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Legeay J, Errafii K, Ziami A, Hijri M. The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13254. [PMID: 38725134 PMCID: PMC11082428 DOI: 10.1111/1758-2229.13254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/14/2024] [Indexed: 05/13/2024]
Abstract
Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment.
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Affiliation(s)
- Jean Legeay
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Khaoula Errafii
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Abdelhadi Ziami
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
| | - Mohamed Hijri
- African Genome CenterUniversity Mohammed VI Polytechnic (UM6P)Ben GuerirMorocco
- Institut de Recherche en Biologie VégétaleDépartement de Sciences Biologiques, Université de MontréalMontrealQuebecCanada
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2
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Khan AL. Silicon: A valuable soil element for improving plant growth and CO 2 sequestration. J Adv Res 2024:S2090-1232(24)00217-0. [PMID: 38806098 DOI: 10.1016/j.jare.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Silicon (Si), the second most abundant and quasi-essential soil element, is locked as a recalcitrant silicate mineral in the Earth's crust. The physical abundance of silicates can play an essential role in increasing plant productivity. Plants store Si as biogenic silica (phytoliths), which is mobilized through a chemical weathering process in the soil. AIM OF REVIEW Although Si is a critical element for plant growth, there is still a considerable need to understand its dissolution, uptake, and translocation in agroecosystems. Here, we show recent progress in understanding the interactome of Si, CO2, the microbiome, and soil chemistry, which can sustainably govern silicate dissolution and cycling in agriculture. KEY SCIENTIFIC CONCEPTS OF THIS REVIEW Si cycling is directly related to carbon cycling, and the resulting climate stability can be enhanced by negative feedback between atmospheric CO2 and the silicate uptake process. Improved Si mobilization in the rhizosphere by the presence of reactive elements (for example, Ca, Na, Al, Zn, and Fe) and Si uptake through genetic transporters in plants are crucial to achieving the dual objectives of (i) enhancing crop productivity and (ii) abiotic stress tolerance. Furthermore, the microbiome is a symbiotic partner of plants. Bacterial and fungal microbiomes can solubilize silicate minerals through intriguingly complex bioweathering mechanisms by producing beneficial metabolites and enzymes. However, the interaction of Si with CO2 and the microbiome's function in mobilization have been understudied. This review shows that enhancing our understanding of Si, CO2, the microbiome, and soil chemistry can help in sustainable crop production during climatic stress events.
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Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, USA; Department of Biology and Biochemistry, University of Houston, Houston TX, USA.
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3
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Ben Zineb A, Lamine M, Khallef A, Hamdi H, Ahmed T, Al-Jabri H, Alsafran M, Mliki A, Sayadi S, Gargouri M. Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects. Front Microbiol 2024; 15:1362722. [PMID: 38646634 PMCID: PMC11027745 DOI: 10.3389/fmicb.2024.1362722] [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: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.
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Affiliation(s)
- Ameni Ben Zineb
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mariem Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Ahlem Khallef
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Helmi Hamdi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Hareb Al-Jabri
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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Coffman L, Mejia HD, Alicea Y, Mustafa R, Ahmad W, Crawford K, Khan AL. Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO 2. FRONTIERS IN PLANT SCIENCE 2024; 14:1295674. [PMID: 38389716 PMCID: PMC10882081 DOI: 10.3389/fpls.2023.1295674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/27/2023] [Indexed: 02/24/2024]
Abstract
Introduction With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2). Methods We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding. Results Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts. Conclusion This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.
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Affiliation(s)
- Lauryn Coffman
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Hector D Mejia
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Yelinska Alicea
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Raneem Mustafa
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Waqar Ahmad
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Kerri Crawford
- Department of Biological Sciences and Chemistry, College of Natural Science and Mathematics, University of Houston, Houston, TX, United States
| | - Abdul Latif Khan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biological Sciences and Chemistry, College of Natural Science and Mathematics, University of Houston, Houston, TX, United States
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Zhu YL, Huang YJ, Nuerhamanti N, Bai XY, Wang HN, Zhu XY, Zhang W. The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere. MICROBIAL ECOLOGY 2023; 87:2. [PMID: 38008827 DOI: 10.1007/s00248-023-02320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/25/2023] [Indexed: 11/28/2023]
Abstract
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.
