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Dostálek T, Rydlová J, Kohout P, Kuťáková E, Kolaříková Z, Frouz J, Münzbergová Z. Beyond the rootzone: Unveiling soil property and biota gradients around plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175032. [PMID: 39059657 DOI: 10.1016/j.scitotenv.2024.175032] [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: 04/15/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Although the effects of plants on soil properties are well known, the effects of distance from plant roots to root-free soil on soil properties and associated soil organisms are much less studied. Previous research on the effects of distance from a plant explored specific soil organisms and properties, however, comparative studies across a wide range of plant-associated organisms and multiple model systems are lacking. We conducted a controlled greenhouse experiment using soil from two contrasting habitats. Within each soil type, we cultivated two plant species, individually and in combination, studying soil organisms and properties in the root centre, the root periphery, and the root-free zones. We showed that the distance from the cultivated plant (representing decreasing amount of plant roots) had a significant impact on the abiotic properties of the soil (pH and available P and N) and also on the composition of the fungal, bacterial, and nematode communities. The specific patterns, however, did not always match our expectations. For example, there was no significant relationship between the abundance of fungal pathogens and the distance from the cultivated plant compared to a strong decrease in the abundance of arbuscular mycorrhizal fungi. Changes in soil chemistry along the distance from the cultivated plant were probably one of the important drivers that affected bacterial communities. The abundance of nematodes also decreased with distance from the cultivated plant, and the rate of their responses reflected the distribution of their food sources. The patterns of soil changes along the gradient from plant to root-free soil were largely similar in two contrasting soil types and four plant species or their mixtures. This suggests that our results can be generalised to other systems and contribute to a better understanding of the mechanisms of soil legacy formation.
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Affiliation(s)
- Tomáš Dostálek
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic; Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague, Czech Republic.
| | - Jana Rydlová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Petr Kohout
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic; Institute of Microbiology, The Czech Academy of Science, Vídeňská 1043, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Eliška Kuťáková
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic; Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague, Czech Republic; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, SE-907 36 Umeå, Sweden
| | - Zuzana Kolaříková
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Jan Frouz
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic; Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague, Czech Republic
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Ortúzar M, Riesco R, Criado M, Alonso MDP, Trujillo ME. Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174277. [PMID: 38944300 DOI: 10.1016/j.scitotenv.2024.174277] [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: 05/07/2024] [Revised: 06/05/2024] [Accepted: 06/23/2024] [Indexed: 07/01/2024]
Abstract
Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.
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Affiliation(s)
- Maite Ortúzar
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
| | - Marco Criado
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - María Del Pilar Alonso
- Area of Edaphology and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, University of Salamanca, 37007 Salamanca, Spain.
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain.
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Adigoun RFR, Durand A, Tchokponhoué DA, Achigan-Dako EG, Aholoukpè HNS, Bokonon-Ganta AH, Benizri E. Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173550. [PMID: 38810760 DOI: 10.1016/j.scitotenv.2024.173550] [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: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.
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Affiliation(s)
- Rabiath F R Adigoun
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France; Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin; Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Alexis Durand
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | - Dèdéou A Tchokponhoué
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Hervé N S Aholoukpè
- Centre de Recherches Agricoles Plantes Pérennes (CRA-PP), Institut National des Recherches Agricoles du Bénin, BP 01 Pobè, Benin
| | - Aimé H Bokonon-Ganta
- Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Emile Benizri
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
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Jiang P, Wang Y, Zhang Y, Fei J, Rong X, Peng J, Yin L, Luo G. Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes. THE NEW PHYTOLOGIST 2024; 243:1506-1521. [PMID: 38874414 DOI: 10.1111/nph.19906] [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: 10/24/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.
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Affiliation(s)
- Pan Jiang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yizhe Wang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
| | - Yuping Zhang
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jiangchi Fei
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Xiangmin Rong
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Jianwei Peng
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
| | - Lichu Yin
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
| | - Gongwen Luo
- College of Resources, Hunan Agricultural University, Changsha, 410128, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Changsha, 410128, China
- Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Changsha, 410128, China
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Jia X, Lin S, Zhang Q, Wang Y, Hong L, Li M, Zhang S, Wang T, Jia M, Luo Y, Ye J, Wang H. The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality. PLANTS (BASEL, SWITZERLAND) 2024; 13:2029. [PMID: 39124147 PMCID: PMC11314174 DOI: 10.3390/plants13152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/11/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024]
Abstract
It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Shuqi Zhang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Tingting Wang
- College of Life Science, Longyan University, Longyan 364012, China
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Yangxin Luo
- College of Life Science, Longyan University, Longyan 364012, China
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.)
- College of Life Science, Longyan University, Longyan 364012, China
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Dietrich M, Panhölzl C, Angel R, Giguere AT, Randi D, Hausmann B, Herbold CW, Pötsch EM, Schaumberger A, Eichorst SA, Woebken D. Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization. Commun Biol 2024; 7:846. [PMID: 38987659 PMCID: PMC11237082 DOI: 10.1038/s42003-024-06522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Fixation of atmospheric N2 by free-living diazotrophs accounts for an important proportion of nitrogen naturally introduced to temperate grasslands. The effect of plants or fertilization on the general microbial community has been extensively studied, yet an understanding of the potential combinatorial effects on the community structure and activity of free-living diazotrophs is lacking. In this study we provide a multilevel assessment of the single and interactive effects of different long-term fertilization treatments, plant species and vicinity to roots on the free-living diazotroph community in relation to the general microbial community in grassland soils. We sequenced the dinitrogenase reductase (nifH) and the 16S rRNA genes of bulk soil and root-associated compartments (rhizosphere soil, rhizoplane and root) of two grass species (Arrhenatherum elatius and Anthoxanthum odoratum) and two herb species (Galium album and Plantago lanceolata) growing in Austrian grassland soils treated with different fertilizers (N, P, NPK) since 1960. Overall, fertilization has the strongest effect on the diazotroph and general microbial community structure, however with vicinity to the root, the plant effect increases. Despite the long-term fertilization, plants strongly influence the diazotroph communities emphasizing the complexity of soil microbial communities' responses to changing nutrient conditions in temperate grasslands.
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Affiliation(s)
- Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christopher Panhölzl
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Andrew T Giguere
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dania Randi
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Erich M Pötsch
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Andreas Schaumberger
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Stephanie A Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Lepinay C, Větrovský T, Chytrý M, Dřevojan P, Fajmon K, Cajthaml T, Kohout P, Baldrian P. Effect of plant communities on bacterial and fungal communities in a Central European grassland. ENVIRONMENTAL MICROBIOME 2024; 19:42. [PMID: 38902816 PMCID: PMC11188233 DOI: 10.1186/s40793-024-00583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Čertoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity. RESULTS High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition. CONCLUSIONS The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.
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Affiliation(s)
- Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Chytrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Pavel Dřevojan
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Karel Fajmon
- Regional Office Protected Landscape Area Bílé Karpaty, Nature Conservation Agency of the Czech Republic, Nádražní 318, 763 26, Luhačovice, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
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Jia X, Lin S, Wang Y, Zhang Q, Jia M, Li M, Chen Y, Cheng P, Hong L, Zhang Y, Ye J, Wang H. Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves. PLANTS (BASEL, SWITZERLAND) 2024; 13:1686. [PMID: 38931118 PMCID: PMC11207862 DOI: 10.3390/plants13121686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.
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Affiliation(s)
- Xiaoli Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qi Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Miao Jia
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan 364012, China
| | - Yiling Chen
- College of Life Science, Longyan University, Longyan 364012, China
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan 364012, China
| | - Lei Hong
- College of Life Science, Longyan University, Longyan 364012, China
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Zhang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Jianghua Ye
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
| | - Haibin Wang
- College of Tea and Food, Wuyi University, Wuyishan 354300, China; (X.J.); (J.Y.)
