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Lahmamsi H, Ananou S, Lahlali R, Tahiri A. Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects. Folia Microbiol (Praha) 2024; 69:465-489. [PMID: 38393576 DOI: 10.1007/s12223-024-01146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.
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Affiliation(s)
- Haitam Lahmamsi
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco
| | - Samir Ananou
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
| | - Rachid Lahlali
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
| | - Abdessalem Tahiri
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
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Nishisaka CS, Ventura JP, Bais HP, Mendes R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. ENVIRONMENTAL MICROBIOME 2024; 19:33. [PMID: 38745256 DOI: 10.1186/s40793-024-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps-TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. RESULTS qPCR revealed that the B. subtilis UD1022eps-TasA- strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. CONCLUSION This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
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Affiliation(s)
- Caroline Sayuri Nishisaka
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - João Paulo Ventura
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center (BPI), Newark, DE, USA
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Azri R, Lamine M, Bensalem-Fnayou A, Hamdi Z, Mliki A, Ruiz-Lozano JM, Aroca R. Genotype-Dependent Response of Root Microbiota and Leaf Metabolism in Olive Seedlings Subjected to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:857. [PMID: 38592857 PMCID: PMC10974243 DOI: 10.3390/plants13060857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Under stress or in optimum conditions, plants foster a specific guild of symbiotic microbes to strengthen pivotal functions including metabolic regulation. Despite that the role of the plant genotype in microbial selection is well documented, the potential of this genotype-specific microbial assembly in maintaining the host homeostasis remains insufficiently investigated. In this study, we aimed to assess the specificity of the foliar metabolic response of contrasting olive genotypes to microbial inoculation with wet-adapted consortia of plant-growth-promoting rhizobacteria (PGPR), to see if previously inoculated plants with indigenous or exogenous microbes would display any change in their leaf metabolome once being subjected to drought stress. Two Tunisian elite varieties, Chetoui (drought-sensitive) and Chemleli (drought-tolerant), were tested under controlled and stressed conditions. Leaf samples were analyzed by gas chromatography-mass spectrometry (GC-TOFMS) to identify untargeted metabolites. Root and soil samples were used to extract microbial genomic DNA destined for bacterial community profiling using 16S rRNA amplicon sequencing. Respectively, the score plot analysis, cluster analysis, heat map, Venn diagrams, and Krona charts were applied to metabolic and microbial data. Results demonstrated dynamic changes in the leaf metabolome of the Chetoui variety in both stress and inoculation conditions. Under the optimum state, the PGPR consortia induced noteworthy alterations in metabolic patterns of the sensitive variety, aligning with the phytochemistry observed in drought-tolerant cultivars. These variations involved fatty acids, tocopherols, phenols, methoxyphenols, stilbenoids, triterpenes, and sugars. On the other hand, the Chemleli variety displaying comparable metabolic profiles appeared unaffected by stress and inoculation probably owing to its tolerance capacity. The distribution of microbial species among treatments was distinctly uneven. The tested seedlings followed variety-specific strategies in selecting beneficial soil bacteria to alleviate stress. A highly abundant species of the wet-adapted inoculum was detected only under optimum conditions for both cultivars, which makes the moisture history of the plant genotype a selective driver shaping microbial community and thereby a useful tool to predict microbial activity in large ecosystems.
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Affiliation(s)
- Rahma Azri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
- National Insitute of Applied Science and Technology, University of Carthage, Centre Urbain Nord, BP 676, Charguia Cedex 1080, Tunisia
| | - Myriam Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Asma Bensalem-Fnayou
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Zohra Hamdi
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Juan Manuel Ruiz-Lozano
- Departament of Microbiology, Soil System and Symbiosis, Zaidín Experimental Station, Spanish Reaserch Council (CSIC), Prof. Albareda 1, 18008 Granada, Spain
| | - Ricardo Aroca
- Departament of Microbiology, Soil System and Symbiosis, Zaidín Experimental Station, Spanish Reaserch Council (CSIC), Prof. Albareda 1, 18008 Granada, Spain
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Roy B, Maitra D, Biswas A, Chowdhury N, Ganguly S, Bera M, Dutta S, Golder S, Roy S, Ghosh J, Mitra AK. Efficacy of High-Altitude Biofilm-Forming Novel Bacillus subtilis Species as Plant Growth-Promoting Rhizobacteria on Zea mays L. Appl Biochem Biotechnol 2024; 196:643-666. [PMID: 37171757 DOI: 10.1007/s12010-023-04563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 05/13/2023]
Abstract
With the global population explosion, the need for increasing crop productivity is reaching its peak. The significance of organic means of cultivation including biofertilizers and biopesticides is undeniable in this context. Over the last few decades, the use of rhizobacteria to induce crop productivity has gained particular interest of researchers. Of these, several Bacillus spp. have been known for their potential plant growth-promoting and phyto-pathogenic actions. Keeping this background in mind, this study was formulated with an aim to unravel the PGPR and phyto-pathogenic potency of Bacillus sp. isolated from extreme environmental conditions, viz. high-altitude waters of Ganges at Gangotri (Basin Extent Longitude Latitude-73° 2' to 89° 5' E 21° 6' to 31° 21' N). Based on recent studies showing the impact of biofilm on bacterial PGPR potency, three novel strains of Bacillus subtilis were isolated on basis of their extremely high biofilm-producing abilities (BRAM_G1: Accession Number MW006633; BRAM_G2: Accession Numbers MT998278-MT998280; BRAM_G3: Accession Number MT998617), and were tested for their PGPR properties like nutrient sequestration, growth hormone production (IAA, GA3), stress-responsive enzyme production (ACC deaminase) and lignocellulolytic and agriculturally important enzyme productions. The strains were further tested for the plethora of metabolites (liquid and VOCs) exuded by them. Finally, the strains both in individually and in an association, i.e. consortium was tested on a test crop, viz. Zea mays L., and the data were collected at regular intervals and the results were statistically analysed. In the present study, the role of high-altitude novel Bacillus subtilis strains as potent PGPR has been analysed statistically.
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Affiliation(s)
- Bedaprana Roy
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India.
| | - Debapriya Maitra
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Abhik Biswas
- Department of Mathematics, St. Xavier's College (Autonomous), Kolkata, India
| | - Niti Chowdhury
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Saswata Ganguly
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Mainak Bera
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Shijini Dutta
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Samriddhi Golder
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Sucharita Roy
- Department of Mathematics, St. Xavier's College (Autonomous), Kolkata, India
| | - Jaydip Ghosh
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
| | - Arup Kumar Mitra
- Department of Microbiology, St. Xavier's College (Autonomous), Kolkata, India
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Li X, Wang C, Zhu X, Ntoukakis V, Cernava T, Jin D. Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance. ENVIRONMENTAL MICROBIOME 2023; 18:78. [PMID: 37876011 PMCID: PMC10594911 DOI: 10.1186/s40793-023-00534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland. RESULTS The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants. CONCLUSION Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.
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Affiliation(s)
- Xinan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, School of Resource and Environmental Sciences, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Chao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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Wang X, Yan G, Liu W, Chen H, Yuan Q, Wang Z, Liu H. Endophytic Beauveria bassiana of Tomato Resisted the Damage from Whitefly Bemisia tabaci by Mediating the Accumulation of Plant-Specialized Metabolites. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13244-13254. [PMID: 37646319 PMCID: PMC10510379 DOI: 10.1021/acs.jafc.3c03679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Beauveria bassiana acts as an endophytic fungus that controls herbivorous pests by stimulating plant defenses and inducing systemic resistance. Through multiomics analysis, 325 differential metabolites and 1739 differential expressed genes were observed in tomatoes treated with B. bassiana by root irrigation; meanwhile, 152 differential metabolites and 1002 differential genes were observed in tomatoes treated by local leaf spraying. Among the upregulated metabolites were α-solanine, 5-O-caffeoylshikimic acid, clerodendrin A, and peucedanin, which demonstrated anti-insect activity. These differential metabolites were primarily associated with alkaloid biosynthesis, flavonoid biosynthesis, and tryptophan metabolism pathways. Furthermore, the gene silencing of UDP-glucose:sterol glucosyltransferase, a gene involved in α-solanine synthesis, indicated that B. bassiana could inhibit the reproduction of whiteflies by regulating α-solanine. This study highlighted the ability of B. bassiana to modulate plant secondary metabolites and emphasized the significance of understanding and harnessing multitrophic interactions of endophytic B. bassiana for sustainable agriculture.
