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Article: Field to Greenhouse: How Stable Is the Soil Microbiome after Removal from the Field?

Kushwaha, Priyanka / Soto Velázquez, Ana L / McMahan, Colleen / Neilson, Julia W

2024 Volume 12, Issue 1

Abstract: Plant-soil feedback (PSF) processes impact plant productivity and ecosystem function, but they are poorly understood because PSFs vary significantly with plant and soil type, plant growth stage, and environmental conditions. Controlled greenhouse studies ...

Abstract	Plant-soil feedback (PSF) processes impact plant productivity and ecosystem function, but they are poorly understood because PSFs vary significantly with plant and soil type, plant growth stage, and environmental conditions. Controlled greenhouse studies are essential to unravel the mechanisms associating PSFs with plant productivity; however, successful implementation of these controlled experiments is constrained by our understanding of the persistence of the soil microbiome during the transition from field to greenhouse. This study evaluates the preservation potential of a field soil microbiome when stored in the laboratory under field temperature and moisture levels. Soil microbial diversity, taxonomic composition, and functional potential were evaluated via amplicon sequencing at the start of storage (W0), week 3 (W3), week 6 (W6), and week 9 (W9) to determine the effect of storage time on soil microbiome integrity. Though microbial richness remained stable, Shannon diversity indices decreased significantly at W6 for bacteria/archaea and W3 for fungi. Bacterial/archaeal community composition also remained stable, whereas the fungal community changed significantly during the first 3 weeks. Functional predictions revealed increased capacity for chemoheterotrophy for bacteria/archaea and decreased relative proportions of arbuscular mycorrhizal and ectomycorrhizal fungi. We show that preservation of the field soil microbiome must be a fundamental component of experimental design. Either greenhouse experiments should be initiated within 3 weeks of field soil collection, or a preliminary incubation study should be conducted to determine the time and storage conditions required to sustain the integrity of the specific field soil microbiome being studied.
Language	English
Publishing date	2024-01-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12010110
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Soil microbial community and abiotic soil properties influence Zn and Cd hyperaccumulation differently in Arabidopsis halleri

Kushwaha, Priyanka / Neilson, Julia W. / Maier, Raina M. / Babst-Kostecka, Alicja

Science of the total environment. 2022 Jan. 10, v. 803

2022

Abstract: Soil contamination with trace metal(loid) elements (TME) is a global concern. This has focused interest on TME-tolerant plants, some of which can hyperaccumulate extraordinary amounts of TME into above-ground tissues, for potential treatment of these ... ...

Abstract	Soil contamination with trace metal(loid) elements (TME) is a global concern. This has focused interest on TME-tolerant plants, some of which can hyperaccumulate extraordinary amounts of TME into above-ground tissues, for potential treatment of these soils. However, intra-species variability in TME hyperaccumulation is not yet sufficiently understood to fully harness this potential. Particularly, little is known about the rhizosphere microbial communities associated with hyperaccumulating plants and whether or not they facilitate TME uptake. The aim of this study is to characterize the diversity and structure of Arabidopsis halleri rhizosphere-influenced and background (i.e., non-Arabidopsis) soil microbial communities in four plant populations with contrasting Zn and Cd hyperaccumulation traits, two each from contaminated and uncontaminated sites. Microbial community properties were assessed along with geographic location, climate, abiotic soil properties, and plant parameters to explain variation in Zn and Cd hyperaccumulation. Site type (TME-contaminated vs. uncontaminated) and location explained 44% of bacterial/archaeal and 28% of fungal community variability. A linear discriminant effect size (LEfSe) analysis identified a greater number of taxa defining rhizosphere microbial communities than associated background soils. Further, in TME-contaminated soils, the number of rhizosphere-defining taxa was 6-fold greater than in the background soils. In contrast, the corresponding ratio for uncontaminated sites, was 3 and 1.6 for bacteria/archaea and fungi, respectively. The variables analyzed explained 71% and 76% of the variance in Zn and Cd hyperaccumulation, respectively; however, each hyperaccumulation pattern was associated with different variables. A. halleri rhizosphere fungal richness and diversity associated most strongly with Zn hyperaccumulation, whereas soil Cd and Zn bioavailability had the strongest associations with Cd hyperaccumulation. Our results indicate strong associations between A. halleri TME hyperaccumulation and rhizosphere microbial community properties, a finding that needs to be further explored to optimize phytoremediation technology that is based on hyperaccumulation.
Keywords	Arabidopsis halleri ; Archaea ; bioavailability ; climate ; environment ; fungal communities ; fungi ; hyperaccumulators ; phytoremediation ; rhizosphere ; soil microorganisms ; soil pollution ; variance
Language	English
Dates of publication	2022-0110
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.150006
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Article ; Online: Soil microbial community and abiotic soil properties influence Zn and Cd hyperaccumulation differently in Arabidopsis halleri.

