1
|
Hnini M, Aurag J. Prevalence, diversity and applications potential of nodules endophytic bacteria: a systematic review. Front Microbiol 2024; 15:1386742. [PMID: 38812696 PMCID: PMC11133547 DOI: 10.3389/fmicb.2024.1386742] [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: 02/16/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule endophytic bacteria, alongside Paenibacillus, Agrobacterium, and Enterobacter. Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
Collapse
Affiliation(s)
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| |
Collapse
|
2
|
Ben Gaied R, Sbissi I, Tarhouni M, Brígido C. Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium. Arch Microbiol 2024; 206:203. [PMID: 38573536 PMCID: PMC10995081 DOI: 10.1007/s00203-024-03943-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.
Collapse
Affiliation(s)
- Roukaya Ben Gaied
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal
| | - Imed Sbissi
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Mohamed Tarhouni
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Clarisse Brígido
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE-Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, Évora, 7006-554, Portugal.
| |
Collapse
|
3
|
Ben Gaied R, Sbissi I, Tarhouni M, Brígido C. Bacterial Endophytes from Legumes Native to Arid Environments Are Promising Tools to Improve Mesorhizobium-Chickpea Symbiosis under Salinity. BIOLOGY 2024; 13:96. [PMID: 38392314 PMCID: PMC10886315 DOI: 10.3390/biology13020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Symbiotic nitrogen fixation is a major contributor of N in agricultural ecosystems, but the establishment of legume-rhizobium symbiosis is highly affected by soil salinity. Our interest is focused on the use of non-rhizobial endophytes to assist the symbiosis between chickpea and its microsymbiont under salinity to avoid loss of production and fertility. Our aims were (1) to investigate the impact of salinity on both symbiotic partners; including on early events of the Mesorhizobium-chickpea symbiosis, and (2) to evaluate the potential of four non-rhizobial endophytes isolated from legumes native to arid regions (Phyllobacterium salinisoli, P. ifriqiyense, Xanthomonas translucens, and Cupriavidus respiraculi) to promote chickpea growth and nodulation under salinity. Our results show a significant reduction in chickpea seed germination rate and in the microsymbiont Mesorhizobium ciceri LMS-1 growth under different levels of salinity. The composition of phenolic compounds in chickpea root exudates significantly changed when the plants were subjected to salinity, which in turn affected the nod genes expression in LMS-1. Furthermore, the LMS-1 response to root exudate stimuli was suppressed by the presence of salinity (250 mM NaCl). On the contrary, a significant upregulation of exoY and otsA genes, which are involved in exopolysaccharide and trehalose biosynthesis, respectively, was registered in salt-stressed LMS-1 cells. In addition, chickpea co-inoculation with LMS-1 along with the consortium containing two non-rhizobial bacterial endophytes, P. salinisoli and X. translucens, resulted in significant improvement of the chickpea growth and the symbiotic performance of LMS-1 under salinity. These results indicate that this non-rhizobial endophytic consortium may be an appropriate ecological and safe tool to improve chickpea growth and its adaptation to salt-degraded soils.
Collapse
Affiliation(s)
- Roukaya Ben Gaied
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
- MED-Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Imed Sbissi
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Mohamed Tarhouni
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Clarisse Brígido
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE-Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| |
Collapse
|
4
|
Msaddak A, Quiñones MA, Mars M, Pueyo JJ. The Beneficial Effects of Inoculation with Selected Nodule-Associated PGPR on White Lupin Are Comparable to Those of Inoculation with Symbiotic Rhizobia. PLANTS (BASEL, SWITZERLAND) 2023; 12:4109. [PMID: 38140436 PMCID: PMC10747367 DOI: 10.3390/plants12244109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Nodule endophytes and associated bacteria are non-symbiotic bacteria that colonize legume nodules. They accompany nodulating rhizobia and can form beneficial associations, as some of them are plant growth-promoting rhizobacteria (PGPR) that are able to promote germination and plant growth and increase tolerance to biotic and abiotic stress. White lupin (Lupinus albus) is a legume crop that is gaining relevance as a suitable alternative to soybean as a plant protein source. Eleven nodule-associated bacteria were isolated from white lupin nodules grown in a Tunisian soil. They belonged to the genera Rhizobium, Ensifer, Pseudomonas and Bacillus. Their plant growth-promoting (PGP) and enzymatic activities were tested in vitro. Strains Pseudomonas sp., L1 and L12, displayed most PGP activities tested, and were selected for in planta assays. Inoculation with strains L1 or L12 increased seed germination and had the same positive effects on all plant growth parameters as did inoculation with symbiotic Bradyrhizobium canariense, with no significant differences among treatments. Inoculation with efficient nitrogen-fixing rhizobia must compete with rhizobia present in the soil that sometimes nodulate efficiently but fix nitrogen poorly, leading to a low response to inoculation. In such cases, inoculation with highly effective PGPR might represent a feasible alternative to boost crop productivity.
Collapse
Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - Miguel A. Quiñones
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia;
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain;
| |
Collapse
|
5
|
Lebrazi S, Fadil M, Chraibi M, Fikri-Benbrahim K. Phenotypic, molecular, and symbiotic characterization of the rhizobial symbionts isolated from Acacia saligna grown in different regions in Morocco: a multivariate approach. World J Microbiol Biotechnol 2023; 39:343. [PMID: 37843647 DOI: 10.1007/s11274-023-03775-1] [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: 04/07/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
The introduced species Acacia saligna is a very promiscuous host as it can be efficiently nodulated with a wide range diversity of rhizobia taxa, including both fast and slow-growing strains. Fourteen nitrogen (N)-fixing bacteria were isolated from root nodules of wild Acacia saligna growing in distinct geographic locations in Morocco and were examined for their symbiotic efficiency and phenotypic properties. Multivariate tools, such as principal component analysis (PCA) and hierarchical clustering analysis (HCA), were used to study the correlation between phenotypic and symbiotic variables and discriminate and describe the similarities between different isolated bacteria with respect to all the phenotypic and symbiotic variables. Phenotypic characterization showed a variable response to extreme temperature, salinity and soil pH. At the plant level, the nodulation, nitrogen fixation, and the shoot and root dry weights were considered. The obtained results show that some of the tested isolates exhibit remarkable tolerances to the studied abiotic stresses while showing significant N2 fixation, indicating their usefulness as effective candidates for the inoculation of acacia trees. The PCA also allowed showing the isolates groups that present a similarity with evaluated phenotypic and symbiotic parameters. The genotypic identification of N2-fixing bacteria, carried out by the 16S rDNA approach, showed a variable genetic diversity among the 14 identified isolates, and their belonging to three different genera, namely Agrobacterium, Phyllobacterium and Rhizobium.
Collapse
Affiliation(s)
- Sara Lebrazi
- Microbial Biotechnology and Bioactive Molecules Laboratory, Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fez, Morocco.
| | - Mouhcine Fadil
- Laboratory of Applied Organic Chemistry, Faculty of Sciences and Techniques, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Marwa Chraibi
- Microbial Biotechnology and Bioactive Molecules Laboratory, Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Kawtar Fikri-Benbrahim
- Microbial Biotechnology and Bioactive Molecules Laboratory, Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| |
Collapse
|
6
|
Bizjak T, Sellstedt A, Gratz R, Nordin A. Presence and activity of nitrogen-fixing bacteria in Scots pine needles in a boreal forest: a nitrogen-addition experiment. TREE PHYSIOLOGY 2023; 43:1354-1364. [PMID: 37073466 PMCID: PMC10423461 DOI: 10.1093/treephys/tpad048] [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: 12/06/2022] [Revised: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. This study aimed to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris L.) needles. The presence and rate of nitrogen fixation by endophytic bacteria were compared between control plots and fertilized plots in a nitrogen-addition experiment. In contrast to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha-1 year-1, which is rather low compared with Scots pine annual nitrogen use but could be important for the nitrogen-poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. In summary, 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole-genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.
Collapse
Affiliation(s)
- Tinkara Bizjak
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Anita Sellstedt
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
| | - Regina Gratz
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| | - Annika Nordin
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
| |
Collapse
|
7
|
Dhole AM, Shelat HN, Patel HK, Jhala YK. Evaluation of the Co-inoculation Effect of Rhizobium and Plant Growth Promoting Non-rhizobial Endophytes on Vigna radiata. Curr Microbiol 2023; 80:167. [PMID: 37024674 DOI: 10.1007/s00284-023-03266-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/11/2023] [Indexed: 04/08/2023]
Abstract
A unique feature of leguminous plants is the establishment of symbiotic bacterial genera inside root or stem nodules that is being recently re-evaluated for investigating the micro-flora discrete to nitrogen fixation. The present research was carried out to evaluate non-rhizobial endophytes and Rhizobium from root nodules of Vigna radiata and ascertain their co-inoculation effect in pot and field conditions. Each strain displayed one or more plant growth-promoting behaviors in varying degrees. The ability to fix nitrogen was observed in all strains; however, a noticeable enhancement in nitrogen fixation was observed when all three strains were co-inoculated. All three strains were found to possess the nifH gene, which plays a key role in the nitrogen fixation process. However, only Rhizobium sp. AAU B3 also had the nodD gene present. Furthermore, combinations of all three strains produced the highest levels of phosphate solubilization, potash mobilisation, Indole Acetic Acid (IAA), and the stress-relieving enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Interestingly, the succession of the root nodule formation within root hairs seedlings was observed under a fluorescence microscope and two NRE were found to be located inside the root nodules, indicating that they are endophytic. Additionally, a pot and field investigation revealed that the combination of chosen Rhizobium and NRE strains had a favorable impact on the growth and yield characteristics of a green gram. Selected bio-inoculants can reduce the utilization of synthetic fertilizers by 75%, which might lead to the restoration of the soil's health. Therefore, these bio-inoculants might be explored commercially for sustainable agriculture production.