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Affiliation(s)
- Yan-Lei Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
| | - Yong-Jie Huang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Naifeisai Nuerhamanti
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Xiao-Yu Bai
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Hui-Nan Wang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Xiao-Ying Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Zhu YL, Huang YJ, Nuerhamanti N, Bai XY, Wang HN, Zhu XY, Zhang W. Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere. MICROBIAL ECOLOGY 2023; 86:2461-2476. [PMID: 37301781 DOI: 10.1007/s00248-023-02252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.
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Affiliation(s)
- Yan-Lei Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China.
| | - Yong-Jie Huang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Naifeisai Nuerhamanti
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Xiao-Yu Bai
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Hui-Nan Wang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
| | - Xiao-Ying Zhu
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, China
| | - Wei Zhang
- College of Life Sciences, Xinjiang Normal University, Urumqi, 830054, Xinjiang, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Key Laboratory of Plant Stress Biology in Arid Land, Urumqi, 830054, Xinjiang, 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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9
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Moraga D, Latorre K, Muñoz-Torres P, Cárdenas S, Jofré-Quispe A, López-Cepeda J, Bustos L, Balada C, Argaluza MF, González P, Guzmán L. Diversity of Culturable Bacteria from Endemic Medicinal Plants of the Highlands of the Province of Parinacota, Chile. BIOLOGY 2023; 12:920. [PMID: 37508351 PMCID: PMC10376134 DOI: 10.3390/biology12070920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023]
Abstract
Endemic medicinal plants that grow at altitudes in northern Chile have been traditionally used for therapeutic applications by Aymara doctors. Several studies have analyzed the biological properties of these plants for therapeutic purposes. The aim was to characterize at molecular and biochemical levels the bacteria that live in the rhizosphere and roots from endemic medicinal plants that grow between 3681-5104 m.a.s.l. in the province of Parinacota. Thirty-nine bacteria were isolated from nine medicinal plants under our laboratory conditions. These bacteria were characterized by Gram stain, hydrolase production, plant-growth promotion, anti-fungal and antibacterial activities, and 16S rDNA sequencing. A phylogenetic study revealed the presence of three major phyla, Actinomycetota (46.2%), Bacillota (43.6%), and Pseudomonadota (10.3%). The rhizobacteria strains associated with the Aymara medicinal plant exhibited several interesting biological activities, such as hydrolytic enzymes, plant-growth-promoting traits, and antibacterial and antifungal properties, indicating their potential for developing new bio-based products for agricultural or clinical applications. These results are promising and highlight the need to point toward the search for explanations of the bio-molecular basis of the therapeutic effects of medicinal plants.
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Affiliation(s)
- Daniel Moraga
- Laboratorio de Fisiología, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad de Tarapacá, Arica 1000000, Chile
| | - Katina Latorre
- Laboratorio de Microbiología, Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Patricio Muñoz-Torres
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Steffany Cárdenas
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Alan Jofré-Quispe
- Departamento de Ciencias Históricas y Geográficas, Universidad de Tarapacá, Arica 1000000, Chile
| | - José López-Cepeda
- Departamento de Biología, Facultad de Ciencias, Universidad de Tarapacá, Arica 1000000, Chile
| | - Luis Bustos
- Subdepartamento de Gestión de Farmacia, Servicio de Salud Arica, Arica 1000871, Chile
| | - Cristóbal Balada
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - María Fernanda Argaluza
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Pablo González
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Leda Guzmán
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
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Luecke NC, de Mesquita CPB, Luong M, Schmidt SK, Suding KN, Crawford KM. Causes and consequences of differences in soil and seed microbiomes for two alpine plants. Oecologia 2022; 200:385-396. [PMID: 36224498 DOI: 10.1007/s00442-022-05271-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/27/2022] [Indexed: 10/17/2022]
Abstract
Seed and soil microbiomes strongly affect plant performance, and these effects can scale-up to influence plant community structure. However, seed and soil microbial community composition are variable across landscapes, and different microbial communities can differentially influence multiple plant metrics (biomass, germination rate), and community stabilizing mechanisms. We determined how microbiomes inside seeds and in soils varied among alpine plant species and communities that differed in plant species richness and density. Across 10 common alpine plant species, we found a total of 318 bacterial and 128 fungal operational taxonomic units (OTUs) associated with seeds, with fungal richness affected by plant species identity more than sampling location. However, seed microbes had only marginally significant effects on plant germination success and timing. In contrast, soil microbes associated with two different plant species had significant effects on plant biomass, and their effect depended both on the plant species and the location the soils were sampled from. This led to significant changes in plant-soil feedback at different locations that varied in plant density and richness, such that plant-soil feedback favored plant species coexistence in some locations and opposed coexistence at other locations. Importantly, we found that coexistence-facilitating feedback was associated with low plant species richness, suggesting that soil microbes may promote the diversity of colonizing plants during the course of climate change and glacial recession.