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Affiliation(s)
- Xian Wang
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Ganwei Yan
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Wenjie Liu
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Haolin Chen
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Qian Yuan
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Ziying Wang
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
| | - Huai Liu
- Key Laboratory of Agricultural Biosafety
and Green Production of Upper Yangtze River, Key Laboratory of Entomology
and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, People’s Republic of China
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Mishcherikova V, Lynikienė J, Marčiulynas A, Gedminas A, Prylutskyi O, Marčiulynienė D, Menkis A. Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe. J Fungi (Basel) 2023; 9:829. [PMID: 37623600 PMCID: PMC10455207 DOI: 10.3390/jof9080829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
We assessed the diversity and composition of fungal communities in different functional tissues and the rhizosphere soil of Pinus sylvestris and Picea abies stands along the latitudinal gradient of these tree species distributions in Europe to model possible changes in fungal communities imposed by climate change. For each tree species, living needles, shoots, roots, and the rhizosphere soil were sampled and subjected to high-throughput sequencing. Results showed that the latitude and the host tree species had a limited effect on the diversity and composition of fungal communities, which were largely explained by the environmental variables of each site and the substrate they colonize. The mean annual temperature and mean annual precipitation had a strong effect on root fungal communities, isothermality on needle fungal communities, mean temperature of the warmest quarter and precipitation of the driest month on shoot fungal communities, and precipitation seasonality on soil fungal communities. Fungal communities of both tree species are predicted to shift to habitats with a lower annual temperature amplitude and with increasing precipitation during the driest month, but the suitability of these habitats as compared to the present conditions is predicted to decrease in the future.
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Affiliation(s)
- Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, V.N. Karazin Kharkiv National University, Svobody Sq., 61022 Kharkiv, Ukraine;
| | - Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
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Chen X, Wang Y, Wang Y, Zhang Y, Shen Y, He X, Xiao C. A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China. J Fungi (Basel) 2023; 9:jof9050549. [PMID: 37233260 DOI: 10.3390/jof9050549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive.
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Affiliation(s)
- Xin Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yujue Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yushu Zhang
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yuting Shen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing 100038, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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Wang Y, Wu F, Li X, Li C, Zhao Y, Gao Y, Liu J. Effects of plants and soil microorganisms on organic carbon and the relationship between carbon and nitrogen in constructed wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:62249-62261. [PMID: 36940031 DOI: 10.1007/s11356-023-26489-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023]
Abstract
Constructed wetland is an ideal place for studying the effects of plants and microorganisms on the nutrient cycling and carbon-nitrogen coupling in wetland for their clear background. This study examined both bare plots and others with plants (Phragmites australis or Typha angustifolia) in constructed wetlands and vegetation and soil samples were collected to investigate the effects of plants and soil microorganisms on carbon and nitrogen content. Results showed that the soil organic carbon content was high in plots with high plant biomass, and the increase of soil organic carbon driven by plant biomass was mainly from light fraction organic carbon (LFOC). Correlation analysis and redundancy analysis (RDA) suggested that plants play an important role in the cycle of carbon and nitrogen elements in constructed wetland soils, and that plant nitrogen components were key factors influencing wetland soil carbon and nitrogen. In addition, this study found that most of the main microbial taxa were significantly correlated with dissolved organic carbon (DOC), ammonium nitrogen (NH4+), and nitrate and nitrite nitrogen (NOx-) indicating that microorganisms might play an important role in regulating soil element cycles in constructed wetlands by affecting the metabolism of activated carbon and reactive nitrogen. This study has implications for increasing the carbon sink of constructed wetlands to mitigate the effects of global warming.
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Affiliation(s)
- Yan Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Fan Wu
- Jinan Environmental Research Academy, Jinan, 250000, China
| | - Xin Li
- Jinan Environmental Research Academy, Jinan, 250000, China
| | - Changchao Li
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Yongkang Zhao
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Yuxue Gao
- Jinan Environmental Research Academy, Jinan, 250000, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao, 266237, China.
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Ren X, Whitton MM, Yu SJ, Trotter T, Bajagai YS, Stanley D. Application of Phytogenic Liquid Supplementation in Soil Microbiome Restoration in Queensland Pasture Dieback. Microorganisms 2023; 11:microorganisms11030561. [PMID: 36985135 PMCID: PMC10054416 DOI: 10.3390/microorganisms11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Pasture production is vital in cattle farming as it provides animals with food and nutrients. Australia, as a significant global beef producer, has been experiencing pasture dieback, a syndrome of deteriorating grassland that results in the loss of grass and the expansion of weeds. Despite two decades of research and many remediation attempts, there has yet to be a breakthrough in understanding the causes or mechanisms involved. Suggested causes of this phenomenon include soil and plant microbial pathogens, insect infestation, extreme heat stress, radiation, and others. Plants produce a range of phytomolecules with antifungal, antibacterial, antiviral, growth-promoting, and immunostimulant effects to protect themselves from a range of environmental stresses. These products are currently used more in human and veterinary health than in agronomy. In this study, we applied a phytogenic product containing citric acid, carvacrol, and cinnamaldehyde, to investigate its ability to alleviate pasture dieback. The phytogenic liquid-based solution was sprayed twice, one week apart, at 5.4 L per hectare. The soil microbial community was investigated longitudinally to determine long-term effects, and pasture productivity and plant morphometric improvements were explored. The phytogenic liquid significantly improved post-drought recovery of alpha diversity and altered temporal and spatial change in the community. The phytogenic liquid reduced biomarker genera associated with poor and polluted soils and significantly promoted plant and soil beneficial bacteria associated with plant rhizosphere and a range of soil benefits. Phytogenic liquid application produced plant morphology improvements and a consistent enhancement of pasture productivity extending beyond 18 months post-application. Our data show that phytogenic products used in the livestock market as an alternative to antibiotics may also have a beneficial role in agriculture, especially in the light of climate change-related soil maintenance and remediation.
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11
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Fu B, Fang C, Xia J, Pan S, Zhou L, Peng Y, Yan Y, Yang Y, He Y, Chen S, Yang H, Wang J. Urbanization alters soil bacterial communities in southern China coastal cities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 250:114492. [PMID: 36603487 DOI: 10.1016/j.ecoenv.2022.114492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/18/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Urbanization carries essential influences to ecosystem of soil bacteria in coastal cities. Comprehending the patterns and drivers of bacterial diversity are essential to understanding how soil ecosystems respond to environmental change. This study aimed to explore how soil bacterial community (SBC) response to distinct urbanization of coastal cities on composition, assembly process and potential function in Guangdong province, south China. 72 samples from 24 sample sites within 3 cities were included in the study. Soil chemical properties were analyzed, and the bacterial community were investigated by high-throughout sequencing. Proteobacteria and Acidobacteria were the main phyla. Assembly processes remained in stochastic processes and co-occurrence network of SBC kept stable, while urbanization altered SBC by influencing the dominant phyla. The indicators of communities in coastal city soils were the genera gamma_proteobacterium and beta_proteobacterium. Urbanized extent was the non-negligible factor which affected soil bacterial community, despite the total carbon was still the most vital. The impact of urbanization on bacterial communities might follow a non-linear pattern. Faprotax function prediction showed different urbanized coastal city soils share similar metabolic potential. Our study improved our understanding of the response of soil bacterial communities to urbanization in subtropical coastal cities and offered a useful strategy to monitor the ecology risk toward the soil under urbanization.