Collapse
Affiliation(s)
- Archana M Dhole
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India.
| | - Harsha N Shelat
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Hiren K Patel
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
| | - Yogeshvari K Jhala
- B. A. College of Agriculture, Anand Agricultural University, Anand, Gujarat, 388110, India
| |
Collapse
|
8
|
Msaddak A, Mars M, Quiñones MA, Lucas MM, Pueyo JJ. Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer. Int J Mol Sci 2023; 24:ijms24076496. [PMID: 37047476 PMCID: PMC10094711 DOI: 10.3390/ijms24076496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin’s adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin’s adaptability to marginal soils and climates.
Collapse
Affiliation(s)
- Abdelhakim Msaddak
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Mohamed Mars
- Laboratory of Biodiversity and Valorization of Arid Areas Bioresources, BVBAA, Faculty of Sciences, University of Gabès, Erriadh, Zrig, Gabès 6072, Tunisia
| | - Miguel A. Quiñones
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - M. Mercedes Lucas
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| | - José J. Pueyo
- Department of Soil. Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, 28006 Madrid, Spain
| |
Collapse
|
9
|
A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing. Microorganisms 2023; 11:microorganisms11030672. [PMID: 36985245 PMCID: PMC10054463 DOI: 10.3390/microorganisms11030672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.
Collapse
|
10
|
Elevated atmospheric CO 2 concentrations caused a shift of the metabolically active microbiome in vineyard soil. BMC Microbiol 2023; 23:46. [PMID: 36809988 PMCID: PMC9942357 DOI: 10.1186/s12866-023-02781-5] [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: 11/09/2021] [Accepted: 01/23/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.
Collapse
|
11
|
Mugani R, El Khalloufi F, Redouane EM, Haida M, Zerrifi SEA, Campos A, Kasada M, Woodhouse J, Grossart HP, Vasconcelos V, Oudra B. Bacterioplankton Associated with Toxic Cyanobacteria Promote Pisum sativum (Pea) Growth and Nutritional Value through Positive Interactions. Microorganisms 2022; 10:microorganisms10081511. [PMID: 35893569 PMCID: PMC9394358 DOI: 10.3390/microorganisms10081511] [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: 07/05/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Research on Plant Growth-Promoting Bacteria (PGPB) has focused much more on rhizospheric bacteria. However, PGPB associated with toxic cyanobacterial bloom (TCB) could enter the rhizosphere through irrigation water, helping plants such as Pisum sativum L. (pea) overcome oxidative stress induced by microcystin (MC) and improve plant growth and nutritional value. This study aimed to isolate bacteria associated with toxic cyanobacteria, test PGPB properties, and inoculate them as a consortium to pea seedlings irrigated with MC to investigate their role in plant protection as well as in improving growth and nutritional value. Two bacterioplankton isolates and one rhizosphere isolate were isolated and purified on a mineral salt medium supplemented with 1000 μg/L MC and identified via their 16S rRNA gene. The mixed strains were inoculated to pea seedlings in pots irrigated with 0, 50, and 100 μg/L MC. We measured the morphological and physiological parameters of pea plants at maturity and evaluated the efficiency of the plant’s enzymatic and non-enzymatic antioxidant responses to assess the role and contribution of PGPB. Both bacterioplankton isolates were identified as Starkeya sp., and the rhizobacterium was identified as Brevundimonas aurantiaca. MC addition significantly (p < 0.05) reduced all the growth parameters of the pea, i.e., total chlorophyll content, leaf quantum yield, stomatal conductance, carotenoids, and polyphenol contents, in an MC concentration-dependent manner, while bacterial presence positively affected all the measured parameters. In the MC treatment, the levels of the pea’s antioxidant traits, including SOD, CAT, POD, PPO, GST, and ascorbic acid, were increased in the sterile pots. In contrast, these levels were reduced with double and triple PGPB addition. Additionally, nutritional values such as sugars, proteins, and minerals (Ca and K) in pea fruits were reduced under MC exposure but increased with PGPB addition. Overall, in the presence of MC, PGPB seem to positively interact with pea plants and thus may constitute a natural alternative for soil fertilization when irrigated with cyanotoxin-contaminated water, increasing the yield and nutritional value of crops.
Collapse
Affiliation(s)
- Richard Mugani
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
| | - Fatima El Khalloufi
- Natural Resources Engineering and Environmental Impacts Team, Multidisciplinary Research and Innovation Laboratory, Polydisciplinary Faculty of Khouribga, Sultan Moulay Slimane University of Beni Mellal, P.O. Box 145, Khouribga 25000, Morocco;
| | - El Mahdi Redouane
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Mohammed Haida
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Soukaina El Amrani Zerrifi
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| | - Alexandre Campos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
| | - Minoru Kasada
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
- Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Jason Woodhouse
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhuette 2, 14775 Stechlin, Germany; (M.K.); (J.W.); (H.-P.G.)
- Institute for Biochemistry and Biology, University of Potsdam, Maulbeeralle 2, 14469 Potsdam, Germany
| | - Vitor Vasconcelos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-223-401-817
| | - Brahim Oudra
- Water, Biodiversity and Climate Change Laboratory, Faculty of Sciences Semlalia, Cadi Ayyad University, Av. Prince My Abdellah, P.O. Box 2390, Marrakech 40000, Morocco; (R.M.); (E.M.R.); (M.H.); (S.E.A.Z.); (B.O.)
| |
Collapse
|
12
|
Jing L, Jia-min A, Xiao-dong L, Ying-ying J, Chao-chao Z, Rui-hua Z, Zhen-shan D. Environmental filtering drives the establishment of the distinctive rhizosphere, bulk, and root nodule bacterial communities of Sophora davidii in hilly and gully regions of the Loess Plateau of China. Front Microbiol 2022; 13:945127. [PMID: 35935225 PMCID: PMC9355530 DOI: 10.3389/fmicb.2022.945127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to the rhizobia, other non-rhizobial endophytes (NREs) have been simultaneously isolated from the root nodules. The existence of NREs in leguminous root nodules is a universal phenomenon, and they have the potential to enhance legume survival, especially under conditions of environmental stress. However, the diversity and biogeographic patterns of microbial communities inhabiting root nodules are not well studied or understood. Here, we explored and characterized the diversity of NRE bacteria by using 16S rRNA gene high-throughput amplicon sequencing. Additionally, we compared the biogeography and co-occurrence patterns in review of the bacterial microbiota inhabiting the rhizosphere, the bulk soil and the root nodule bacterial communities associated with Sophora davidii, a native N-fixing wild leguminous shrub in hilly and gully regions of the Loess Plateau of China. The results showed the presence of a large diversity of bacteria belonging to 81 phyla, 154 classes, 333 orders, 463 families, and 732 genera inside the nodules. Proteobacteria were dominant in the nodule and rhizosphere soil samples, and Actinomycetes were dominant in the bulk soil samples. Mesorhizobium was the dominant genus in the nodules, accounting for between 60.15 and 83.74% of the bacteria. The microbial community composition of the NRE in the root nodules differed from that in the rhizosphere soil and the bulk soil of S. davidii. Moreover, we found that the biogeographic patterns and assembly process of the rhizobia and non-rhizobia communities differed in the root nodule, the rhizosphere soil and the bulk soil. Furthermore, the correlation analysis between the soil’s physical and chemical properties and the bacteria showed that available phosphorus was the predominant factor affecting the bacterial diversity within the rhizosphere soil. Finally, our results revealed that the microbial network diagram of co-occurrence patterns showed more complexes in the soil than in the root nodules. This indicates that only specific microorganisms could colonize and thrive in the rhizosphere through the selection and filtering effects of roots. In conclusion, there are significant differences in bacterial community composition in the nodules, rhizosphere and bulk soil in the hilly and gully region of the Loess Plateau, which is the result of environmental filtration. Our study improves the understanding of the biogeographic patterns and diversity of bacterial microbiota inhabiting root nodules and can help quantify and define the root nodule assemblage process of S. davidii.
