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references.yaml
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---
references:
- id: abarenkov2023
abstract: >-
This release consists of a single FASTA file: the RepS/RefS of all SHs,
adopting the dynamically use of clustering thresholds whenever available.
Includes global and 97% singletons.
accessed:
- year: 2024
month: 2
day: 4
author:
- family: Abarenkov
given: Kessy
- family: Zirk
given: Allan
- family: Piirmann
given: Timo
- family: Pöhönen
given: Raivo
- family: Ivanov
given: Filipp
- family: Nilsson
given: R. Henrik
- family: Kõljalg
given: Urmas
citation-key: abarenkov2023
DOI: 10.15156/BIO/2938068
issued:
- year: 2023
month: 7
day: 18
license: Attribution-ShareAlike (CC BY-SA)
medium: application/gzip
publisher: UNITE Community
source: DOI.org (Datacite)
title: UNITE general FASTA release for Fungi 2
type: dataset
URL: https://doi.plutof.ut.ee/doi/10.15156/BIO/2938068
- id: abarenkov2023a
abstract: >-
This release consists of a single FASTA file: the RepS/RefS of all SHs,
adopting the dynamically use of clustering thresholds whenever available.
accessed:
- year: 2024
month: 2
day: 4
author:
- family: Abarenkov
given: Kessy
- family: Zirk
given: Allan
- family: Piirmann
given: Timo
- family: Pöhönen
given: Raivo
- family: Ivanov
given: Filipp
- family: Nilsson
given: R. Henrik
- family: Kõljalg
given: Urmas
citation-key: abarenkov2023a
DOI: 10.15156/BIO/2938067
issued:
- year: 2023
month: 7
day: 18
license: Attribution-ShareAlike (CC BY-SA)
medium: application/gzip
publisher: UNITE Community
source: DOI.org (Datacite)
title: UNITE general FASTA release for Fungi
type: dataset
URL: https://doi.plutof.ut.ee/doi/10.15156/BIO/2938067
- id: adams2002
accessed:
- year: 2024
month: 5
day: 2
author:
- family: Adams
given: David G.
citation-key: adams2002
container-title: The Ecology of Cyanobacteria
DOI: 10.1007/0-306-46855-7_19
editor:
- family: Whitton
given: Brian A.
- family: Potts
given: Malcolm
event-place: Dordrecht
ISBN: 978-0-7923-4735-4
issued:
- year: 2002
language: en
page: 523-561
publisher: Kluwer Academic Publishers
publisher-place: Dordrecht
source: DOI.org (Crossref)
title: Symbiotic Interactions
type: chapter
URL: http://link.springer.com/10.1007/0-306-46855-7_19
- id: aimone2023
abstract: >-
Foliar fungal endophytes are known to alter plant physiology but the
mechanisms by which they do so remain poorly understood. We focused on how
plant gene expression was altered by six fungal strains that generated
“water-saver” and “water-spender” drought physiologies in a C4 grass,
Panicum hallii. Water-saver physiologies have lower plant water loss,
improved wilt resistance, and higher survival compared with water-spender
strategies. We expected that fungi within each functional group would have
similar effects on P. hallii, and this was largely true for plant physiology
but not for plant gene expression. When we focused only on genes that were
differentially expressed relative to fungus-free controls, we found
surprisingly little overlap in plant differentially expressed genes or gene
regulatory pathways across the fungal treatments, including within and
between the water-saver and water-spender strategies. Nevertheless, using
lasso regression, we identified a small subset of genes that predicted 39
and 53% of the variation in plant wilt resistance and water loss,
respectively. These results suggest that fungal effects on plant
transcription may identify how they extend the plant phenotype, and the
comparison across multiple fungi allows us to differentiate broadly
fungal-responsive plant genes versus those plant genes that respond only to
single fungal taxa. The genes identified here could be targeted for future
study to understand their function and, ultimately, represent candidates for
precision breeding efforts to increase plant drought tolerance.
[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
accessed:
- year: 2024
month: 4
day: 8
author:
- family: Aimone
given: Catherine D.
