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Zhang X, Li Q, Zhong Z, Huang Z, Bian F. Characterization of the composition, structure, and functional potential of bamboo rhizosphere archaeal communities along a chromium gradient. Front Microbiol 2024; 15:1372403. [PMID: 38694797 PMCID: PMC11061513 DOI: 10.3389/fmicb.2024.1372403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/29/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction Bamboo can be used in the phytoremediation of heavy metal pollution. However, the characteristics of the bamboo rhizosphere archaeal community in Cr-contaminated soil under field conditions remain unclear. Methods In this study, high-throughput sequencing was used to examine the rhizosphere soil archaeal communities of Lei bamboo (Phyllostachys precox) plantations along a Cr pollution gradient. Results The results revealed U-shaped relationships between Cr [total Cr (TCr) or HCl-extractable Cr (ACr)] and two alpha indices (Chao1 and Shannon) of archaea. We also established that high Cr concentrations were associated with a significant increase in the abundance of Thaumarchaeota and significant reductions in the abundances of Crenarchaeota and Euryarchaeota. The archaeal co-occurrence networks reduced in complexity with Cr pollution, decreasing the community's resistance to environmental disturbance. Candidatus nitrosotalea and Nitrososphaeraceae_unclassified (two genera of Thaumarchaeota) were identified as keystone taxa. The community structure of soil archaeal communities was also found to be affected by TCr, ACr, pH, total organic C, and available nutrient (N, P, and K) concentrations, with pH being identified as the most reliable predictor of the archaeal community in assessed soils. Discussion These findings enhance our understanding of microbial responses to Cr pollution and provide a basis for developing more refined approaches for the use of bamboo in the remediation of Cr-contaminated soils.
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Affiliation(s)
- Xiaoping Zhang
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Engineering Research Center of Biochar of Zhejiang Province, Hangzhou, China
| | - Qiaoling Li
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
| | - Zheke Zhong
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou, China
| | - Zhiyuan Huang
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
| | - Fangyuan Bian
- Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, China National Bamboo Research Center, Hangzhou, China
- National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Hangzhou, China
- Key Laboratory of High Efficient Processing of Bamboo of Zhejiang Province, Hangzhou, China
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Khan AL. The phytomicrobiome: solving plant stress tolerance under climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1219366. [PMID: 37746004 PMCID: PMC10513501 DOI: 10.3389/fpls.2023.1219366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.
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Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, United States
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Jara-Servin A, Silva A, Barajas H, Cruz-Ortega R, Tinoco-Ojanguren C, Alcaraz LD. Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.). PLoS One 2023; 18:e0285978. [PMID: 37205698 DOI: 10.1371/journal.pone.0285978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Buffelgrass (Pennisetum ciliare) is an invasive plant introduced into Mexico's Sonoran desert for cattle grazing and has converted large areas of native thorn scrub. One of the invasion mechanisms buffelgrass uses to invade is allelopathy, which consists of the production and secretion of allelochemicals that exert adverse effects on other plants' growth. The plant microbiome also plays a vital role in establishing invasive plants and host growth and development. However, little is known about the buffelgrass root-associated bacteria and the effects of allelochemicals on the microbiome. We used 16S rRNA gene amplicon sequencing to obtain the microbiome of buffelgrass and compare it between samples treated with root exacknudates and aqueous leachates as allelochemical exposure and samples without allelopathic exposure in two different periods. The Shannon diversity values were between H' = 5.1811-5.5709, with 2,164 reported bacterial Amplicon Sequence Variants (ASVs). A total of 24 phyla were found in the buffelgrass microbiome, predominantly Actinobacteria, Proteobacteria, and Acidobacteria. At the genus level, 30 different genera comprised the buffelgrass core microbiome. Our results show that buffelgrass recruits microorganisms capable of thriving under allelochemical conditions and may be able to metabolize them (e.g., Planctomicrobium, Aurantimonas, and Tellurimicrobium). We also found that the community composition of the microbiome changes depending on the developmental state of buffelgrass (p = 0.0366; ANOSIM). These findings provide new insights into the role of the microbiome in the establishment of invasive plant species and offer potential targets for developing strategies to control buffelgrass invasion.
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Affiliation(s)
- Angélica Jara-Servin
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adán Silva
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Hugo Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Clara Tinoco-Ojanguren
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Khan AL, Lopes LD, Bilal S, Asaf S, Crawford KM, Balan V, Al-Rawahi A, Al-Harrasi A, Schachtman DP. Microbiome Variation Across Populations of Desert Halophyte Zygophyllum qatarensis. FRONTIERS IN PLANT SCIENCE 2022; 13:841217. [PMID: 35432394 PMCID: PMC9009292 DOI: 10.3389/fpls.2022.841217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Microbial symbionts play a significant role in plant health and stress tolerance. However, few studies exist that address rare species of core-microbiome function during abiotic stress. In the current study, we compared the microbiome composition of succulent dwarf shrub halophyte Zygophyllum qatarensis Hadidi across desert populations. The results showed that rhizospheric and endosphere microbiome greatly varied due to soil texture (sandy and gravel). No specific bacterial amplicon sequence variants were observed in the core-microbiome of bulk soil and rhizosphere, however, bacterial genus Alcaligenes and fungal genus Acidea were abundantly distributed across root and shoot endospheres. We also analyzed major nutrients such as silicon (Si), magnesium, and calcium across different soil textures and Z. qatarensis populations. The results showed that the rhizosphere and root parts had significantly higher Si content than the bulk soil and shoot parts. The microbiome variation can be attributed to markedly higher Si - suggesting that selective microbes are contributing to the translocation of soluble Si to root. In conclusion, low core-microbiome species abundance might be due to the harsh growing conditions in the desert - making Z. qatarensis highly selective to associate with microbial communities. Utilizing rare microbial players from plant microbiomes may be vital for increasing crop stress tolerance and productivity during stresses.