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Affiliation(s)
- Bing Fu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Chang Fang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Jun Xia
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences (Research Center for Veterinary Clinical Medicine, Xinjiang Academy of Animal Sciences), Key Laboratory of Herbivore Disease Prevention and Control, Ministry of Agriculture and Rural Affairs, Urumqi 830000, China
| | - Sentao Pan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Lei Zhou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yisheng Peng
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yumeng Yan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yan Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yinglin He
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China
| | - Shijun Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China.
| | - Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Zhongshan Innovation Center of South China Agricultural University, Zhongshan 528400, China.
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
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12
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Wang Y, He Y, Ding M, Wang Z, Zhou S. Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest. Curr Microbiol 2022; 79:368. [PMID: 36253615 DOI: 10.1007/s00284-022-03049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022]
Abstract
Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.
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Affiliation(s)
- Yukun Wang
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Yuran He
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Mao Ding
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Zhi Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, Nanjing, 210042, China
| | - Shoubiao Zhou
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China.
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, 241002, China.
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13
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Adoni P, Romanyuk A, Overton TW, Fernandez-Trillo P. Polymer-induced biofilms for enhanced biocatalysis. MATERIALS HORIZONS 2022; 9:2592-2602. [PMID: 35912866 PMCID: PMC9528183 DOI: 10.1039/d2mh00607c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The intrinsic resilience of biofilms to environmental conditions makes them an attractive platform for biocatalysis, bioremediation, agriculture or consumer health. However, one of the main challenges in these areas is that beneficial bacteria are not necessarily good at biofilm formation. Currently, this problem is solved by genetic engineering or experimental evolution, techniques that can be costly and time consuming, require expertise in molecular biology and/or microbiology and, more importantly, are not suitable for all types of microorganisms or applications. Here we show that synthetic polymers can be used as an alternative, working as simple additives to nucleate the formation of biofilms. Using a combination of controlled radical polymerization and dynamic covalent chemistry, we prepare a set of synthetic polymers carrying mildly cationic, aromatic, heteroaromatic or aliphatic moieties. We then demonstrate that hydrophobic polymers induce clustering and promote biofilm formation in MC4100, a strain of Escherichia coli that forms biofilms poorly, with aromatic and heteroaromatic moieties leading to the best performing polymers. Moreover, we compare the effect of the polymers on MC4100 against PHL644, an E. coli strain that forms biofilms well due to a single point mutation which increases expression of the adhesin curli. In the presence of selected polymers, MC4100 can reach levels of biomass production and curli expression similar or higher than PHL644, demonstrating that synthetic polymers promote similar changes in microbial physiology than those introduced following genetic modification. Finally, we demonstrate that these polymers can be used to improve the performance of MC4100 biofilms in the biocatalytic transformation of 5-fluoroindole into 5-fluorotryptophan. Our results show that incubation with these synthetic polymers helps MC4100 match and even outperform PHL644 in this biotransformation, demonstrating that synthetic polymers can underpin the development of beneficial applications of biofilms.
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Affiliation(s)
- Pavan Adoni
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Andrey Romanyuk
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tim W Overton
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Paco Fernandez-Trillo
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain
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14
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Malik G, Chugh S, Madan A. The Potential of Plant Growth-Promoting Rhizobacteria (PGPR) as Biological Tools in Enhancing Agricultural Sustainability. Fungal Biol 2022. [DOI: 10.1007/978-3-031-04805-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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15
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Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc 2021; 16:5030-5082. [PMID: 34635859 PMCID: PMC10824140 DOI: 10.1038/s41596-021-00593-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Affiliation(s)
- Ilija Dukovski
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael Quintin
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kirill S Korolev
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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16
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Fan X, Zhou X, Chen H, Tang M, Xie X. Cross-Talks Between Macro- and Micronutrient Uptake and Signaling in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:663477. [PMID: 34721446 PMCID: PMC8555580 DOI: 10.3389/fpls.2021.663477] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/30/2021] [Indexed: 05/05/2023]
Abstract
In nature, land plants as sessile organisms are faced with multiple nutrient stresses that often occur simultaneously in soil. Nitrogen (N), phosphorus (P), sulfur (S), zinc (Zn), and iron (Fe) are five of the essential nutrients that affect plant growth and health. Although these minerals are relatively inaccessible to plants due to their low solubility and relative immobilization, plants have adopted coping mechanisms for survival under multiple nutrient stress conditions. The double interactions between N, Pi, S, Zn, and Fe have long been recognized in plants at the physiological level. However, the molecular mechanisms and signaling pathways underlying these cross-talks in plants remain poorly understood. This review preliminarily examined recent progress and current knowledge of the biochemical and physiological interactions between macro- and micro-mineral nutrients in plants and aimed to focus on the cross-talks between N, Pi, S, Zn, and Fe uptake and homeostasis in plants. More importantly, we further reviewed current studies on the molecular mechanisms underlying the cross-talks between N, Pi, S, Zn, and Fe homeostasis to better understand how these nutrient interactions affect the mineral uptake and signaling in plants. This review serves as a basis for further studies on multiple nutrient stress signaling in plants. Overall, the development of an integrative study of multiple nutrient signaling cross-talks in plants will be of important biological significance and crucial to sustainable agriculture.
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Affiliation(s)
| | | | | | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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17
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Mauger S, Ricono C, Mony C, Chable V, Serpolay E, Biget M, Vandenkoornhuyse P. Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:235-248. [PMID: 37284513 PMCID: PMC10168034 DOI: 10.1002/pei3.10062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 06/08/2023]
Abstract
Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.
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Affiliation(s)
- Solène Mauger
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Claire Ricono
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | - Cendrine Mony
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
| | | | | | - Marine Biget
- Université de Rennes 1CNRSUMR6553 ECOBIORennes CedexFrance
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18
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Sangiorgio D, Cellini A, Spinelli F, Farneti B, Khomenko I, Muzzi E, Savioli S, Pastore C, Rodriguez-Estrada MT, Donati I. Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity? Microorganisms 2021; 9:microorganisms9081617. [PMID: 34442697 PMCID: PMC8400319 DOI: 10.3390/microorganisms9081617] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/24/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022] Open
Abstract
Plant-associated microbes can shape plant phenotype, performance, and productivity. Cultivation methods can influence the plant microbiome structure and differences observed in the nutritional quality of differently grown fruits might be due to variations in the microbiome taxonomic and functional composition. Here, the influence of organic and integrated pest management (IPM) cultivation on quality, aroma and microbiome of raspberry (Rubus idaeus L.) fruits was evaluated. Differences in the fruit microbiome of organic and IPM raspberry were examined by next-generation sequencing and bacterial isolates characterization to highlight the potential contribution of the resident-microflora to fruit characteristics and aroma. The cultivation method strongly influenced fruit nutraceutical traits, aroma and epiphytic bacterial biocoenosis. Organic cultivation resulted in smaller fruits with a higher anthocyanidins content and lower titratable acidity content in comparison to IPM berries. Management practices also influenced the amounts of acids, ketones, aldehydes and monoterpenes, emitted by fruits. Our results suggest that the effects on fruit quality could be related to differences in the population of Gluconobacter, Sphingomonas, Rosenbergiella, Brevibacillus and Methylobacterium on fruit. Finally, changes in fruit aroma can be partly explained by volatile organic compounds (VOCs) emitted by key bacterial genera characterizing organic and IPM raspberry fruits.