- family: Giauque
given: Hannah
- family: Hawkes
given: Christine V.
citation-key: aimone2023
container-title: Phytobiomes Journal
container-title-short: Phytobiomes Journal
DOI: 10.1094/PBIOMES-01-22-0006-FI
ISSN: 2471-2906
issue: '2'
issued:
- year: 2023
month: 9
language: en
page: 172-183
source: DOI.org (Crossref)
title: >-
Fungal Symbionts Generate Water-Saver and Water-Spender Plant Drought
Strategies via Diverse Effects on Host Gene Expression
type: article-journal
URL: https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-01-22-0006-FI
volume: '7'
- id: albrectsen2010
accessed:
- year: 2024
month: 4
day: 14
author:
- family: Albrectsen
given: Benedicte R.
- family: Björkén
given: Lars
- family: Varad
given: Akkamahadevi
- family: Hagner
given: Åsa
- family: Wedin
given: Mats
- family: Karlsson
given: Jan
- family: Jansson
given: Stefan
citation-key: albrectsen2010
container-title: Fungal Diversity
container-title-short: Fungal Diversity
DOI: 10.1007/s13225-009-0011-y
ISSN: 1560-2745, 1878-9129
issue: '1'
issued:
- year: 2010
month: 3
language: en
license: http://www.springer.com/tdm
page: 17-28
source: DOI.org (Crossref)
title: >-
Endophytic fungi in European aspen (Populus tremula) leaves—diversity,
detection, and a suggested correlation with herbivory resistance
type: article-journal
URL: http://link.springer.com/10.1007/s13225-009-0011-y
volume: '41'
- id: ali2016
abstract: |-
Abstract
Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.
accessed:
- year: 2024
month: 4
day: 7
author:
- family: Ali
given: Omar A
- family: O’Rourke
given: Sean M
- family: Amish
given: Stephen J
- family: Meek
given: Mariah H
- family: Luikart
given: Gordon
- family: Jeffres
given: Carson
- family: Miller
given: Michael R
citation-key: ali2016
container-title: Genetics
DOI: 10.1534/genetics.115.183665
ISSN: 1943-2631
issue: '2'
issued:
- year: 2016
month: 2
day: 1
language: en
license: >-
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model
page: 389-400
source: DOI.org (Crossref)
title: 'RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping'
title-short: RAD Capture (Rapture)
type: article-journal
URL: https://academic.oup.com/genetics/article/202/2/389/5930231
volume: '202'
- id: anderson2017
abstract: >-
PERMANOVA is a computer program for testing the simultaneous response of one
or more variables to one or more factors in an ANOVA experimental design on
the basis of any distance measure, using permutation methods. These notes
for users assume knowledge of multi-factorial ANOVA, which has the same
basic logic in multivariate as in univariate analysis, and an understanding
of what it means to test a multivariate hypothesis. A more complete
description of the method is given in Anderson (2001a) and McArdle &
Anderson (2001). The program includes: choice of appropriate transformation
and/or standardization of the data; choice of 19 distance (or dissimilarity)
measures to use as the basis of the analysis; option to rank the distances
in the distance matrix before the analysis; analysis and partitioning of the
total sum of squares according to the full model, including appropriate
treatment of factors that are fixed or random, crossed (orthogonal) or
nested (hierarchical), and all interaction terms; correct calculation of an
appropriate distance-based pseudo F-statistic for each term in the model,
based on expected mean squares as in univariate ANOVA (Winer et al. 1991,
Searle et al.1992); correct permutation procedures to obtain P-values for
each term in the model, using the correct permutable units (Anderson & ter
Braak 2003); choice of permutation method: raw data units or residuals under
either a reduced or a full model (Anderson 2001b, Anderson & Legendre 1999,
Anderson & Robinson 2001); correct P-values also obtained through Monte
Carlo random draws from the asymptotic permutation distribution (Anderson &
Robinson 2003); option to include one or more covariables (i.e., to perform
ANCOVA or MANCOVA); pair-wise a posteriori comparisons of levels for single
factors, including within individual levels of other factors in the case of
significant interactions and the use of correct permutable units in each
case.
author:
- family: Anderson
given: Marti J.
