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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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Salazar B, Ortiz A, Keswani C, Minkina T, Mandzhieva S, Pratap Singh S, Rekadwad B, Borriss R, Jain A, Singh HB, Sansinenea E. Bacillus spp. as Bio-factories for Antifungal Secondary Metabolites: Innovation Beyond Whole Organism Formulations. MICROBIAL ECOLOGY 2023; 86:1-24. [PMID: 35604432 DOI: 10.1007/s00248-022-02044-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Several fungi act as parasites for crops causing huge annual crop losses at both pre- and post-harvest stages. For years, chemical fungicides were the solution; however, their wide use has caused environmental contamination and human health problems. For this reason, the use of biofungicides has been in practice as a green solution against fungal phytopathogens. In the context of a more sustainable agriculture, microbial biofungicides have the largest share among the commercial biocontrol products that are available in the market. Precisely, the genus Bacillus has been largely studied for the management of plant pathogenic fungi because they offer a chemically diverse arsenal of antifungal secondary metabolites, which have spawned a heightened industrial engrossment of it as a biopesticide. In this sense, it is indispensable to know the wide arsenal that Bacillus genus has to apply these products for sustainable agriculture. Having this idea in our minds, in this review, secondary metabolites from Bacillus having antifungal activity are chemically and structurally described giving details of their action against several phytopathogens. Knowing the current status of Bacillus secreted antifungals is the base for the goal to apply these in agriculture and it is addressed in depth in the second part of this review.
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Affiliation(s)
- Bruno Salazar
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México
| | - Chetan Keswani
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Saglara Mandzhieva
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344006, Russia
| | - Satyendra Pratap Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Bhagwan Rekadwad
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India
| | - Rainer Borriss
- Institut Für Agrar- Und Gartenbauwissenschaften, Fachgebiet Phytomedizin, Humboldt-Universität Zu Berlin, Lentze-Allee 55-57, 14195, Berlin, Germany
| | - Akansha Jain
- Division of Plant Biology, Bose Institute, CIT Road, Kankurgachi, Kolkata, India
| | - Harikesh B Singh
- Department of Biotechnology, GLA University, Mathura, 281406, India
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590, Puebla, Pue, México.
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Zuo Y, He C, Zhang D, Zhao L, He X, Sun X. Soil variables driven by host plant and growth season affect soil microbial composition and metabolism in extremely arid desert ecosystems. Microbiol Res 2023; 269:127315. [PMID: 36738491 DOI: 10.1016/j.micres.2023.127315] [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: 01/25/2022] [Revised: 11/27/2022] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
Assessment changes of soil microbial community structure and function is important in understanding the response to desert ecosystem management. In present study, variations of soil microbial community and edaphic factors associated with five desert shrubs were determined in Anxi extremely arid desert in Northwest China in growing (summer), deciduous (autumn), and snowfall (winter) seasons. For that, the microbial composition and catabolic metabolism were examined using methods of phospholipid fatty acid (PLFA) and Biolog EcoPlate, respectively. Regardless of plant species and seasonal patterns, the microbial community was mostly dominated by gram-negative bacteria (GN); and the carbohydrates, amino acids and polymers were the main carbon sources for desert microbial metabolism. Microbial biomass and metabolic levels were significantly higher in both summer and winter than those of autumn. There was no correlation between soil microbial community and carbon utilization in winter; but GN was positively correlated with metabolism of amines carbon sources in summer, while fungal community presented the strongest correlation with suites of carbon sources' metabolic levels in autumn, indicating the uncoupled relationship between microbial community and function in desert ecosystems. Desert shrubs significantly influenced the composition of soil microbial community, whereas the variation of microbial catabolic metabolism was most attributed to seasonality. Nevertheless, the effects of both plant species (21.3 %) and climate variation (84.9 %) interacted with soil properties, indicating the seasonality of soil nutrients predominately determined the changes in composition and metabolism of desert microbes. Both the comprehensive seasonal level and the intra-seasonal paired correlation analysis proved that phosphorus was the key factor in determining microbial community composition, while ammonia and nitrate nitrogen were more correlated to microbial functional metabolism. Additionally, soil moisture and organic carbon in desert environment also induced the shifts in ratio of fungi and bacterial communities. We conclude that the seasonal patterns of soil microbial community and metabolic function in extremely arid desert are predictable, and mainly influenced by specific soil factors driven by desert shrubs and climate factors. These findings will provide a basis for evaluating the management of soil resources and microbial function in desert environments.
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Affiliation(s)
- Yiling Zuo
- School of Life Sciences, Hebei University, Baoding 071002, China; College of Traditional Chinese Medicine, Hebei University, Baoding 071002, China.
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Dongdong Zhang
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Lili Zhao
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xueli He
- School of Life Sciences, Hebei University, Baoding 071002, China.
| | - Xiang Sun
- School of Life Sciences, Hebei University, Baoding 071002, China.