- College of Life Science, Longyan University, Longyan 364012, China
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Han Y, Teng Y, Wang X, Wen D, Gao P, Yan D, Yang N. Biodegradable PBAT microplastics adversely affect pakchoi (Brassica chinensis L.) growth and the rhizosphere ecology: Focusing on rhizosphere microbial community composition, element metabolic potential, and root exudates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169048. [PMID: 38061654 DOI: 10.1016/j.scitotenv.2023.169048] [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: 07/21/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024]
Abstract
Biodegradable plastics (BPs) have gained increased attention as a promising solution to plastics pollution problem. However, BPs often exhibited limited in situ biodegradation in the soil environment, so they may also release microplastics (MPs) into soils just like conventional non-degradable plastics. Therefore, it is necessary to evaluate the impacts of biodegradable MPs (BMPs) on soil ecosystem. Here, we explored the effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT) MPs and conventional polyethylene (PE) MPs on soil-plant (pakchoi) system at three doses (0.02 %, 0.2 %, and 2 %, w/w). Results showed that PBAT MPs reduced plant growth in a dose-dependent pattern, while PE MPs exhibited no significant phytotoxicity. High-dose PBAT MPs negatively affected the rhizosphere soil nutrient availability, e.g., decreased available phosphorus and available potassium. Metagenomics analysis revealed that PBAT MPs caused more serious interference with the rhizosphere microbial community composition and function than PE MPs. In particular, compared with PE MPs, PBAT MPs induced greater changes in functional potential of carbon, nitrogen, phosphorus, and sulfur cycles, which may lead to alterations in soil biogeochemical processes and ecological functions. Moreover, untargeted metabolomics showed that PBAT MPs and PE MPs differentially affect plant root exudates. Mantel tests, correlation analysis, and partial least squares path model analysis showed that changes in plant growth and root exudates were significantly correlated with soil properties and rhizosphere microbiome driven by the MPs-rhizosphere interactions. This work improves our knowledge of how biodegradable and conventional non-degradable MPs affect plant growth and the rhizosphere ecology, highlighting that BMPs might pose greater threat to soil ecosystems than non-degradable MPs.
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Affiliation(s)
- Yujuan Han
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiao Wang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dan Wen
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Peixin Gao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dong Yan
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ning Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
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10
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Mészárošová L, Kuťáková E, Kohout P, Münzbergová Z, Baldrian P. Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland. ENVIRONMENTAL MICROBIOME 2024; 19:8. [PMID: 38268048 PMCID: PMC10809484 DOI: 10.1186/s40793-024-00550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence of other plants growing nearby is. RESULTS To determine the extent to which a focal host plant influences its soil and root microbiome when growing in a diverse community, we sampled the belowground bacterial and fungal communities of three plant species across a primary successional grassland sequence. The magnitude of the host effect on its belowground microbiome varied among microbial groups, soil and root habitats, and successional stages characterized by different levels of diversity of plant neighbours. Soil microbial communities were most strongly structured by sampling site and showed significant spatial patterns that were partially driven by soil chemistry. The influence of focal plant on soil microbiome was low but tended to increase with succession and increasing plant diversity. In contrast, root communities, particularly bacterial, were strongly structured by the focal plant species. Importantly, we also detected a significant effect of neighbouring plant community composition on bacteria and fungi associating with roots of the focal plants. The host influence on root microbiome varied across the successional grassland sequence and was highest in the most diverse site. CONCLUSIONS Our results show that in a species rich natural grassland, focal plant influence on the belowground microbiome depends on environmental context and is modulated by surrounding plant community. The influence of plant neighbours is particularly pronounced in root communities which may have multiple consequences for plant community productivity and stability, stressing the importance of plant diversity for ecosystem functioning.
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Affiliation(s)
- Lenka Mészárošová
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic.
- University of Chemistry and Technology, Technická 5, Praha 6, 166 28, Czech Republic.
| | - Eliška Kuťáková
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd 17, Umeå, 901 83, Sweden
| | - Petr Kohout
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
| | - Zuzana Münzbergová
- Institute of Botany of the CAS, v. v. i., Zámek 1, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the CAS, v. v. i., Vídeňská 1083, Prague 4, 142 20, Czech Republic
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11
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Dreyling L, Penone C, Schenk NV, Schmitt I, Dal Grande F. Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests. ISME COMMUNICATIONS 2024; 4:ycae012. [PMID: 38500703 PMCID: PMC10945369 DOI: 10.1093/ismeco/ycae012] [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: 12/15/2023] [Revised: 01/18/2024] [Indexed: 03/20/2024]
Abstract
Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
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Affiliation(s)
- Lukas Dreyling
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Department of Biology, University of Padova, Padua 35122, Italy
- National Biodiversity Future Center (NBFC), Palermo 90133, Italy
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12
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Blakney AJC, St-Arnaud M, Hijri M. Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages? ISME COMMUNICATIONS 2024; 4:ycae019. [PMID: 38500702 PMCID: PMC10944699 DOI: 10.1093/ismeco/ycae019] [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: 01/17/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/20/2024]
Abstract
Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- Present address: Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Ontario, M1C 1A4, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
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13
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Song W, Wang Y, Peng B, Yang L, Gao J, Xiao C. Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes. FRONTIERS IN PLANT SCIENCE 2023; 14:1297399. [PMID: 38130486 PMCID: PMC10733484 DOI: 10.3389/fpls.2023.1297399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Introduction Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP). Methods Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing. Results Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms. Conclusion Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.
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Affiliation(s)
- Wenchen Song
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Bo Peng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Linyan Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
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14
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Schober I, Bunk B, Carril G, Freese HM, Ojeda N, Riedel T, Meier-Kolthoff JP, Göker M, Spröer C, Flores-Herrera PA, Nourdin-Galindo G, Gómez F, Cárdenas C, Vásquez-Ponce F, Labra A, Figueroa J, Olivares-Pacheco J, Nübel U, Sikorski J, Marshall SH, Overmann J. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. THE ISME JOURNAL 2023; 17:2247-2258. [PMID: 37853183 PMCID: PMC10689435 DOI: 10.1038/s41396-023-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
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Affiliation(s)
- Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabriela Carril
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nicolás Ojeda
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Patricio A Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Guillermo Nourdin-Galindo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Fernando Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Constanza Cárdenas
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alvaro Labra
- Laboratorio de Patógenos Acuícolas, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio para la Investigación Colaborativa en Resistencia Antimicrobiana (MICROB-R), Santiago, Chile
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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15
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Brunetti AE, Lyra ML, Bauermeister A, Bunk B, Boedeker C, Müsken M, Neto FC, Mendonça JN, Caraballo-Rodríguez AM, Melo WG, Pupo MT, Haddad CF, Cabrera GM, Overmann J, Lopes NP. Host macrocyclic acylcarnitines mediate symbiotic interactions between frogs and their skin microbiome. iScience 2023; 26:108109. [PMID: 37867936 PMCID: PMC10587524 DOI: 10.1016/j.isci.2023.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/23/2023] [Accepted: 09/28/2023] [Indexed: 10/24/2023] Open
Abstract
The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts' health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs' skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs' skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs' multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.