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Affiliation(s)
- Daniela Sangiorgio
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Antonio Cellini
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
- Correspondence: ; Tel.: +39-051-2096443
| | - Brian Farneti
- Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (B.F.); (I.K.)
| | - Iuliia Khomenko
- Research and Innovation Center, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (B.F.); (I.K.)
| | - Enrico Muzzi
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Stefano Savioli
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Chiara Pastore
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - María Teresa Rodriguez-Estrada
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
| | - Irene Donati
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy; (D.S.); (A.C.); (E.M.); (S.S.); (C.P.); (M.T.R.-E.); (I.D.)
- Zespri Fresh Produce, 40132 Bologna, Italy
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19
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Li Z, Cabana H, Lecka J, Brar SK, Galvez R, Bellenger JP. Efficiencies of selected biotreatments for the remediation of PAH in diluted bitumen contaminated soil microcosms. Biodegradation 2021; 32:563-576. [PMID: 34086180 DOI: 10.1007/s10532-021-09952-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Unconventional oils such as diluted bitumen from oil sands differs from most of conventional oils in terms of physiochemical properties and PAHs composition. This raises concerns regarding the effectiveness of current remediation strategies and protocols originally developed for conventional oil. Here we evaluated the efficiency of different biotreatment approaches, such as fungi inoculation (bioaugmentation), sludge addition (bioaugmentation/biostimulation), perennial grasses plantation (phytoremediation) and their combinations as well as natural attenuation (as control condition), for the remediation of soil contaminated by synthetic crude oil (a product of diluted bitumen) in laboratory microcosms. We specifically monitored the PAHs loss percentage (alkylated PAHs and unsubstituted 16 EPA Priority PAHs), the residue of PAHs and evaluated the ecotoxicity of soil after treatment. All treatments were highly efficient with more than ~ 80% of ∑PAHs loss after 60 days. Distinctive loss efficiencies between light PAHs (≤ 3 rings, ~ 96% average loss) and heavy PAHs (4-6 rings, ~ 29% average loss) were observed. The lowest average PAHs residue (0.10 ± 0.02 mg·kg-1, for an initial concentration of 0.29 ± 0.12 mg·kg-1) was achieved with the "sludge-plants (grasses)" combination. Sludge addition was the only treatment that achieved significantly lower ecotoxicity (3% ± 4% of growth inhibition of L. sativa) than the control (natural attenuation, 13% ± 4% of inhibition). Sludge addition, grasses plantation and "sludge-fungi combination" treatments could result in lower PAH exposure (than other treatments) in post-treated soil when using the Canadian Soil Quality Guidelines for the protection of environmental and human health for potentially carcinogenic and other PAHs.
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Affiliation(s)
- Ziang Li
- Department of Civil Engineering, Faculty of Science and Engineering, Laval University, Quebec City, Canada.,Department of Chemistry, Faculty of Sciences, Sherbrooke University, Sherbrooke, Canada
| | - Hubert Cabana
- Department of Civil and Building Engineering, Faculty of Engineering, Sherbrooke University, Sherbrooke, Canada
| | - Joanna Lecka
- Eau Terre Environnement Research Centre, INRS, Quebec City, Canada
| | - Satinder K Brar
- Eau Terre Environnement Research Centre, INRS, Quebec City, Canada
| | - Rosa Galvez
- Department of Civil Engineering, Faculty of Science and Engineering, Laval University, Quebec City, Canada
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20
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Grandel NE, Reyes Gamas K, Bennett MR. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol 2021; 29:1095-1105. [PMID: 33966922 DOI: 10.1016/j.tim.2021.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.
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Affiliation(s)
- Nicolas E Grandel
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA.
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21
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Garaycochea S, Romero H, Beyhaut E, Neal AL, Altier N. Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities. FEMS Microbiol Ecol 2021; 96:5920615. [PMID: 33038219 DOI: 10.1093/femsec/fiaa207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/08/2020] [Indexed: 12/26/2022] Open
Abstract
Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.
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Affiliation(s)
- Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma/Unidad de Genómica Evolutiva, Departamento de Ecología y Evolución, Facultad de Ciencias/CURE, Universidad de la República, Maldonado, Uruguay
| | - Elena Beyhaut
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
| | - Andrew L Neal
- Department of Sustainable Agricultural Sciences, Rothamsted Research, North Wyke, Devon EX22 2SB, UK
| | - Nora Altier
- Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Las Brujas, Ruta 48 Km 10, Canelones, 90200, Uruguay
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22
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Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application. SUSTAINABILITY 2021. [DOI: 10.3390/su13084422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.
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23
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Ares A, Costa J, Joaquim C, Pintado D, Santos D, Messmer MM, Mendes-Moreira PM. Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population). Front Microbiol 2021; 12:636009. [PMID: 33717028 PMCID: PMC7953162 DOI: 10.3389/fmicb.2021.636009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.
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Affiliation(s)
- Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Carolina Joaquim
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Duarte Pintado
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Daniela Santos
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Monika M Messmer
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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24
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de Souza AJ, Pereira APDA, Andreote FD, Tornisielo VL, Tizioto PC, Coutinho LL, Regitano JB. Sulfadiazine dissipation as a function of soil bacterial diversity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116374. [PMID: 33412451 DOI: 10.1016/j.envpol.2020.116374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/02/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Antibiotic residues in the environment are concerning since results in dispersion of resistance genes. Their degradation is often closely related to microbial metabolism. However, the impacts of soil bacterial community on sulfadiazine (SDZ) dissipation remains unclear, mainly in tropical soils. Our main goals were to evaluate effects of long-term swine manure application on soil bacterial structure as well as effects of soil microbial diversity depletion on SDZ dissipation, using "extinction dilution approach" and 14C-SDZ. Manure application affected several soil attributes, such as pH, organic carbon (OC), and macronutrient contents as well as bacterial community structure and diversity. Even minor bacterial diversity depletion impacted SDZ mineralization and non-extractible residue (NER) formation rates, but NER recovered along 42 d likely due to soil diversity recovery. However, this period may be enough to spread resistance genes into the environment. Surprisingly, the non-manured natural soil (NS-S1) showed faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a great number of bacterial families involved in major SDZ dissipation pathways (mineralization and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_(Subgroup_1), Micromonosporaceae, and Sphingobacteriaceae. This result is unique and contrasts our hypothesis that long-term manured soils would present adaptive advantages and, consequently, have higher SDZ dissipation rates. The literature suggests instantaneous chemical degradation of SDZ in acidic soils responsible to the fast formation of NER. Our results show that if chemical degradation happens, it is soon followed by microbial metabolism (biodegradation) performed by a pool of bacteria and the newly formed metabolites should favors NER formation since SDZ presented low sorption. It also showed that SDZ mineralization is a low redundancy function.
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Affiliation(s)
- Adijailton Jose de Souza
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Fernando Dini Andreote
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Valdemar Luiz Tornisielo
- Center of Nuclear Energy for Agriculture (CENA), University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Jussara Borges Regitano
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, São Paulo, Brazil.
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25
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Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil. Sci Rep 2021; 11:831. [PMID: 33437021 PMCID: PMC7804402 DOI: 10.1038/s41598-020-80840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.
