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Anderson MD, Taylor DL, Olson K, Ruess RW. Composition of soil Frankia assemblages across ecological drivers parallels that of nodule assemblages in Alnus incana ssp. tenuifolia in interior Alaska. Ecol Evol 2024; 14:e11458. [PMID: 38979008 PMCID: PMC11229434 DOI: 10.1002/ece3.11458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 07/10/2024] Open
Abstract
In root nodule symbioses (RNS) between nitrogen (N)-fixing bacteria and plants, bacterial symbionts cycle between nodule-inhabiting and soil-inhabiting niches that exert differential selection pressures on bacterial traits. Little is known about how the resulting evolutionary tension between host plants and symbiotic bacteria structures naturally occurring bacterial assemblages in soils. We used DNA cloning to examine soil-dwelling assemblages of the actinorhizal symbiont Frankia in sites with long-term stable assemblages in Alnus incana ssp. tenuifolia nodules. We compared: (1) phylogenetic diversity of Frankia in soil versus nodules, (2) change in Frankia assemblages in soil versus nodules in response to environmental variation: both across succession, and in response to long-term fertilization with N and phosphorus, and (3) soil assemblages in the presence and absence of host plants. Phylogenetic diversity was much greater in soil-dwelling than nodule-dwelling assemblages and fell into two large clades not previously observed. The presence of host plants was associated with enhanced representation of genotypes specific to A. tenuifolia, and decreased representation of genotypes specific to a second Alnus species. The relative proportion of symbiotic sequence groups across a primary chronosequence was similar in both soil and nodule assemblages. Contrary to expectations, both N and P enhanced symbiotic genotypes relative to non-symbiotic ones. Our results provide a rare set of field observations against which predictions from theoretical and experimental work in the evolutionary ecology of RNS can be compared.
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Affiliation(s)
- M. D. Anderson
- Biology DepartmentMacalester CollegeSaint PaulMinnesotaUSA
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - D. L. Taylor
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - K. Olson
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
| | - R. W. Ruess
- Institute of Arctic BiologyUniversity of AlaskaFairbanksAlaskaUSA
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Liu H, Ni B, Duan A, He C, Zhang J. High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule. FRONTIERS IN PLANT SCIENCE 2024; 15:1301447. [PMID: 38450407 PMCID: PMC10915256 DOI: 10.3389/fpls.2024.1301447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Introduction Actinorhizal symbioses are gaining attention due to the importance of symbiotic nitrogen fixation in sustainable agriculture. Sea buckthorn (Hippophae L.) is an important actinorhizal plant, yet research on the microbial community and nitrogen cycling in its nodules is limited. In addition, the influence of environmental differences on the microbial community of sea buckthorn nodules and whether there is a single nitrogen-fixing actinomycete species in the nodules are still unknown. Methods We investigated the diversity, community composition, network associations and nitrogen cycling pathways of the microbial communities in the root nodule (RN), nodule surface soil (NS), and bulk soil (BS) of Mongolian sea buckthorn distributed under three distinct ecological conditions in northern China using 16S rRNA gene and metagenomic sequencing. Combined with the data of environmental factors, the effects of environmental differences on different sample types were analyzed. Results The results showed that plants exerted a clear selective filtering effect on microbiota, resulting in a significant reduction in microbial community diversity and network complexity from BS to NS to RN. Proteobacteria was the most abundant phylum in the microbiomes of BS and NS. While RN was primarily dominated by Actinobacteria, with Frankia sp. EAN1pec serving as the most dominant species. Correlation analysis indicated that the host determined the microbial community composition in RN, independent of the ecological and geographical environmental changes of the sea buckthorn plantations. Nitrogen cycle pathway analyses showed that RN microbial community primarily functions in nitrogen fixation, and Frankia sp. EAN1pec was a major contributor to nitrogen fixation genes in RN. Discussion This study provides valuable insights into the effects of eco-geographical environment on the microbial communities of sea buckthorn RN. These findings further prove that the nodulation specificity and stability of sea buckthorn root and Frankia sp. EAN1pec may be the result of their long-term co-evolution.
