019.02.006
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Article: Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

Hackel, Jan / Henkel, Terry W. / Moreau, Pierre‐Arthur / De Crop, Eske / Verbeken, Annemieke / Sà, Mariana / Buyck, Bart / Neves, Maria‐Alice / Vasco‐Palacios, Aída / Wartchow, Felipe / Schimann, Heidy / Carriconde, Fabian / Garnica, Sigisfredo / Courtecuisse, Régis / Gardes, Monique / Manzi, Sophie / Louisanna, Eliane / Roy, Mélanie

The new phytologist. 2022 Oct., v. 236, no. 2

2022

Abstract	The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae. We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia. The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid‐Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north‐temperate origins and are associated with North Andean uplift and the general north–south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas. Neotropical Russulaceae have multiple biogeographic origins since the mid‐Eocene involving dispersal and co‐migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.
Keywords	Neotropics ; Russulaceae ; biogeography ; ectomycorrhizae ; fungi ; geographical distribution ; internal transcribed spacers ; Africa ; Andes region ; Argentina ; Panama
Language	English
Dates of publication	2022-10
Size	p. 698-713.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	208885-x
ISSN	1469-8137 ; 0028-646X
ISSN (online)	1469-8137
ISSN	0028-646X
DOI	10.1111/nph.18365
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Article ; Online: Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia.

Houles, Anne / Vincent, Bryan / David, Magali / Ducousso, Marc / Galiana, Antoine / Juillot, Farid / Hannibal, Laure / Carriconde, Fabian / Fritsch, Emmanuel / Jourand, Philippe

Microbial ecology

2018 Volume 76, Issue 4, Page(s) 964–975

Abstract: 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- ... ...

Abstract	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.
MeSH term(s)	Acacia/growth & development ; Acacia/microbiology ; Basidiomycota/classification ; Basidiomycota/physiology ; Mycorrhizae/classification ; Mycorrhizae/physiology ; New Caledonia ; Soil/chemistry ; Soil Microbiology ; Symbiosis
Chemical Substances	Soil
Language	English
Publishing date	2018-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-018-1193-1
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Article ; Online: Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (

Data in brief

2019 Volume 22, Page(s) 794–811

Abstract: The myrtle rust disease, caused by the ... ...

Abstract	The myrtle rust disease, caused by the fungus
Language	English
Publishing date	2019-01-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.12.080
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Article ; Online: Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.

Gourmelon, Véronique / Maggia, Laurent / Powell, Jeff R / Gigante, Sarah / Hortal, Sara / Gueunier, Claire / Letellier, Kelly / Carriconde, Fabian

PloS one

2016 Volume 11, Issue 12, Page(s) e0167405

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Bacteria/genetics ; Ecosystem ; Fungi/genetics ; Genetic Variation ; Metagenomics ; New Caledonia ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2016-12-01
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0167405
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Article: Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota)

Jargeat, Patricia / Martos, Florent / Carriconde, Fabian / Gryta, Herve / Moreau, Pierre-Arthur / Gardes, Monique

Molecular ecology. 2010 Dec., v. 19, no. 23

2010

Abstract: Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine ... ...

Abstract	Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.
Keywords	DNA barcoding ; Tricholoma ; ectomycorrhizae ; fungi ; genetic distance ; genotype ; internal transcribed spacers ; nuclear genome ; phenotype ; phylogeny ; ribosomal DNA ; type collections ; Western European region
Language	English
Dates of publication	2010-12
Size	p. 5216-5230.
Publishing place	Blackwell Publishing Ltd
Document type	Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/j.1365-294X.2010.04863.x
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