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26
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Ribeiro IDA, Volpiano CG, Vargas LK, Granada CE, Lisboa BB, Passaglia LMP. Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review. FRONTIERS IN PLANT SCIENCE 2020; 11:590774. [PMID: 33362817 PMCID: PMC7759553 DOI: 10.3389/fpls.2020.590774] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/26/2020] [Indexed: 05/19/2023]
Abstract
Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Camila Gazolla Volpiano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciano Kayser Vargas
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
| | | | - Bruno Brito Lisboa
- Laboratório de Microbiologia Agrícola, Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Desenvolvimento Rural, Porto Alegre, Brazil
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27
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Andrade PAMD, de Souza AJ, Lira SP, Assis MA, Berlinck RGS, Andreote FD. The bacterial and fungal communities associated with Anthurium ssp. leaves: Insights into plant endemism and microbe association. Microbiol Res 2020; 244:126667. [PMID: 33338969 DOI: 10.1016/j.micres.2020.126667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 11/18/2022]
Abstract
It is known that different plant species select specific microbes to live inside their tissues in a process determined by the host genotype, phenotype and geographic location, which can introduce discussion on plant endemism and the assembly of specific microbial communities. Herein, we report the results of an investigation relating the geographic distribution of plant species and the composition of microbial communities associated with plant hosts. The bacterial and fungal community associated with Anthurium plant leaves was mapped to assess the diversity and ecology of the endophytic community associated with Anthurium spp. collected on islands and on the Brazilian mainland. Twenty-six Anthurium specimens were surveyed, distributed throughout the São Paulo state coastline, including Alcatrazes Island, some coastal islands and distinct mainland environments. Bacterial and fungal endophytes were obtained from the leaves of A. alcatrazense, A. loefgrenii, A. penthaphyllum, A. urvellianum and A. intermedium and subjected to massive bacterial 16S rRNA and fungal ITS sequencing. The results indicated that A. alcatrazense, endemic to Alcatrazes Island, hosted a specific bacterial community structure, while its fungal community was similar to that of Anthurium species from other locations. Betaproteobacteria showed a high differential occurrence in A. alcatrazense. Some groups of fungi were found mainly inhabiting A. loefgrenii plants. While Alphaproteobacteria, Gammaproteobacteria, Actinobacteria and Sordariomycetes, Dothiodeomycetes and Tremellomycetes composed the core microbial community among Anthurium plants. The results suggest crucial role for the bacterial communities to endemic plants, while endophytic fungal diversity is less specifically distributed among endemic and nonendemic plant species.
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Affiliation(s)
- Pedro Avelino Maia de Andrade
- Department of Soil Science, "Luiz de Queiroz" Superior College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Adijailton José de Souza
- Department of Soil Science, "Luiz de Queiroz" Superior College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Simone Possedente Lira
- Department of Exact Science, "Luiz de Queiroz" Superior College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Marco Antonio Assis
- Department of Botany, São Paulo State University, Piracicaba, São Paulo, Brazil
| | - Roberto G S Berlinck
- São Carlos Institute of Chemistry, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, "Luiz de Queiroz" Superior College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
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28
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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29
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Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
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Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
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30
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Li M, Chen Z, Qian J, Wei F, Zhang G, Wang Y, Wei G, Hu Z, Dong L, Chen S. Composition and function of rhizosphere microbiome of Panax notoginseng with discrepant yields. Chin Med 2020; 15:85. [PMID: 32793300 PMCID: PMC7418314 DOI: 10.1186/s13020-020-00364-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Background Panax notoginseng is a highly valuable medicinal plant. Reduced P. notoginseng yield is a common and serious problem that arises in a continuous cropping system. Variation in the composition and function of soil microbial community is considered the primary cause of yield reduction. Methods This study used shotgun metagenomic sequencing approaches to describe the taxonomic and functional features of P. notoginseng rhizosphere microbiome and screen microbial taxa and functional traits related to yields. Results At the family and genus level, a total of 43 families and 45 genera (relative abundance > 0.1%) were obtained, and the correlation with the yield of P. notoginseng was further analyzed. Nitrosomonadaceae, Xanthomonadaceae, Mycobacterium and Arthrobacter that were enriched in soils with higher yields were positively correlated with P. notoginseng yields, thereby suggesting that they might increase yields. Negative correlation coefficients indicated that Xanthobacteraceae, Caulobacteraceae, Oxalobacteraceae, Chitinophagaceae, Sphingomonas, Hyphomicrobium, Variovorax and Phenylobacterium might be detrimental to P. notoginseng growth. A total of 85 functional traits were significantly (P < 0.05) correlated with P. notoginseng yields. Functional traits, likely steroid biosynthesis and MAPK signaling pathway were positively correlated with P. notoginseng yields. In contrast, functional traits, such as bacterial secretion system, ABC transporters, metabolism of xenobiotics by cytochrome P450 and drug metabolism–cytochrome P450, were negatively associated with yields. Conclusions This study describes an overview of the rhizosphere microbiome of P. notoginseng with discrepant yields and identifies the taxa and functional traits related to yields. Our results provide valuable information to guide the isolation and culture of potentially beneficial microorganisms and to utilize the power of the microbiome to increase plant yields in a continuous cropping system.
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Affiliation(s)
- Mengzhi Li
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China.,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, 663000 China.,Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, 663000 China
| | - Jun Qian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China.,College of Pharmaceutical Science, Dali University, Dali, 671000 China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, 663000 China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, 663000 China
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Shilin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China.,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, 100700 China
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31
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Baptistella JLC, de Andrade SAL, Favarin JL, Mazzafera P. Urochloa in Tropical Agroecosystems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00119] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Carvalho CR, Dias AC, Homma SK, Cardoso EJ. Phyllosphere bacterial assembly in citrus crop under conventional and ecological management. PeerJ 2020; 8:e9152. [PMID: 32547860 PMCID: PMC7274167 DOI: 10.7717/peerj.9152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/17/2020] [Indexed: 11/20/2022] Open
Abstract
Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.
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Affiliation(s)
- Carolinne R Carvalho
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Armando Cf Dias
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Elke Jbn Cardoso
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
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33
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Pettifor BJ, Doonan J, Denman S, McDonald JE. Survival of Brenneria goodwinii and Gibbsiella quercinecans, associated with acute oak decline, in rainwater and forest soil. Syst Appl Microbiol 2020; 43:126052. [PMID: 31932140 DOI: 10.1016/j.syapm.2019.126052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/19/2019] [Accepted: 12/26/2019] [Indexed: 10/25/2022]
Abstract
Acute oak decline (AOD) affects native UK oak species causing rapid decline and mortality in as little as five years. A major symptom of AOD is black weeping stem lesions associated with bacterial phytopathogens, Brenneria goodwinii and Gibbsiella quercinecans. However, there is limited knowledge on the ecological and environmental reservoirs of these phytopathogens. Rainwater and soils are common reservoirs of plant pathogens in a forest environment; therefore, the aim of this study was to investigate the survival of B. goodwinii and G. quercinecans in vitro when inoculated into rainwater and forest soil using a combination of agar-based colony counts and gyrB gene-targeted quantitative PCR (qPCR). Brenneria goodwinii lost viability on inoculation into soil and rainwater, but was detectable at low abundance in soil for 28 days using qPCR, suggesting a limited ability to persist outside of the host, potentially in a viable but non-culturable (VBNC) state. Conversely, Gibbsiella quercinecans, was re-isolated from rainwater for the entire duration of the experiment (84 days) and was re-isolated from forest soil after 28 days, with qPCR analysis corroborating these trends. These data demonstrate that B. goodwinii is unable to survive in forest soils and rainwater, suggesting that it may be an endosymbiont of oak trees, whereas G. quercinecans remains viable in soil and rainwater biomes, suggesting a broad ecological distribution. These data advance understanding of the potential epidemiology of AOD-associated bacteria and their ecological reservoirs, thus increasing the overall knowledge of the pathology of AOD, which assists the development of future management strategies.
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Affiliation(s)
- Bethany J Pettifor
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - James Doonan
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Sandra Denman
- Forest Research, Centre for Forestry and Climate Change, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - James E McDonald
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK.