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Affiliation(s)
- Noah C Luecke
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.
| | | | - Madeline Luong
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334, USA
| | - Katharine N Suding
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, 80309-0450, USA
| | - Kerri M Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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11
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Vu MT, Geraldi A, Do HDK, Luqman A, Nguyen HD, Fauzia FN, Amalludin FI, Sadila AY, Wijaya NH, Santoso H, Manuhara YSW, Bui LM, Hariyanto S, Wibowo AT. Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes. BIOLOGY 2022; 11:biology11050695. [PMID: 35625422 PMCID: PMC9138652 DOI: 10.3390/biology11050695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/15/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.
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Affiliation(s)
- Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Almando Geraldi
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Arif Luqman
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia;
| | - Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam; (M.T.V.); (H.D.K.D.); (H.D.N.)
| | - Faiza Nur Fauzia
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Fahmi Ikhlasul Amalludin
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Aliffa Yusti Sadila
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Nabilla Hapsari Wijaya
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
| | - Heri Santoso
- Generasi Biologi Indonesia (Genbinesia) Foundation, Gresik 61171, Indonesia;
| | - Yosephine Sri Wulan Manuhara
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
| | - Le Minh Bui
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Department of Biotechnology, NTT Hi-tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Sucipto Hariyanto
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Correspondence: (S.H.); (A.T.W.)
| | - Anjar Tri Wibowo
- Departement of Biology, Faculty of Science and Technology, Airlangga University, Surabaya 60115, Indonesia; (A.G.); (F.N.F.); (F.I.A.); (A.Y.S.); (N.H.W.); (Y.S.W.M.); (L.M.B.)
- Biotechnology of Tropical Medicinal Plants Research Group, Airlangga University, Surabaya 60115, Indonesia
- Correspondence: (S.H.); (A.T.W.)
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12
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Marasco R, Fusi M, Mosqueira M, Booth JM, Rossi F, Cardinale M, Michoud G, Rolli E, Mugnai G, Vergani L, Borin S, De Philippis R, Cherif A, Daffonchio D. Rhizosheath-root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment. ENVIRONMENTAL MICROBIOME 2022; 17:14. [PMID: 35365219 PMCID: PMC8973986 DOI: 10.1186/s40793-022-00407-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath-root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert. RESULTS The belowground rhizosheath-root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath-root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath-root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment. CONCLUSIONS Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Joint Nature Conservation Committee, Monkstone House, City Road, Peterborough, PE1 1JY, UK
| | - Maria Mosqueira
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Jenny Marie Booth
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Federico Rossi
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University, Giessen, Germany
| | - Grégoire Michoud
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | | | - Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Roberto De Philippis
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Ameur Cherif
- Institut Supérieur de Biotechnologie Sidi Thabet (ISBST), BVBGR-LR11ES31, Biotechpole Sidi Thabet, University Manouba, Ariana, Tunisia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
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13
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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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14
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Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem. Sci Rep 2022; 12:3741. [PMID: 35260670 PMCID: PMC8904503 DOI: 10.1038/s41598-022-07765-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.
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15
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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16
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Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano. DIVERSITY 2021. [DOI: 10.3390/d14010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth.
