Journal ArticleDOI
Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits.
Laurent Bordez,Philippe Jourand,Marc Ducousso,Fabian Carriconde,Yvon Cavaloc,Sébastien Santini,Jean-Michel Claverie,Laurent Wantiez,Antoine Leveau,Hamid Amir +9 more
TLDR
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.Abstract:
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.read more
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Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
TL;DR: It is found that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied, and stringent quality-based trimming of 16S pyrotags and clustering threshold no greater than 97% identity should be used to avoid overestimates of the rare biosphere.
Journal ArticleDOI
Soil microbial diversity during 30 years of grassland restoration on the Loess Plateau, China: Tight linkages with plant diversity
TL;DR: Investigation of linkages between soil microbial and plant diversity across a 30‐year chronosequence of restored grasslands on the Loess Plateau in Northwestern China showed that plant, bacterial, and fungal species richness all increased with increased years of grassland restoration, during which their community compositions shifted among six different habitats.
Journal ArticleDOI
Nickel drives bacterial community diversity in the rhizosphere of the hyperaccumulator Alyssum murale
Séverine Lopez,Séverine Lopez,Séverine Piutti,Séverine Piutti,Jessica Vallance,Jean Louis Morel,Jean Louis Morel,Guillaume Echevarria,Guillaume Echevarria,Emile Benizri,Emile Benizri +10 more
TL;DR: The objectives were to understand the specific changes in the structure of A. murale rhizosphere bacterial community that occur across two gradients: 1) elevation and 2) bioavailable Ni.
Journal ArticleDOI
Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.
Véronique Gourmelon,Laurent Maggia,Jeff R. Powell,Sarah Gigante,Sara Hortal,Claire Gueunier,Kelly Letellier,Fabian Carriconde +7 more
TL;DR: Assessment of soil bacterial and fungal diversity in New Caledonian ultramafic substrates indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species.
Journal ArticleDOI
Assessing the agromining potential of Mediterranean nickel-hyperaccumulating plant species at field-scale in ultramafic soils under humid-temperate climate.
Tania Pardo,Beatriz Rodríguez-Garrido,Ramez F. Saad,Jose Luis Soto-Vázquez,Mariana Loureiro-Viñas,Ángeles Prieto-Fernández,Guillaume Echevarria,Emil Benizri,Petra Kidd +8 more
TL;DR: Both Ni-hyperaccumulating Mediterranean species showed great potential for their use in Ni agromining systems, although optimising soil and crop management practices could improve the phytoextraction efficiency.
References
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Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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Journal ArticleDOI
Biodiversity hotspots for conservation priorities
Norman Myers,Russell A. Mittermeier,Cristina G. Mittermeier,Gustavo A. B. da Fonseca,Jennifer Kent +4 more
TL;DR: A ‘silver bullet’ strategy on the part of conservation planners, focusing on ‘biodiversity hotspots’ where exceptional concentrations of endemic species are undergoing exceptional loss of habitat, is proposed.
Journal ArticleDOI
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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