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34
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Selvarajan R, Sibanda T, Venkatachalam S, Ogola HJO, Christopher Obieze C, Msagati TA. Distribution, Interaction and Functional Profiles of Epiphytic Bacterial Communities from the Rocky Intertidal Seaweeds, South Africa. Sci Rep 2019; 9:19835. [PMID: 31882618 PMCID: PMC6934600 DOI: 10.1038/s41598-019-56269-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/05/2019] [Indexed: 11/16/2022] Open
Abstract
Interrelations between epiphytic bacteria and macroalgae are multifaceted and complicated, though little is known about the community structure, interaction and functions of those epiphytic bacteria. This study comprehensively characterized the epiphytic bacterial communities associated with eight different common seaweeds collected from a rocky intertidal zone on the Indian Ocean at Cape Vidal, South Africa. High-throughput sequencing analyses indicated that seaweed-associated bacterial communities were dominated by the phyla Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Energy-dispersive X-ray (EDX) analysis showed the presence of elemental composition in the surface of examined seaweeds, in varying concentrations. Cluster analysis showed that bacterial communities of brown seaweeds (SW2 and SW4) were closely resembled those of green seaweeds (SW1) and red seaweeds (SW7) while those of brown seaweeds formed a separate branch. Predicted functional capabilities of epiphytic bacteria using PICRUSt analysis revealed abundance of genes related to metabolic and biosynthetic activities. Further important identified functional interactions included genes for bacterial chemotaxis, which could be responsible for the observed association and network of elemental-microbes interaction. The study concludes that the diversity of epiphytic bacteria on seaweed surfaces is greatly influenced by algal organic exudates as well as elemental deposits on their surfaces, which triggers chemotaxis responses from epiphytic bacteria with the requisite genes to metabolise those substrates.
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Affiliation(s)
- Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.
| | - Timothy Sibanda
- Department of Biological Sciences, University of Namibia, Mandume Ndemufayo Ave, Pionierspark, Windhoek, Namibia
| | | | - Henry J O Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, UNISA, Johannesburg, South Africa.,Centre for Research, Innovation and Technology, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | | | - Titus A Msagati
- Nanotechnology and Water Sustainability Research Unit, College of Science, Engineering and Technology, University of South Africa-Science Campus, Florida, South Africa
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35
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Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants. PLoS One 2019; 14:e0223847. [PMID: 31703074 PMCID: PMC6839845 DOI: 10.1371/journal.pone.0223847] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/30/2019] [Indexed: 11/19/2022] Open
Abstract
Plants harbor diverse bacterial communities, which play crucial roles in plant health and growth, in their rhizosphere, phyllosphere and endosphere. Tomato is an important model for studying plant-microbe interactions, but comparison of its associated bacterial community is still lacking. In this study, using Illumina sequencing of 16S rRNA amplicons, we characterized and compared the bacterial size and community from rootzone soil as well as the rhizosphere, phyllosphere and endosphere of roots, stems, leaves, fruits and seeds of tomato plants that were grown in greenhouse conditions. Habitat (soil, phyllospheric, and endophytic) structured the community. The bacterial communities from the soil-type samples (rootzone soil and rhizosphere) showed the highest richness and diversity. The lowest bacterial diversity occurred in the phyllospheric samples, while the lowest richness occurred in the endosphere. Among the endophytic samples, both bacterial diversity and richness varied in different tissues, with the highest values in roots. The most abundant phyla in the tomato-associated community was Proteobacteria, with the exception of the seeds and jelly, where both Proteobacteria and Firmicutes were dominant. At the genus level, the sequences of Pseudomonas and Acinetobacter were prevalent in the rhizosphere, and in the phyllosphere, more than 97% of the sequences were assigned to Acinetobacter. For the endophytes, Acinetobacter, Enterobacter, and Pseudomonas were the abundant genera in the roots, stems and leaves. In the fruits, the bacterial endophytes varied in different compartments, with Enterobacter being enriched in the pericarp and seeds, Acinetobacter in the placenta, and Weissella in the jelly. The present data provide a comprehensive description of the tomato-associated bacterial community and will be useful for better understanding plant-microbe interactions and selecting suitable bacterial taxa for tomato production.
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36
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Feng K, Zhang Y, He Z, Ning D, Deng Y. Interdomain ecological networks between plants and microbes. Mol Ecol Resour 2019; 19:1565-1577. [PMID: 31479575 DOI: 10.1111/1755-0998.13081] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022]
Abstract
While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above-belowground ecology in natural ecosystems has been poorly understood, especially for the plant-microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant-microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant-forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta-communities across different domain species.
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Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuguang Zhang
- Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Beijing, China
| | - Zhili He
- Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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37
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics‐Driven Discovery of NO‐Donating Diazeniumdiolate Siderophores in Diverse Plant‐Associated Bacteria. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906326] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Jule L. Mehl
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology at the Doherty Institute University of Melbourne Melbourne VIC 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstrasse 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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38
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Hermenau R, Mehl JL, Ishida K, Dose B, Pidot SJ, Stinear TP, Hertweck C. Genomics-Driven Discovery of NO-Donating Diazeniumdiolate Siderophores in Diverse Plant-Associated Bacteria. Angew Chem Int Ed Engl 2019; 58:13024-13029. [PMID: 31276269 PMCID: PMC6771848 DOI: 10.1002/anie.201906326] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/05/2019] [Indexed: 01/13/2023]
Abstract
Siderophores are key players in bacteria–host interactions, with the main function to provide soluble iron for their producers. Gramibactin from rhizosphere bacteria expands siderophore function and diversity as it delivers iron to the host plant and features an unusual diazeniumdiolate moiety for iron chelation. By mutational analysis of the grb gene cluster, we identified genes (grbD and grbE) necessary for diazeniumdiolate formation. Genome mining using a GrbD‐based network revealed a broad range of orthologous gene clusters in mainly plant‐associated Burkholderia/Paraburkholderia species. Two new types of diazeniumdiolate siderophores, megapolibactins and plantaribactin were fully characterized. In vitro assays and in vivo monitoring experiments revealed that the iron chelators also liberate nitric oxide (NO) in plant roots. This finding is important since NO donors are considered as biofertilizers that maintain iron homeostasis and increase overall plant fitness.
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Affiliation(s)
- Ron Hermenau
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Jule L Mehl
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745, Jena, Germany.,Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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39
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Patz S, Witzel K, Scherwinski AC, Ruppel S. Culture Dependent and Independent Analysis of Potential Probiotic Bacterial Genera and Species Present in the Phyllosphere of Raw Eaten Produce. Int J Mol Sci 2019; 20:ijms20153661. [PMID: 31357436 PMCID: PMC6696213 DOI: 10.3390/ijms20153661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
The plant phyllosphere is colonized by a complex ecosystem of microorganisms. Leaves of raw eaten vegetables and herbs are habitats for bacteria important not only to the host plant, but also to human health when ingested via meals. The aim of the current study was to determine the presence of putative probiotic bacteria in the phyllosphere of raw eaten produce. Quantification of bifidobacteria showed that leaves of Lepidium sativum L., Cichorium endivia L., and Thymus vulgaris L. harbor between 103 and 106 DNA copies per gram fresh weight. Total cultivable bacteria in the phyllosphere of those three plant species ranged from 105 to 108 CFU per gram fresh weight. Specific enrichment of probiotic lactic acid bacteria from C. endivia, T. vulgaris,Trigonella foenum-graecum L., Coriandrum sativum L., and Petroselinum crispum L. led to the isolation of 155 bacterial strains, which were identified as Pediococcus pentosaceus, Enterococcus faecium, and Bacillus species, based on their intact protein pattern. A comprehensive community analysis of the L. sativum leaves by PhyloChip hybridization revealed the presence of genera Bifidobacterium, Lactobacillus, and Streptococcus. Our results demonstrate that the phyllosphere of raw eaten produce has to be considered as a substantial source of probiotic bacteria and point to the development of vegetables and herbs with added probiotic value.