citation-key: anderson2017
container-title: 'Wiley StatsRef: Statistics Reference Online'
DOI: 10.1002/9781118445112.stat07841
issued:
- year: 2017
month: 11
day: 15
page: 1-15
publisher: Wiley
title: Permutational Multivariate Analysis of Variance ( PERMANOVA )
type: chapter
- id: andrews2010
abstract: >-
FastQC aims to provide a simple way to do some quality control checks on raw
sequence data coming from high throughput sequencing pipelines. It provides
a modular set of analyses which you can use to give a quick impression of
whether your data has any problems of which you should be aware before doing
any further analysis.
author:
- family: Andrews
given: Simon
- family: Krueger
given: Felix
- family: Segonds-Pichon
given: Anne
- family: Biggins
given: Laura
- family: Krueger
given: Christel
- family: Wingett
given: Steven
citation-key: andrews2010
event-place: Babraham, UK
issued:
- year: 2010
publisher-place: Babraham, UK
title: FastQC
type: software
version: 0.12.1
- id: apigo2022
abstract: |-
Abstract
Understanding the origins and maintenance of host specificity, or why horizontally‐acquired symbionts associate with some hosts but not others, remains elusive. In this study, we explored whether patterns of host specificity in foliar fungal endophytes, a guild of highly diverse fungi that occur within the photosynthetic tissues of all major plant lineages, were related to characteristics of the plant community. We comprehensively sampled all plant host species within a single community and tested the relationship between plant abundance or plant evolutionary relatedness and metrics of endophyte host specificity. We quantified host specificity with methods that considered the total endophyte community per plant host (i.e., multivariate methods) along with species‐based methods (i.e., univariate metrics) that considered host specificity from the perspective of each endophyte. Univariate host specificity metrics quantified plant alpha‐diversity (structural specificity), plant beta‐diversity (beta‐specificity), and plant phylogenetic diversity (phylogenetic specificity) per endophyte. We standardized the effect sizes of univariate host specificity metrics to randomized distributions to avoid spurious correlations between host specificity metrics and endophyte abundance. We found that more abundant plant species harbored endophytes that occupied fewer plant species (higher structural specificity) and were consistently found in the same plant species across the landscape (higher beta‐specificity). There was no relationship between plant phylogenetic distance and endophyte community dissimilarity. We still found that endophyte community composition significantly varied among plant species, families, and major groups, supporting a plant identity effect. In particular, endophytes in angiosperm lineages associated with narrower phylogenetic breadths of plants (higher phylogenetic specificity) compared to endophytes within conifer and fern lineages. Overall, an effect of plant species abundance may help explain why horizontally‐transmitted endophytes vary geographically within host species ranges.
accessed:
- year: 2024
month: 3
day: 8
author:
- family: Apigo
given: Austen
- family: Oono
given: Ryoko
citation-key: apigo2022
container-title: Ecosphere
container-title-short: Ecosphere
DOI: 10.1002/ecs2.3879
ISSN: 2150-8925, 2150-8925
issue: '1'
issued:
- year: 2022
month: 1
language: en
page: e03879
source: DOI.org (Crossref)
title: >-
Plant abundance, but not plant evolutionary history, shapes patterns of host
specificity in foliar fungal endophytes
type: article-journal
URL: https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.3879
volume: '13'
- id: aponterolon2023
author:
- family: Aponte Rolón
given: Bolívar
citation-key: aponterolon2023
issued:
- year: 2023
title: >-
High-Molecular-Weight SPRI-aided DNA extraction from Mimulus (Phrymaceae)
leaf tissue.
type: webpage
URL: dx.doi.org/10.17504/protocols.io.bp2l6xn8rlqe/v2
- id: armstrong2022
abstract: >-
Dimensionality reduction techniques are a key component of most microbiome
studies, providing both the ability to tractably visualize complex
microbiome datasets and the starting point for additional, more formal,
statistical analyses. In this review, we discuss the motivation for applying
dimensionality reduction techniques, the special characteristics of
microbiome data such as sparsity and compositionality that make this
difficult, the different categories of strategies that are available for
dimensionality reduction, and examples from the literature of how they have
been successfully applied (together with pitfalls to avoid). We conclude by
describing the need for further development in the field, in particular
combining the power of phylogenetic analysis with the ability to handle
sparsity, compositionality, and non-normality, as well as discussing current
techniques that should be applied more widely in future analyses.
accessed:
- year: 2024
month: 6
day: 11
author:
- family: Armstrong
given: George
- family: Rahman
given: Gibraan
- family: Martino
given: Cameron
- family: McDonald
given: Daniel
- family: Gonzalez
given: Antonio
- family: Mishne
given: Gal
- family: Knight
given: Rob
citation-key: armstrong2022
container-title: Frontiers in Bioinformatics
container-title-short: Front. Bioinform.