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Cleveland CC, Reis CRG, Perakis SS, Dynarski KA, Batterman SA, Crews TE, Gei M, Gundale MJ, Menge DNL, Peoples MB, Reed SC, Salmon VG, Soper FM, Taylor BN, Turner MG, Wurzburger N. Exploring the Role of Cryptic Nitrogen Fixers in Terrestrial Ecosystems: A Frontier in Nitrogen Cycling Research. Ecosystems 2022. [DOI: 10.1007/s10021-022-00804-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Srinivasan J, Khadka J, Novoplansky N, Gillor O, Grafi G. Endophytic Bacteria Colonizing the Petiole of the Desert Plant Zygophyllum dumosum Boiss: Possible Role in Mitigating Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040484. [PMID: 35214818 PMCID: PMC8924888 DOI: 10.3390/plants11040484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 05/13/2023]
Abstract
Zygophyllum dumosum is a dominant shrub in the Negev Desert whose survival is accomplished by multiple mechanisms including abscission of leaflets to reduce whole plant transpiration while leaving the fleshy, wax-covered petioles alive but dormant during the dry season. Petioles that can survive for two full growing seasons maintain cell component integrity and resume metabolic activity at the beginning of the winter. This remarkable survival prompted us to investigate endophytic bacteria colonizing the internal tissues of the petiole and assess their role in stress tolerance. Twenty-one distinct endophytes were isolated by culturing from surface-sterile petioles and identified by sequencing of the 16S rDNA. Sequence alignments and the phylogenetic tree clustered the isolated endophytes into two phyla, Firmicutes and Actinobacteria. Most isolated endophytes displayed a relatively slow growth on nutrient agar, which was accelerated by adding petiole extracts. Metabolic analysis of selected endophytes showed several common metabolites whose level is affected by petiole extract in a species-dependent manner including phosphoric acid, pyroglutamic acid, and glutamic acid. Other metabolites appear to be endophyte-specific metabolites, such as proline and trehalose, which were implicated in stress tolerance. These results demonstrate the existence of multiple endophytic bacteria colonizing Z. dumosum petioles with the potential role in maintaining cell integrity and functionality via synthesis of multiple beneficial metabolites that mitigate stress and contribute to stress tolerance.
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Affiliation(s)
- Jansirani Srinivasan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel; (J.S.); (J.K.); (N.N.)
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel;
| | - Janardan Khadka
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel; (J.S.); (J.K.); (N.N.)
| | - Nurit Novoplansky
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel; (J.S.); (J.K.); (N.N.)
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel;
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion 84990, Israel; (J.S.); (J.K.); (N.N.)
- Correspondence:
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Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future. BIOLOGY 2021; 10:biology10100961. [PMID: 34681060 PMCID: PMC8533330 DOI: 10.3390/biology10100961] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 01/14/2023]
Abstract
Simple Summary Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today. Abstract Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.
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Bahadur A, Zhang W, Sajjad W, Nasir F, Zhang G, Liu G, Chen T. Bacterial diversity patterns of desert dunes in the northeastern Qinghai-Tibet Plateau, China. Arch Microbiol 2021; 203:2809-2823. [PMID: 33730221 DOI: 10.1007/s00203-021-02272-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/02/2023]
Abstract
Limited knowledge about the variation patterns of bacterial community composition in the sand and vegetative ecosystems confines our understanding regarding the contribution of the sand dune to desert areas. In this study, 454 pyrosequencing platforms were adopted to determine the community structure of bacteria and diversity of sand dunes in northeastern Qinghai-Tibet Plateau, China: 50 cm deep, rhizosphere, physical crusts, and biological crusts representing sand and vegetative ecosystems, respectively. The findings revealed significant variation in bacterial diversities and the structure of communities in the sand and vegetative ecosystems. The dominant bacterial phyla of sand and vegetative ecosystems were Firmicutes (47%), Actinobacteria (21%), Proteobacteria (16%), and Bacteroidetes (13%), while Lactococcus (50%) was found to be the dominant genus. Furthermore, samples with high alpha-diversity indices (Chao 1 and Shannon) for the vegetative ecosystem have the lowest modularity index and the largest number of biomarkers, with some exceptions. Redundancy analysis exhibited that environmental factors could explain 72% (phyla) and 67% (genera) of the bacterial communities, with EC, TC, and TOC being the major driving factors. This study expands our understanding of bacterial community composition in the desert ecosystem. The findings suggest that variations in the sand and vegetative ecosystems, such as those predicted by environmental factors, may reduce the abundance and diversity of bacteria, a response that likely affects the provision of key ecosystem processes by desert regions.
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Affiliation(s)
- Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences (CAS), ChangchunJilin Province, 130102, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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Rodríguez-Berbel N, Ortega R, Lucas-Borja ME, Solé-Benet A, Miralles I. Long-term effects of two organic amendments on bacterial communities of calcareous mediterranean soils degraded by mining. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110920. [PMID: 32579515 DOI: 10.1016/j.jenvman.2020.110920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
The application of organic amendments to improve the chemical and biological properties of degraded soils from calcareous quarries is necessary to accelerate restoration processes. The aim of this study is to assess the success of different restoration treatments in the long-term using two organic amendments (sewage sludge from urban waste water (SS) and compost from domestic solid waste (CW)). The chemical properties and bacterial communities of restored soils were compared with unamended soils (NA) and surrounding natural soils (NS) from a limestone quarry in a semi-arid ecosystem. After 10 years of the addition of organic amendments, the abundance of soil bacteria, diversity, and taxonomic composition at the phylum and genus level in each soil type was analysed by rRNA 16 S amplification (PCR), sequencing using Illumina, and comparison with the SILVA database using QIIME2 software. The relationships between soil bacterial taxa and chemical soil properties (pH, electrical conductivity (EC), total organic carbon (TOC), and total nitrogen content (TN)) were also studied, as well as the interrelations between soil bacterial taxa at the genus level or the next upper taxonomic level identified. The organic amendments changed the chemical properties of the restored soils, influencing the microbial communities of the restored soils. CW treatment was the organic amendment that most resembled NS, favouring in the long-term a greater diversity and proliferation of bacteria. Several bacterial communities, more abundant in NA and CW soils, were strongly correlated with each other (Craurococcus, Phaselicystis, Crossiella, etc.), forming a bacterial co-occurrence pattern (Co-occurrence pattern 1). Those bacteria showed high significant positive correlations with TOC, TN, and EC and negative correlations with the soil pH. In contrast, NA soils presented other groups of bacterial communities (Co-occurrence pattern 2) represented by Sphingomonas, Rubellimicrobium, Noviherbaspirillum, Psychroglaciecola and Caenimonas, which showed high significant positive correlations with soil pH and negative correlations with TOC, TN, and EC. The distance-based redundancy analysis indicated that SS soils remained in an intermediate stage of chemical and biological quality between NS and NA soils. Our results demonstrate that soil chemical properties and soil bacterial communities significantly changed with organic amendments in calcareous Mediterranean soils degraded by mining.