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Affiliation(s)
- Sascha Patz
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Ann-Christin Scherwinski
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
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40
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Sinnesael A, Leroux O, Janssens SB, Smets E, Panis B, Verstraete B. Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant. PLoS One 2019; 14:e0219863. [PMID: 31310638 PMCID: PMC6634412 DOI: 10.1371/journal.pone.0219863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND & AIMS The bacterial leaf nodule symbiosis is an interaction where bacteria are housed in specialised structures in the leaves of their plant host. In the Rubiaceae plant family, host plants interact with Burkholderia bacteria. This interaction might play a role in the host plant defence system. It is unique due to its high specificity; the vertical transmission of the endophyte to the next generation of the host plant; and its supposedly obligatory character. Although previous attempts have been made to investigate this obligatory character by developing Burkholderia-free plants, none have succeeded and nodulating plants were still produced. In order to investigate the obligatory character of this endosymbiosis, our aims were to develop Burkholderia-free Psychotria umbellata plants and to investigate the effect of the absence of the endophytes on the host in a controlled environment. METHODS The Burkholderia-free plants were obtained via embryo culture, a plant cultivation technique. In order to analyse the endophyte-free status, we screened the plants morphologically, microscopically and molecularly over a period of three years. To characterise the phenotype and growth of the in vitro aposymbiotic plants, we compared the growth of the Burkholderia-free plants to the nodulating plants under the same in vitro conditions. KEY RESULTS All the developed plants were Burkholderia-free and survived in a sterile in vitro environment. The growth analysis showed that plants without endophytes had a slower development. CONCLUSIONS Embryo culture is a cultivation technique with a high success rate for the development of Burkholderia-free plants of P. umbellata. The increased growth rate in vitro when the specific endophyte is present cannot be explained by possible benefits put forward in previous studies. This might indicate that the benefits of the endosymbiosis are not yet completely understood.
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Affiliation(s)
- Arne Sinnesael
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | | | - Steven B. Janssens
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Bart Panis
- Bioversity International, Leuven, Belgium
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41
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Giard-Laliberté C, Azarbad H, Tremblay J, Bainard L, Yergeau É. A water stress-adapted inoculum affects rhizosphere fungi, but not bacteria nor wheat. FEMS Microbiol Ecol 2019; 95:5499018. [DOI: 10.1093/femsec/fiz080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
- Charlotte Giard-Laliberté
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hamed Azarbad
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, 6100 avenue Royalmount, Montreal, QC, H4P 2R2, Canada
| | - Luke Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport road, Swift Current, SK, S9H 3X2, Canada
| | - Étienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
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42
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Sugiyama A. The soybean rhizosphere: Metabolites, microbes, and beyond-A review. J Adv Res 2019; 19:67-73. [PMID: 31341671 PMCID: PMC6630087 DOI: 10.1016/j.jare.2019.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 11/17/2022] Open
Abstract
Rhizosphere microbial communities are important for plant health. Specialized metabolites in the rhizosphere influence the microbial communities. Isoflavones and saponins are major specialized metabolites secreted by soybean. Secretion is regulated developmentally and nutritionally. Possible links between specialized metabolites and microbial communities are highlighted.
The rhizosphere is the region close to a plant’s roots, where various interactions occur. Recent evidence indicates that plants influence rhizosphere microbial communities by secreting various metabolites and, in turn, the microbes influence the growth and health of the plants. Despite the importance of plant-derived metabolites in the rhizosphere, relatively little is known about their spatiotemporal distribution and dynamics. In addition to being an important crop, soybean (Glycine max) is a good model plant with which to study these rhizosphere interactions, because soybean plants have symbiotic relationships with rhizobia and arbuscular mycorrhizal fungi and secrete various specialized metabolites, such as isoflavones and saponins, into the soil. This review summarizes the characteristics of the soybean rhizosphere from the viewpoint of specialized metabolites and microbes and discusses future research perspectives. In sum, secretion of these metabolites is developmentally and nutritionally regulated and potentially alters the rhizosphere microbial communities.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
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43
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Santhanam R, Menezes RC, Grabe V, Li D, Baldwin IT, Groten K. A suite of complementary biocontrol traits allows a native consortium of root-associated bacteria to protect their host plant from a fungal sudden-wilt disease. Mol Ecol 2019; 28:1154-1169. [PMID: 30633416 DOI: 10.1111/mec.15012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/05/2023]
Abstract
The beneficial effects of plant--bacterial interactions in controlling plant pests have been extensively studied with single bacterial isolates. However, in nature, bacteria interact with plants in multitaxa consortia, systems which remain poorly understood. Previously, we demonstrated that a consortium of five native bacterial isolates protected their host plant Nicotiana attenuata from a sudden wilt disease. Here we explore the mechanisms behind the protection effect against the native pathosystem. Three members of the consortium, Pseudomonas azotoformans A70, P. frederiksbergensis A176 and Arthrobacter nitroguajacolicus E46, form biofilms when grown individually in vitro, and the amount of biofilm increased synergistically in the five-membered consortium, including two Bacillus species, B. megaterium and B. mojavensis. Fluorescence in situ hybridization and scanning electron microscopy in planta imaging techniques confirmed biofilm formation and revealed locally distinct distributions of the five bacterial strains colonizing different areas on the plant-root surface. One of the five isolates, K1 B. mojavensis produces the antifungal compound surfactin, under in vitro and in vivo conditions, clearly inhibiting fungal growth. Furthermore, isolates A70 and A176 produce siderophores under in vitro conditions. Based on these results we infer that the consortium of five bacterial isolates protects its host against fungal phytopathogens via complementary traits. The study should encourage researchers to create synthetic communities from native strains of different genera to improve bioprotection against wilting diseases.
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Affiliation(s)
- Rakesh Santhanam
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Riya C Menezes
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Dapeng Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
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Wille L, Messmer MM, Studer B, Hohmann P. Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. PLANT, CELL & ENVIRONMENT 2019; 42:20-40. [PMID: 29645277 DOI: 10.1111/pce.13214] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 05/19/2023]
Abstract
Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
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Wu L, Chen J, Khan MU, Wang J, Wu H, Xiao Z, Zhang Z, Lin W. Rhizosphere Fungal Community Dynamics Associated with Rehmannia glutinosa Replant Disease in a Consecutive Monoculture Regime. PHYTOPATHOLOGY 2018; 108:1493-1500. [PMID: 29975158 DOI: 10.1094/phyto-02-18-0038-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Consecutive monoculture of Rehmannia glutinosa in the same field leads to a severe decline in both quality and yield of tuberous roots, the most useful part in traditional Chinese medicine. Fungi are an important and diverse group of microorganisms in the soil ecosystem and play crucial roles in soil health. In this study, high-throughput pyrosequencing of internal transcribed spacer 2 ribosomal DNA amplicons was applied to gain insight into how consecutive monoculture practice influence and stimulate R. glutinosa rhizosphere and bulk soil fungal communities. The results from nonmetric multidimensional scaling ordination and clustering analysis revealed distinctive differences between rhizosphere and bulk soil fungal communities. However, longer-term monocultured bulk soils were more similar to the rhizosphere soils in comparison with the shorter-term monocultured bulk soils. Moreover, consecutive monoculture caused a gradual shift in the composition and structure of the soil fungal community. The cultivation of this plant led to the appearance of some exclusive operational taxonomic units in rhizosphere or bulk soils that were assigned to the genera Fusarium, Rhizoctonia, and so on. Furthermore, the sum of the relative abundance of species of Fusarium, Cylindrocarpon, and Gibberella (belonging to the family Nectriaceae); Rhizoctonia, Thanatephorus, and Ceratobasidium (belonging to the family Ceratobasidiaceae); and Lectera and Plectosporium (belonging to the family Plectosphaerellaceae) was significantly higher in consecutively monocultured (CM) than in newly planted (NP) soil in both rhizosphere and bulk soils. In particular, Fusarium abundance was significantly higher in CM than in NP in the rhizosphere, and higher in rhizosphere soils than in bulk soils for each treatment. A pathogenicity test showed that both Fusarium strains isolated were pathogenic to R. glutinosa seedlings. In addition, the culture filtrate and mycotoxins produced by Fusarium oxysporum significantly repressed the growth of the antagonistic bacterium, Pseudomonas aeruginosa. In conclusion, consecutive monoculture of R. glutinosa restructured the fungal communities in both rhizosphere and bulk soils but bulk effects developed more slowly over time in comparison with rhizosphere effects. Furthermore, microbial interactions might lead to a reduction in the abundance of beneficial microbes.