Collapse
|
13
|
Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum. Int J Mol Sci 2022; 23:ijms23126609. [PMID: 35743053 PMCID: PMC9224216 DOI: 10.3390/ijms23126609] [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: 05/06/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Microbacterium foliorum is a Gram-positive bacteria found in organic matter. Three lytic bacteriophages, KaiHaiDragon, OneinaGillian, and YuuY, were isolated from M. foliorum strain NRRL B-24224. Phage YuuY in particular expresses a broad host range as it possesses the ability to infect closely related bacterial species Microbacterium aerolatum at a high plating efficiency. Characterization tests were performed on all three Microbacterium phage to assess morphology, genomic characteristics, pH and thermal stabilities, life cycle, and the type of receptor used for infection. All three phages showed similar pH stability, ranging from pH 5-11, except for KaiHaiDragon, which had a reduced infection effectiveness at a pH of 11. YuuY possessed a significantly higher temperature tolerance compared to the other Microbacterium phages as some phage particles remained viable after incubation temperatures of up to 80 °C. Based on the one-step growth curve assay, all three Microbacterium phages possessed a relatively short latent period of 90 min and an approximately two-fold burst size factor. Moreover, all three phages utilize a carbohydrate receptor to initiate infection. Based on bioinformatics analysis, YuuY, KaiHaiDragon and OneinaGillian were assigned to clusters EA10, EC, and EG, respectively.
Collapse
|
14
|
Etesami H. Root nodules of legumes: A suitable ecological niche for isolating non-rhizobial bacteria with biotechnological potential in agriculture. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
15
|
Bhagat N, Sharma S, Ambardar S, Raj S, Trakroo D, Horacek M, Zouagui R, Sbabou L, Vakhlu J. Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility Study. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.688393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Host–microbiome interactions are specific and not random, making them defining entities for the host. The hypothesis proposed by various researchers earlier, that both plants and animals harbor specific inheritable core microbiome, is being augmented in the present study. Additionally, a case for using microbial fingerprint as a biomarker, not only for plant identification but also as a geographical indicator, has been investigated, taking Crocus sativus, saffron, as a study material. Crocus sativus, a monogenetic herb, on account of its male sterility and vegetative propagation, is reported to lack genome based molecular markers. Cormosphere microbiome (microbiome associated with corm) has been compared across three geographical locations, in two continents, to identify the core and unique microbiome, during the vegetative phase of its growth. Microbiome analysis done at phylum and genus level, using next generation sequencing technology, revealed that cormosphere at three locations harbored common phyla. At genus level, 24 genera were found common to all three geographical locations, indicating them to be part of the core microbiome of saffron. However, there were some bacterial genera unique to Kashmir, Kishtwar, and Morocco that can be used to develop microbial markers/geographical indicators for saffron grown in these regions. This is a preliminary study, indicating that the location specific bacterial community can be used to develop microbial barcodes but needs further augmentation with high coverage data from other saffron growing geographical regions.
Collapse
|
16
|
Martínez‐Romero E, Aguirre‐Noyola JL, Bustamante‐Brito R, González‐Román P, Hernández‐Oaxaca D, Higareda‐Alvear V, Montes‐Carreto LM, Martínez‐Romero JC, Rosenblueth M, Servín‐Garcidueñas LE. We and herbivores eat endophytes. Microb Biotechnol 2021; 14:1282-1299. [PMID: 33320440 PMCID: PMC8313258 DOI: 10.1111/1751-7915.13688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Health depends on the diet and a vegetal diet promotes health by providing fibres, vitamins and diverse metabolites. Remarkably, plants may also provide microbes. Fungi and bacteria that reside inside plant tissues (endophytes) seem better protected to survive digestion; thus, we investigated the reported evidence on the endophytic origin of some members of the gut microbiota in animals such as panda, koala, rabbits and tortoises and several herbivore insects. Data examined here showed that some members of the herbivore gut microbiota are common plant microbes, which derived to become stable microbiota in some cases. Endophytes may contribute to plant fibre or antimetabolite degradation and synthesis of metabolites with the plethora of enzymatic activities that they display; some may have practical applications, for example, Lactobacillus plantarum found in the intestinal tract, plants and in fermented food is used as a probiotic that may defend animals against bacterial and viral infections as other endophytic-enteric bacteria do. Clostridium that is an endophyte and a gut bacterium has remarkable capabilities to degrade cellulose by having cellulosomes that may be considered the most efficient nanomachines. Cellulose degradation is a challenge in animal digestion and for biofuel production. Other endophytic-enteric bacteria may have cellulases, pectinases, xylanases, tannases, proteases, nitrogenases and other enzymatic capabilities that may be attractive for biotechnological developments, indeed many endophytes are used to promote plant growth. Here, a cycle of endophytic-enteric-soil-endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.
Collapse
Affiliation(s)
| | | | | | - Pilar González‐Román
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | | | | | | | | - Mónica Rosenblueth
- Programa de Ecología GenómicaCentro de Ciencias GenómicasUNAMCuernavacaMorelosMexico
| | | |
Collapse
|
17
|
Bakhtiyarifar M, Enayatizamir N, Mehdi Khanlou K. Biochemical and molecular investigation of non-rhizobial endophytic bacteria as potential biofertilisers. Arch Microbiol 2021; 203:513-521. [PMID: 32965526 DOI: 10.1007/s00203-020-02038-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/29/2020] [Accepted: 09/12/2020] [Indexed: 11/29/2022]
Abstract
This study was performed to isolate non-rhizobial endophytic bacteria from the root nodules of Glycine max (soybean), Vigna radiata (mung bean) and Vigna unguiculata (cowpea). The bacteria were characterized for plant growth promoting properties such as indole acetic acid production, phosphate and zinc solubilisation, nitrogen fixation and hydrogen cyanide production. Phylogenetic identification was performed using the Neighbour-Joining method on16S rRNA gene sequences. The impact of salt tolerant isolates on some properties of wheat cv. Chamran was evaluated by a completely randomised factorial design. Nine isolates having some characteristics related to plant growth promotion were identified as Staphylococcus hominis 7E, Streptomyces sp. 11E, Bacillus sp. 13E, Acinetobacter sp. 19E, from mung bean, Bacillus endophyticus 1E from cowpea, Staphylococcus hominis 9E, Bacillus endophyticus 14E, Brevundimonas sp. 16E and Kocuria sp. 26E from soybean nodules. Isolates 7E and 19E caused maximum growth inhibition of Fusarium on PDA plate. All isolates were able to grow at salinity levels of mixtures containing up to 400 mM of NaCl, CaCl2 and MgCl2, but their growth was inhibited by increasing salinity level. Only the growth of isolate 14E increased at three levels of salinity compared with control. Some isolates, i.e. 7E, 14E, 19E and 26E had higher colony diameter at 45 °C after 48 h of incubation compared to the growth at 30 and 40 °C. Inoculation of soil with isolate 1E and isolate 26E caused to ameliorate salinity stress in wheat and increased the weight of 1000-grains as compared with non-inoculated treatments.
Collapse
Affiliation(s)
- Marzieh Bakhtiyarifar
- Soil Science & Engineering Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Naeimeh Enayatizamir
- Soil Science & Engineering Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Khosro Mehdi Khanlou
- Production Engineering & Plant Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
18
|
Turnau K, Fiałkowska E, Ważny R, Rozpądek P, Tylko G, Bloch S, Nejman-Faleńczyk B, Grabski M, Węgrzyn A, Węgrzyn G. Extraordinary Multi-Organismal Interactions Involving Bacteriophages, Bacteria, Fungi, and Rotifers: Quadruple Microbial Trophic Network in Water Droplets. Int J Mol Sci 2021; 22:ijms22042178. [PMID: 33671687 PMCID: PMC7926626 DOI: 10.3390/ijms22042178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 12/01/2022] Open
Abstract
Our observations of predatory fungi trapping rotifers in activated sludge and laboratory culture allowed us to discover a complicated trophic network that includes predatory fungi armed with bacteria and bacteriophages and the rotifers they prey on. Such a network seems to be common in various habitats, although it remains mostly unknown due to its microscopic size. In this study, we isolated and identified fungi and bacteria from activated sludge. We also noticed abundant, virus-like particles in the environment. The fungus developed absorptive hyphae within the prey. The bacteria showed the ability to enter and exit from the hyphae (e.g., from the traps into the caught prey). Our observations indicate that the bacteria and the fungus share nutrients obtained from the rotifer. To narrow the range of bacterial strains isolated from the mycelium, the effects of bacteria supernatants and lysed bacteria were studied. Bacteria isolated from the fungus were capable of immobilizing the rotifer. The strongest negative effect on rotifer mobility was shown by a mixture of Bacillus sp. and Stenotrophomonas maltophilia. The involvement of bacteriophages in rotifer hunting was demonstrated based on molecular analyses and was discussed. The described case seems to be an extraordinary quadruple microbiological puzzle that has not been described and is still far from being understood.