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Affiliation(s)
- N Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - M E Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - A Solé-Benet
- EEZA-CSIC, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Carretera de Sacramento S/n, 04120, La Cañada de San Urbano, Almería, Spain
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
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Alsharif W, Saad MM, Hirt H. Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments. Front Microbiol 2020; 11:1666. [PMID: 32793155 PMCID: PMC7387410 DOI: 10.3389/fmicb.2020.01666] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/25/2020] [Indexed: 11/13/2022] Open
Abstract
A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.
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Affiliation(s)
- Wiam Alsharif
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maged M. Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
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Khan N, Martínez-Hidalgo P, Humm EA, Maymon M, Kaplan D, Hirsch AM. Inoculation With a Microbe Isolated From the Negev Desert Enhances Corn Growth. Front Microbiol 2020; 11:1149. [PMID: 32636811 PMCID: PMC7316896 DOI: 10.3389/fmicb.2020.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/06/2020] [Indexed: 11/13/2022] Open
Abstract
Corn (Zea mays L.) is not only an important food source, but also has numerous uses, including for biofuels, fillers for cosmetics, glues, and so on. The amount of corn grown in the U.S. has significantly increased since the 1960's and with it, the demand for synthetic fertilizers and pesticides/fungicides to enhance its production. However, the downside of the continuous use of these products, especially N and P fertilizers, has been an increase in N2O emissions and other greenhouse gases into the atmosphere as well as run-off into waterways that fuel pollution and algal blooms. These approaches to agriculture, especially if exacerbated by climate change, will result in decreased soil health as well as human health. We searched for microbes from arid, native environments that are not being used for agriculture because we reasoned that indigenous microbes from such soils could promote plant growth and help restore degraded soils. Employing cultivation-dependent methods to isolate bacteria from the Negev Desert in Israel, we tested the effects of several microbial isolates on corn in both greenhouse and small field studies. One strain, Dietzia cinnamea 55, originally identified as Planomicrobium chinense, significantly enhanced corn growth over the uninoculated control in both greenhouse and outside garden experiments. We sequenced and analyzed the genome of this bacterial species to elucidate some of the mechanisms whereby D. cinnamea 55 promoted plant growth. In addition, to ensure the biosafety of this previously unknown plant growth promoting bacterial (PGPB) strain as a potential bioinoculant, we tested the survival and growth of Caenorhabditis elegans and Galleria mellonella (two animal virulence tests) as well as plants in response to D. cinnamea 55 inoculation. We also looked for genes for potential virulence determinants as well as for growth promotion.
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Affiliation(s)
- Noor Khan
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Pilar Martínez-Hidalgo
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biology, Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Ethan A Humm
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maskit Maymon
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Drora Kaplan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ann M Hirsch
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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11
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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12
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Ortiz Y, Restrepo C, Vilanova-Cuevas B, Santiago-Valentin E, Tringe SG, Godoy-Vitorino F. Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla. PLoS One 2020; 15:e0231083. [PMID: 32255799 PMCID: PMC7138329 DOI: 10.1371/journal.pone.0231083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/17/2020] [Indexed: 11/19/2022] Open
Abstract
Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.
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Affiliation(s)
- Yakshi Ortiz
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Carla Restrepo
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Brayan Vilanova-Cuevas
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
| | | | - Susannah G. Tringe
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
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13
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Abdelshafy Mohamad OA, Ma JB, Liu YH, Zhang D, Hua S, Bhute S, Hedlund BP, Li WJ, Li L. Beneficial Endophytic Bacterial Populations Associated With Medicinal Plant Thymus vulgaris Alleviate Salt Stress and Confer Resistance to Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2020; 11:47. [PMID: 32117385 PMCID: PMC7033553 DOI: 10.3389/fpls.2020.00047] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
As a result of climate change, salinity has become a major abiotic stress that reduces plant growth and crop productivity worldwide. A variety of endophytic bacteria alleviate salt stress; however, their ecology and biotechnological potential has not been fully realized. To address this gap, a collection of 117 endophytic bacteria were isolated from wild populations of the herb Thymus vulgaris in Sheikh Zuweid and Rafah of North Sinai Province, Egypt, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 17 genera and 30 species. The number of bacterial species obtained from root tissues was higher (n = 18) compared to stem (n = 14) and leaf (n = 11) tissue. The endophytic bacteria exhibited several plant growth-promoting activities in vitro, including auxin synthesis, diazotrophy, phosphate solubilization, siderophore production, and production of lytic enzymes (i.e., chitinase, cellulase, protease, and lipase). Three endophytes representing Bacillus species associated with T. vulgaris such as EGY05, EGY21, and EGY25 were selected based on their ex-situ activities for growth chamber assays to test for their ability to promote the growth of tomato (Solanum lycopersicum L.) under various NaCl concentrations (50-200 mM). All three strains significantly (P < 0.05) promoted the growth of tomato plants under salt stress, compared to uninoculated controls. In addition, inoculated tomato plants by all tested strains decreased (P < 0.05) the activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidase). Six strains, representing Bacillus and Enterobacter species EGY01, EGY05, EGY16, EGY21, EGY25, and EGY31 were selected based on in vitro antagonistic activity to F. oxysporum for pot experiments under salt stress. All tested strains reduced the disease severity index (DSI) of tomato plants at all tested salt concentrations. Gas-chromatography/mass-spectrometry analysis of cell-free extracts of B. subtilis (EGY16) showed at least ten compounds were known to have antimicrobial activity, with the major peaks being benzene, 1,3-dimethyl-, p-xylene, dibutyl phthalate, bis (2-ethylhexyl) phthalate, and tetracosane. This study demonstrates that diverse endophytes grow in wild thyme populations and that some are able to alleviate salinity stress and inhibit F. oxysporum pathogenesis, making them promising candidates for biofertilizers and biocontrol agents.