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Affiliation(s)
- Andrés E. Brunetti
- Instituto de Biología Subtropical (IBS, UNaM-CONICET), Posadas, Misiones N3300LQH, Argentina
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Straße 8, 07745 Jena, Germany
| | - Mariana L. Lyra
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi 129188, United Arab Emirates
| | - Anelize Bauermeister
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Christian Boedeker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Niedersachsen, Germany
| | - Fausto Carnevale Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Jacqueline Nakau Mendonça
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Weilan G.P. Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Mônica T. Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Célio F.B. Haddad
- Departamento de Biodiversidade e Centro de Aquicultura da UNESP (CAUNESP), Instituto de Biociências, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900, Brazil
| | - Gabriela M. Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad de Microanálisis y Métodos Físicos aplicados a la Química Orgánica (UMYMFOR), Buenos Aires C1428EGA, Argentina
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Niedersachsen, Germany
| | - Norberto P. Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
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16
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Flocco CG, Methner A, Burkart F, Geppert A, Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol 2023; 14:1197837. [PMID: 37601377 PMCID: PMC10435870 DOI: 10.3389/fmicb.2023.1197837] [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: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
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Affiliation(s)
- Cecilia G. Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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Li L, Liu Y, Xiao Q, Xiao Z, Meng D, Yang Z, Deng W, Yin H, Liu Z. Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota. Front Microbiol 2023; 14:1173748. [PMID: 37485539 PMCID: PMC10361621 DOI: 10.3389/fmicb.2023.1173748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Qinzhi Xiao
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Zhipeng Xiao
- Hengyang Tobacco Company of Hunan Province, Hengyang, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Wenqiao Deng
- Changsha Institute of Agricultural Science, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Zhu CL, Lü HX, Huang YH, Cheng JL, Li H, Li YW, Mo CH, Zhao HM, Xiang L, Cai QY. Rice genotypes and root-associated niches shifted bacterial community in response to pollution of di-(2-ethylhexyl) phthalate (DEHP) for promoting DEHP removal. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131227. [PMID: 37004445 DOI: 10.1016/j.jhazmat.2023.131227] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Organic pollutants influenced root-associated bacterial community. However, the response variation of root-associated bacterial community among different rice genotypes exposed to phthalates (PAEs) and their removal mechanism remains unknown. Here, bacterial community and PAE-degrading genes in root-associated niches were analyzed between low (Fengyousimiao) and high (Hhang) PAE-accumulating rice cultivars exposed to di-(2-ethylhexyl) phthalate (DEHP). DEHP dissipation percentages in rhizosphere of Hhang were significantly higher than those of Fengyousimiao. The bacterial community diversities (including Chao1 and Shannon index) significantly decreased along bulk soil - rhizosphere - rhizoplane - endosphere. The bacterial community structures were shaped mainly by root-associated niches, DEHP pollution and rice genotypes, with significant differences in rhizosphere and rhizoplane between Fengyousimiao and Hhang. Rhizosphere enriched more PAE-degrading bacteria than in bulk soil, and exhibited significantly higher expression of PAE-degrading genes (hydrolase 65, phtab, phtC, pcaF and pcaI) than in bulk soil. Furthermore, rhizosphere of Hhang demonstrated significantly stronger bacterial functions related to xenobiotics biodegradation and higher expression of PAE-degrading genes than those of Fengyousimiao, leading to significantly higher DEHP dissipation percentages in rhizosphere of Hhang. The findings demonstrate that Hhang shaped specific root-associated bacterial community with higher abundances of PAE-degrading bacteria and genes than Fengyousimiao to promote DEHP degradation.
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Affiliation(s)
- Cui-Lan Zhu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui-Xiong Lü
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yu-Hong Huang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ji-Liang Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Acharya SM, Yee MO, Diamond S, Andeer PF, Baig NF, Aladesanmi OT, Northen TR, Banfield JF, Chakraborty R. Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots. ISME COMMUNICATIONS 2023; 3:54. [PMID: 37280433 PMCID: PMC10244434 DOI: 10.1038/s43705-023-00265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
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Affiliation(s)
- Shwetha M Acharya
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mon Oo Yee
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Peter F Andeer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nameera F Baig
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Omolara T Aladesanmi
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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20
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Liu Y, Wang H, Qian X, Gu J, Chen W, Shen X, Tao S, Jiao S, Wei G. Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy. MICROBIOME 2023; 11:109. [PMID: 37211607 DOI: 10.1186/s40168-023-01511-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 03/07/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments. RESULTS Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings. CONCLUSIONS Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xun Qian
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jie Gu
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, 3 Taicheng Road, Yangling, Shaanxi, 712100, People's Republic of China.
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Liu L, Zhu L, Yan R, Yang Y, Adams JM, Liu J. Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162178. [PMID: 36775144 DOI: 10.1016/j.scitotenv.2023.162178] [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: 10/26/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO3--N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Zhu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Rong Yan
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Yang
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Jinshan Liu
- Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture and Rural Affairs/College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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22
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Castellano-Hinojosa A, Albrecht U, Strauss SL. Interactions between rootstocks and compost influence the active rhizosphere bacterial communities in citrus. MICROBIOME 2023; 11:79. [PMID: 37076924 PMCID: PMC10116748 DOI: 10.1186/s40168-023-01524-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizosphere bacterial communities and the availability of root nutrients for plant uptake. Rootstocks are developed to provide resistance to disease or tolerance of abiotic stresses, and compost application is a common practice to also control biotic and abiotic stresses in crops. In this field study, we examined: (i) the effect of four citrus rootstocks and/or compost application on the abundance, diversity, composition, and predicted functionality of active rhizosphere bacterial communities, and (ii) the relationships between active rhizosphere bacterial communities and root nutrient concentrations, with identification of bacterial taxa significantly correlated with changes in root nutrients in the rhizosphere. RESULTS The rootstock genotype determined differences in the diversity of active rhizosphere bacterial communities and also impacted how compost altered the abundance, diversity, composition, and predicted functions of these active communities. Variations in the active bacterial rhizobiome were strongly linked to root nutrient cycling, and these interactions were root-nutrient- and rootstock-specific. Direct positive relationships between enriched taxa in treated soils and specific root nutrients were detected, and potentially important taxa for root nutrient uptake were identified. Significant differences in specific predicted functions were related to soil nutrient cycling (carbon, nitrogen, and tryptophan metabolisms) in the active bacterial rhizobiome among rootstocks, particularly in soils treated with compost. CONCLUSIONS This study illustrates that interactions between citrus rootstocks and compost can influence active rhizosphere bacterial communities, which impact root nutrient concentrations. In particular, the response of the rhizobiome bacterial abundance, diversity, and community composition to compost was determined by the rootstock. Specific bacterial taxa therefore appear to be driving changes in root nutrient concentrations in the active rhizobiome of different citrus rootstocks. Several potential functions of active bacterial rhizobiomes recruited by different citrus rootstocks did not appear to be redundant but rather rootstock-specific. Together, these findings have important agronomic implications as they indicate the potential for agricultural production systems to maximize benefits from rhizobiomes through the choice of selected rootstocks and the application of compost. Video Abstract.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Department of Soil, Water, and Ecosystem Sciences, Southwest Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
| | - Ute Albrecht
- Department of Horticultural Sciences, Southwest Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA
| | - Sarah L Strauss
- Department of Soil, Water, and Ecosystem Sciences, Southwest Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL, 34142, USA.
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Mierzejewska E, Tołoczko W, Urbaniak M. Behind the plant-bacteria system: The role of zucchini and its secondary metabolite in shaping functional microbial diversity in MCPA-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161312. [PMID: 36603641 DOI: 10.1016/j.scitotenv.2022.161312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
MCPA (2-methyl-4-chlorophenoxyacetic acid) contamination is an emerging problem, especially in water reservoirs. The early removal of MCPA residues from soil can prevent its spread to untreated areas. It has been found that the growth of cucurbits and the addition of selected plant secondary metabolites (PSMs) can stimulate MCPA removal from soil. However, the effect of these treatments on soil microbial activity remains poorly studied. Hence, the aim of this research was to evaluate the influence of zucchini (C. pepo cv Atena Polka) and its characteristic PSM: syringic acid (SA) on the functional diversity of soil microorganisms in MCPA-contaminated soil using Biolog® EcoPlates™. It also examines soil physicochemical properties and the growth parameters of zucchini. Microbial activity was enhanced by both zucchini cultivation and SA. All unplanted variants showed significantly lower microbial activity (average well color development, AWCD, ranging from 0.35 to 0.51) than the planted ones (AWCD ranging from 0.77 to 1.16). SA also stimulated microbial activity in the soil: a positive effect was observed from the beginning of the experiment in the unplanted variants, but over a longer time span in the planted variants. SA ameliorated the toxic effect of MCPA on the studied plants, especially in terms of photosynthetic pigment production: the MCPA+SA group demonstrated significantly increased chlorophyll content (401 ± 4.83 μg/g), compared to the MCPA group without SA (338 ± 50.1 μg/g). Our findings demonstrated that zucchini and the amendment of soils with SA, the characteristic PSM of cucurbits, can shape functional diversity in MCPA-contaminated soil. The changes of soil properties caused by the application of both compounds can trigger changes in functional diversity. Hence, both SA and MCPA exert indirect and direct effects on soil microbial activity.