Collapse
Affiliation(s)
- Katarzyna Turnau
- Institute of Environmental Sciences, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland;
- Correspondence: ; Tel.: +48-506-006-642
| | - Edyta Fiałkowska
- Institute of Environmental Sciences, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Rafał Ważny
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7a, 30-387 Krakow, Poland; (R.W.); (P.R.)
| | - Piotr Rozpądek
- Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Gronostajowa 7a, 30-387 Krakow, Poland; (R.W.); (P.R.)
| | - Grzegorz Tylko
- Institute of Zoology and Biomedical Research, Jagiellonian University in Krakow, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Sylwia Bloch
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kladki 24, 80-822 Gdansk, Poland; (S.B.); (A.W.)
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (B.N.-F.); (M.G.); (G.W.)
| | - Michał Grabski
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (B.N.-F.); (M.G.); (G.W.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kladki 24, 80-822 Gdansk, Poland; (S.B.); (A.W.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (B.N.-F.); (M.G.); (G.W.)
| |
Collapse
|
19
|
Bünger W, Sarkar A, Grönemeyer JL, Zielinski J, Revermann R, Hurek T, Reinhold-Hurek B. Root Nodule Rhizobia From Undomesticated Shrubs of the Dry Woodlands of Southern Africa Can Nodulate Angolan Teak Pterocarpus angolensis, an Important Source of Timber. Front Microbiol 2021; 12:611704. [PMID: 33584615 PMCID: PMC7876412 DOI: 10.3389/fmicb.2021.611704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 11/17/2022] Open
Abstract
Pterocarpus angolensis, a leguminous tree native to the dry woodlands of Southern Africa, provides valuable timber, but is threatened by land conversion and overharvesting while showing limited natural regeneration. Nitrogen-fixing root nodule symbionts that could improve establishment of young seedlings have not yet been described. Therefore, we investigated the ability of P. angolensis to form nodules with a diverse range of rhizobia. In drought-prone areas under climate change with higher temperatures, inoculants that are heat-tolerant and adapted to these conditions are likely to be of advantage. Sources of bacterial isolates were roots of P. angolensis from nurseries in the Kavango region, other shrubs from this area growing near Pterocarpus such as Indigofera rautanenii, Desmodium barbatum, Chamaecrista sp., or shrubs from drought-prone areas in Namaqualand (Wiborgia monoptera, Leobordea digitata) or Kalahari (Indigofera alternans). Only slight protrusions were observed on P. angolensis roots, from which a non-nodulating Microbacterium sp. was isolated. Rhizobia that were isolated from nodules of other shrubs were affiliated to Bradyrhizobium ripae WR4T, Bradyrhizobium spp. (WR23/WR74/WR93/WR96), or Ensifer/Mesorhizobium (WR41/WR52). As many plant growth-promoting rhizobacteria (PGPR), nodule isolates produced siderophores and solubilized phosphate. Among them, only the Bradyrhizobium strains nodulated P. angolensis under controlled conditions in the laboratory. Isolates were further characterized by multilocus sequence analysis and were found to be distant from known Bradyrhizobium species. Among additional reference species tested for nodulation on P. angolensis, Bradyrhizobium vignae 7-2T and Bradyrhizobium namibiense 5-10T from the Kavango region of Namibia as well as Bradyrhizobium elkanii LMG6234T and Bradyrhizobium yuanmingense LMG21728T induced nitrogen-fixing nodules, while Bradyrhizobium diazoefficiens USDA110T and Bradyrhizobium tropiciagri SEMIA6148T did not. This suggests a broad microsymbiont range from Bradyrhizobium japonicum and B. elkanii lineages. Phylogenetic analysis of nodC genes indicated that nodulating bradyrhizobia did not belong to a specific symbiovar. Also, for I. rautanenii and Wiborgia, nodule isolates B. ripae WR4T or Mesorhizobium sp. WR52, respectively, were authenticated. Characterization of symbionts inducing effective root nodules in P. angolensis and other shrubs from Subsahara Africa (SSA) give insights in their symbiotic partners for the first time and might help in future to develop bioinoculants for young seedlings in nurseries, and for reforestation efforts in Southern Africa.
Collapse
Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Abhijit Sarkar
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Jann Lasse Grönemeyer
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Janina Zielinski
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rasmus Revermann
- Department of Biodiversity, Ecology and Evolution of Plants, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
- Faculty of Natural Resources and Spatial Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| |
Collapse
|
20
|
Jacobs-Sera D, Abad LA, Alvey RM, Anders KR, Aull HG, Bhalla SS, Blumer LS, Bollivar DW, Bonilla JA, Butela KA, Coomans RJ, Cresawn SG, D'Elia T, Diaz A, Divens AM, Edgington NP, Frederick GD, Gainey MD, Garlena RA, Grant KW, Gurney SMR, Hendrickson HL, Hughes LE, Kenna MA, Klyczek KK, Kotturi H, Mavrich TN, McKinney AL, Merkhofer EC, Moberg Parker J, Molloy SD, Monti DL, Pape-Zambito DA, Pollenz RS, Pope WH, Reyna NS, Rinehart CA, Russell DA, Shaffer CD, Sivanathan V, Stoner TH, Stukey J, Sunnen CN, Tolsma SS, Tsourkas PK, Wallen JR, Ware VC, Warner MH, Washington JM, Westover KM, Whitefleet-Smith JL, Wiersma-Koch HI, Williams DC, Zack KM, Hatfull GF. Genomic diversity of bacteriophages infecting Microbacterium spp. PLoS One 2020; 15:e0234636. [PMID: 32555720 PMCID: PMC7302621 DOI: 10.1371/journal.pone.0234636] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/29/2020] [Indexed: 11/19/2022] Open
Abstract
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
Collapse
Affiliation(s)
- Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Lawrence A. Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Richard M. Alvey
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - Kirk R. Anders
- Department of Biology, Gonzaga University, Spokane, Washington, United States of America
| | - Haley G. Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Suparna S. Bhalla
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Lawrence S. Blumer
- Department of Biology, Morehouse College, Atlanta, Georgia, United States of America
| | - David W. Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, Illinois, United States of America
| | - J. Alfred Bonilla
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Kristen A. Butela
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Roy J. Coomans
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina, United States of America
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America
| | - Tom D'Elia
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Arturo Diaz
- Department of Biology, La Sierra University, Riverside, California, United States of America
| | - Ashley M. Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nicholas P. Edgington
- Department of Biology, Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Gregory D. Frederick
- Department of Biology and Kinesiology, LeTourneau University, Longview, Texas, United States of America
| | - Maria D. Gainey
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kenneth W. Grant
- Department of Pathology, Wake Forest Baptist Health, Winston-Salem, North Carolina, United States of America
| | - Susan M. R. Gurney
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | | | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Margaret A. Kenna
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Karen K. Klyczek
- Department of Biology, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Hari Kotturi
- Department of Biology, University of Central Oklahoma, Edmond, Oklahoma, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Angela L. McKinney
- Department of Biology, Nebraska Wesleyan University, Lincoln, Nebraska, United States of America
| | - Evan C. Merkhofer
- Department of Natural Sciences, Mount Saint Mary College, Newburgh, New York, United States of America
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Sally D. Molloy
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, United States of America
| | - Denise L. Monti
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Dana A. Pape-Zambito
- Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard S. Pollenz
- Department Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Nathan S. Reyna
- Department of Biology, Ouachita Baptist University, Arkadelphia, Arkansas, United States of America
| | - Claire A. Rinehart
- Department of Biology, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher D. Shaffer
- Department of Biology, University of Washington in St. Louis, St. Louis, Missouri, United States of America
| | - Viknesh Sivanathan
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Ty H. Stoner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joseph Stukey
- Biology Department, Hope College, Holland, Michigan, United States of America
| | - C. Nicole Sunnen
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Sara S. Tolsma
- Biology Department, Northwestern College, Orange City, Iowa, United States of America
| | - Philippos K. Tsourkas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, United States of America
| | - Jamie R. Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina, United States of America
| | - Vassie C. Ware
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Marcie H. Warner
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Kristi M. Westover
- Department of Biology, Winthrop University, Rock Hill, South Carolina, United States of America
| | - JoAnn L. Whitefleet-Smith
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Helen I. Wiersma-Koch
- Department of Biological Sciences, Indian River State College, Fort Pierce, Florida, United States of America
| | - Daniel C. Williams
- Department of Biology, Coastal Carolina University, Conway, South Carolina, United States of America
| | - Kira M. Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
21
|
The ACC-Deaminase Producing Bacterium Variovorax sp . CT7.15 as a Tool for Improving Calicotome villosa Nodulation and Growth in Arid Regions of Tunisia. Microorganisms 2020; 8:microorganisms8040541. [PMID: 32283666 PMCID: PMC7232455 DOI: 10.3390/microorganisms8040541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Calicotome villosa is a spontaneous Mediterranean legume that can be a good candidate as pioneer plants to limit regression of vegetation cover and loss of biodiversity in Tunisian arid soils. In order to grow legumes in such soils, pairing rhizobia and nodule associated bacteria (NAB) might provide numerous advantages. In this work, cultivable biodiversity of rhizobial symbionts and NAB in nodules of C. villosa plants growing in five arid regions of south Tunisia was characterized. Phylogenetic analysis using 16S rDNA gene, dnak, recA and nodD sequences separated nodule-forming bacteria in six clades associated to genera Ensifer, Neorhizobium, Phyllobacterium and Rhizobium. Among NAB, the strain Variovorax sp. CT7.15 was selected due to its capacity to solubilise phosphate and, more interestingly, its high level of aminocyclopropane-1-carboxylate deaminase (ACC deaminase) activity. C. villosa plants were inoculated with representative rhizobia of each phylogenetic group and co-inoculated with the same rhizobia and strain CT7.15. Compared with single rhizobia inoculation, co-inoculation significantly improved plant growth and nodulation, ameliorated plant physiological state and increased nitrogen content in the plants, independently of the rhizobia used. These results support the benefits of pairing rhizobia and selected NAB to promote legume growth in arid or degraded soils.