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17
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Marasco R, Fusi M, Rolli E, Ettoumi B, Tambone F, Borin S, Ouzari H, Boudabous A, Sorlini C, Cherif A, Adani F, Daffonchio D. Aridity modulates belowground bacterial community dynamics in olive tree. Environ Microbiol 2021; 23:6275-6291. [PMID: 34490977 PMCID: PMC9290347 DOI: 10.1111/1462-2920.15764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Marco Fusi
- School of Applied SciencesEdinburgh Napier UniversityEdinburghUK
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Besma Ettoumi
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Fulvia Tambone
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Hadda‐Imene Ouzari
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Abdellatif Boudabous
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de TunisUniversité Tunis El ManarTunisTunisia
| | - Claudia Sorlini
- Department of Food, Environmental and Nutritional Sciences (DeFENS)University of MilanoMilanItaly
| | - Ameur Cherif
- Institut Supérieur de Biotechnologie Sidi Thabet (ISBST)BVBGR‐LR11ES31, Biotechpole Sidi Thabet, University ManoubaArianaTunisia
| | - Fabrizio Adani
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla LabUniversity of MilanoMilanItaly
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
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18
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Wang J, Wu H, Wu L, Liu Y, Letuma P, Qin X, Chen T, Rensing C, Lin S, Lin W. Revealing Microbiome Structure and Assembly Process in Three Rhizocompartments of Achyranthes bidentata Under Continuous Monoculture Regimes. Front Microbiol 2021; 12:677654. [PMID: 34194412 PMCID: PMC8236951 DOI: 10.3389/fmicb.2021.677654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The complex composition and interaction of root-associated microbes are critical to plant health and performance. In this study, we presented a detailed characterization of three rhizocompartment (rhizosphere, rhizoplane, and root) microbiomes of Achyranthes bidentata under different years of consecutive monoculture by deep sequencing in order to determine keystone microorganisms via co-occurrence network analysis. The network analysis showed that multiple consecutive monoculture (MCM, represented 5Y and 10Y) soils generated some distinct beneficial bacterial taxa such as Bacillus, Fictibacillus, Bradyrhizobium, Shinella, and Herbaspirillum. For fungi, Mortierella substituted for Fusarium in occupying an important position in different rhizocompartments under A. bidentate monoculture. Quantitative PCR analysis confirmed a significant increase in Bacillus, Pseudomonas, and Burkholderia spp. The results of the inoculation assay showed that addition of beneficial bacteria Bacillus subtilis 74 and Bacillus halodurans 75 significantly increased the root length and fresh weight of A. bidentata. Furthermore, three types of phytosterones, as the main allochemicals, were identified both in the rhizosphere soil and in culture medium under sterile conditions by LC-MS/MS. When looking at in vitro interactions, it was found that phytosterones displayed a positive interaction with dominant beneficial species (Bacillus amyloliquefaciens 4 and B. halodurans 75) and had a negative effect on the presence of the pathogenic fungi Fusarium solani and Fusarium oxysporum. Overall, this study demonstrated that consecutive monoculture of A. bidentata can alter the bacterial and fungal community by secreting root exudates, leading to recruitment of beneficial microbes and replacement of plant-specific pathogenic fungi with plant beneficial fungi.
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Affiliation(s)
- Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Department of Crop Science, National University of Lesotho, Maseru, Lesotho
| | - Xianjin Qin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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19
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Hernandez DJ, David AS, Menges ES, Searcy CA, Afkhami ME. Environmental stress destabilizes microbial networks. THE ISME JOURNAL 2021; 15:1722-1734. [PMID: 33452480 PMCID: PMC8163744 DOI: 10.1038/s41396-020-00882-x] [Citation(s) in RCA: 369] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil microbiomes along 40 replicate stress gradients (elevation/water availability gradients) in the Florida scrub ecosystem, we show that: (1) prokaryotic and fungal diversity decline in high stress, and (2) two network properties of stable microbial communities-modularity and negative:positive cohesion-have a clear negative relationship with environmental stress, explaining 51-78% of their variation. Interestingly, pathogenic taxa/functional guilds decreased in relative abundance along the stress gradient, while oligotrophs and mutualists increased, suggesting that the shift in negative:positive cohesion could result from decreasing negative:positive biotic interactions consistent with the predictions of the Stress Gradient Hypothesis. Given the crucial role microbiomes play in ecosystem functions, our results suggest that, by limiting the compartmentalization of microbial associations and creating communities dominated by positive associations, increasing stress in the Anthropocene could destabilize microbiomes and undermine their ecosystem services.