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Affiliation(s)
- Elżbieta Mierzejewska
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.
| | - Wojciech Tołoczko
- Department of Physical Geography, Faculty of Geography, University of Lodz, Prez. Gabriela Narutowicz 88, 90-139 Lodz, Poland
| | - Magdalena Urbaniak
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland; European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90-364 Lodz, Poland; Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology in Prague, Technicka 3, 166 28 Prague, Czech Republic
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24
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Liu L, Ma L, Zhu M, Liu B, Liu X, Shi Y. Rhizosphere microbial community assembly and association networks strongly differ based on vegetation type at a local environment scale. Front Microbiol 2023; 14:1129471. [PMID: 36998396 PMCID: PMC10043216 DOI: 10.3389/fmicb.2023.1129471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
IntroductionRhizosphere microbes perform critical functions for their hosts, and their structure is strongly influenced by vegetation type. Although studies on the effects of vegetation on rhizosphere microbial community structure have been conducted at large and global environment scales, studies at local environment scales would eliminate numerous external factors such as climate and soil type, while highlighting the potential influence of local vegetation type.MethodsHere, we compared rhizosphere microbial communities using 54 samples under three vegetation types (herb, shrubs, and arbors, with bulk soil as the control) at the campus of Henan University. 16S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing.Results and DiscussionRhizosphere bacterial and fungal community structures were influenced considerably by vegetation type. Bacterial alpha diversity under herbs was significantly different from that under arbors and shrubs. The abundance of phyla such as Actinobacteria was extremely higher in bulk soil than in the rhizosphere soils. Herb rhizosphere harbored more unique species than other vegetation type soils. Furthermore, bacterial community assembly in bulk soil was more dominated by deterministic process, whereas the rhizosphere bacterial community assembly was dominated by stochasticity and the construction of fungal communities was all dominated by deterministic processes. In addition, rhizosphere microbial networks were less complex than bulk soil networks, and their keystone species differed based on vegetation type. Notably, bacterial community dissimilarities were strongly correlated with plant phylogenetic distance. Exploring rhizosphere microbial community patterns under different vegetation types could enhance our understanding of the role of rhizosphere microbes in ecosystem function and service provision, as well as basic information that could facilitate plant and microbial diversity conservation at the local environment scale.
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Affiliation(s)
- Luxian Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Liya Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Mengmeng Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Bo Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
- *Correspondence: Yu Shi,
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Microbial Communities of Peaty Permafrost Tundra Soils along the Gradient of Environmental Conditions and Anthropogenic Disturbance in Pechora River Delta in the Eastern European Arctic. DIVERSITY 2023. [DOI: 10.3390/d15020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Microbial communities play crucial roles in the global carbon cycle, particularly in peatland and tundra ecosystems experiencing climate change. The latest IPCC assessments highlight the anthropogenic changes in the Arctic peatlands and their consequences due to global climate change. These disturbances could trigger permafrost degradation and intensification of the biogeochemical processes resulting in greenhouse gas formation. In this study, we describe the variation in diversity and composition of soil microbial communities from shallow peat tundra sites with different anthropogenic loads and applied restoration interventions in the landscape of remnant fragments of terraces in the Pechora River delta, the Russian Arctic, Nenets Autonomous Okrug. The molecular approaches, including quantitative real-time PCR and high-throughput Illumina sequencing of 16S RNA and ITS, were applied to examine the bacterial and fungal communities in the soil samples. Anthropogenic disturbance leads to a significant decrease in the representation of Acidobacteria and Verrucomicrobia, while the proportion and diversity of Proteobacteria increase. Fungal communities in undisturbed sites may be characterized as monodominant, and anthropogenic impact increases the fungal diversity. Only the verrucomicrobial methanotrophs Methyloacifiphilaceae were found in the undisturbed sites, but proteobacterial methanotrophs Methylobacterium-Methylorubrum, as well as different methylotrophs affiliated with Methylophilaceae, and Beijerinckiaceae (Methylorosula), were detected in disturbed sites.
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Araujo ASF, Miranda ARL, Pereira APDA, de Melo WJ, Melo VMM, Ventura SH, Brito Junior ES, de Medeiros EV, Araujo FF, Mendes LW. Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination. CHEMOSPHERE 2023; 313:137417. [PMID: 36460149 DOI: 10.1016/j.chemosphere.2022.137417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/18/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg-1 Cr) and Cr-contaminated soils (∼250 mg kg-1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.
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Affiliation(s)
| | | | | | - Wanderley José de Melo
- Universidade Estadual Paulista (Unesp), Faculdade de Agronomia e Veterinaria, Jaboticabal, Brazil
| | | | | | | | | | | | - Lucas William Mendes
- Centro de Energia Nuclear Na Agricultura, Universidade de Sao Paulo, Piracicaba, SP, Brazil
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Wang Y, Zhang X, Xiao L, Lin H. The in-depth revelation of the mechanism by which a downflow Leersia hexandra Swartz constructed wetland-microbial fuel cell synchronously removes Cr(VI) and p-chlorophenol and generates electricity. ENVIRONMENTAL RESEARCH 2023; 216:114451. [PMID: 36183789 DOI: 10.1016/j.envres.2022.114451] [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: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
The composite pollution by Cr(VI) and p-chlorophenol (4-CP) has high toxicity and harms water safety. However, research on the effective removal of Cr(VI) and 4-CP composite-polluted wastewater (C&P) and efficient synchronous electricity generation with reclaimed resources is limited. In this study, a downflow Leersia hexandra constructed wetland-microbial fuel cell (DLCW-MFC) was builded to treat C&P, as well as wastewater singularly polluted by Cr(VI) (SC) and 4-CP (SP), respectively, to reveal the mechanism by which DLCW-MFC treats C&P and synchronously generates electricity. The results demonstrate that the cathode layer had a stronger removal effect on pollutants than the middle layer and anode zone layer. Moreover, SC and SP had stronger pollutant removal effects than C&P. Cr(VI) had more competitive with electrons than 4-CP, and they had a synergistic effect on efficient electricity generation. The L.hexandra in SC and SP had a better growth state and lower Cr enrichment concentration than that in C&P. Cr existed in the DLCW-MFC mainly in the form of Cr(III). Gas chromatography-mass spectrometry was used to investigate the degradation pathway of 4-CP in C&P, and indicated that Phenol, 2,4-bis(1,1-dimethylethyl)- and benzoic acid compounds were the main intermediates formed at the cathode, and further mineralized to form medium-long-chain organic compounds to form CO2. The microbial community distribution results revealed that Simplicispira, Cloacibacterium, and Rhizobium are associated with Cr(VI) removal and 4-CP degradation, and were found to be rich in the cathode of C&P. The anode of C&P was found to have more Acinetobacter (1.34%) and Spirochaeta (4.83%) than SC and SP, and the total relative abundance of electricigens at the anode of C&P (7.46%) was higher than that at the anodes of SC and SP. This study can provide a theoretical foundation for the DLCW-MFC to treat heavy metal and chlorophenol composite-polluted wastewater and synchronously generate electricity.