DOI: 10.3389/fbinf.2022.821861
ISSN: 2673-7647
issued:
- year: 2022
month: 2
day: 24
page: '821861'
source: DOI.org (Crossref)
title: >-
Applications and Comparison of Dimensionality Reduction Methods for
Microbiome Data
type: article-journal
URL: https://www.frontiersin.org/articles/10.3389/fbinf.2022.821861/full
volume: '2'
- id: arnold2003
abstract: >-
Every plant species examined to date harbors endophytic fungi within its
asymptomatic aerial tissues, such that endophytes rep-resent a ubiquitous,
yet cryptic, component of terrestrial plant communities. Fungal endophytes
associated with leaves of woody angiosperms are especially diverse; yet,
fundamental aspects of their interactions with hosts are unknown. In
contrast to the relatively species-poor endophytes that are vertically
transmitted and act as defensive mutualists of some temperate grasses, the
diverse, horizontally transmitted endophytes of woody angio-sperms are
thought to contribute little to host defense. Here, we document high
diversity, spatial structure, and host affinity among foliar endophytes
associated with a tropical tree (Theobroma cacao, Malvaceae) across lowland
Panama. We then show that inoculation of endophyte-free leaves with
endophytes isolated frequently from naturally infected, asymptomatic hosts
signifi-cantly decreases both leaf necrosis and leaf mortality when T. cacao
seedlings are challenged with a major pathogen (Phytophthora sp.). In
contrast to reports of fungal inoculation inducing systemic defense, we
found that protection was primarily localized to endophyte-infected tissues.
Further, endophyte-mediated protec-tion was greater in mature leaves, which
bear less intrinsic defense against fungal pathogens than do young leaves.
In vitro studies suggest that host affinity is mediated by leaf chemistry,
and that protection may be mediated by direct interactions of endophytes
with foliar pathogens. Together, these data demonstrate the capacity of
diverse, horizontally transmitted endophytes of woody angiosperms to play an
important but previously unappreciated role in host defense.
author:
- family: Arnold
given: A Elizabeth
- family: Mejía
given: Luis Carlos
- family: Kyllo
given: Damond
- family: Rojas
given: Enith I
- family: Maynard
given: Zuleyka
- family: Robbins
given: Nancy
- family: Herre
given: Edward Allen
citation-key: arnold2003
container-title: Proceedings of the National Academy of Sciences
issue: '26'
issued:
- year: 2003
page: 15649-15654
title: Fungal endophytes limit pathogen damage in a tropical tree
type: article-journal
volume: '100'
- id: arnold2007
abstract: >-
Drought strongly influences plant phenology, growth and mortality in
tropical forests, thereby shaping plant performance, population dynamics and
community structure (Bunker & Carson 2005, Condit
et al.
1995). Microbial symbionts of plants profoundly influence host water relations (Lösch & Gansert 2002), but are rarely considered in studies of tropical plant physiology. In particular, plant–fungus associations, which are ubiquitous in plant communities and especially common in tropical forests, play important and varied roles in plant water status. Fungal pathogens associated with roots, vascular tissue and foliage may interfere with water uptake and transport, increase rates of foliar transpiration, and induce xylem embolism and tissue death (Agrios 1997). In contrast, rhizosphere mutualists such as ecto- and arbuscular mycorrhizal fungi may benefit hosts by increasing surface area for water uptake, enhancing stomatal regulation of water loss, and increasing root hydraulic conductivity (Auge 2001, Lösch & Gansert 2002).
accessed:
- year: 2024
month: 1
day: 20
author:
- family: Arnold
given: A. Elizabeth
- family: Engelbrecht
given: Bettina M. J.
citation-key: arnold2007
container-title: Journal of Tropical Ecology
container-title-short: J. Trop. Ecol.