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Affiliation(s)
- Linkun Wu
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Jun Chen
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Muhammad Umar Khan
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Juanying Wang
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Hongmiao Wu
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Zhigang Xiao
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Zhongyi Zhang
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Wenxiong Lin
- First, second, third, fourth, fifth, sixth, and eighth authors: College of Life Sciences and Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring; seventh and eighth authors: Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Province University; and seventh author: College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
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Xing H, Ma J, Xu B, Zhang S, Wang J, Cao L, Yang X. Mycobiota of maize seeds revealed by rDNA-ITS sequence analysis of samples with varying storage times. Microbiologyopen 2018; 7:e00609. [PMID: 29573223 PMCID: PMC6291794 DOI: 10.1002/mbo3.609] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/17/2018] [Accepted: 01/25/2018] [Indexed: 11/16/2022] Open
Abstract
Fungi are an integral component of the plant microbiome. However, the composition and variation in the fungal communities (mycobiota) associated with seeds are poorly understood. In this study, we investigated the mycobiota of 11 maize seed samples with storage times ranging from 6 months to 12 years. Mycobiota were characterized by a culture-based approach, and fungal species were identified through rDNA-ITS sequence analyses. From a total of 169 pure fungal isolates obtained from both the seed surface and internal tissues, we identified 16 distinct species (belonging to 10 genera) associated with maize seeds, all but one of which were ascomycetes. Among these species, seven were exclusively isolated from internal tissues, two species were isolated only from the seed surface, and another six species were isolated from both the surface and internal tissues. Aspergillus niger was consistently found under all storage conditions and dominated fungal communities with a relative abundance of 36%-100%. Species of Fusarium (9%-40%) and Penicillium (9%-20%) were also frequently isolated, but other species appeared sporadically and were isolated from fewer than three seed stocks. According to our results, while the overall incidence of fungal infection generally declined with storage time, there was no consistent association between seed storage time and fungal species richness or relative abundance; furthermore, the composition of the mycobiota associated with maize seeds was highly variable among the samples. The detection of the four major mycotoxigenic fungal genera, specifically Aspergillus, Fusarium, Penicillium, and Alternaria, was alarming, and the isolation of a potential controlling agent as well as information about their temporal occurrence will contribute to the management of mycotoxins in the future.
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Affiliation(s)
- Hui‐Qin Xing
- College of Plant ProtectionGansu Agricultural University and Biocontol Engineering Laboratory of Crop Diseases and Pests of Gansu ProvinceLanzhouGansuChina
- College of Agriculture and BiotechnologyHexi UniversityZhangyeGansuChina
| | - Jian‐Cang Ma
- Zhangye Maize Stock Production BaseZhangyeGansuChina
| | - Bing‐Liang Xu
- College of Plant ProtectionGansu Agricultural University and Biocontol Engineering Laboratory of Crop Diseases and Pests of Gansu ProvinceLanzhouGansuChina
| | - Shu‐Wu Zhang
- College of Plant ProtectionGansu Agricultural University and Biocontol Engineering Laboratory of Crop Diseases and Pests of Gansu ProvinceLanzhouGansuChina
| | - Jin Wang
- College of Agriculture and BiotechnologyHexi UniversityZhangyeGansuChina
| | - Li Cao
- College of Agriculture and BiotechnologyHexi UniversityZhangyeGansuChina
| | - Xue‐Mei Yang
- College of Agriculture and BiotechnologyHexi UniversityZhangyeGansuChina
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Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D, Ricci E, Subramanian S, Smith DL. Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2018; 9:1473. [PMID: 30405652 PMCID: PMC6206271 DOI: 10.3389/fpls.2018.01473] [Citation(s) in RCA: 581] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/20/2018] [Indexed: 05/02/2023]
Abstract
Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.
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Affiliation(s)
- Rachel Backer
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - J. Stefan Rokem
- School of Medicine, Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - John Lamont
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Dana Praslickova
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Emily Ricci
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | | | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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Kim YC, Anderson AJ. Rhizosphere pseudomonads as probiotics improving plant health. MOLECULAR PLANT PATHOLOGY 2018; 19:2349-2359. [PMID: 29676842 PMCID: PMC6638116 DOI: 10.1111/mpp.12693] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/08/2018] [Accepted: 04/18/2018] [Indexed: 05/25/2023]
Abstract
Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.
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Affiliation(s)
- Young Cheol Kim
- Department of Applied Biology, College of Agriculture and Life SciencesChonnam National UniversityGwangju 61186South Korea
| | - Anne J. Anderson
- Department of Biological EngineeringUtah State UniversityLoganUT 84322‐4105USA
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Vargas-Albores F, Martínez-Córdova LR, Martínez-Porchas M, Calderón K, Lago-Lestón A. Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences. Biotechnol Genet Eng Rev 2018; 35:69-91. [PMID: 30221593 DOI: 10.1080/02648725.2018.1513230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.
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Affiliation(s)
- Francisco Vargas-Albores
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Luis R Martínez-Córdova
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
| | - Marcel Martínez-Porchas
- a Centro de Investigación en Alimentación y Desarrollo , A.C. Coordinación de Tecnología de Alimentos de Origen Animal , Hermosillo , Mexico
| | - Kadiya Calderón
- b Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora , Universidad de Sonora , Hermosillo , Mexico
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50
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Brugman S, Ikeda-Ohtsubo W, Braber S, Folkerts G, Pieterse CMJ, Bakker PAHM. A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research. Front Nutr 2018; 5:80. [PMID: 30234124 PMCID: PMC6134018 DOI: 10.3389/fnut.2018.00080] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
During recent years the impact of microbial communities on the health of their host (being plants, fish, and terrestrial animals including humans) has received increasing attention. The microbiota provides the host with nutrients, induces host immune development and metabolism, and protects the host against invading pathogens (1-6). Through millions of years of co-evolution bacteria and hosts have developed intimate relationships. Microbial colonization shapes the host immune system that in turn can shape the microbial composition (7-9). However, with the large scale use of antibiotics in agriculture and human medicine over the last decades an increase of diseases associated with so-called dysbiosis has emerged. Dysbiosis refers to either a disturbed microbial composition (outgrowth of possible pathogenic species) or a disturbed interaction between bacteria and the host (10). Instead of using more antibiotics to treat dysbiosis there is a need to develop alternative strategies to combat disturbed microbial control. To this end, we can learn from nature itself. For example, the plant root (or "rhizosphere") microbiome of sugar beet contains several bacterial species that suppress the fungal root pathogen Rhizoctonia solani, an economically important fungal pathogen of this crop (11). Likewise, commensal bacteria present on healthy human skin produce antimicrobial molecules that selectively kill skin pathogen Staphylococcus aureus. Interestingly, patients with atopic dermatitis (inflammation of the skin) lacked antimicrobial peptide secreting commensal skin bacteria (12). In this review, we will give an overview of microbial manipulation in fish, plants, and terrestrial animals including humans to uncover conserved mechanisms and learn how we might restore microbial balance increasing the resilience of the host species.
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Affiliation(s)
- Sylvia Brugman
- Cell Biology and Immunology Group, Animal Sciences Group, Wageningen University and Research, Wageningen, Netherlands
| | - Wakako Ikeda-Ohtsubo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Saskia Braber
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
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