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Affiliation(s)
- Damian J. Hernandez
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Aaron S. David
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA ,grid.508985.9USDA-ARS, Invasive Plant Research Laboratory, Fort Lauderdale, FL 33314 USA
| | - Eric S. Menges
- grid.248717.f0000 0000 9407 7092Archbold Biological Station, Venus, FL 33960 USA
| | - Christopher A. Searcy
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Michelle E. Afkhami
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL 33146 USA
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20
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The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México. J Fungi (Basel) 2021; 7:jof7030210. [PMID: 33809206 PMCID: PMC7999539 DOI: 10.3390/jof7030210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/15/2023] Open
Abstract
The abundance and diversity of fungi were evaluated in a hypersaline microbial mat from Guerrero Negro, México, using a combination of quantitative polymerase chain reaction (qPCR) amplification of domain-specific primers, and metagenomic sequencing. Seven different layers were analyzed in the mat (Layers 1–7) at single millimeter resolution (from the surface to 7 mm in depth). The number of copies of the 18S rRNA gene of fungi ranged between 106 and 107 copies per g mat, being two logarithmic units lower than of the 16S rRNA gene of bacteria. The abundance of 18S rRNA genes of fungi varied significantly among the layers with layers 2–5 mm from surface contained the highest numbers of copies. Fifty-six fungal taxa were identified by metagenomic sequencing, classified into three different phyla: Ascomycota, Basidiomycota and Microsporidia. The prevalent genera of fungi were Thermothelomyces, Pyricularia, Fusarium, Colletotrichum, Aspergillus, Botrytis, Candida and Neurospora. Genera of fungi identified in the mat were closely related to genera known to have saprotrophic and parasitic lifestyles, as well as genera related to human and plant pathogens and fungi able to perform denitrification. This research suggests that fungi in the mat may participate in nutrient recycling, modification of community composition through parasitic activities, and denitrification.
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21
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Rodriguez R, Durán P. Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. Front Bioeng Biotechnol 2020; 8:568. [PMID: 32582678 PMCID: PMC7287022 DOI: 10.3389/fbioe.2020.00568] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
In the current scenario of climate change, the future of agriculture is uncertain. Climate change and climate-related disasters have a direct impact on biotic and abiotic factors that govern agroecosystems compromising the global food security. In the last decade, the advances in high throughput sequencing techniques have significantly improved our understanding about the composition, function and dynamics of plant microbiome. However, despite the microbiome have been proposed as a new platform for the next green revolution, our knowledge about the mechanisms that govern microbe-microbe and microbe-plant interactions are incipient. Currently, the adaptation of plants to environmental changes not only suggests that the plants can adapt or migrate, but also can interact with their surrounding microbial communities to alleviate different stresses by natural microbiome selection of specialized strains, phenomenon recently called "Cry for Help". From this way, plants have been co-evolved with their microbiota adapting to local environmental conditions to ensuring the survival of the entire holobiome to improve plant fitness. Thus, the strong selective pressure of native extreme microbiomes could represent a remarkable microbial niche of plant stress-amelioration to counteract the negative effect of climate change in food crops. Currently, the microbiome engineering has recently emerged as an alternative to modify and promote positive interactions between microorganisms and plants to improve plant fitness. In the present review, we discuss the possible use of extreme microbiome to alleviate different stresses in crop plants under the current scenario of climate change.
