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Strong coupling of plant and fungal community structure across western Amazonian rainforests

TLDR
It is found that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type, and strong correlations between α- and β-diversity of soil fungi and trees.
Abstract
The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.

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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

TL;DR: Fungi typically live in highly diverse communities composed of multiple ecological guilds, and FUNGuild is a tool that can be used to taxonomically parse fungal OTUs by ecological guild independent of sequencing platform or analysis pipeline.
Journal ArticleDOI

Embracing the unknown: disentangling the complexities of the soil microbiome.

TL;DR: Although most soil microorganisms remain undescribed, the field is now poised to identify how to manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve the understanding of how terrestrial ecosystems will respond to environmental change.
Journal ArticleDOI

Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing.

TL;DR: The results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs, and the potential for continuous integration of older datasets with newer technology is demonstrated.
Journal ArticleDOI

Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees

TL;DR: The effect of trees on the composition of microbial community was demonstrated to be stronger than other soil properties and to explain a large proportion of variation in community composition, especially in fungi.
Journal ArticleDOI

Endemism and functional convergence across the North American soil mycobiome

TL;DR: This work isolates different geographic and local processes hypothesized to shape fungal community composition and activity in pine forests across the continental United States and shows that the principal ecological processes controlling community structure and function operate at different scales.
References
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Journal Article

R: A language and environment for statistical computing.

R Core Team
- 01 Jan 2014 - 
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Journal ArticleDOI

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar
- 01 Oct 2010 - 
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI

A new method for non-parametric multivariate analysis of variance

TL;DR: In this article, a non-parametric method for multivariate analysis of variance, based on sums of squared distances, is proposed. But it is not suitable for most ecological multivariate data sets.
Journal ArticleDOI

UCHIME improves sensitivity and speed of chimera detection

TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
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