DOI: 10.1017/S0266467407004038
ISSN: 0266-4674, 1469-7831
issue: '3'
issued:
- year: 2007
month: 5
language: en
page: 369-372
source: DOI.org (Crossref)
title: >-
Fungal endophytes nearly double minimum leaf conductance in seedlings of a
neotropical tree species
type: article-journal
URL: >-
https://www.cambridge.org/core/product/identifier/S0266467407004038/type/journal_article
volume: '23'
- id: arnold2019
abstract: |-
Summary
Plant biology is experiencing a renewed interest in the mechanistic underpinnings and evolution of phenotypic plasticity that calls for a re‐evaluation of how we analyse phenotypic responses to a rapidly changing climate. We suggest that dissecting plant plasticity in response to increasing temperature needs an approach that can represent plasticity over multiple environments, and considers both population‐level responses and the variation between genotypes in their response. Here, we outline how a random regression mixed model framework can be applied to plastic traits that show linear or nonlinear responses to temperature. Random regressions provide a powerful and efficient means of characterising plasticity and its variation. Although they have been used widely in other fields, they have only recently been implemented in plant evolutionary ecology. We outline their structure and provide an example tutorial of their implementation.
accessed:
- year: 2024
month: 5
day: 10
author:
- family: Arnold
given: Pieter A.
- family: Kruuk
given: Loeske E. B.
- family: Nicotra
given: Adrienne B.
citation-key: arnold2019
container-title: New Phytologist
container-title-short: New Phytologist
DOI: 10.1111/nph.15656
ISSN: 0028-646X, 1469-8137
issue: '3'
issued:
- year: 2019
month: 5
language: en
page: 1235-1241
source: DOI.org (Crossref)
title: How to analyse plant phenotypic plasticity in response to a changing climate
type: article-journal
URL: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15656
volume: '222'
- id: arya.hoffmann2011
abstract: >-
Evolutionary adaptation can be rapid and potentially help species counter
stressful conditions or realize ecological opportunities arising from
climate change. The challenges are to understand when evolution will occur
and to identify potential evolutionary winners as well as losers, such as
species lacking adaptive capacity living near physiological limits.
Evolutionary processes also need to be incorporated into management
programmes designed to minimize biodiversity loss under rapid climate
change. These challenges can be met through realistic models of evolutionary
change linked to experimental data across a range of taxa.
author:
- literal: Ary A. Hoffmann
- family: Hoffmann
given: Ary A.
- literal: Carla M. Sgrò
- family: Sgrò
given: Carla M.
citation-key: arya.hoffmann2011
container-title: Nature
DOI: 10.1038/nature09670
issue: '7335'
issued:
- year: 2011
month: 2
day: 24
note: 'MAG ID: 2008951609'
page: 479-485
PMID: '21350480'
title: Climate change and evolutionary adaptation
type: article-journal
volume: '470'
- id: barton2023
author:
- family: Bartoń
given: Kamil
citation-key: barton2023
genre: manual
issued:
- year: 2023
title: 'MuMIn: Multi-model inference'
type: report
URL: https://CRAN.R-project.org/package=MuMIn
- id: belisle2012
accessed:
- year: 2024
month: 6
day: 13
author:
- family: Belisle
given: Melinda
- family: Peay
given: Kabir G.
- family: Fukami
given: Tadashi
citation-key: belisle2012
container-title: Microbial Ecology
container-title-short: Microb Ecol
DOI: 10.1007/s00248-011-9975-8
ISSN: 0095-3628, 1432-184X
issue: '4'
issued:
- year: 2012
month: 5
language: en
license: http://www.springer.com/tdm
page: 711-718
source: DOI.org (Crossref)
title: >-
Flowers as Islands: Spatial Distribution of Nectar-Inhabiting Microfungi
among Plants of *Mimulus aurantiacus*, a Hummingbird-Pollinated Shrub
title-short: Flowers as Islands
type: article-journal
URL: http://link.springer.com/10.1007/s00248-011-9975-8
volume: '63'
- id: benjamini1995
abstract: >-
SUMMARY The common approach to the multiplicity problem calls for
controlling the familywise error rate (FWER). This approach, though, has
faults, and we point out a few. A different approach to problems of multiple
significance testing is presented. It calls for controlling the expected
proportion of falsely rejected hypotheses — the false discovery rate. This
error rate is equivalent to the FWER when all hypotheses are true but is
smaller otherwise. Therefore, in problems where the control of the false
discovery rate rather than that of the FWER is desired, there is potential
for a gain in power. A simple sequential Bonferronitype procedure is proved
to control the false discovery rate for independent test statistics, and a
simulation study shows that the gain in power is substantial. The use of the
new procedure and the appropriateness of the criterion are illustrated with
examples.