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Affiliation(s)
- Osama Abdalla Abdelshafy Mohamad
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
- Department of Biological, Marine Sciences, and Environmental Agriculture, Institute for Post Graduate Environmental Studies, Arish University, Al-Arish, Egypt
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish, Egypt
| | - Jin-Biao Ma
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
| | - Yong-Hong Liu
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
| | - Daoyuan Zhang
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
| | - Shao Hua
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
| | - Shrikant Bhute
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish, Egypt
| | - Brian P. Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Wen-Jun Li
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Li Li
- CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, China
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14
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Eida AA, Ziegler M, Lafi FF, Michell CT, Voolstra CR, Hirt H, Saad MM. Desert plant bacteria reveal host influence and beneficial plant growth properties. PLoS One 2018; 13:e0208223. [PMID: 30540793 PMCID: PMC6291088 DOI: 10.1371/journal.pone.0208223] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/14/2018] [Indexed: 11/19/2022] Open
Abstract
Deserts, such as those found in Saudi Arabia, are one of the most hostile places for plant growth. However, desert plants are able to impact their surrounding microbial community and select beneficial microbes that promote their growth under these extreme conditions. In this study, we examined the soil, rhizosphere and endosphere bacterial communities of four native desert plants Tribulus terrestris, Zygophyllum simplex, Panicum turgidum and Euphorbia granulata from the Southwest (Jizan region), two of which were also found in the Midwest (Al Wahbah area) of Saudi Arabia. While the rhizosphere bacterial community mostly resembled that of the highly different surrounding soils, the endosphere composition was strongly correlated with its host plant phylogeny. In order to assess whether any of the native bacterial endophytes might have a role in plant growth under extreme conditions, we analyzed the properties of 116 cultured bacterial isolates that represent members of the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Our analysis shows that different strains have highly different biochemical properties with respect to nutrient acquisition, hormone production and growth under stress conditions. More importantly, eleven of the isolated strains could confer salinity stress tolerance to the experimental model plant Arabidopsis thaliana suggesting some of these plant-associated bacteria might be useful for improving crop desert agriculture.
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Affiliation(s)
- Abdul Aziz Eida
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Maren Ziegler
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Feras F. Lafi
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Craig T. Michell
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Heribert Hirt
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
- * E-mail:
| | - Maged M. Saad
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
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15
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Khan N, Martínez-Hidalgo P, Ice TA, Maymon M, Humm EA, Nejat N, Sanders ER, Kaplan D, Hirsch AM. Antifungal Activity of Bacillus Species Against Fusarium and Analysis of the Potential Mechanisms Used in Biocontrol. Front Microbiol 2018; 9:2363. [PMID: 30333816 PMCID: PMC6176115 DOI: 10.3389/fmicb.2018.02363] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/14/2018] [Indexed: 12/05/2022] Open
Abstract
Fusarium is a complex genus of ascomycete fungi that consists of plant pathogens of agricultural relevance. Controlling Fusarium infection in crops that leads to substantial yield losses is challenging. These economic losses along with environmental and human health concerns over the usage of chemicals in attaining disease control are shifting focus toward the use of biocontrol agents for effective control of phytopathogenic Fusarium spp. In the present study, an analysis of the plant-growth promoting (PGP) and biocontrol attributes of four bacilli (Bacillus simplex 30N-5, B. simplex 11, B. simplex 237, and B. subtilis 30VD-1) has been conducted. The production of cellulase, xylanase, pectinase, and chitinase in functional assays was studied, followed by in silico gene analysis of the PGP-related and biocontrol-associated genes. Of all the bacilli included in this study, B. subtilis 30VD-1 (30VD-1) demonstrated the most effective antagonism against Fusarium spp. under in vitro conditions. Additionally, 100 μg/ml of the crude 1-butanol extract of 30VD-1’s cell-free culture filtrate caused about 40% inhibition in radial growth of Fusarium spp. Pea seed bacterization with 30VD-1 led to considerable reduction in wilt severity in plants with about 35% increase in dry plant biomass over uninoculated plants growing in Fusarium-infested soil. Phase contrast microscopy demonstrated distortions and abnormal swellings in F. oxysporum hyphae on co-culturing with 30VD-1. The results suggest a multivariate mode of antagonism of 30VD-1 against phytopathogenic Fusarium spp., by producing chitinase, volatiles, and other antifungal molecules, the characterization of which is underway.
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Affiliation(s)
- Noor Khan
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Pilar Martínez-Hidalgo
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Tyler A Ice
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maskit Maymon
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ethan A Humm
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Najmeh Nejat
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Erin R Sanders
- Center for Education Innovation and Learning in the Sciences, University of California, Los Angeles, Los Angeles, CA, United States
| | - Drora Kaplan
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Ann M Hirsch
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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16
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Gairola S, Al Shaer KI, Al Harthi EK, Mosa KA. Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:521-533. [PMID: 30042610 PMCID: PMC6041242 DOI: 10.1007/s12298-018-0551-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/19/2018] [Accepted: 05/08/2018] [Indexed: 05/09/2023]
Abstract
The biotechnology of desert plants is a vast subject. The main applications in this broad field of study comprises of plant tissue culture, genetic engineering, molecular markers and others. Biotechnology applications have the potential to address biodiversity conservation as well as agricultural, medicinal, and environmental issues. There is a need to increase our knowledge of the genetic diversity through the use of molecular genetics and biotechnological approaches in desert plants in the Arabian Gulf region including those in the United Arab Emirates (UAE). This article provides a prospective research for the study of UAE desert plant diversity through DNA fingerprinting as well as understanding the mechanisms of both abiotic stress resistance (including salinity, drought and heat stresses) and biotic stress resistance (including disease and insect resistance). Special attention is given to the desert halophytes and their utilization to alleviate the salinity stress, which is one of the major challenges in agriculture. In addition, symbioses with microorganisms are thought to be hypothesized as important components of desert plant survival under stressful environmental conditions. Thus, factors shaping the diversity and functionality of plant microbiomes in desert ecosystems are also emphasized in this article. It is important to establish a critical mass for biotechnology research and applications while strengthening the channels for collaboration among research/academic institutions in the area of desert plant biotechnology.