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Affiliation(s)
- Yian Wang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
| | - Xuehong Zhang
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
| | - Ling Xiao
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
| | - Hua Lin
- College of Environmental Science and Engineering, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Areas, Guilin University of Technology, 319 Yanshan Street, Guilin, 541000, China.
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Sun X, Zhang X, Zhang G, Miao Y, Zeng T, Zhang M, Zhang H, Zhang L, Huang L. Environmental Response to Root Secondary Metabolite Accumulation in Paeonia lactiflora: Insights from Rhizosphere Metabolism and Root-Associated Microbial Communities. Microbiol Spectr 2022; 10:e0280022. [PMID: 36318022 PMCID: PMC9769548 DOI: 10.1128/spectrum.02800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Paeonia lactiflora is a commercial crop with horticultural and medicinal value. Although interactions between plants and microbes are increasingly evident and considered to be drivers of ecosystem service, the regulatory relationship between microbial communities and the growth and root metabolites of P. lactiflora is less well known. Here, soil metabolomics indicated that carbohydrates and organic acids were enriched in the rhizosphere (RS) with higher diversity. Moreover, the variation of root-associated microbiotas between the bulk soil (BS) and the RS of P. lactiflora was investigated via 16S rRNA and internally transcribed spacer (ITS) amplicon sequencing. The RS displayed a low-diversity community dominated by copiotrophs, whereas the BS showed an oligotroph-dominated, high-diversity community. Hierarchical partitioning showed that cation exchange capacity (CEC) was the main factor affecting microbial community diversity. The null model and the dispersion niche continuum index (DNCI) suggested that stochastic processes (dispersal limitation) dominated the community assembly of both the RS and BS. The bacterial-fungal interkingdom networks illustrated that the RS possessed more complex and stable co-occurrence patterns. Meanwhile, positive link numbers and positive cohesion results revealed more cooperative relationships among microbes in the RS. Additionally, random forest model prediction and two partial least-squares path model (PLS-PM) analyses showed that the P. lactiflora root secondary metabolites were comprehensively impacted by soil water content (SWC), mean annual precipitation (MAP), pH (abiotic), and Alternaria (biotic). Collectively, this study provides a theoretical basis for screening the microbiome associated with the active components of P. lactiflora. IMPORTANCE Determining the taxonomic and functional components of the rhizosphere microbiome, as well as how they differ from those of the bulk soil microbiome, is critical for manipulating them to improve plant growth performance and increase agricultural yields. Soil metabolic profiles can help enhance the understanding of rhizosphere exudates. Here, we explored the regulatory relationship across environmental variables (root-associated microbial communities and soil metabolism) in the accumulation of secondary metabolites of P. lactiflora. Overall, this work improves our knowledge of how the rhizosphere affects soil and microbial communities. These observations improve the understanding of plant-microbiome interactions and introduce new horizons for synthetic community investigations as well as the creation of microbiome technologies for agricultural sustainability.
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Affiliation(s)
- Xiao Sun
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xinke Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guoshuai Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yujing Miao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tiexin Zeng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Min Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Huihui Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Zhang
- College of Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, China
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Shao M, Zhang S, Niu B, Pei Y, Song S, Lei T, Yun H. Soil texture influences soil bacterial biomass in the permafrost-affected alpine desert of the Tibetan plateau. Front Microbiol 2022; 13:1007194. [PMID: 36578569 PMCID: PMC9791195 DOI: 10.3389/fmicb.2022.1007194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022] Open
Abstract
Under warm climate conditions, permafrost thawing results in the substantial release of carbon (C) into the atmosphere and potentially triggers strong positive feedback to global warming. Soil microorganisms play an important role in decomposing organic C in permafrost, thus potentially regulating the ecosystem C balance in permafrost-affected regions. Soil microbial community and biomass are mainly affected by soil organic carbon (SOC) content and soil texture. Most studies have focused on acidic permafrost soil (pH < 7), whereas few examined alkaline permafrost-affected soil (pH > 7). In this study, we analyzed soil microbial communities and biomass in the alpine desert and steppe on the Tibetan plateau, where the soil pH values were approximately 8.7 ± 0.2 and 8.5 ± 0.1, respectively. Our results revealed that microbial biomass was significantly associated with mean grain size (MGS) and SOC content in alkaline permafrost-affected soils (p < 0.05). In particular, bacterial and fungal biomasses were affected by SOC content in the alpine steppe, whereas bacterial and fungal biomasses were mainly affected by MGS and SOC content, respectively, in the alpine desert. Combined with the results of the structural equation model, those findings suggest that SOC content affects soil texture under high pH-value (pH 8-9) and that soil microbial biomass is indirectly affected. Soils in the alpine steppe and desert are dominated by plagioclase, which provides colonization sites for bacterial communities. This study aimed to highlight the importance of soil texture in managing soil microbial biomass and demonstrate the differential impacts of soil texture on fungal and bacterial communities in alkaline permafrost-affected regions.
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Affiliation(s)
- Ming Shao
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Shengyin Zhang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Bin Niu
- University of Chinese Academy of Sciences, Beijing, China,Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Yu Pei
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Sen Song
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China,University of Chinese Academy of Sciences, Beijing, China
| | - Tianzhu Lei
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China,*Correspondence: Tianzhu Lei, ; Hanbo Yun,
| | - Hanbo Yun
- State Key Laboratory of Frozen Soil Engineering, BeiLu'He Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China,Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark,Department of Earth, Atmospheric and Planetary Sciences, Purdue University, West Lafayette, IN, United States,*Correspondence: Tianzhu Lei, ; Hanbo Yun,
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Zahid MS, Hussain M, Song Y, Li J, Guo D, Li X, Song S, Wang L, Xu W, Wang S. Root-Zone Restriction Regulates Soil Factors and Bacterial Community Assembly of Grapevine. Int J Mol Sci 2022; 23:ijms232415628. [PMID: 36555269 PMCID: PMC9778885 DOI: 10.3390/ijms232415628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Root-zone restriction induces physiological stress on roots, thus limiting the vegetative and enhancing reproductive development, which promotes fruit quality and growth. Numerous bacterial-related growth-promoting, stress-mitigating, and disease-prevention activities have been described, but none in root-restricted cultivation. The study aimed to understand the activities of grapevine bacterial communities and plant-bacterial relationships to improve fruit quality. We used High-throughput sequencing, edaphic soil factors, and network analysis to explore the impact of restricted cultivation on the diversity, composition and network structure of bacterial communities of rhizosphere soil, roots, leaves, flowers and berries. The bacterial richness, diversity, and networking were indeed regulated by root-zone restriction at all phenological stages, with a peak at the veraison stage, yielding superior fruit quality compared to control plants. Moreover, it also handled the nutrient availability in treated plants, such as available nitrogen (AN) was 3.5, 5.7 and 0.9 folds scarcer at full bloom, veraison and maturity stages, respectively, compared to control plants. Biochemical indicators of the berry have proved that high-quality berry is yielded in association with the bacteria. Cyanobacteria were most abundant in the phyllosphere, Proteobacteria in the rhizosphere, and Firmicutes and Bacteroidetes in the endosphere. These bacterial phyla were most correlated and influenced by different soil factors in control and treated plants. Our findings are a comprehensive approach to the implications of root-zone restriction on the bacterial microbiota, which will assist in directing a more focused procedure to uncover the precise mechanism, which is still undiscovered.