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Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, United States
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Lucas Dantas Lopes
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Saqib Bilal
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Kerri M. Crawford
- Department of Biology and Biochemistry, College of Natural Science and Mathematics, University of Houston, Houston, TX, United States
| | - Venkatesh Balan
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, TX, United States
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Daniel P. Schachtman
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
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Ravi S, Law DJ, Caplan JS, Barron-Gafford GA, Dontsova KM, Espeleta JF, Villegas JC, Okin GS, Breshears DD, Huxman TE. Biological invasions and climate change amplify each other's effects on dryland degradation. GLOBAL CHANGE BIOLOGY 2022; 28:285-295. [PMID: 34614285 DOI: 10.1111/gcb.15919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Climate models predict that, in the coming decades, many arid regions will experience increasingly hot conditions and will be affected more frequently by drought. These regions are also experiencing rapid vegetation change, notably invasion by exotic grasses. Invasive grasses spread rapidly into native desert ecosystems due, in particular, to interannual variability in precipitation and periodic fires. The resultant destruction of non-fire-adapted native shrub and grass communities and of the inherent soil resource heterogeneity can yield invader-dominated grasslands. Moreover, recurrent droughts are expected to cause widespread physiological stress and mortality of both invasive and native plants, as well as the loss of soil resources. However, the magnitude of these effects may differ between invasive and native grasses, especially under warmer conditions, rendering the trajectory of vegetated communities uncertain. Using the Biosphere 2 facility in the Sonoran Desert, we evaluated the viability of these hypothesized relationships by simulating combinations of drought and elevated temperature (+5°C) and assessing the ecophysiological and mortality responses of both a dominant invasive grass (Pennisetum ciliare or buffelgrass) and a dominant native grass (Heteropogan contortus or tanglehead). While both grasses survived protracted drought at ambient temperatures by inducing dormancy, drought under warmed conditions exceeded the tolerance limits of the native species, resulting in greater and more rapid mortality than exhibited by the invasive. Thus, two major drivers of global environmental change, biological invasion and climate change, can be expected to synergistically accelerate ecosystem degradation unless large-scale interventions are enacted.
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Affiliation(s)
- Sujith Ravi
- Department of Earth & Environmental Science, Temple University, Philadelphia, Pennsylvania, USA
| | - Darin J Law
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
| | - Joshua S Caplan
- Department of Architecture & Environmental Design, Temple University, Ambler, Pennsylvania, USA
| | - Greg A Barron-Gafford
- School of Geography, Development & Environment, University of Arizona, Tucson, Arizona, USA
| | - Katerina M Dontsova
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | | | - Juan C Villegas
- Grupo de Investigación en Ecología Aplicada, Facultad de Ingeniería, Universidad de Antioquia, Medellín, Colombia
| | - Gregory S Okin
- Department of Geography, University of California, Los Angeles, California, USA
| | - David D Breshears
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
| | - Travis E Huxman
- Department of Ecology & Evolutionary Biology, University of California, Irvine, California, USA
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Yang B, Balazs KR, Butterfield BJ, Laushman KM, Munson SM, Gornish ES, Barberán A. Does restoration of plant diversity trigger concomitant soil microbiome changes in dryland ecosystems? J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ben Yang
- Department of Environmental Science University of Arizona Tucson AZ USA
| | - Kathleen R. Balazs
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff AZ USA
| | - Bradley J. Butterfield
- Department of Biological Sciences Northern Arizona University Flagstaff AZ USA
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff AZ USA
| | | | - Seth M. Munson
- U.S. Geological Survey Southwest Biological Science Center Flagstaff AZ USA
| | - Elise S. Gornish
- University of Arizona School of Natural Resources and the Environment Tucson AZ USA
| | - Albert Barberán
- Department of Environmental Science University of Arizona Tucson AZ USA
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Williams JP, Gornish ES, Barberán A. Effects of buffelgrass removal and nitrogen addition on soil microbial communities during an extreme drought in the Sonoran Desert. Restor Ecol 2021. [DOI: 10.1111/rec.13570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jared P. Williams
- Department of Environmental Science University of Arizona Tucson AZ 85721 U.S.A
| | - Elise S. Gornish
- School of Natural Resources and the Environment University of Arizona Tucson AZ 85721 U.S.A
| | - Albert Barberán
- Department of Environmental Science University of Arizona Tucson AZ 85721 U.S.A
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