accessed:
- year: 2024
month: 1
day: 14
author:
- family: Benjamini
given: Yoav
- family: Hochberg
given: Yosef
citation-key: benjamini1995
container-title: 'Journal of the Royal Statistical Society: Series B (Methodological)'
container-title-short: 'Journal of the Royal Statistical Society: Series B (Methodological)'
DOI: 10.1111/j.2517-6161.1995.tb02031.x
ISSN: 0035-9246, 2517-6161
issue: '1'
issued:
- year: 1995
month: 1
language: english
page: 289–300
title: >-
Controlling the False Discovery Rate: A Practical and Powerful Approach to
Multiple Testing
title-short: Controlling the False Discovery Rate
type: article-journal
URL: https://rss.onlinelibrary.wiley.com/doi/10.1111/j.2517-6161.1995.tb02031.x
volume: '57'
- id: bergelson2021
accessed:
- year: 2024
month: 4
day: 10
author:
- family: Bergelson
given: Joy
- family: Brachi
given: Benjamin
- family: Roux
given: Fabrice
- family: Vailleau
given: Fabienne
citation-key: bergelson2021
container-title: Current Opinion in Biotechnology
container-title-short: Current Opinion in Biotechnology
DOI: 10.1016/j.copbio.2021.05.007
ISSN: '09581669'
issued:
- year: 2021
month: 8
language: en
page: 167-173
source: DOI.org (Crossref)
title: Assessing the potential to harness the microbiome through plant genetics
type: article-journal
URL: https://linkinghub.elsevier.com/retrieve/pii/S0958166921000744
volume: '70'
- id: blanchet2008
abstract: >-
This paper proposes a new way of using forward selection of explanatory
variables in regression or canonical redundancy analysis. The classical
forward selection method presents two problems: a highly inflated Type I
error and an overestimation of the amount of explained variance. Correcting
these problems will greatly improve the performance of this very useful
method in ecological modeling. To prevent the first problem, we propose a
two‐step procedure. First, a global test using all explanatory variables is
carried out. If, and only if, the global test is significant, one can
proceed with forward selection. To prevent overestimation of the explained
variance, the forward selection has to be carried out with two stopping
criteria: (1) the usual alpha significance level and (2) the adjusted
coefficient of multiple determination (
) calculated using all explanatory variables. When forward selection identifies a variable that brings one or the other criterion over the fixed threshold, that variable is rejected, and the procedure is stopped. This improved method is validated by simulations involving univariate and multivariate response data. An ecological example is presented using data from the Bryce Canyon National Park, Utah, USA.
accessed:
- year: 2024
month: 1
day: 14
author:
- family: Blanchet
given: F. Guillaume
- family: Legendre
given: Pierre
- family: Borcard
given: Daniel
citation-key: blanchet2008
container-title: Ecology
container-title-short: Ecology
DOI: 10.1890/07-0986.1
ISSN: 0012-9658, 1939-9170
issue: '9'
issued:
- year: 2008
month: 9
language: en
page: 2623-2632
source: DOI.org (Crossref)
title: FORWARD SELECTION OF EXPLANATORY VARIABLES
type: article-journal
URL: https://esajournals.onlinelibrary.wiley.com/doi/10.1890/07-0986.1
volume: '89'
- id: bodenhausen2014
abstract: >-
The identity of plant host genetic factors controlling the composition of
the plant microbiota and the extent to which plant genes affect associated
microbial populations is currently unknown. Here, we use a candidate gene
approach to investigate host effects on the phyllosphere community
composition and abundance. To reduce the environmental factors that might
mask genetic factors, the model plant Arabidopsis thaliana was used in a
gnotobiotic system and inoculated with a reduced complexity synthetic
bacterial community composed of seven strains representing the most abundant
phyla in the phyllosphere. From a panel of 55 plant mutants with alterations
in the surface structure, cell wall, defense signaling, secondary
metabolism, and pathogen recognition, a small number of single host
mutations displayed an altered microbiota composition and/or abundance. Host
alleles that resulted in the strongest perturbation of the microbiota
relative to the wild-type were lacs2 and pec1. These mutants affect cuticle
formation and led to changes in community composition and an increased
bacterial abundance relative to the wild-type plants, suggesting that
different bacteria can benefit from a modified cuticle to different extents.