Collapse
|
22
|
Alishahi F, Alikhani HA, Khoshkholgh-Sima NA, Etesami H. Mining the roots of various species of the halophyte Suaeda for halotolerant nitrogen-fixing endophytic bacteria with the potential for promoting plant growth. Int Microbiol 2020; 23:415-427. [PMID: 31898032 DOI: 10.1007/s10123-019-00115-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022]
Abstract
Saline area may tend to be a productive land; however, many of salt-affected soils have nitrogen limitation and depend on plant-associated diazotrophs as their source of 'new' nitrogen. Herein, a total of 316 salinity tolerant nitrogen-fixing endophytic bacteria were isolated from roots of the halophyte Suaeda sp. sampled from 22 different areas of Iran to prepare the collection of nitrogen-fixing bacterial endophytes and evaluate the plant growth-promoting effect of effective isolates on growth of the halophyte Suaeda maritima. All of the identified nitrogen-fixing endophytes were classified to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes phylum while we did not detect common nitrogen-fixing endophyte of glycophytes like Azospirillum. The genera Pseudomonas and Microbacterium were both encountered in high abundance in all samples, indicating that they might play an advanced role in the micro-ecosystem of the halophyte Suaeda. In addition, the results also showed that not only soil salinity can affect halophyte endophytic composition but also other factors such as geographical location, plant species, and other soil properties may be involved. Interestingly, only Zhihengliuella halotolerans and Brachybacterium sp. belonging to Actinobacteria could grow in semi-solid N-free (NFb) medium supplemented with 6% NaCl and highly enhanced growth of S. maritima in vitro. Overall, this study offers useful new resources for nitrogen-fixing endophytic bacteria which may be utilized to improve approaches for providing bio-fertilizer useful in saline-based agriculture.
Collapse
Affiliation(s)
- Frashad Alishahi
- Department of Soil Science, Agriculture & Natural Resources Campus, Faculty of Agricultural Engineering & Technology, University of Tehran, Daneshkadeh Ave., Karaj, Tehran, 31587-77871, Iran
| | - Hossein Ali Alikhani
- Department of Soil Science, Agriculture & Natural Resources Campus, Faculty of Agricultural Engineering & Technology, University of Tehran, Daneshkadeh Ave., Karaj, Tehran, 31587-77871, Iran.
| | - Nayer Azam Khoshkholgh-Sima
- Agriculture Biotechnology Research Institute of Iran (ABRII), Agriculture Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hassan Etesami
- Department of Soil Science, Agriculture & Natural Resources Campus, Faculty of Agricultural Engineering & Technology, University of Tehran, Daneshkadeh Ave., Karaj, Tehran, 31587-77871, Iran.
| |
Collapse
|
23
|
Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
Collapse
Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| |
Collapse
|
24
|
Deng ZS, Kong ZY, Zhang BC, Zhao LF. Insights into non-symbiotic plant growth promotion bacteria associated with nodules of Sphaerophysa salsula growing in northwestern China. Arch Microbiol 2019; 202:399-409. [DOI: 10.1007/s00203-019-01752-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 11/25/2022]
|
25
|
Zhang HL, Jia F, Li M, Yu F, Zhou B, Hao QH, Wang XL. Endophytic Bacillus
strains isolated from alfalfa (Medicago sativa
L.) seeds: enhancing the lifespan of Caenorhabditis elegans. Lett Appl Microbiol 2019; 68:226-233. [DOI: 10.1111/lam.13102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 07/31/2018] [Accepted: 11/22/2018] [Indexed: 11/28/2022]
Affiliation(s)
- H.-L. Zhang
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - F. Jia
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - M. Li
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - F. Yu
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - B. Zhou
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - Q.-H. Hao
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| | - X.-L. Wang
- College of Life Sciences; Agricultural University of Hebei; Baoding China
| |
Collapse
|
26
|
Muresu R, Porceddu A, Sulas L, Squartini A. Nodule-associated microbiome diversity in wild populations of Sulla coronaria reveals clues on the relative importance of culturable rhizobial symbionts and co-infecting endophytes. Microbiol Res 2019; 221:10-14. [PMID: 30825937 DOI: 10.1016/j.micres.2019.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/30/2023]
Abstract
The culturable bacteria from root nodules of Sulla coronaria growing in spontaneous conditions in Sardinia were characterized. This plant's peculiarity is to represent a legume still found in both wild and cropped statuses. We tested whether culturable bacteria would differ from those commonly isolated from its field-cropped varieties, to date exclusively represented by Rhizobium sullae. 63 isolates from 60 surface-sterilized nodules were analyzed by ARDRA and 16S rDNA sequencing. The official nitrogen-fixing symbiont Rhizobium sullae was found only in 25 nodules out of 60. The remaining nodules did not yield culturable rhizobia but a number of different endophytic genera including Pseudomonas sp. (17 nodules), Microbacterium sp. (15 nodules), Pantoea agglomerans (5 nodules). The situation appears therefore a hybrid between what is commonly observed in other Mediterranean legumes occurring only in wild status (featuring non-culturable rhizobia and arrays of culturable endophytes within nodules), as opposed to cropped legumes (endowed with fully culturable rhizobia and minimal endophytic occurrence). These findings, within a species bridging the ecology between native and cropped conditions, suggest insights on the relative importance of endophytic co-occupancy vs. true N-fixing symbiont culturability within nodules. The latter trait thus appears to accompany the domestication path of plants with a main trade-off of renouncing to interactions with a diversity of endophytic co-invaders; the relationships with those being critical in the non-cropped status. In fact, endophytes are known to promote plant growth in harsh conditions, which can be particularly stressful in the Mediterranean due to drought, highly calcareous soils, and pathogens outbreaks.
Collapse
Affiliation(s)
- Rosella Muresu
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, University of Sassari, Viale Italia 1, 07100, Sassari, Italy
| | - Leonardo Sulas
- Institute for the Animal Production System in Mediterranean Environment-National Research Council (ISPAAM CNR), Traversa La Crucca 3, 07100, Sassari, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Università 16, Legnaro, Padova, Italy.
| |
Collapse
|
27
|
Lu T, Ke M, Lavoie M, Jin Y, Fan X, Zhang Z, Fu Z, Sun L, Gillings M, Peñuelas J, Qian H, Zhu YG. Rhizosphere microorganisms can influence the timing of plant flowering. MICROBIOME 2018; 6:231. [PMID: 30587246 PMCID: PMC6307273 DOI: 10.1186/s40168-018-0615-0] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/17/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant phenology has crucial biological, physical, and chemical effects on the biosphere. Phenological drivers have largely been studied, but the role of plant microbiota, particularly rhizosphere microbiota, has not been considered. RESULTS We discovered that rhizosphere microbial communities could modulate the timing of flowering of Arabidopsis thaliana. Rhizosphere microorganisms that increased and prolonged N bioavailability by nitrification delayed flowering by converting tryptophan to the phytohormone indole acetic acid (IAA), thus downregulating genes that trigger flowering, and stimulating further plant growth. The addition of IAA to hydroponic cultures confirmed this metabolic network. CONCLUSIONS We document a novel metabolic network in which soil microbiota influenced plant flowering time, thus shedding light on the key role of soil microbiota on plant functioning. This opens up multiple opportunities for application, from helping to mitigate some of the effects of climate change and environmental stress on plants (e.g. abnormal temperature variation, drought, salinity) to manipulating plant characteristics using microbial inocula to increase crop potential.