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Affiliation(s)
- Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Khawla I. Al Shaer
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Eman K. Al Harthi
- Plant Molecular Biology and Biotechnology Laboratory, Sharjah Research Academy, University City, Sharjah, P. Box 60999, Sharjah, UAE
| | - Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
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17
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Schmidt JE, Gaudin ACM. What is the agronomic potential of biofertilizers for maize? A meta-analysis. FEMS Microbiol Ecol 2018; 94:4999898. [DOI: 10.1093/femsec/fiy094] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 01/07/2023] Open
Affiliation(s)
- Jennifer E Schmidt
- Department of Plant Sciences, University of California at Davis, 2136 Plant and Environmental Sciences One Shields Avenue, Davis, CA 95616, USA
| | - Amélie C M Gaudin
- Department of Plant Sciences, University of California at Davis, 2136 Plant and Environmental Sciences One Shields Avenue, Davis, CA 95616, USA
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18
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Li L, Mohamad OAA, Ma J, Friel AD, Su Y, Wang Y, Musa Z, Liu Y, Hedlund BP, Li W. Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F. Antonie van Leeuwenhoek 2018. [PMID: 29516314 DOI: 10.1007/s10482-018-1062-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue. Geographically, the diversity of culturable endophytic genera was higher at the Tekesi (n = 14) and Xinyuan (n = 12) sites than the Gongliu site (n = 4), reflecting the extremely low organic carbon content, high salinity, and low nutrient status of Gongliu soils. The endophytic bacteria exhibited a number of plant growth-promoting activities ex situ, including diazotrophy, phosphate and potassium solubilization, siderophore production, auxin synthesis, and production of hydrolytic enzymes. Twelve endophytes were selected based on their ex situ plant growth-promoting activities for growth chamber assays to test for their ability to promote growth of G. uralensis F. and Triticum aestivum (wheat) plants. Several strains belonging to the genera Bacillus (n = 6) and Achromobacter (n = 1) stimulated total biomass production in both G. uralensis and T. aestivum under low-nutrient conditions. This work is the first report on the isolation and characterization of endophytes associated with G. uralensis F. in arid lands. The results demonstrate the broad diversity of endophytes associated with wild licorice and suggest that some Bacillus strains may be promising candidates for biofertilizers to promote enhanced survival and growth of licorice and other valuable crops in arid environments.
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Affiliation(s)
- Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Osama Abdalla Abdelshafy Mohamad
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- Institute for Post Graduate Environmental Studies, Environmental Science Department, Arish University, North-Sinai, 45516, Egypt
| | - Jinbiao Ma
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Yangui Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Yun Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Zulpiya Musa
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yonghong Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
| | - Wenjun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences (CAS), Urumqi, 830011, China.
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat Sen University, Guangzhou, 510275, China.
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19
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de Zélicourt A, Synek L, Saad MM, Alzubaidy H, Jalal R, Xie Y, Andrés-Barrao C, Rolli E, Guerard F, Mariappan KG, Daur I, Colcombet J, Benhamed M, Depaepe T, Van Der Straeten D, Hirt H. Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2-keto-4-methylthiobutyric acid production. PLoS Genet 2018; 14:e1007273. [PMID: 29554117 PMCID: PMC5875868 DOI: 10.1371/journal.pgen.1007273] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 03/29/2018] [Accepted: 02/23/2018] [Indexed: 11/18/2022] Open
Abstract
Several plant species require microbial associations for survival under different biotic and abiotic stresses. In this study, we show that Enterobacter sp. SA187, a desert plant endophytic bacterium, enhances yield of the crop plant alfalfa under field conditions as well as growth of the model plant Arabidopsis thaliana in vitro, revealing a high potential of SA187 as a biological solution for improving crop production. Studying the SA187 interaction with Arabidopsis, we uncovered a number of mechanisms related to the beneficial association of SA187 with plants. SA187 colonizes both the surface and inner tissues of Arabidopsis roots and shoots. SA187 induces salt stress tolerance by production of bacterial 2-keto-4-methylthiobutyric acid (KMBA), known to be converted into ethylene. By transcriptomic, genetic and pharmacological analyses, we show that the ethylene signaling pathway, but not plant ethylene production, is required for KMBA-induced plant salt stress tolerance. These results reveal a novel molecular communication process during the beneficial microbe-induced plant stress tolerance.