Moreover, we identified ein2, which is involved in ethylene signaling, as a
host factor modulating the community's composition. Finally, we found that
different Arabidopsis accessions exhibited different communities, indicating
that plant host genetic factors shape the associated microbiota, thus
harboring significant potential for the identification of novel plant
factors affecting the microbiota of the communities.
author:
- family: Bodenhausen
given: Natacha
- family: Bortfeld-Miller
given: Miriam
- family: Ackermann
given: Martin
- family: Vorholt
given: Julia A.
citation-key: bodenhausen2014
container-title: PLOS Genetics
DOI: 10.1371/journal.pgen.1004283
issue: '4'
issued:
- year: 2014
month: 4
day: 17
note: 'MAG ID: 1990582630'
PMCID: '3990490'
PMID: '24743269'
title: >-
A Synthetic Community Approach Reveals Plant Genotypes Affecting the
Phyllosphere Microbiota
type: article-journal
volume: '10'
- id: bowman2021
abstract: >-
Fungal communities associated with plants often decrease in similarity as
the distance between sampling sites increases (i.e., they demonstrate
distance decay). In the southwestern USA, forests occur in highlands
separated from one another by warmer, drier biomes with plant and fungal
communities that differ from those at higher elevations. These disjunct
forests are broadly similar in climate to one another, offering an
opportunity to examine drivers of distance decay in plant-associated fungi
across multiple ecologically similar yet geographically disparate
landscapes. We examined ectomycorrhizal and foliar endophytic fungi
associated with a dominant forest tree (Pinus ponderosa) in forests across
ca. 550 km of geographic distance from northwestern to southeastern Arizona
(USA). Both guilds of fungi showed distance decay, but drivers differed for
each: ectomycorrhizal fungi are constrained primarily by dispersal
limitation, whereas foliar endophytes are constrained by specific
environmental conditions. Most ectomycorrhizal fungi were found in only a
single forested area, as were many endophytic fungi. Such regional-scale
perspectives are needed for baseline estimates of fungal diversity
associated with forest trees at a landscape scale, with attention to the
sensitivity of different guilds of fungal symbionts to decreasing areas of
suitable habitat, increasing disturbance, and related impacts of climate
change.
accessed:
- year: 2023
month: 11
day: 16
author:
- family: Bowman
given: Elizabeth A.
- family: Arnold
given: A. Elizabeth
citation-key: bowman2021
container-title: The ISME Journal
container-title-short: ISME J
DOI: 10.1038/s41396-021-01006-9
ISSN: 1751-7362, 1751-7370
issue: '12'
issued:
- year: 2021
month: 12
language: en
page: 3437-3454
source: DOI.org (Crossref)
title: >-
Drivers and implications of distance decay differ for ectomycorrhizal and
foliar endophytic fungi across an anciently fragmented landscape
type: article-journal
URL: https://www.nature.com/articles/s41396-021-01006-9
volume: '15'
- id: bowsher2020
abstract: >-
Plant root−microbe interactions influence plant productivity, health, and
resistance to stress. Although there is evidence that plant species and even
genotypes can alter soil microbial community structure, environmental
conditions can potentially outweigh plant genetic effects. Here, we used a
reciprocal transplant experiment to understand the contributions of the
environment and the host plant to rhizosphere microbiome composition in
locally adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata). Two
genotypes of a coastal ecotype and two genotypes of an inland ecotype were
planted at coastal and inland sites. After 3 months, we collected
rhizosphere and bulk soil and assessed microbial communities by 16S rRNA
gene sequencing. We found that local environment (coastal versus inland
site) strongly influenced rhizosphere communities, at least in part due to
distinct local microbial species pools. Host identity played a smaller role:
at each site, the ecotypes exhibited remarkably similar composition of
microbial communities at the class level, indicating that divergent M.
