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Article ; Online: The role of innate immunity in asthma development and protection: Lessons from the environment.

Pivniouk, Vadim / Gimenes Junior, Joao Antonio / Honeker, Linnea K / Vercelli, Donata

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology

2020 Volume 50, Issue 3, Page(s) 282–290

Abstract: Asthma, a complex, chronic disease characterized by airway inflammation, hyperresponsiveness and remodelling, affects over 300 million people worldwide. While the disease is typically associated with exaggerated allergen-induced type 2 immune responses, ... ...

Abstract	Asthma, a complex, chronic disease characterized by airway inflammation, hyperresponsiveness and remodelling, affects over 300 million people worldwide. While the disease is typically associated with exaggerated allergen-induced type 2 immune responses, these responses are strongly influenced by environmental exposures that stimulate innate immune pathways capable of promoting or protecting from asthma. The dual role played by innate immunity in asthma pathogenesis offers multiple opportunities for both research and clinical interventions and is the subject of this review.
MeSH term(s)	Allergens/immunology ; Asthma/immunology ; Environmental Exposure/adverse effects ; Humans ; Immunity, Innate ; Th2 Cells/immunology
Chemical Substances	Allergens
Language	English
Publishing date	2020-06-09
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	645204-8
ISSN	1365-2222 ; 0954-7894 ; 0960-2178
ISSN (online)	1365-2222
ISSN	0954-7894 ; 0960-2178
DOI	10.1111/cea.13508
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Article: Automating methods for estimating metabolite volatility.

Meredith, Laura K / Ledford, S Marshall / Riemer, Kristina / Geffre, Parker / Graves, Kelsey / Honeker, Linnea K / LeBauer, David / Tfaily, Malak M / Krechmer, Jordan

Frontiers in microbiology

2023 Volume 14, Page(s) 1267234

Abstract: The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility ... ...

Abstract	The volatility of metabolites can influence their biological roles and inform optimal methods for their detection. Yet, volatility information is not readily available for the large number of described metabolites, limiting the exploration of volatility as a fundamental trait of metabolites. Here, we adapted methods to estimate vapor pressure from the functional group composition of individual molecules (SIMPOL.1) to predict the gas-phase partitioning of compounds in different environments. We implemented these methods in a new open pipeline called
Language	English
Publishing date	2023-12-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1267234
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Article: Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings.

Honeker, Linnea K / Gullo, Catherine F / Neilson, Julia W / Chorover, Jon / Maier, Raina M

Frontiers in microbiology

2019 Volume 10, Page(s) 1209

Abstract: Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized ... ...

Abstract	Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N
Language	English
Publishing date	2019-05-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2019.01209
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Article ; Online: Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF).

Honeker, Linnea K / Root, Robert A / Chorover, Jon / Maier, Raina M

Journal of microbiological methods

2016 Volume 131, Page(s) 23–33

Abstract: Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field ... ...

Abstract	Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME μXRF. The FISH and ME μXRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49±0.19) than to bacteria (0.072±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate.
MeSH term(s)	Actinobacteria/genetics ; Actinobacteria/isolation & purification ; Bacteria/classification ; Bacteria/genetics ; Bacteria/growth & development ; Bacteria/isolation & purification ; DNA, Bacterial ; Electron Probe Microanalysis/methods ; Environmental Monitoring/methods ; Gammaproteobacteria/genetics ; Gammaproteobacteria/isolation & purification ; Genes, Bacterial ; In Situ Hybridization, Fluorescence/methods ; Metals/analysis ; Phylogeny ; Plant Roots/chemistry ; Plant Roots/microbiology ; Plant Roots/radiation effects ; Plants/chemistry ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Soil Pollutants/analysis ; Synchrotrons/instrumentation ; X-Rays
Chemical Substances	DNA, Bacterial ; Metals ; RNA, Ribosomal, 16S ; Soil Pollutants
Language	English
Publishing date	2016-09-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	604916-3
ISSN	1872-8359 ; 0167-7012
ISSN (online)	1872-8359
ISSN	0167-7012
DOI	10.1016/j.mimet.2016.09.018
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Zs.A 1849: Show issues

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Article ; Online: Asthma-protective agents in dust from traditional farm environments.