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Affiliation(s)
- Axel de Zélicourt
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Lukas Synek
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Maged M. Saad
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Hanin Alzubaidy
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Rewaa Jalal
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Yakun Xie
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Cristina Andrés-Barrao
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Eleonora Rolli
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Florence Guerard
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Kiruthiga G. Mariappan
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
| | - Ihsanullah Daur
- King Abdulaziz University, Faculty of Meteorology, Environment and Arid Land Agriculture, Jeddah, Saudi Arabia
| | - Jean Colcombet
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Moussa Benhamed
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
| | - Thomas Depaepe
- Ghent University, Department of Physiology, Laboratory of Functional Plant Biology, Ghent, Belgium
| | | | - Heribert Hirt
- King Abdullah University of Science and Technology, Division of Biological and Environmental Sciences and Engineering, Thuwal, Kingdom of Saudi Arabia
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, France
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Etesami H, Beattie GA. Mining Halophytes for Plant Growth-Promoting Halotolerant Bacteria to Enhance the Salinity Tolerance of Non-halophytic Crops. Front Microbiol 2018; 9:148. [PMID: 29472908 PMCID: PMC5809494 DOI: 10.3389/fmicb.2018.00148] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/23/2018] [Indexed: 11/20/2022] Open
Abstract
Salinity stress is one of the major abiotic stresses limiting crop production in arid and semi-arid regions. Interest is increasing in the application of PGPRs (plant growth promoting rhizobacteria) to ameliorate stresses such as salinity stress in crop production. The identification of salt-tolerant, or halophilic, PGPRs has the potential to promote saline soil-based agriculture. Halophytes are a useful reservoir of halotolerant bacteria with plant growth-promoting capabilities. Here, we review recent studies on the use of halophilic PGPRs to stimulate plant growth and increase the tolerance of non-halophytic crops to salinity. These studies illustrate that halophilic PGPRs from the rhizosphere of halophytic species can be effective bio-inoculants for promoting the production of non-halophytic species in saline soils. These studies support the viability of bioinoculation with halophilic PGPRs as a strategy for the sustainable enhancement of non-halophytic crop growth. The potential of this strategy is discussed within the context of ensuring sustainable food production for a world with an increasing population and continuing climate change. We also explore future research needs for using halotolerant PGPRs under salinity stress.
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Affiliation(s)
- Hassan Etesami
- Department of Soil Science, Faculty of Agricultural Engineering & Technology, University of Tehran, Tehran, Iran
| | - Gwyn A. Beattie
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
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Khan AL, Asaf S, Al-Rawahi A, Lee IJ, Al-Harrasi A. Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree. PLoS One 2017; 12:e0186939. [PMID: 29053752 PMCID: PMC5650177 DOI: 10.1371/journal.pone.0186939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022] Open
Abstract
Boswellia sacra, a frankincense producing endemic tree, has been well known for its cultural, religious and economic values. However, the tree has been least explored for the associated microsymbiota in the rhizosphere. The current study elucidates the fungal and bacterial communities of the rhizospheric regions of the wild and cultivated B. sacra tree populations through next generation sequencing. The sequence analysis showed the existence of 1006±8.9 and 60.6±3.1 operational taxonomic unit (OTUs) for bacterial and fungal communities respectively. In fungal communities, five major phyla were found with significantly higher abundance of Ascomycota (60.3%) in wild population and Basidiomycota (52%) in cultivated tree rhizospheres. Among bacterial communities, 31 major phyla were found, with significant distribution of Actinobacteria in wild tree rhizospheres, whereas Proteobacteria and Acidobacteria were highly abundant in cultivated trees. The diversity and abundance of microbiome varied significantly depending upon soil characteristics of the three different populations. In addition, significantly higher glucosidases, cellulases and indole-3-acetic acid were found in cultivated tree’s rhizospheres as compared to wild tree populations. for these plants to survive the harsh arid-land environmental conditions. The current study is a first comprehensive work and advances our knowledge about the core fungal and bacterial microbial microbiome associated with this economically important tree.
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Affiliation(s)
- Abdul Latif Khan
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Rawahi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ahmed Al-Harrasi
- UoN Chair of Oman’s Medicinal Plants and Marine Natural Products, University of Nizwa, Nizwa, Oman
- * E-mail:
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Del Rocío Bustillos-Cristales M, Corona-Gutierrez I, Castañeda-Lucio M, Águila-Zempoaltécatl C, Seynos-García E, Hernández-Lucas I, Muñoz-Rojas J, Medina-Aparicio L, Fuentes-Ramírez LE. Culturable Facultative Methylotrophic Bacteria from the Cactus Neobuxbaumia macrocephala Possess the Locus xoxF and Consume Methanol in the Presence of Ce 3+ and Ca 2. Microbes Environ 2017; 32:244-251. [PMID: 28855445 PMCID: PMC5606694 DOI: 10.1264/jsme2.me17070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanol-consuming culturable bacteria were isolated from the plant surface, rhizosphere, and inside the stem of Neobuxbaumia macrocephala. All 38 isolates were facultative methylotrophic microorganisms. Their classification included the Classes Actinobacteria, Sphingobacteriia, Alpha-, Beta-, and Gammaproteobacteria. The deduced amino acid sequences of methanol dehydrogenase obtained by PCR belonging to Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria showed high similarity to rare-earth element (REE)-dependent XoxF methanol dehydrogenases, particularly the group XoxF5. The sequences included Asp301, the REE-coordinating amino acid, present in all known XoxF dehydrogenases and absent in MxaF methanol dehydrogenases. The quantity of the isolates showed positive hybridization with a xoxF probe, but not with a mxaF probe. Isolates of all taxonomic groups showed methylotrophic growth in the presence of Ce3+ or Ca2+. The presence of xoxF-like sequences in methylotrophic bacteria from N. macrocephala and its potential relationship with their adaptability to xerophytic plants are discussed.
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23
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Veliz EA, Martínez-Hidalgo P, Hirsch AM. Chitinase-producing bacteria and their role in biocontrol. AIMS Microbiol 2017; 3:689-705. [PMID: 31294182 PMCID: PMC6604996 DOI: 10.3934/microbiol.2017.3.689] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 11/30/2022] Open
Abstract
Chitin is an important component of the exteriors of insects and fungi. Upon degradation of chitin by a number of organisms, severe damage and even death may occur in pathogens and pests whose external surfaces contain this polymer. Currently, chemical fungicides and insecticides are the major means of controlling these disease-causing agents. However, due to the potential harm that these chemicals cause to the environment and to human and animal health, new strategies are being developed to replace or reduce the use of fungal- and pest-killing compounds in agriculture. In this context, chitinolytic microorganisms are likely to play an important role as biocontrol agents and pathogen antagonists and may also function in the control of postharvest rot. In this review, we discuss the literature concerning chitin and the basic knowledge of chitin-degrading enzymes, and also describe the biocontrol effects of chitinolytic microorganisms and their potential use as more sustainable pesticides and fungicides in the field.