guttatus ecotypes recruit phylogenetically similar rhizosphere communities,
even in environments to which they are maladapted. Nevertheless, the two
ecotypes significantly differed in community composition at both sites due,
in part, to an exclusive set of taxa associated with each ecotype. They also
differed in alpha diversity at the inland site. Although this indicates that
locally adapted M. guttatus ecotypes are genetically diverged in factors
shaping rhizosphere communities, our findings highlight the context-specific
interactions between host identity and local environment that shape those
communities.
[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
accessed:
- year: 2024
month: 4
day: 8
author:
- family: Bowsher
given: Alan W.
- family: Kearns
given: Patrick J.
- family: Popovic
given: Damian
- family: Lowry
given: David B.
- family: Shade
given: Ashley
citation-key: bowsher2020
container-title: Phytobiomes Journal
container-title-short: Phytobiomes Journal
DOI: 10.1094/PBIOMES-05-19-0026-R
ISSN: 2471-2906, 2471-2906
issue: '1'
issued:
- year: 2020
month: 1
language: en
page: 53-63
source: DOI.org (Crossref)
title: >-
Locally Adapted *Mimulus* Ecotypes Differentially Impact Rhizosphere
Bacterial and Archaeal Communities in an Environment-Dependent Manner
type: article-journal
URL: https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-05-19-0026-R
volume: '4'
- id: brachi2022
abstract: >-
Although complex interactions between hosts and microbial associates are
increasingly well documented, we still know little about how and why hosts
shape microbial communities in nature. In addition, host genetic effects on
microbial communities vary widely depending on the environment, obscuring
conclusions about which microbes are impacted and which plant functions are
important. We characterized the leaf microbiota of 200
Arabidopsis thaliana
genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
accessed:
- year: 2024
month: 4
day: 10
author:
- family: Brachi
given: Benjamin
- family: Filiault
given: Daniele
- family: Whitehurst
given: Hannah
- family: Darme
given: Paul
- family: Le Gars
given: Pierre
- family: Le Mentec
given: Marine
- family: Morton
given: Timothy C.
- family: Kerdaffrec
given: Envel
- family: Rabanal
given: Fernando
- family: Anastasio
given: Alison
- family: Box
given: Mathew S.
- family: Duncan
given: Susan
- family: Huang
given: Feng
- family: Leff
given: Riley
- family: Novikova
given: Polina
- family: Perisin
given: Matthew
- family: Tsuchimatsu
given: Takashi
- family: Woolley
given: Roderick
- family: Dean
given: Caroline
- family: Nordborg
given: Magnus
- family: Holm
given: Svante
- family: Bergelson
given: Joy
citation-key: brachi2022
container-title: Proceedings of the National Academy of Sciences
container-title-short: Proc. Natl. Acad. Sci. U.S.A.
DOI: 10.1073/pnas.2201285119
ISSN: 0027-8424, 1091-6490
issue: '30'
issued:
- year: 2022
month: 7
day: 26
language: en
page: e2201285119
source: DOI.org (Crossref)
title: >-
Plant genetic effects on microbial hubs impact host fitness in repeated
field trials
type: article-journal
URL: https://pnas.org/doi/full/10.1073/pnas.2201285119
volume: '119'
- id: brandvain2014
accessed:
- year: 2024
month: 7
day: 13
author:
- family: Brandvain
given: Yaniv
- family: Kenney
given: Amanda M.
- family: Flagel
given: Lex
- family: Coop
given: Graham
- family: Sweigart
given: Andrea L.
citation-key: brandvain2014
container-title: PLoS Genetics
container-title-short: PLoS Genet
DOI: 10.1371/journal.pgen.1004410
editor:
- family: Jiggins
given: Chris D.
ISSN: 1553-7404
issue: '6'
issued:
- year: 2014
month: 6