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Affiliation(s)
- Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100045, China
| | - Yue Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiajia Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dinghan Guo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangyi Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence:
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Yang YZ, Luo MX, Yan HX, Gao RH, Chang JT, Chao CT, Liao PC. Physicochemical and Biotic Changes and the Phylogenetic Evenness of Microbial Community in Soil Subjected to Phytoreclamation. MICROBIAL ECOLOGY 2022; 84:1182-1194. [PMID: 34741194 DOI: 10.1007/s00248-021-01890-w] [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: 06/11/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Phytoreclamation is the intervention of plants to improve degraded soil quality, changing soil biotic and abiotic properties. Many studies have focused on microbial composition and bioactivity, but few explored the changes in phylogenetic assemblages of soil microbiota after phytoreclamation. This study compared microbiomes of bare land to those of planted soils and investigated how the rhizosphere environment affects microbial assemblages from monocot Poa pratensis and eudicot Dianthus plumarius plantings using 16S rRNA metabarcoding. The results showed that the biotic susceptibility of soil to the rhizosphere environment was higher than that of the abiotic. A noticeable change was in some soil physicochemical properties like Na, P, Zn, Cu, C, and sand-to-silt proportion before and after phytoreclamation, but not between the rhizosphere and bulk soil of plantings. Contrastingly, microbial composition and diversity were significantly affected by both turfing and rhizosphere effects and were more susceptible to differences in turfing or not than in planting species. In the turfgrass, the microbiome differences between plants were greater in the rhizosphere than in the surrounding bulk soil, indicating the proximal influence of root exudates. We also found that the main abiotic factors that influenced microbial composition were Na, Zn, NOx, N, and S; as for the phylogenetic assemblages, were by K levels and the increase of silt. Turfgrass decomposes soil aggregates and changes the physicochemical properties, thereby evens the phylogenetic clustering of the soil microbial community. We demonstrated that the deterministic process affects the microbial assemblage and acts as a selective agent of the soil microbiota in fundamental and realized niches. Phytoreclamation may lead to abiotic soil changes that reallocate resources to microbes. This could affect the phylogeny of the microbial assemblages and increase microbial richness.
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Affiliation(s)
- Yong-Zhi Yang
- College of Forestry, Inner Mongolia Agricultural University, Huhhot, 010019, China
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Hai-Xia Yan
- Inner Mongolia Autonomous Region Hohhot Ecological Environment Monitoring Station, Hohhot, 010030, China
| | - Run-Hong Gao
- College of Forestry, Inner Mongolia Agricultural University, Huhhot, 010019, China.
| | - Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, 116, Taiwan.
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Faggioli VS, Covacevich F, Grilli G, Lorenzon C, Aimetta B, Sagadin M, Langarica-Fuentes A, Cabello MN. Environmental response of arbuscular mycorrhizal fungi under soybean cultivation at a regional scale. MYCORRHIZA 2022; 32:425-438. [PMID: 36207539 DOI: 10.1007/s00572-022-01093-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Climate change, the shortage of fertilizers and reduced land for cultivation have drawn attention to the potential aid provided by soil-borne organisms. Arbuscular mycorrhizal fungi (AMF) offer a wide range of ecosystem benefits and hence, understanding the mechanisms that control AMF occurrence and maintenance is essential for resilient crop production. We conducted a survey of 123 soybean fields located across a 75,000-km2 area of Argentina to explore AMF community composition and to quantify the impact of soil, climate, and geographical distance on these key soil organisms. First, based upon morphological identification of spores, we compiled a list of the AMF species found in the studied area and identified Acaulospora scrobiculata and Glomus fuegianum as the most frequent species. G. fuegianum abundance was negatively correlated with precipitation seasonality and positively correlated with mean annual precipitation as well as mycorrhizal colonisation of soybean roots. Second, we observed that species richness was negatively correlated with soil P availability (Bray I), clay content and mean annual precipitation. Finally, based on partitioning variation analysis, we found that AMF exhibited spatial patterning at a broad scale. Therefore, we infer that geographical distance was positively associated with spore community composition heterogeneity across the region. Nevertheless, we highlight the importance of precipitation sensitivity of frequent species, overall AMF richness and community composition, revealing a crucial challenge to forthcoming agriculture considering an expected change in global climate patterns.
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Affiliation(s)
- Valeria Soledad Faggioli
- Instituto Nacional de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km 36, 2580, Marcos Juárez, Córdoba, Argentina.
| | - Fernanda Covacevich
- Instituto de Investigaciones en Biodiversidad Y Biotecnología (CONICET)-Fundación Para Las Investigaciones Biológicas Aplicadas, Ruta 226 km 73.5, 7620, Balcarce, Argentina
| | - Gabriel Grilli
- FCEFyN (CONICET, Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba), Vélez Sarsfield 1611, CC 495, Córdoba, Argentina
| | - Claudio Lorenzon
- Instituto Nacional de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km 36, 2580, Marcos Juárez, Córdoba, Argentina
| | - Bethania Aimetta
- Instituto Nacional de Tecnología Agropecuaria, EEA Marcos Juárez, Ruta 12 km 36, 2580, Marcos Juárez, Córdoba, Argentina
| | - Monica Sagadin
- Centro de Investigación Agropecuaria (CIAP), Instituto Nacional de Tecnología Agropecuaria, Instituto de Fisiología Y Recursos Genéticos Vegetales (IFRGV), CONICET, Camino 60 Cuadras km, 51/2 C.P. 5119, Córdoba, Argentina
| | - Adrián Langarica-Fuentes
- Department of Geosciences, Eberhard-Karls-University Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
| | - Marta Noemí Cabello
- Instituto Spegazzini (Facultad de Ciencias Naturales Y Museo, UNLP), Comisión de Investigaciones Científicas de La Prov. de Buenos Aires (CICPBA), Av 53 # 477, 1900, La Plata, Argentina
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Tan X, Xie H, Yu J, Wang Y, Xu J, Xu P, Ma B. Host genetic determinants drive compartment-specific assembly of tea plant microbiomes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2174-2186. [PMID: 35876474 PMCID: PMC9616527 DOI: 10.1111/pbi.13897] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Diverse host factors drive microbial variation in plant-associated environments, whereas their genetic mechanisms remain largely unexplored. To address this, we coupled the analyses of plant genetics and microbiomes in this study. Using 100 tea plant (Camellia sinensis) cultivars, the microbiomes of rhizosphere, root endosphere and phyllosphere showed clear compartment-specific assembly, whereas the subpopulation differentiation of tea cultivars exhibited small effects on microbial variation in each compartment. Through microbiome genome-wide association studies, we examined the interactions between tea genetic loci and microbial variation. Notably, genes related to the cell wall and carbon catabolism were heavily linked to root endosphere microbial composition, whereas genes related to the metabolism of metal ions and small organic molecules were overrepresented in association with rhizosphere microbial composition. Moreover, a set of tea genetic variants, including the cytoskeleton-related formin homology interacting protein 1 gene, were strongly associated with the β-diversity of phyllosphere microbiomes, implying their interactions with the overall structure of microbial communities. Our results create a catalogue of tea genetic determinants interacting with microbiomes and reveal the compartment-specific microbiome assembly driven by host genetics.
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Affiliation(s)
- Xiangfeng Tan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Hengtong Xie
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jingwen Yu
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Yuefei Wang
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
| | - Ping Xu
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
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Karpouzas DG, Vryzas Z, Martin-Laurent F. Pesticide soil microbial toxicity: setting the scene for a new pesticide risk assessment for soil microorganisms (IUPAC Technical Report). PURE APPL CHEM 2022. [DOI: 10.1515/pac-2022-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.