Marques Dos Santos, Mauricius / Pivniouk, Vadim / Rankl, Bettina / Walker, Alesia / Pagani, Giulia / Hertkorn, Norbert / Schmitt-Kopplin, Philippe / Müller, Christoph / Bracher, Franz / Merl-Pham, Juliane / Hauck, Stefanie M / Schloter, Michael / Michael, Ashley N / Anderson, Dayna / Honeker, Linnea / Gozdz, Justyna / Pivniouk, Oksana / Ober, Carole / Holbreich, Mark /

Martinez, Fernando D / Snyder, Shane A / von Mutius, Erika / Vercelli, Donata

The Journal of allergy and clinical immunology

2023 Volume 152, Issue 3, Page(s) 610–621

Abstract: Background: Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma ... ...

Abstract	Background: Growing up on traditional European or US Amish dairy farms in close contact with cows and hay protects children against asthma, and airway administration of extracts from dust collected from cowsheds of those farms prevents allergic asthma in mice. Objectives: This study sought to begin identifying farm-derived asthma-protective agents. Methods: Our work unfolded along 2 unbiased and independent but complementary discovery paths. Dust extracts (DEs) from protective and nonprotective farms (European and Amish cowsheds vs European sheep sheds) were analyzed by comparative nuclear magnetic resonance profiling and differential proteomics. Bioactivity-guided size fractionation focused on protective Amish cowshed DEs. Multiple in vitro and in vivo functional assays were used in both paths. Some of the proteins thus identified were characterized by in-solution and in-gel sodium dodecyl sulfate-polyacrylamide gel electrophoresis enzymatic digestion/peptide mapping followed by liquid chromatography/mass spectrometry. The cargo carried by these proteins was analyzed by untargeted liquid chromatography-high-resolution mass spectrometry. Results: Twelve carrier proteins of animal and plant origin, including the bovine lipocalins Bos d 2 and odorant binding protein, were enriched in DEs from protective European cowsheds. A potent asthma-protective fraction of Amish cowshed DEs (≈0.5% of the total carbon content of unfractionated extracts) contained 7 animal and plant proteins, including Bos d 2 and odorant binding protein loaded with fatty acid metabolites from plants, bacteria, and fungi. Conclusions: Animals and plants from traditional farms produce proteins that transport hydrophobic microbial and plant metabolites. When delivered to mucosal surfaces, these agents might regulate airway responses.
MeSH term(s)	Female ; Animals ; Cattle ; Mice ; Sheep ; Farms ; Dust/analysis ; Asthma/prevention & control ; Allergens ; Respiratory System
Chemical Substances	Dust ; Allergens
Language	English
Publishing date	2023-06-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2023.05.013
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Article ; Online: Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants.

The Science of the total environment

2023 Volume 899, Page(s) 165689

Abstract: Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant- ... ...

Abstract	Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific
MeSH term(s)	Soil Microbiology ; Rainforest ; Droughts ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Carbon/metabolism ; Soil ; Bacteria/metabolism ; Metabolome ; Plant Roots/metabolism
Chemical Substances	RNA, Ribosomal, 16S ; Carbon (7440-44-0) ; Soil
Language	English
Publishing date	2023-07-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.165689
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Article: Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME Î¼XRF)

Honeker, Linnea K / Jon Chorover / Raina M. Maier / Robert A. Root

Journal of microbiological methods. 2016 Dec., v. 131

2016

Abstract	Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME Î¼XRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME Î¼XRF. The FISH and ME Î¼XRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49Â±0.19) than to bacteria (0.072Â±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate.
Keywords	Actinobacteria ; alpha-Proteobacteria ; anthropogenic activities ; arsenic ; bacteria ; computer software ; environmental factors ; fluorescence ; fluorescence in situ hybridization ; gamma-Proteobacteria ; image analysis ; iron ; iron oxides ; mechanistic models ; metal tolerance ; mine tailings ; nucleic acids ; plant tissues ; quantitative analysis ; roots ; X-radiation
Language	English
Dates of publication	2016-12
Size	p. 23-33.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	604916-3
ISSN	1872-8359 ; 0167-7012
ISSN (online)	1872-8359
ISSN	0167-7012
DOI	10.1016/j.mimet.2016.09.018
Database	NAL-Catalogue (AGRICOLA)