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Affiliation(s)
- Hong Liu
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bingbing Ni
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Zhang L, Jin Q, Guan Y, Liu Z, Pan X, Zhang Y, Zhang Y, Wang Q. Trichoderma spp. promotes ginseng biomass by influencing the soil microbial community. Front Microbiol 2024; 15:1283492. [PMID: 38357355 PMCID: PMC10864653 DOI: 10.3389/fmicb.2024.1283492] [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: 08/26/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Ginseng (Panax ginseng C.A. Meyer) has multiple effects on human health; however, soil degradation seriously affects its yield. Trichoderma spp. play an important role in improving plant biomass by influencing the soil environment. Therefore, it is necessary to screen efficient Trichoderma strains that can increase ginseng biomass and determine their mechanisms. Methods Herein, we selected six Trichoderma species (T. brevicompactum, T. velutinum, T. viridescens, T. atroviride, T. koningiopsis, and T. saturnisporum) isolated from ginseng rhizosphere soil, and evaluated their growth promoting effects on ginseng and their influence on the microbiome and chemical attributes of the ginseng rhizosphere soil. Results Except for T. saturnisporum (F), compared with the control, the other five species increased ginseng biomass. In terms of chemical properties, the pH value, available potassium content, and available phosphorus content in the ginseng rhizosphere soil increased by 1.16-5.85%, 0.16-14.03%, and 3.92-38.64%, respectively, after root irrigation with spores of Trichoderma species. For the soil microbiome, fungal Chao1 and Ace richness indices decreased. Application of Trichoderma enhanced the relative level of Proteobacteria, but reduced the relative level of Ascomycota. At the genus level, application of Trichoderma enhanced the relative levels of Sphingomonas, Blastomonas, and Trichoderma, but reduced the relative level of Fusarium. Available K and available P were the most important elements that affected the structure of the bacterial community, while total K was the most influential element for the structure of the fungal community structure. Conclusion The results indicated that the application of Trichoderma spp. could increase soil nutrients and regulate the structure and composition of the soil microbial community, thereby enhancing the biomass of ginseng. The results will provide guidance for soil improvement in ginseng cultivation.
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Affiliation(s)
- Linlin Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiao Jin
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yiming Guan
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Zhengbo Liu
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaoxi Pan
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yue Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yayu Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
- Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiuxia Wang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
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Groß C, Hossen S, Dittrich S, Knorr KH, Borken W, Noll M. Biological nitrogen fixation, diversity and community structure of diazotrophs in two mosses in 25 temperate forests. Environ Microbiol 2024; 26:e16555. [PMID: 38148519 DOI: 10.1111/1462-2920.16555] [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: 07/19/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Many moss species are associated with nitrogen (N)-fixing bacteria (diazotrophs) that support the N supply of mosses. Our knowledge relates primarily to pristine ecosystems with low atmospheric N input, but knowledge of biological N fixation (BNF) and diazotrophic communities in mosses in temperate forests with high N deposition is limited. We measured BNF rates using the direct stable isotope method and studied the total and potentially active diazotrophic communities in two abundant mosses, Brachythecium rutabulum and Hypnum cupressiforme, both growing on lying deadwood trunks in 25 temperate forest sites. BNF rates in both mosses were similar to those observed in moss species of pristine ecosystems. H. cupressiforme fixed three times more N2 and exhibited lower diazotrophic richness than B. rutabulum. Frankia was the most prominent diazotroph followed by cyanobacteria Nostoc. Manganese, iron, and molybdenum contents in mosses were positively correlated with BNF and diazotrophic communities. Frankia maintained high BNF rates in H. cupressiforme and B. rutabulum even under high chronic N deposition in Central European forests. Moss N concentration and 15 N abundance indicate a rather minor contribution of BNF to the N nutrition of these mosses.