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Affiliation(s)
- Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology , Laboratory of Plant and Environmental Biotechnology, University of Thessaly , Viopolis 41500 , Larissa , Greece
| | - Zisis Vryzas
- Department of Agricultural Development , Democritus University of Thrace , Orestiada , Greece
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Luo J, Gu S, Guo X, Liu Y, Tao Q, Zhao HP, Liang Y, Banerjee S, Li T. Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12975-12987. [PMID: 36067360 DOI: 10.1021/acs.est.1c08832] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Persistent microbial symbioses can confer greater fitness to their host under unfavorable conditions, but manipulating such beneficial interactions necessitates a mechanistic understanding of the consistently important microbiomes for the plant. Here, we examined the phylogenetic profiles and plant-beneficial traits of the core microbiota that consistently inhabits the rhizosphere of four divergent Cd hyperaccumulators and an accumulator. We evidenced the existence of a conserved core rhizosphere microbiota in each plant distinct from that in the non-hyperaccumulating plant. Members of Burkholderiaceae and Sphingomonas were the shared cores across hyperaccumulators and accumulators. Several keystone taxa in the rhizosphere networks were part of the core microbiota, the abundance of which was an important predictor of plant Cd accumulation. Furthermore, an inoculation experiment with synthetic communities comprising isolates belonging to the shared cores indicated that core microorganisms could facilitate plant growth and metal tolerance. Using RNA-based stable isotope probing, we discovered that abundant core taxa overlapped with active rhizobacteria utilizing root exudates, implying that the core rhizosphere microbiota assimilating plant-derived carbon may provide benefits to plant growth and host phenotype such as Cd accumulation. Our study suggests common principles underpinning hyperaccumulator-microbiome interactions, where plants consistently interact with a core set of microbes contributing to host fitness and plant performance. These findings lay the foundation for harnessing the persistent root microbiomes to accelerate the restoration of metal-disturbed soils.
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Affiliation(s)
- Jipeng Luo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shaohua Gu
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, 100091 Beijing, China
| | - Xinyu Guo
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuankun Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - He-Ping Zhao
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota 58108-6050, United States
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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Guajardo-Leiva S, Alarcón J, Gutzwiller F, Gallardo-Cerda J, Acuña-Rodríguez IS, Molina-Montenegro M, Crandall KA, Pérez-Losada M, Castro-Nallar E. Source and acquisition of rhizosphere microbes in Antarctic vascular plants. Front Microbiol 2022; 13:916210. [PMID: 36160194 PMCID: PMC9493328 DOI: 10.3389/fmicb.2022.916210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Florence Gutzwiller
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Gallardo-Cerda
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - Marco Molina-Montenegro
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigación en Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
- Division of Emergency Medicine, Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Children’s National Hospital, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- *Correspondence: Eduardo Castro-Nallar,
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Wang B, Huang S, Li Z, Zhou Z, Huang J, Yu H, Peng T, Song Y, Na X. Factors driving the assembly of prokaryotic communities in bulk soil and rhizosphere of Torreya grandis along a 900-year age gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155573. [PMID: 35504392 DOI: 10.1016/j.scitotenv.2022.155573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/24/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Excessive nutrient inputs imperil the stability of forest ecosystems via modifying the interactions among soil properties, microbes, and plants, particularly in forests composed of cash crops that are under intensive disturbances of agricultural activities, such as Torreya grandis. Understanding the potential drivers of soil microbial community helps scientists develop effective strategies for balancing the protection and productivity of the ancient Torreya forest. Here, we assayed the link between plant and soil parameters and prokaryote communities in bulk soil and T. grandis rhizosphere in 900-year-old stands by detecting plant and soil properties in two independent sites in southeastern China. Our results showed no apparent influence of stand age on the compositions of prokaryote communities in bulk soil and T. grandis rhizosphere. In contrast, soil abiotic factors (i.e., soil pH) overwhelm plant characteristics (i.e., height, plant tissue carbon, nitrogen, and phosphorus content) and contribute most to the shift in prokaryote communities in bulk soil and T. grandis rhizosphere. Soil pH leads to an increase in microbiota alpha diversity in both compartments. With the help of a random forest, we found a critical transition point of pH (pH = 4.9) for the dominance of acidic and near-neutral bacterial groups. Co-occurrence network analysis further revealed a substantially simplified network in plots with a pH of <4.9 versus samples with a pH of ≥4.9, indicating that soil acidification induces biodiversity loss and disrupts potential interactions among soil microbes. Our findings provide empirical evidence that soil abiotic properties nearly completely offset the roles of host plants in the assembly and potential interactions of rhizosphere microorganisms. Hence, reduction in inorganic fertilization and proper liming protocols should be seriously considered by local farmers to protect ancient Torreya forests.
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Affiliation(s)
- Bin Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Shengyi Huang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Zhengcai Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Zhichun Zhou
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China
| | - Juying Huang
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Hailong Yu
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Tong Peng
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
| | - Yanfang Song
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
| | - Xiaofan Na
- School of Life Science, Lanzhou University, Lanzhou 730000, China; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China.
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Dastogeer KMG, Yasuda M, Okazaki S. Microbiome and pathobiome analyses reveal changes in community structure by foliar pathogen infection in rice. Front Microbiol 2022; 13:949152. [PMID: 35983324 PMCID: PMC9379101 DOI: 10.3389/fmicb.2022.949152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Increasing evidence suggests that the plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogens, but microbiome assembly due to foliar pathogen infection and ecological mechanisms that govern microbiome assembly and functions in the diseased host are not fully understood. To provide a comprehensive view of the rice-associated microbiome, we compared bacterial and fungal communities of healthy rice and those infected with Magnaporthe oryzae, the causal agent of blast disease. We found that the soil had a greater diversity of bacterial and fungal communities than plant endospheric communities. There was no significant dysbiosis of bacterial and fungal microbiome diversity due to disease, but it caused a substantial alteration of bacterial community structure in the root and rhizosphere compartments. The pathobiome analysis showed that the microbiome community structure of leaf and grain tissues was changed markedly at the pathogen infection site, although the alpha diversity did not change. Correspondingly, the relative abundances of some bacteria and fungi were clearly altered in symptomatic tissues. We noted an increase in Rhizobium bacteria and a decline of Tylospora, Clohesyomyces, and Penicillium fungi in the symptomatic leaf and grain tissues from both locations. According to the inferred microbial network, several direct interactions between M. oryzae and other microbes were identified. The majority of edges in the interaction network were positive in diseased samples; contrastingly, the number of edges was much lower in the healthy samples. With source tracking analysis, we observed a sharp contrast in the source of root endosphere bacteria due to Magnaporthe infection. Whereas the majority (71%) of healthy root bacteria could be tracked from the soil, only a very small portion (17%) could be tracked from the soil for diseased samples. These results advanced our understanding and provided potential ideas and a theoretical basis for studying pathobiome and exploiting the microbiome for sustainable agriculture.
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Affiliation(s)
- Khondoker M. G. Dastogeer
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- *Correspondence: Khondoker M. G. Dastogeer
| | - Michiko Yasuda
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Shin Okazaki
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Kaushal M, Kolombia Y, Alakonya AE, Kuate AF, Ortega-Beltran A, Amah D, Masso C. Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa. MICROBIAL ECOLOGY 2022; 84:580-593. [PMID: 34585290 PMCID: PMC9436888 DOI: 10.1007/s00248-021-01873-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.
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Affiliation(s)
- Manoj Kaushal
- International Institute of Tropical Agriculture (IITA), Mikocheni B, Dar es Salaam, Tanzania.
| | - Yao Kolombia
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, 200001, Nigeria
| | - Amos Emitati Alakonya
- International Maize and Wheat Improvement Center (CIMMYT), México-Veracruz, El Batán Km. 45, 56237, Texcoco, Mexico
| | - Apollin Fotso Kuate
- International Institute of Tropical Agriculture (IITA), BP 2008 (Messa), Yaounde, Cameroon
| | - Alejandro Ortega-Beltran
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, 200001, Nigeria
| | - Delphine Amah
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, 200001, Nigeria
| | - Cargele Masso
- International Institute of Tropical Agriculture (IITA), BP 2008 (Messa), Yaounde, Cameroon
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Li P, Liu J, Saleem M, Li G, Luan L, Wu M, Li Z. Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems. MICROBIOME 2022; 10:108. [PMID: 35841078 PMCID: PMC9287909 DOI: 10.1186/s40168-022-01287-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with 13CO2, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP). RESULTS Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem. CONCLUSIONS Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.