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Affiliation(s)
- Rodrigo Rodriguez
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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22
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Astorga-Eló M, Zhang Q, Larama G, Stoll A, Sadowsky MJ, Jorquera MA. Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile. Front Microbiol 2020; 11:571. [PMID: 32322245 PMCID: PMC7156552 DOI: 10.3389/fmicb.2020.00571] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/16/2020] [Indexed: 12/22/2022] Open
Abstract
Flowering desert (FD) events consist of the rapid flowering of a wide variety of native plants in the Atacama Desert of Chile, which is categorized as the driest desert in the world. While ephemeral plants are an integral part of the desert ecosystem, there is little knowledge on plant-microbe interactions that occur during FD events. Consequently, the overall goals of this present study were to investigate changes in the composition and potential functions of rhizobacterial community of Cistanthe longiscapa (Montiaceae) during the 2014 and 2015 FD events and determine the composition, potential functions, and co-occurrence networks of rhizobacterial community associated with the root zone of C. longiscapa during pre- (PF) and full-flowering (FF) phenological stages. Results of this study showed that the Proteobacteria and Actinobacteria were the dominant taxa in rhizosphere soils during the three FD events (2014, 2015, and 2017) examined. In general, greater microbial richness and diversity were observed in rhizosphere soils during the 2015-, compared with the 2014-FD event. Similarly, predicted functional analyses indicated that a larger number of sequences were assigned to information processing (e.g., ion channel, transporters and ribosome) and metabolism (e.g., lipids, nitrogen, and sulfur) during 2015 compared with 2014. Despite the lack of significant differences in diversity among PF and FF stages, the combined analysis of rhizobacterial community data, along with data concerning rhizosphere soil properties, evidenced differences among both phenological stages and suggested that sodium is a relevant abiotic factor shaping the rhizosphere. In general, no significant differences in predicted functions (most of them assigned to chemoheterotrophy, magnesium metabolisms, and fermentation) were observed among PF and FF. Co-occurrence analysis revealed the complex rhizobacterial interactions that occur in C. longiscapa during FD, highlighting to Kouleothrixaceae family as keystone taxa. Taken together this study shows that the composition and function of rhizobacteria vary among and during FD events, where some bacterial groups and their activity may influence the growth and flowering of native plants, and therefore, the ecology and trophic webs in Atacama Desert.
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Affiliation(s)
- Marcia Astorga-Eló
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Giovanni Larama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States.,Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States.,Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,The Network for Extreme Environment Research (NEXER), Scientific and Biotechnological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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23
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Astorga-Eló M, Zhang Q, Larama G, Stoll A, Sadowsky MJ, Jorquera MA. Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile. Front Microbiol 2020. [PMID: 32322245 DOI: 10.3389/fmicb.2020.00571/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Flowering desert (FD) events consist of the rapid flowering of a wide variety of native plants in the Atacama Desert of Chile, which is categorized as the driest desert in the world. While ephemeral plants are an integral part of the desert ecosystem, there is little knowledge on plant-microbe interactions that occur during FD events. Consequently, the overall goals of this present study were to investigate changes in the composition and potential functions of rhizobacterial community of Cistanthe longiscapa (Montiaceae) during the 2014 and 2015 FD events and determine the composition, potential functions, and co-occurrence networks of rhizobacterial community associated with the root zone of C. longiscapa during pre- (PF) and full-flowering (FF) phenological stages. Results of this study showed that the Proteobacteria and Actinobacteria were the dominant taxa in rhizosphere soils during the three FD events (2014, 2015, and 2017) examined. In general, greater microbial richness and diversity were observed in rhizosphere soils during the 2015-, compared with the 2014-FD event. Similarly, predicted functional analyses indicated that a larger number of sequences were assigned to information processing (e.g., ion channel, transporters and ribosome) and metabolism (e.g., lipids, nitrogen, and sulfur) during 2015 compared with 2014. Despite the lack of significant differences in diversity among PF and FF stages, the combined analysis of rhizobacterial community data, along with data concerning rhizosphere soil properties, evidenced differences among both phenological stages and suggested that sodium is a relevant abiotic factor shaping the rhizosphere. In general, no significant differences in predicted functions (most of them assigned to chemoheterotrophy, magnesium metabolisms, and fermentation) were observed among PF and FF. Co-occurrence analysis revealed the complex rhizobacterial interactions that occur in C. longiscapa during FD, highlighting to Kouleothrixaceae family as keystone taxa. Taken together this study shows that the composition and function of rhizobacteria vary among and during FD events, where some bacterial groups and their activity may influence the growth and flowering of native plants, and therefore, the ecology and trophic webs in Atacama Desert.
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Affiliation(s)
- Marcia Astorga-Eló
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Giovanni Larama
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), La Serena, Chile
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Química y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- The Network for Extreme Environment Research (NEXER), Scientific and Biotechnological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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