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Affiliation(s)
- Christina Groß
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Sebastian Dittrich
- Biodiversity and Conservation, Technical University of Dresden, Tharandt, Germany
| | - Klaus-Holger Knorr
- Institute of Landscape Ecology, Ecohydrology and Biogeochemistry Group, University of Münster, Münster, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
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Yuan Y, Chen Z, Huang X, Wang F, Guo H, Huang Z, Yang H. Comparative analysis of nitrogen content and its influence on actinorhizal nodule and rhizospheric microorganism diversity in three Alnus species. Front Microbiol 2023; 14:1230170. [PMID: 38169791 PMCID: PMC10758417 DOI: 10.3389/fmicb.2023.1230170] [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: 05/28/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Alnus spp. (alder) are typical nonleguminous nitrogen-fixing trees that have a symbiotic relationship with Frankia. To explore the differences in nitrogen-fixing microorganisms between three alders (A. cremastogyne, A. glutinosa, and A. formosana) with different chromosome ploidies, the community structure and compositional diversity of potential nitrogen-fixing microorganism in root nodules and rhizosphere soil were comparatively analyzed using 16S rRNA and nitrogenase (nifH) gene sequencing. The nitrogen contents in the root nodules and rhizosphere soil were also determined. The results showed that the contents of total nitrogen and nitrate nitrogen in the root nodules of the three alders are significantly higher than those in the rhizosphere soils, while the ammonium nitrogen content show the opposite trend. The family, genus, and species levels showed obviously differences between root nodules and rhizosphere soils, while there were no significant differences at the classification level between the three alders. At the phylum level, the dominant phyla from 16S rRNA and nifH gene data in the root nodules and rhizosphere soil of the three alders are phylum Actinomycetota and phylum Pseudomonadota, respectively. The LEfSe results showed that there are significant differences in the dominant groups in the root nodules and rhizosphere oil of the three alders. The relative abundances of dominant groups also showed obvious differences between the root nodules and rhizosphere soils of three alders. The relative abundances of Frankia and unclassified_Frankia in root nodules are obviously higher than those in rhizosphere soils, and their relative abundances in A. glutinosa root nodules are significantly higher than those in A. cremastogyne and A. formosana at the genus and species levels. The diversity of potential nitrogen-fixing microorganism from 16S rRNA and nifH gene data in the A. glutinosa root nodules and rhizosphere soils are all higher than those in A. cremastogyne and A. formosana. The results of functional prediction also showed that the OTUs for nitrogen fixation, nitrate respiration, and ureolysis in A. glutinosa root nodules are higher than those in the other two alders. Redundancy analysis revealed that the total nitrogen content mostly affects the Frankia community. Overall, there are significant differences in the community composition and structure of potential nitrogen-fixing microorganism in the root nodules and rhizosphere soils between the three alders. A. glutinosa showed a relatively stronger nitrogen fixation capacity than A. formosana and A. cremastogyne. The results help elucidates how the community structure and nitrogen-fixing ability of potential nitrogen-fixing microorganism differ between alder species and serve as a reference for applying Frankia to alder plantations.
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Affiliation(s)
- Yuwei Yuan
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Zhi Chen
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Xin Huang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Fang Wang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Hongying Guo
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Zhen Huang
- Sichuan Key Laboratory of Ecological Restoration and Conservation for Forest and Wetland, Sichuan Academy of Forestry, Chengdu, China
| | - Hanbo Yang
- Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, National Forestry and Grassland Administration Key Laboratory of Forest Resource Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Rainy Area of West China Plantation Ecosystem Permanent Scientific Research Base, College of Forestry, Sichuan Agricultural University, Chengdu, China
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Nouioui I, Neumann-Schaal M, Pujic P, Fournier P, Normand P, Herrera-Belaroussi A, Vemulapally S, Guerra T, Hahn D. Frankia nepalensis sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Coriaria nepalensis Wall. Int J Syst Evol Microbiol 2023; 73. [PMID: 38098135 DOI: 10.1099/ijsem.0.006199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Strains CN4T, CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus. The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N2-fixing vesicles and do not fix nitrogen in vitro. The peptidoglycan of strain CN4T contains meso-diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H4) and MK-9(H6) are the predominant menaquinones (>15 %), and iso-C16 : 0 and C17 : 1ω8c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4T is most closely related to Frankia saprophytica CN 3T. An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3T , Frankia asymbiotica M16386T and Frankia inefficax EuI1cT with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4T, CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4T has a 10.76 Mb genome. CN4T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4T (=DSM 114740T = LMG 32595T) to a novel species, with CN4T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.