Kushwaha, Priyanka / Neilson, Julia W / Maier, Raina M / Babst-Kostecka, Alicja

The Science of the total environment

2021 Volume 803, Page(s) 150006

Abstract	Soil contamination with trace metal(loid) elements (TME) is a global concern. This has focused interest on TME-tolerant plants, some of which can hyperaccumulate extraordinary amounts of TME into above-ground tissues, for potential treatment of these soils. However, intra-species variability in TME hyperaccumulation is not yet sufficiently understood to fully harness this potential. Particularly, little is known about the rhizosphere microbial communities associated with hyperaccumulating plants and whether or not they facilitate TME uptake. The aim of this study is to characterize the diversity and structure of Arabidopsis halleri rhizosphere-influenced and background (i.e., non-Arabidopsis) soil microbial communities in four plant populations with contrasting Zn and Cd hyperaccumulation traits, two each from contaminated and uncontaminated sites. Microbial community properties were assessed along with geographic location, climate, abiotic soil properties, and plant parameters to explain variation in Zn and Cd hyperaccumulation. Site type (TME-contaminated vs. uncontaminated) and location explained 44% of bacterial/archaeal and 28% of fungal community variability. A linear discriminant effect size (LEfSe) analysis identified a greater number of taxa defining rhizosphere microbial communities than associated background soils. Further, in TME-contaminated soils, the number of rhizosphere-defining taxa was 6-fold greater than in the background soils. In contrast, the corresponding ratio for uncontaminated sites, was 3 and 1.6 for bacteria/archaea and fungi, respectively. The variables analyzed explained 71% and 76% of the variance in Zn and Cd hyperaccumulation, respectively; however, each hyperaccumulation pattern was associated with different variables. A. halleri rhizosphere fungal richness and diversity associated most strongly with Zn hyperaccumulation, whereas soil Cd and Zn bioavailability had the strongest associations with Cd hyperaccumulation. Our results indicate strong associations between A. halleri TME hyperaccumulation and rhizosphere microbial community properties, a finding that needs to be further explored to optimize phytoremediation technology that is based on hyperaccumulation.
MeSH term(s)	Arabidopsis ; Biodegradation, Environmental ; Cadmium ; Microbiota ; Rhizosphere ; Soil ; Soil Microbiology ; Soil Pollutants/analysis ; Zinc
Chemical Substances	Soil ; Soil Pollutants ; Cadmium (00BH33GNGH) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2021-08-30
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.2021.150006
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Article: Progressive belowground soil development associated with sustainable plant establishment during copper mine waste revegetation.

Ossanna, Lia Q R / Serrano, Karen / Jennings, Lydia L / Dillon, Jesse / Maier, Raina M / Neilson, Julia W

Applied soil ecology : a section of Agriculture, Ecosystems & Environment

2023 Volume 186

Abstract: Critical to the environmental sustainability of hard rock mining is the reclamation of disturbed lands following mine closure through revegetation. Improved understanding of associations between above- and belowground processes that characterize ... ...

Abstract	Critical to the environmental sustainability of hard rock mining is the reclamation of disturbed lands following mine closure through revegetation. Improved understanding of associations between above- and belowground processes that characterize successful plant establishment is critical to the implementation of more efficient revegetation strategies for nutrient-poor mine waste materials. The specific objective of this five-year temporal study was to identify progressive biotic and abiotic indicators of primary soil development on mine waste rock (WR) on a slope hydroseeded with native plant species and to quantify comparative effects of plant lifeform on soil development. Aboveground plant diversity and belowground substrate properties were measured annually at 67 m intervals along transects following the slope contour. Seeded WR was compared to unseeded WR and the adjacent native ecosystem. A temporal increase in WR microbial biomass was observed in seeded WR relative to unseeded areas. Microbial community analysis found the unseeded WR to be defined by oligotrophic microbes, whereas targeted grass and shrub root zones samples demonstrated significant increases in specific cellulose and lignin degrading and N-cycling phylotypes. More extensive chemical and biological fertility development was observed in shrub root zones relative to grass. Ten chemical and biological indicators increased significantly in shrub WR relative to unseeded WR, whereas grass WR was only enriched in bacterial 16S rRNA gene copy number/g substrate and bacterial/archaeal and fungal diversity. In addition, the shrub root zone had significantly higher nitrogen-cycling potential than grass root zones or unseeded WR. Thus, both grasses and shrubs improve belowground WR development; however, shrub establishment had greater fertility outcomes. Concurrent belowground fertility development is critical to sustainable plant establishment. Coupled evaluation of above- and belowground metrics provides an improved quantitative assessment of revegetation progress and a valuable tool to guide management decisions.
Language	English
Publishing date	2023-01-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1196758-4
ISSN	0929-1393
ISSN	0929-1393
DOI	10.1016/j.apsoil.2023.104813
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Article ; Online: Life-history strategies of soil microbial communities in an arid ecosystem.