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Affiliation(s)
- Pengfa Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jia Liu
- Soil and Fertilizer & Resources and Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104 USA
| | - Guilong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 China
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Upadhyay SK, Srivastava AK, Rajput VD, Chauhan PK, Bhojiya AA, Jain D, Chaubey G, Dwivedi P, Sharma B, Minkina T. Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production. Front Microbiol 2022; 13:916488. [PMID: 35910633 PMCID: PMC9329127 DOI: 10.3389/fmicb.2022.916488] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022] Open
Abstract
The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.
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Affiliation(s)
- Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | | | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Prabhat K. Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - Ali Asger Bhojiya
- Department of Agriculture and Veterinary Sciences, Mewar University, Chittorgarh, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Bechan Sharma
- Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad, India
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
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Kanukollu S, Remus R, Rücker AM, Buchen-Tschiskale C, Hoffmann M, Kolb S. Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species. ENVIRONMENTAL MICROBIOME 2022; 17:35. [PMID: 35794633 PMCID: PMC9258066 DOI: 10.1186/s40793-022-00428-y] [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: 08/06/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking. RESULTS We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of 13C derived from 13C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, 13C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant 13C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). 14C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere. CONCLUSIONS Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.
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Affiliation(s)
- Saranya Kanukollu
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Rainer Remus
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Present Address: Johann Heinrich von Thünen-Institut, Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Mathias Hoffmann
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Medina-Paz F, Herrera-Estrella L, Heil M. All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean ( Phaseolus vulgaris) in Its Centre of Domestication. PLANTS (BASEL, SWITZERLAND) 2022; 11:1631. [PMID: 35807585 PMCID: PMC9269403 DOI: 10.3390/plants11131631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.
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Affiliation(s)
- Francisco Medina-Paz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato 36824, GTO, Mexico; or
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79424, USA
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
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Blakney AJC, Bainard LD, St-Arnaud M, Hijri M. Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought. Environ Microbiol 2022; 24:3529-3548. [PMID: 35590462 DOI: 10.1111/1462-2920.16046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Luke D Bainard
- Agassiz Research and Development Centre, AgricuSlture and Agri-Food Canada, Agassiz, BC, V0M 1A2, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, QC, Canada.,African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco
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Zhang S, Liu X, Zhou L, Deng L, Zhao W, Liu Y, Ding W. Alleviating Soil Acidification Could Increase Disease Suppression of Bacterial Wilt by Recruiting Potentially Beneficial Rhizobacteria. Microbiol Spectr 2022; 10:e0233321. [PMID: 35254141 PMCID: PMC9045175 DOI: 10.1128/spectrum.02333-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/11/2022] [Indexed: 01/04/2023] Open
Abstract
Bacterial wilt is accompanied by microbial communities shift and soil acidification. However, the relationship between the changes of bacterial communities and bacterial wilt under the influence of different acidification levels has not been fully elucidated. Here, we analyzed the abundance of Ralstonia solanacearum, rhizosphere bacterial communities and carbon metabolism at differently acidic levels (pH 6.45, pH 5.60, pH 5.35, pH 4.90 and pH 4.45) and soil amendment treatment (CaO). The results indicated that both the abundance of R. solanacearum and the incidence of bacterial wilt showed a significant trend of first increasing and then decreasing with the increase of soil pH. The Firmicutes phylum and potentially beneficial genera Bacillus, Paenibacillus, Flavobacterium and Pseudomonas were significantly enriched at pH 6.45. The metabolic ability in response to the l-arginine and 4-hydroxybenzoic acid was significantly increased at pH 6.45. After using CaO to increase the pH of diseased soil from 5.45 to 6.05, the abundance of R. solanacearum and the incidence of bacterial wilt were significantly reduced, the Firmicutes and potentially beneficial genera Bacillus and Pseudomonas were significantly enriched. Overall, alleviating soil acidification to a slightly acidic level (pH 6.0-6.5) could suppress bacterial wilt by suppressing the growth of R. solanacearum and enriching the rhizosphere potentially beneficial bacteria, and further emphasized the importance of increasing soil pH in biological control of bacterial wilt. IMPORTANCE The rhizosphere microbiota and soil acidification have been shown to have impacts on bacterial wilt. However, the influence of different acidification levels on the rhizosphere communities and bacterial wilt has not been fully studied. In this study, the potentially beneficial bacteria (Bacillus and Pseudomonas) were significantly enriched in the slightly acidic soil (pH 6.45), leading to the increase of the metabolism of 4-hydroxybenzoic acid and the decrease of pathogenic R. solanacearum, thereby alleviating the occurrence of bacterial wilt. The changes of potentially beneficial bacteria and pathogenic R. solanacearum in strongly acidic soil (pH 5.35) with the highest incidence of bacterial wilt were just the opposite. These findings help clarify the mechanisms by which soil bacteria exert influence on bacterial wilt outbreak under different soil acidification levels.
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Affiliation(s)
- Shuting Zhang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xiaojiao Liu
- College of Plant Protection, Southwest University, Chongqing, China
| | - Lihua Zhou
- College of Plant Protection, Southwest University, Chongqing, China
| | - Liyuan Deng
- College of Plant Protection, Southwest University, Chongqing, China
| | - Wenzhuo Zhao
- College of Plant Protection, Southwest University, Chongqing, China
| | - Ying Liu
- College of Plant Protection, Southwest University, Chongqing, China
| | - Wei Ding
- College of Plant Protection, Southwest University, Chongqing, China
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Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere. Sci Rep 2022; 12:3472. [PMID: 35236879 PMCID: PMC8891268 DOI: 10.1038/s41598-022-06860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/08/2022] [Indexed: 12/31/2022] Open
Abstract
Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.
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Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 2022; 20:415-430. [DOI: 10.1038/s41579-022-00695-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/18/2022]
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Huber KJ, Vieira S, Sikorski J, Wüst PK, Fösel BU, Gröngröft A, Overmann J. Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils. Front Microbiol 2022; 13:750456. [PMID: 35222321 PMCID: PMC8874233 DOI: 10.3389/fmicb.2022.750456] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the β-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.
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Affiliation(s)
- Katharina J. Huber
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Selma Vieira
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K. Wüst
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Bärbel U. Fösel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Gröngröft
- Department of Geosciences, Institute of Soil Science, University of Hamburg, Hamburg, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
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Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fösel BU, Friedrich MW, Göker M, Hölzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schöning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J. The Evolution of Ecological Diversity in Acidobacteria. Front Microbiol 2022; 13:715637. [PMID: 35185839 PMCID: PMC8847707 DOI: 10.3389/fmicb.2022.715637] [Citation(s) in RCA: 3] [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: 05/27/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.
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Affiliation(s)
- Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vanessa Baumgartner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Runa S. Boeddinghaus
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Boyke Bunk
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Bärbel U. Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Markus Göker
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group, Institute of Landscape Ecology, University Münster, Münster, Germany
| | - Sixing Huang
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katharina J. Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ellen Kandeler
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | | | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, University of GieBen, GieBen, Germany
| | - Sven Marhan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Kathleen M. Regan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - João F. Matias Rodrigues
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Barbara Schmitt
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Emily F. Solly
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
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Herms CH, Hennessy RC, Bak F, Dresbøll DB, Nicolaisen MH. Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions. Environ Microbiol 2022; 24:3264-3272. [PMID: 35106901 PMCID: PMC9543362 DOI: 10.1111/1462-2920.15926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high‐yielding crop cultivars.
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Affiliation(s)
- Courtney Horn Herms
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Rosanna Catherine Hennessy
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Frederik Bak
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Dorte Bodin Dresbøll
- Section for Crop Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 30, Taastrup, 2630, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
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