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Affiliation(s)
- Imen Nouioui
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Petar Pujic
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Pascale Fournier
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Philippe Normand
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Aude Herrera-Belaroussi
- Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne 69622 Cedex, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Normand P, Pujic P, Abrouk D, Vemulapally S, Guerra T, Carlos-Shanley C, Hahn D. Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions. J Genomics 2022; 10:61-68. [PMID: 35979511 PMCID: PMC9379372 DOI: 10.7150/jgen.75779] [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: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species. Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.
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Affiliation(s)
- Philippe Normand
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Petar Pujic
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Danis Abrouk
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Sarkar I, Sen G, Bhattacharyya S, Gtari M, Sen A. Inter-cluster competition and resource partitioning may govern the ecology of Frankia. Arch Microbiol 2022; 204:326. [PMID: 35576077 DOI: 10.1007/s00203-022-02910-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/25/2022]
Abstract
Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality, as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Since the co-existence of two different genera in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario. Here, we exploited an 'R' package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host-specific nature. According to their plant host, Frankia has already been sub-divided into four clusters C-I, C-II, C-III, and C-IV. Our results revealed a strong competing nature of CI Frankia. Among the clusters of Frankia studied, the competition index between C-I and C-III was the largest. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV groups.
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Affiliation(s)
- I Sarkar
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - G Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
| | - S Bhattacharyya
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India
| | - M Gtari
- Unité de Bactériologie Moléculaire and Génomique, Département de Génie Biologique and Chimique, Institut National Des Sciences Appliquéeset de Technologie, Université de Carthage, Carthage, Tunisia
| | - A Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India.
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India.
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India.
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Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction. BIOLOGY 2020; 9:biology9060116. [PMID: 32498442 PMCID: PMC7344409 DOI: 10.3390/biology9060116] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022]
Abstract
Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world’s population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.
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In Planta Sporulation of Frankia spp. as a Determinant of Alder-Symbiont Interactions. Appl Environ Microbiol 2018; 84:AEM.01737-18. [PMID: 30217853 DOI: 10.1128/aem.01737-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
The Alnus genus forms symbiosis with the actinobacteria Frankia spp. and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta Spore-positive (Sp+) strains are predominant on Alnus incana and Alnus viridis in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, as well as the effect of the sporulation genotype on the ectomycorrhizal (ECM) communities. Trapping experiments were conducted using A. glutinosa, A. incana, and A. viridis plantlets on 6 soils, differing in the alder species and the frequency of Sp+ nodules in the field. Higher diversity of Frankia spp. and variation in Sp+ frequencies were observed in the trapping than in the fields. Both indigenous and trapping species shape Frankia community structure in trapped nodules. Nodulation impediments were observed under several trapping conditions in Sp+ soils, supporting a narrower host range of Sp+ Frankia species. A. incana and A. viridis were able to associate equally with compatible Sp+ and Sp- strains in the greenhouse. Additionally, no host shift was observed for Alnus-specific ECM, and the sporulation genotype of Frankia spp. defined the ECM communities on the host roots. The symbiotic association is likely determined by the host range, the soil history, and the type of in planta Frankia species. These results provide an insight into the biogeographical drivers of alder symbionts in the Holarctic region.IMPORTANCE Most Frankia-actinorhiza plant symbioses are capable of high rates of nitrogen fixation comparable to those found on legumes. Yet, our understanding of the ecology and distribution of Frankia spp. is still very limited. Several studies have focused on the distribution patterns of Frankia spp., demonstrating a combination of host and pedoclimatic parameters in their biogeography. However, very few have considered the in planta sporulation form of the strain, although it is a unique feature among all symbiotic plant-associated microbes. Compared with Sp- Frankia strains, Sp+ strains would be obligate symbionts that are highly dependent on the presence of a compatible host species and with lower efficiency in nitrogen fixation. Understanding the biogeographical drivers of Sp+ Frankia strains might help elucidate the ecological role of in planta sporulation and the extent to which this trait mediates host-partner interactions in the alder-Frankia-ECM fungal symbiosis.
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