Chen, Yongjian / Neilson, Julia W / Kushwaha, Priyanka / Maier, Raina M / Barberán, Albert

The ISME journal

2020 Volume 15, Issue 3, Page(s) 649–657

Abstract: The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense ...

Abstract	The overwhelming taxonomic diversity and metabolic complexity of microorganisms can be simplified by a life-history classification; copiotrophs grow faster and rely on resource availability, whereas oligotrophs efficiently exploit resource at the expense of growth rate. Here, we hypothesize that community-level traits inferred from metagenomic data can distinguish copiotrophic and oligotrophic microbial communities. Moreover, we hypothesize that oligotrophic microbial communities harbor more unannotated genes. To test these hypotheses, we conducted metagenomic analyses of soil samples collected from copiotrophic vegetated areas and from oligotrophic bare ground devoid of vegetation in an arid-hyperarid region of the Sonoran Desert, Arizona, USA. Results supported our hypotheses, as we found that multiple ecologically informed life-history traits including average 16S ribosomal RNA gene copy number, codon usage bias in ribosomal genes and predicted maximum growth rate were higher for microbial communities in vegetated than bare soils, and that oligotrophic microbial communities in bare soils harbored a higher proportion of genes that are unavailable in public reference databases. Collectively, our work demonstrates that life-history traits can distill complex microbial communities into ecologically coherent units and highlights that oligotrophic microbial communities serve as a rich source of novel functions.
MeSH term(s)	Ecosystem ; Metagenome ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology
Chemical Substances	RNA, Ribosomal, 16S ; Soil
Language	English
Publishing date	2020-10-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/s41396-020-00803-y
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Article: Hyperarid soil microbial community response to simulated rainfall.

Demergasso, Cecilia / Neilson, Julia W / Tebes-Cayo, Cinthya / Véliz, Roberto / Ayma, Diego / Laubitz, Daniel / Barberán, Albert / Chong-Díaz, Guillermo / Maier, Raina M

Frontiers in microbiology

2023 Volume 14, Page(s) 1202266

Abstract: The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal ... ...

Abstract	The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to
Language	English
Publishing date	2023-09-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1202266
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Article: Corrigendum: Hyperarid soil microbial community response to simulated rainfall.

Demergasso, Cecilia / Neilson, Julia W / Tebes-Cayo, Cinthya / Véliz, Roberto / Ayma, Diego / Laubitz, Daniel / Barberán, Albert / Chong-Díaz, Guillermo / Maier, Raina M

Frontiers in microbiology

2023 Volume 14, Page(s) 1327998

Abstract: This corrects the article DOI: 10.3389/fmicb.2023.1202266.]. ...

Abstract	[This corrects the article DOI: 10.3389/fmicb.2023.1202266.].
Language	English
Publishing date	2023-12-01
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1327998
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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: Arid Ecosystem Vegetation Canopy-Gap Dichotomy: Influence on Soil Microbial Composition and Nutrient Cycling Functional Potential.

Kushwaha, Priyanka / Neilson, Julia W / Barberán, Albert / Chen, Yongjian / Fontana, Catherine G / Butterfield, Bradley J / Maier, Raina M

Applied and environmental microbiology

2020 Volume 87, Issue 5

Abstract: Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity ... ...

Abstract	Increasing temperatures and drought in desert ecosystems are predicted to cause decreased vegetation density combined with barren ground expansion. It remains unclear how nutrient availability, microbial diversity, and the associated functional capacity vary between vegetated-canopy and gap soils. The specific aim of this study was to characterize canopy vs gap microsite effect on soil microbial diversity, the capacity of gap soils to serve as a canopy-soil microbial reservoir, nitrogen (N)-mineralization genetic potential (
Language	English
Publishing date	2020-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02780-20
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Article: Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions

Valentín-Vargas, Alexis / Neilson, Julia W / Root, Robert A / Chorover, Jon / Maier, Raina M

Science of the total environment. 2018 Mar. 15, v. 618

2018

Abstract: Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant ... ...

Abstract	Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.
Keywords	Atriplex lentiformis ; Leptospirillum ; Thiobacillus ; Thiomonas ; acidification ; composts ; hydrochemistry ; inoculum ; land restoration ; metals ; microbial communities ; mine tailings ; pH ; phylogeny ; phylotype ; phytoremediation ; plant establishment ; semiarid zones ; sulfides ; weathering ; wind
Language	English
Dates of publication	2018-0315
Size	p. 357-368.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2017.11.010
Database	NAL-Catalogue (AGRICOLA)

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