Collapse
Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Michel Lavoie
- Quebec-Ocean and Takuvik Joint International Research Unit, Université Laval, Québec, G1VOA6 Canada
| | - Yujian Jin
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Xiaoji Fan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
| | - Michael Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109 Australia
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Barcelona, Catalonia Spain
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032 People’s Republic of China
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 People’s Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 People’s Republic of China
- State Key Lab of Urban and Regional Ecology, Research Center for Ecoenvironmental Sciences, Chinese Academy of Sciences, Beijing, 100085 People’s Republic of China
| |
Collapse
|
28
|
Cardoso P, Alves A, Silveira P, Sá C, Fidalgo C, Freitas R, Figueira E. Bacteria from nodules of wild legume species: Phylogenetic diversity, plant growth promotion abilities and osmotolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1094-1102. [PMID: 30248834 DOI: 10.1016/j.scitotenv.2018.06.399] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/04/2018] [Accepted: 06/30/2018] [Indexed: 05/23/2023]
Abstract
The demand for food with high nutritional value that can sustain the growth of human population while safeguarding sustainability deserves urgent attention. A possible strategy is the inoculation of crops with plant growth promoting (PGP) bacteria. Plants are naturally colonized by bacteria that can exert beneficial effects on growth and stress tolerance. N2 fixation by rhizobia in the root nodules of legumes is a well-known PGP effect. These bacteria can be used as inoculants to boost legumes productivity and can be especially interesting if they are able to survive to abiotic stresses, such as drought. Herein we report the phylogenetic diversity of bacteria colonizing the root nodules of several wild legume species, from four geographic locations in Portugal with different bioclimates. Interestingly, the vast majority of strains belonged to Flavobacterium, Pseudomonas and other genera apart from rhizobia. PGP abilities other than N2 fixation (production of indol acetic acid, siderophores and volatile organic compounds) and osmotolerance were screened. Location and host plant species did not influence PGP abilities and osmotolerance. Taken together, results evidenced that bacterial strains from wild legumes displaying PGP abilities and osmotolerance can be regarded as good candidates for inoculants of a broad range of hosts, including non-legumes.
Collapse
Affiliation(s)
- Paulo Cardoso
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Artur Alves
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Paulo Silveira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carina Sá
- Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Fidalgo
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Rosa Freitas
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Etelvina Figueira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| |
Collapse
|
29
|
Lima FR, Ferreira AJ, Menezes CG, Miranda VFO, Dourado MN, Araújo WL. Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil. Braz J Microbiol 2018; 49:714-722. [PMID: 29661568 PMCID: PMC6175710 DOI: 10.1016/j.bjm.2017.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/10/2017] [Accepted: 12/24/2017] [Indexed: 11/30/2022] Open
Abstract
Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic isolation site (São Paulo and Mato Grosso) but not the analyzed organs (utricle and stolon). We reported that six genera were common to both sample sites (São Paulo and Mato Grosso). These genera have previously been reported to be beneficial to plants, as well as related to the bioremediation process, showing that these isolates present great biotechnological and agricultural potential. This is the first report of an Acidobacteria isolated from U. breviscapa. The role of these bacteria inside the plant must be further investigated in order to understand their population dynamics within the host.
Collapse
Affiliation(s)
- Felipe Rezende Lima
- Departmento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, 05508-900 São Paulo, SP, Brazil; Núcleo Integrado de Biotecnologia, NIB, Universidade de Mogi das Cruzes, Av. Dr. Cândido Xavier de Almeida Souza, 200, Centro cívico, 08780-911 Mogi das Cruzes, SP, Brazil
| | - Almir José Ferreira
- Departmento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, 05508-900 São Paulo, SP, Brazil; Núcleo Integrado de Biotecnologia, NIB, Universidade de Mogi das Cruzes, Av. Dr. Cândido Xavier de Almeida Souza, 200, Centro cívico, 08780-911 Mogi das Cruzes, SP, Brazil
| | - Cristine Gobbo Menezes
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista UNESP, Via de acesso Prof. Paulo Donato Castellane s/n, Centro, 14884-900 Jaboticabal, SP, Brazil
| | - Vitor Fernandes Oliveira Miranda
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista UNESP, Via de acesso Prof. Paulo Donato Castellane s/n, Centro, 14884-900 Jaboticabal, SP, Brazil
| | - Manuella Nóbrega Dourado
- Departmento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, 05508-900 São Paulo, SP, Brazil.
| | - Welington Luiz Araújo
- Departmento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, 05508-900 São Paulo, SP, Brazil; Núcleo Integrado de Biotecnologia, NIB, Universidade de Mogi das Cruzes, Av. Dr. Cândido Xavier de Almeida Souza, 200, Centro cívico, 08780-911 Mogi das Cruzes, SP, Brazil.
| |
Collapse
|
30
|
Mahdhi M, Houidheg N, Mahmoudi N, Msaadek A, Rejili M, Mars M. Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils. Pol J Microbiol 2018; 65:331-339. [PMID: 29334057 DOI: 10.5604/17331331.1215612] [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] [Indexed: 11/13/2022] Open
Abstract
Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole carbon and nitrogen source. The majority of isolate grew at pHs between 6 and 9, at temperatures up to 40°C and tolerated 3% NaCl concentrations. Phylogenetically, the new isolates were affiliated to four genera Sinorhizobium, Rhizobium, Mesorhizobium and Agrobacterium. About 73% of the isolates were species within the genera Sinorhizobium and Rhizobium. The isolates which failed to nodulate their host plants of origin were associated to Agrobacterium genus (three isolates).
Collapse
Affiliation(s)
- Mosbah Mahdhi
- Center for Environmental Research and Studies, Jazan University, Jazan, Kingdom of Saudi Arabia
| | - Nadia Houidheg
- Research Unit Biodiversity and Valorization of Arid Areas, Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, Gabès, Tunisia
| | - Neji Mahmoudi
- Research Unit Biodiversity and Valorization of Arid Areas, Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, Gabès, Tunisia
| | - Abdelhakim Msaadek
- Research Unit Biodiversity and Valorization of Arid Areas, Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, Gabès, Tunisia
| | - Mokhtar Rejili
- Research Unit Biodiversity and Valorization of Arid Areas, Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, Gabès, Tunisia
| | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas, Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, Gabès, Tunisia
| |
Collapse
|
31
|
Zhao L, Xu Y, Lai X. Antagonistic endophytic bacteria associated with nodules of soybean (Glycine max L.) and plant growth-promoting properties. Braz J Microbiol 2018; 49:269-278. [PMID: 29117917 PMCID: PMC5914205 DOI: 10.1016/j.bjm.2017.06.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 06/07/2017] [Accepted: 06/19/2017] [Indexed: 11/16/2022] Open
Abstract
A total of 276 endophytic bacteria were isolated from the root nodules of soybean (Glycine max L.) grown in 14 sites in Henan Province, China. The inhibitory activity of these bacteria against pathogenic fungus Phytophthora sojae 01 was screened in vitro. Six strains with more than 63% inhibitory activities were further characterized through optical epifluorescence microscopic observation, sequencing, and phylogenetic analysis of 16S rRNA gene, potential plant growth-promoting properties analysis, and plant inoculation assay. On the basis of the phylogeny of 16S rRNA genes, the six endophytic antagonists were identified as belonging to five genera: Enterobacter, Acinetobacter, Pseudomonas, Ochrobactrum, and Bacillus. The strain Acinetobacter calcoaceticus DD161 had the strongest inhibitory activity (71.14%) against the P. sojae 01, which caused morphological abnormal changes of fungal mycelia; such changes include fracture, lysis, formation of a protoplast ball at the end of hyphae, and split ends. Except for Ochrobactrum haematophilum DD234, other antagonistic strains showed the capacity to produce siderophore, indole acetic acid, and nitrogen fixation activity. Regression analysis suggested a significant positive correlation between siderophore production and inhibition ratio against P. sojae 01. This study demonstrated that nodule endophytic bacteria are important resources for searching for inhibitors specific to the fungi and for promoting effects for soybean seedlings.
Collapse
Affiliation(s)
- LongFei Zhao
- Shangqiu Normal University, College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu, Henan, PR China.
| | - YaJun Xu
- Shangqiu Normal University, College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu, Henan, PR China
| | - XinHe Lai
- The First Affiliated Hospital of Wenzhou Medical University, Institute of Inflammation & Diseases, Wenzhou, China
| |
Collapse
|
32
|
Molecular and phenotypic characterization of endophytic bacteria isolated from sulla nodules. Microb Pathog 2017; 111:225-231. [DOI: 10.1016/j.micpath.2017.08.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/18/2017] [Accepted: 08/30/2017] [Indexed: 11/30/2022]
|
33
|
Benito P, Alonso-Vega P, Aguado C, Luján R, Anzai Y, Hirsch AM, Trujillo ME. Monitoring the colonization and infection of legume nodules by Micromonospora in co-inoculation experiments with rhizobia. Sci Rep 2017; 7:11051. [PMID: 28887555 PMCID: PMC5591303 DOI: 10.1038/s41598-017-11428-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/23/2017] [Indexed: 11/11/2022] Open
Abstract
The discovery that the actinobacterium Micromonospora inhabits nitrogen-fixing nodules raised questions as to its potential ecological role. The capacity of two Micromonospora strains to infect legumes other than their original host, Lupinus angustifolius, was investigated using Medicago and Trifolium as test plants. Compatible rhizobial strains were used for coinoculation of the plants because Micromonospora itself does not induce nodulation. Over 50% of nodules from each legume housed Micromonospora, and using 16S rRNA gene sequence identification, we verified that the reisolated strains corresponded to the microorganisms inoculated. Entry of the bacteria and colonization of the plant hosts were monitored using a GFP-tagged Lupac 08 mutant together with rhizobia, and by using immunogold labeling. Strain Lupac 08 was localized in plant tissues, confirming its capacity to enter and colonize all hosts. Based on studying three different plants, our results support a non-specific relationship between Micromonospora and legumes. Micromonospora Lupac 08, originally isolated from Lupinus re-enters root tissue, but only when coinoculated with the corresponding rhizobia. The ability of Micromonospora to infect and colonize different legume species and function as a potential plant-growth promoting bacterium is relevant because this microbe enhances the symbiosis without interfering with the host and its nodulating and nitrogen-fixing microbes.