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Affiliation(s)
- Esteban A Veliz
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
| | | | - Ann M Hirsch
- Department of Molecular Cell and Developmental Biology, Molecular Biology Institute, University of California, Los Angeles, 90095-1606, USA
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24
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Yuan Z, Druzhinina IS, Labbé J, Redman R, Qin Y, Rodriguez R, Zhang C, Tuskan GA, Lin F. Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity. Sci Rep 2016; 6:32467. [PMID: 27572178 PMCID: PMC5004162 DOI: 10.1038/srep32467] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/09/2016] [Indexed: 12/18/2022] Open
Abstract
Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.
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Affiliation(s)
- Zhilin Yuan
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, P. R. China
| | - Irina S. Druzhinina
- Research Area Biochemical Technology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | | | - Yuan Qin
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, P. R. China
| | - Russell Rodriguez
- Adaptive Symbiotic Technologies, Seattle, USA
- Depart of Biology, University of Washington, Seattle, USA
| | - Chulong Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, P. R. China
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, USA
| | - Fucheng Lin
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, P. R. China
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Teymouri M, Akhtari J, Karkhane M, Marzban A. Assessment of phosphate solubilization activity of Rhizobacteria in mangrove forest. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2016. [DOI: 10.1016/j.bcab.2016.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Rodríguez‐Echeverría S, Lozano YM, Bardgett RD. Influence of soil microbiota in nurse plant systems. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12594] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susana Rodríguez‐Echeverría
- CFE‐Centre for Functional Ecology Department of Life Sciences University of Coimbra Calçada Martim de Freitas 3000‐456 Coimbra Portugal
| | - Yudi M. Lozano
- Estación Experimental de Zonas Áridas Consejo Superior de Investigaciones Científicas Carretera de Sacramento s/n E‐04120 La Cañada de San Urbano Almería Spain
| | - Richard D. Bardgett
- Faculty of Life Sciences The University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT UK
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Draft Genome Sequence of Bacillus Species from the Rhizosphere of the Desert Plant Rhazya stricta. GENOME ANNOUNCEMENTS 2015; 3:3/6/e00957-15. [PMID: 26543104 PMCID: PMC4645189 DOI: 10.1128/genomea.00957-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to better understand the ecology and diversity of microbes in the rhizosphere of desert plants, we undertook a survey of Bacillus species isolated from soil around Rhazya stricta plants from the area around Jeddah, in The Kingdom, Saudi Arabia. We have sequenced the genomes of 8 Bacillus isolates representing four different species.
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28
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Massimo NC, Nandi Devan MM, Arendt KR, Wilch MH, Riddle JM, Furr SH, Steen C, U'Ren JM, Sandberg DC, Arnold AE. Fungal endophytes in aboveground tissues of desert plants: infrequent in culture, but highly diverse and distinctive symbionts. MICROBIAL ECOLOGY 2015; 70:61-76. [PMID: 25645243 PMCID: PMC4457668 DOI: 10.1007/s00248-014-0563-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 12/26/2014] [Indexed: 05/02/2023]
Abstract
In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in aboveground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on nonsucculent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity, and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert-plant communities and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.
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Affiliation(s)
- Nicholas C Massimo
- School of Plant Sciences, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ, 85721, USA
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29
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Maymon M, Martínez-Hidalgo P, Tran SS, Ice T, Craemer K, Anbarchian T, Sung T, Hwang LH, Chou M, Fujishige NA, Villella W, Ventosa J, Sikorski J, Sanders ER, Faull KF, Hirsch AM. Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth. FRONTIERS IN PLANT SCIENCE 2015; 6:784. [PMID: 26442090 PMCID: PMC4585168 DOI: 10.3389/fpls.2015.00784] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/10/2015] [Indexed: 05/02/2023]
Abstract
In previous work, we showed that coinoculating Rhizobium leguminosarum bv. viciae 128C53 and Bacillus simplex 30N-5 onto Pisum sativum L. roots resulted in better nodulation and increased plant growth. We now expand this research to include another alpha-rhizobial species as well as a beta-rhizobium, Burkholderia tuberum STM678. We first determined whether the rhizobia were compatible with B. simplex 30N-5 by cross-streaking experiments, and then Medicago truncatula and Melilotus alba were coinoculated with B. simplex 30N-5 and Sinorhizobium (Ensifer) meliloti to determine the effects on plant growth. Similarly, B. simplex 30N-5 and Bu. tuberum STM678 were coinoculated onto Macroptilium atropurpureum. The exact mechanisms whereby coinoculation results in increased plant growth are incompletely understood, but the synthesis of phytohormones and siderophores, the improved solubilization of inorganic nutrients, and the production of antimicrobial compounds are likely possibilities. Because B. simplex 30N-5 is not widely recognized as a Plant Growth Promoting Bacterial (PGPB) species, after sequencing its genome, we searched for genes proposed to promote plant growth, and then compared these sequences with those from several well studied PGPB species. In addition to genes involved in phytohormone synthesis, we detected genes important for the production of volatiles, polyamines, and antimicrobial peptides as well as genes for such plant growth-promoting traits as phosphate solubilization and siderophore production. Experimental evidence is presented to show that some of these traits, such as polyamine synthesis, are functional in B. simplex 30N-5, whereas others, e.g., auxin production, are not.