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Article: Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions

Honeker, Linnea K / Julia W. Neilson / Robert A. Root / Juliana Gil-Loaiza / Jon Chorover / Raina M. Maier

Microbial ecology. 2017 Nov., v. 74, no. 4

2017

Abstract: Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly ... ...

Abstract	Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly important under these harsh conditions because of their beneficial services to plants. We hypothesize that bacterial colonization profiles on rhizoplane surfaces reflect deterministic processes that are governed by plant health and the root environment. The aim of this study was to identify associations between bacterial colonization patterns on buffalo grass (Buchloe dactyloides) rhizoplanes and both plant status (leaf chlorophyll and plant cover) and substrate biogeochemistry (pH, electrical conductivity, total organic carbon, total nitrogen, and rhizosphere microbial community). Buffalo grass plants from mesocosm- and field-scale phytostabilization trials conducted with tailings from the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, Arizona, were analyzed. These tailings are extremely acidic and have arsenic and lead concentrations of 2â4Â gÂ kgâ»Â¹ substrate. Bacterial communities on rhizoplanes and in rhizosphere-associated substrate were characterized using fluorescence in situ hybridization and 16S rRNA gene amplicon sequencing, respectively. The results indicated that the metabolic status of rhizoplane bacterial colonizers is significantly related to plant health. Principal component analysis revealed that root-surface Alphaproteobacteria relative abundance was associated most strongly with substrate pH and Gammaproteobacteria relative abundance associated strongly with substrate pH and plant cover. These factors also affected the phylogenetic profiles of the associated rhizosphere communities. In summary, rhizoplane bacterial colonization patterns are plant specific and influenced by plant status and rhizosphere biogeochemical conditions.
Keywords	Bouteloua dactyloides ; alpha-Proteobacteria ; arsenic ; bacterial colonization ; bacterial communities ; biogeochemistry ; chlorophyll ; electrical conductivity ; fluorescence in situ hybridization ; gamma-Proteobacteria ; genes ; lead ; leaves ; mine tailings ; nitrogen content ; nutrients ; organic carbon ; pH ; phylogeny ; phytoremediation ; plant establishment ; plant health ; principal component analysis ; rhizoplane ; ribosomal RNA ; semiarid zones ; toxicity ; Arizona
Language	English
Dates of publication	2017-11
Size	p. 853-867.
Publishing place	Springer US
Document type	Article
ZDB-ID	1462065-0
ISSN	1432-184X ; 0095-3628
ISSN (online)	1432-184X
ISSN	0095-3628
DOI	10.1007/s00248-017-0998-7
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Article: Elucidating Drought-Tolerance Mechanisms in Plant Roots through ¹H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques

Environmental science & technology. 2022 Jan. 20, v. 56, no. 3

2022

Abstract: As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. ... ...

Abstract	As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific ¹³C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.
Keywords	Clitoria fairchildiana ; Hibiscus rosa-sinensis ; Piper ; carbohydrates ; carbon ; drought ; drought tolerance ; environmental science ; legumes ; lignin ; metabolomics ; organic matter ; rhizosphere ; secretion ; soil ; trees ; tropical rain forests
Language	English
Dates of publication	2022-0120
Size	p. 2021-2032.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.1c06772
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Article ; Online: Elucidating Drought-Tolerance Mechanisms in Plant Roots through

Environmental science & technology

2022 Volume 56, Issue 3, Page(s) 2021–2032

Abstract	As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific
MeSH term(s)	Droughts ; Metabolomics ; Plant Roots/metabolism ; Plants ; Proton Magnetic Resonance Spectroscopy ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Stress, Physiological
Language	English
Publishing date	2022-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c06772
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