Collapse
Affiliation(s)
- Patricia Benito
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Pablo Alonso-Vega
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain
| | - Carolina Aguado
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha Albacete, Ciudad Real, Spain
| | - Rafael Luján
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Departamento Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha Albacete, Ciudad Real, Spain
| | - Yojiro Anzai
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Chiba, Japan
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology and Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, USA
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Campus Miguel de Unamuno, Universidad de Salamanca, Salamanca, Spain.
| |
Collapse
|
34
|
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat Biotechnol 2017; 35:676-683. [DOI: 10.1038/nbt.3886] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/21/2017] [Indexed: 12/16/2022]
Abstract
Abstract
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
Collapse
|
35
|
Bouchiba Z, Boukhatem ZF, Ighilhariz Z, Derkaoui N, Kerdouh B, Abdelmoumen H, Abbas Y, Missbah El Idrissi M, Bekki A. Diversity of nodular bacteria ofScorpiurus muricatusin western Algeria and their impact on plant growth. Can J Microbiol 2017; 63:450-463. [DOI: 10.1139/cjm-2016-0493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A total of 51 bacterial strains were isolated from root nodules of Scorpiurus muricatus sampled from 6 regions of western Algeria. Strain diversity was assessed by rep-PCR amplification fingerprinting, which grouped the isolates into 28 different clusters. Partial nucleotide sequencing of the 16S rRNA gene and BLAST analysis revealed that root nodules of S. muricatus were colonized by different species close to Rhizobium vignae, Rhizobium radiobacter, Rhizobium leguminosarum, Phyllobacterium ifriqiyense, Phyllobacterium endophyticum, Starkeya sp., and Pseudomonas sp. However, none of these strains was able to form nodules on its host plant; even nodC was present in a single strain (SMT8a). The inoculation test showed a great improvement in the growth of inoculated plants compared with noninoculated control plants. A significant amount of indole acetic acid was produced by some strains, but only 2 strains could solubilize phosphate. In this report we described for the first time the diversity of bacteria isolated from root nodules of S. muricatus growing in different regions in western Algeria and demonstrated their potential use in promoting plant growth.
Collapse
Affiliation(s)
- Zoulikha Bouchiba
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes, Université d’Oran1 Ahmed Ben Bella, Oran, Algérie
| | - Zineb Faiza Boukhatem
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes, Université d’Oran1 Ahmed Ben Bella, Oran, Algérie
| | - Zohra Ighilhariz
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes, Université d’Oran1 Ahmed Ben Bella, Oran, Algérie
| | - Nouria Derkaoui
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes, Université d’Oran1 Ahmed Ben Bella, Oran, Algérie
| | | | - Hanaa Abdelmoumen
- Laboratoire de Microbiologie et Biologie Moléculaire, Faculté des sciences, Université Mohammed V, Rabat, Maroc
| | - Younes Abbas
- Faculté Polydisciplinaire de Béni Mellal, Mghila B.P. 592, Université Sultan Moulay Slimane, Béni Mellal – Maroc
| | - Mustapha Missbah El Idrissi
- Laboratoire de Microbiologie et Biologie Moléculaire, Faculté des sciences, Université Mohammed V, Rabat, Maroc
| | - Abdelkader Bekki
- Laboratoire de Biotechnologie des Rhizobiums et Amélioration des Plantes, Université d’Oran1 Ahmed Ben Bella, Oran, Algérie
| |
Collapse
|
36
|
Korir H, Mungai NW, Thuita M, Hamba Y, Masso C. Co-inoculation Effect of Rhizobia and Plant Growth Promoting Rhizobacteria on Common Bean Growth in a Low Phosphorus Soil. FRONTIERS IN PLANT SCIENCE 2017; 8:141. [PMID: 28224000 PMCID: PMC5293795 DOI: 10.3389/fpls.2017.00141] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/23/2017] [Indexed: 05/22/2023]
Abstract
Nitrogen (N) fixation through legume-Rhizobium symbiosis is important for enhancing agricultural productivity and is therefore of great economic interest. Growing evidence indicates that other soil beneficial bacteria can positively affect symbiotic performance of rhizobia. Nodule endophytic plant growth promoting rhizobacteria (PGPR) were isolated from common bean nodules from Nakuru County in Kenya and characterized 16S rDNA partial gene sequencing. The effect of co-inoculation of rhizobium and PGPR, on nodulation and growth of common bean (Phaseolus vulgaris L.) was also investigated using a low phosphorous soil under greenhouse conditions. Gram-positive nodule endophytic PGPR belonging to the genus Bacillus were successfully isolated and characterized. Two PGPR strains (Paenibacillus polymyxa and Bacillus megaterium), two rhizobia strains (IITA-PAU 987 and IITA-PAU 983) and one reference rhizobia strain (CIAT 899) were used in the co-inoculation study. Two common bean varieties were inoculated with Rhizobium strains singly or in a combination with PGPR to evaluate the effect on nodulation and growth parameters. Co-inoculation of IITA-PAU 987 + B. megaterium recorded the highest nodule weight (405.2 mg) compared to IITA-PAU 987 alone (324.8 mg), while CIAT 899 + B. megaterium (401.2 mg) compared to CIAT 899 alone (337.2 mg). CIAT 899 + B. megaterium recorded a significantly higher shoot dry weight (7.23 g) compared to CIAT 899 alone (5.80 g). However, there was no significant difference between CIAT 899 + P. polymyxa and CIAT 899 alone. Combination of IITA-PAU 987 and B. megaterium led to significantly higher shoot dry weight (6.84 g) compared to IITA-PAU 987 alone (5.32 g) but no significant difference was observed when co-inoculated with P. polymyxa. IITA-PAU 983 in combination with P. polymyxa led to significantly higher shoot dry weight (7.15 g) compared to IITA-PAU 983 alone (5.14 g). Plants inoculated with IITA-PAU 987 and B. megaterium received 24.0 % of their nitrogen demand from atmosphere, which showed a 31.1% increase compared to rhizobium alone. Contrast analysis confirmed the difference between the co-inoculation of rhizobia strains and PGPR compared to single rhizobia inoculation on the root dry weight. These results show that co-inoculation of PGPR and Rhizobia has a synergistic effect on bean growth. Use of PGPR may improve effectiveness of Rhizobium biofertilizers for common bean production. Testing of PGPR under field conditions will further elucidate their effectiveness on grain yields of common bean.