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Affiliation(s)
- Maskit Maymon
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Pilar Martínez-Hidalgo
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Stephen S. Tran
- Bioinformatics, University of California, Los AngelesLos Angeles, CA, USA
| | - Tyler Ice
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Karena Craemer
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Teni Anbarchian
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Tiffany Sung
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Lin H. Hwang
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
| | - Minxia Chou
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - Nancy A. Fujishige
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
| | - William Villella
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Jérôme Ventosa
- Biotechnology, Plants, and Microorganisms Biology, University of Montpellier IIMontpellier, France
| | - Johannes Sikorski
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany
| | - Erin R. Sanders
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los AngelesLos Angeles, CA, USA
| | - Kym F. Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
| | - Ann M. Hirsch
- Departments of Molecular, Cell, and Developmental Biology, University of California, Los AngelesLos Angeles, CA, USA
- Molecular Biology Institute, University of California, Los AngelesLos Angeles, CA, USA
- *Correspondence: Ann M. Hirsch, Departments of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, 621 Charles Young Drive South, Los Angeles, CA 90095-1606, USA
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Angus AA, Agapakis CM, Fong S, Yerrapragada S, Estrada-de los Santos P, Yang P, Song N, Kano S, Caballero-Mellado J, de Faria SM, Dakora FD, Weinstock G, Hirsch AM. Plant-associated symbiotic Burkholderia species lack hallmark strategies required in mammalian pathogenesis. PLoS One 2014; 9:e83779. [PMID: 24416172 PMCID: PMC3885511 DOI: 10.1371/journal.pone.0083779] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/13/2013] [Indexed: 11/18/2022] Open
Abstract
Burkholderia is a diverse and dynamic genus, containing pathogenic species as well as species that form complex interactions with plants. Pathogenic strains, such as B. pseudomallei and B. mallei, can cause serious disease in mammals, while other Burkholderia strains are opportunistic pathogens, infecting humans or animals with a compromised immune system. Although some of the opportunistic Burkholderia pathogens are known to promote plant growth and even fix nitrogen, the risk of infection to infants, the elderly, and people who are immunocompromised has not only resulted in a restriction on their use, but has also limited the application of non-pathogenic, symbiotic species, several of which nodulate legume roots or have positive effects on plant growth. However, recent phylogenetic analyses have demonstrated that Burkholderia species separate into distinct lineages, suggesting the possibility for safe use of certain symbiotic species in agricultural contexts. A number of environmental strains that promote plant growth or degrade xenobiotics are also included in the symbiotic lineage. Many of these species have the potential to enhance agriculture in areas where fertilizers are not readily available and may serve in the future as inocula for crops growing in soils impacted by climate change. Here we address the pathogenic potential of several of the symbiotic Burkholderia strains using bioinformatics and functional tests. A series of infection experiments using Caenorhabditis elegans and HeLa cells, as well as genomic characterization of pathogenic loci, show that the risk of opportunistic infection by symbiotic strains such as B. tuberum is extremely low.
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Affiliation(s)
- Annette A. Angus
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Christina M. Agapakis
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Fong
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | | | - Paulina Estrada-de los Santos
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Ciudad de México, Distrito Federal, México
| | - Paul Yang
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Nannie Song
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Kano
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jésus Caballero-Mellado
- Genomic Sciences Center, National Autonomous University of México, Cuernavaca, Morelos, México
| | | | - Felix D. Dakora
- Chemistry Department, Tshwane University of Technology, Arcadia Campus, Pretoria, South Africa
| | - George Weinstock
- Dept. of Genetics, Washington Univ. School of Medicine, St. Louis, Missouri, United States of America
| | - Ann M. Hirsch
- Dept. of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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31
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Gopal M, Gupta A, Thomas GV. Bespoke microbiome therapy to manage plant diseases. Front Microbiol 2013; 4:355. [PMID: 24348466 PMCID: PMC3847548 DOI: 10.3389/fmicb.2013.00355] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/08/2013] [Indexed: 12/26/2022] Open
Abstract
Information gathered with advanced nucleotide sequencing technologies, small molecule detection systems and computational biology is revealing that a community of microbes and their genes, now termed "the microbiome," located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a "core-microbiome" exists that plays the pivotal role in well being of humans and plants. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, though not exactly in similar manner as in medicine, success in plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. A study more similar to artificial gut microbiome transfer in medical field has been recently reported in agriculture, in which transfer of microbiome via soil solutions (filtered and unfiltered) has shown ability to alleviate drought stress in Arabidopsis thaliana. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information drawn from all recent works in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can be a success in agriculture too and it could become a viable strategy for management of plant diseases in future.
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Affiliation(s)
- Murali Gopal
- Microbiology Section, Central Plantation Crops Research InstituteKudlu, Kasaragod, India
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32
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Rout ME, Southworth D. The root microbiome influences scales from molecules to ecosystems: The unseen majority. AMERICAN JOURNAL OF BOTANY 2013; 100:1689-91. [PMID: 24008514 DOI: 10.3732/ajb.1300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants are teeming with microbial organisms including those that colonize internal tissues as well as those that adhere to external surfaces. In the rhizosphere, the plant-associated microbiome is intricately involved in plant health and serves as a reservoir of additional genes that plants can access when needed. Microbiome regulation of plant trait expression affects plant performance, which in turn influences various ecosystem functions, such as primary productivity and soil health. Understanding these plant- and microbe-driven interactions requires a study of the nature and effects of the plant microbiome. Conceptualizing the microbiome requires a synthesis of microbial ecology, physiology, and bioinformatics, integrated with insight into host biology and ecology. Microbiome structure and function analyses are recognized as essential components to understand the genetic and functional capacity of the host (previously assigned solely to the host) and include vital aspects of metabolism and physiology. Here, as a special section, we present a set of papers that address the complex interactions between plants and root microbiomes in the rhizosphere. This unseen majority spans scales; with its microorganisms numerically dominant in terrestrial ecosystems, the root microbiome is also involved in plant genetics through integral roles in plant trait expression that can effect community composition and ecosystem functions, such as soil health.
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Affiliation(s)
- Marnie E Rout
- University of North Texas Health Science Center, Department of Forensics and Investigative Genetics, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, USA
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