Collapse
Affiliation(s)
- Hezekiah Korir
- Department of Crops, Horticulture and Soils, Egerton UniversityNjoro, Kenya
| | - Nancy W. Mungai
- Department of Crops, Horticulture and Soils, Egerton UniversityNjoro, Kenya
| | - Moses Thuita
- International Institute of Tropical AgricultureNairobi, Kenya
| | - Yosef Hamba
- Department of Molecular Biology and Biotechnology, Pan African University Institute of Basic Science, Technology and Innovation, Jomo Kenyatta University of Agriculture and TechnologyNairobi, Kenya
| | - Cargele Masso
- International Institute of Tropical AgricultureNairobi, Kenya
| |
Collapse
|
37
|
Bacterial Endophytes of Plants: Diversity, Invasion Mechanisms and Effects on the Host. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2017. [DOI: 10.1007/978-3-319-66541-2_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
38
|
|
39
|
Nonnodulating Bradyrhizobium spp. Modulate the Benefits of Legume-Rhizobium Mutualism. Appl Environ Microbiol 2016; 82:5259-68. [PMID: 27316960 DOI: 10.1128/aem.01116-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Rhizobia are best known for nodulating legume roots and fixing atmospheric nitrogen for the host in exchange for photosynthates. However, the majority of the diverse strains of rhizobia do not form nodules on legumes, often because they lack key loci that are needed to induce nodulation. Nonnodulating rhizobia are robust heterotrophs that can persist in bulk soil, thrive in the rhizosphere, or colonize roots as endophytes, but their role in the legume-rhizobium mutualism remains unclear. Here, we investigated the effects of nonnodulating strains on the native Acmispon-Bradyrhizobium mutualism. To examine the effects on both host performance and symbiont fitness, we performed clonal inoculations of diverse nonnodulating Bradyrhizobium strains on Acmispon strigosus hosts and also coinoculated hosts with mixtures of sympatric nodulating and nonnodulating strains. In isolation, nonnodulating Bradyrhizobium strains did not affect plant performance. In most cases, coinoculation of nodulating and nonnodulating strains reduced host performance compared to that of hosts inoculated with only a symbiotic strain. However, coinoculation increased host performance only under one extreme experimental treatment. Nearly all estimates of nodulating strain fitness were reduced in the presence of nonnodulating strains. We discovered that nonnodulating strains were consistently capable of coinfecting legume nodules in the presence of nodulating strains but that the fitness effects of coinfection for hosts and symbionts were negligible. Our data suggest that nonnodulating strains most often attenuate the Acmispon-Bradyrhizobium mutualism and that this occurs via competitive interactions at the root-soil interface as opposed to in planta IMPORTANCE Rhizobia are soil bacteria best known for their capacity to form root nodules on legume plants and enhance plant growth through nitrogen fixation. Yet, most rhizobia in soil do not have this capacity, and their effects on this symbiosis are poorly understood. We investigated the effects of diverse nonnodulating rhizobia on a native legume-rhizobium symbiosis. Nonnodulating strains did not affect plant growth in isolation. However, compared to inoculations with symbiotic rhizobia, coinoculations of symbiotic and nonnodulating strains often reduced plant and symbiont fitness. Coinoculation increased host performance only under one extreme treatment. Nonnodulating strains also invaded nodule interiors in the presence of nodulating strains, but this did not affect the fitness of either partner. Our data suggest that nonnodulating strains may be important competitors at the root-soil interface and that their capacity to attenuate this symbiosis should be considered in efforts to use rhizobia as biofertilizers.
Collapse
|
40
|
Fidalgo C, Riesco R, Henriques I, Trujillo ME, Alves A. Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2016; 66:4492-4500. [PMID: 27498827 DOI: 10.1099/ijsem.0.001379] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three actinobacterial strains were isolated from roots of the salt-marsh plant Halimione portulacoides collected in Ria de Aveiro, Portugal. Molecular typing using enterobacterial repetitive intergenic consensus ERIC-PCR fingerprinting showed the strains to be highly similar. Phylogenetic analyses based on the 16S rRNA gene sequence and multilocus sequence analysis (MLSA) using gyrB, rpoB, recA and ppk and 16S rRNA genes sequences showed that the strains represented a member of the genus Microbacterium, with Microbacterium lacus DSM 18910T as the closest phylogenetic relative. DNA-DNA hybridization between strain RZ63T and its closest relative was below 70 %, supporting the hypothesis that it represented a distinct genomic species. Chemotaxonomic analyses of the novel strains and their DNA G+C contents confirmed their affiliation to the genus Microbacterium, however, the peptidoglycan of RZ63T contained diaminobutyric acid as the diagnostic diamino acid. In addition, physiological and fatty acid analyses revealed differences between these strains and their phylogenetic relatives, reinforcing their status as a distinct species. Based on the physiological, genetic and chemotaxonomic characterisation it is proposed that the strains studied represent a novel species of the genus Microbacterium for which the name Microbacterium diaminobutyricum sp. nov. is proposed (type strain RZ63T=DSM 27101T=CECT 8355T).
Collapse
Affiliation(s)
- Cátia Fidalgo
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.,Departamento de Biologia, iBiMED, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Isabel Henriques
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.,Departamento de Biologia, iBiMED, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab. 214, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Artur Alves
- Departamento de Biologia, CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| |
Collapse
|
41
|
HANNANE FZ, KACEM M, KAID HARCHE M. Preliminary characterization of slow growing rhizobial strains isolated from Retama monosperma (L.) Boiss. root nodules from Northwest coast of Algeria. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2016.15226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
42
|
Fidalgo C, Henriques I, Rocha J, Tacão M, Alves A. Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:10200-14. [PMID: 26875822 DOI: 10.1007/s11356-016-6208-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/29/2016] [Indexed: 05/27/2023]
Abstract
Halimione portulacoides is abundant in salt marshes, accumulates mercury (Hg), and was proposed as useful for phytoremediation and pollution biomonitoring. Endophytic bacteria promote plant growth and provide compounds with industrial applications. Nevertheless, information about endophytic bacteria from H. portulacoides is scarce. Endophytic isolates (n = 665) were obtained from aboveground and belowground plant tissues, from two Hg-contaminated sites (sites E and B) and a noncontaminated site (site C), in the estuary Ria de Aveiro. Representative isolates (n = 467) were identified by 16S rRNA gene sequencing and subjected to functional assays. Isolates affiliated with Proteobacteria (64 %), Actinobacteria (23 %), Firmicutes (10 %), and Bacteroidetes (3 %). Altererythrobacter (7.4 %), Marinilactibacillus (6.4 %), Microbacterium (10.2 %), Salinicola (8.8 %), and Vibrio (7.8 %) were the most abundant genera. Notably, Salinicola (n = 58) were only isolated from site C; Hoeflea (17), Labrenzia (22), and Microbacterium (67) only from belowground tissues. This is the first report of Marinilactibacillus in the endosphere. Principal coordinate analysis showed that community composition changes with the contamination gradient and tissue. Our results suggest that the endosphere of H. portulacoides represents a diverse bacterial hotspot including putative novel species. Many isolates, particularly those affiliated to Altererythrobacter, Marinilactibacillus, Microbacterium, and Vibrio, tested positive for enzymatic activities and plant growth promoters, exposing H. portulacoides as a source of bacteria and compounds with biotechnological applications.
Collapse
Affiliation(s)
- Cátia Fidalgo
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Jaqueline Rocha
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Marta Tacão
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Artur Alves
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| |
Collapse
|
43
|
Biodiversity and biogeography of rhizobia associated with common bean (Phaseolus vulgaris L.) in Shaanxi Province. Syst Appl Microbiol 2016; 39:211-219. [DOI: 10.1016/j.syapm.2016.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 11/23/2022]
|
44
|
Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 933] [Impact Index Per Article: 116.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
Collapse
Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
| |
Collapse
|
45
|
Trujillo ME, Riesco R, Benito P, Carro L. Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants. Front Microbiol 2015; 6:1341. [PMID: 26648923 PMCID: PMC4664631 DOI: 10.3389/fmicb.2015.01341] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.
Collapse
Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Patricia Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| |
Collapse
|
46
|
Cold-Active, Heterotrophic Bacteria from the Highly Oligotrophic Waters of Lake Vanda, Antarctica. Microorganisms 2015; 3:391-406. [PMID: 27682095 PMCID: PMC5023249 DOI: 10.3390/microorganisms3030391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/05/2015] [Accepted: 07/09/2015] [Indexed: 11/16/2022] Open
Abstract
The permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica are distinctive ecosystems that consist strictly of microbial communities. In this study, water samples were collected from Lake Vanda, a stratified Dry Valley lake whose upper waters (from just below the ice cover to nearly 60 m) are highly oligotrophic, and used to establish enrichment cultures. Six strains of psychrotolerant, heterotrophic bacteria were isolated from lake water samples from a depth of 50 or 55 m. Phylogenetic analyses showed the Lake Vanda strains to be species of Nocardiaceae, Caulobacteraceae, Sphingomonadaceae, and Bradyrhizobiaceae. All Lake Vanda strains grew at temperatures near or below 0 °C, but optimal growth occurred from 18 to 24 °C. Some strains showed significant halotolerance, but no strains required NaCl for growth. The isolates described herein include cold-active species not previously reported from Dry Valley lakes, and their physiological and phylogenetic characterization broadens our understanding of these limnologically unique lakes.
Collapse
|
47
|
Extra-slow-growing Tardiphaga strains isolated from nodules of Vavilovia formosa (Stev.) Fed. Arch Microbiol 2015; 197:889-98. [PMID: 26013968 DOI: 10.1007/s00203-015-1122-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Eleven extra-slow-growing strains were isolated from nodules of the relict legume Vavilovia formosa growing in North Ossetia (Caucasus) and Armenia. All isolates formed a single rrs cluster together with the type strain Tardiphaga robiniae LMG 26467(T), while the sequencing of the 16S-23S rDNA intergenic region (ITS) and housekeeping genes glnII, atpD, dnaK, gyrB, recA and rpoB divided them into three groups. North Ossetian isolates (in contrast to the Armenian ones) were clustered separately from the type strain LMG 26467(T). However, all isolates were classified as T. robiniae because the DNA-DNA relatedness between them and the type strain LMG 26467(T) was 69.6% minimum. Two symbiosis-related genes (nodM and nodT) were amplified in all isolated Tardiphaga strains. It was shown that the nodM gene phylogeny is similar to that of ITS and housekeeping genes. The presence of the other symbiosis-related genes in described Tardiphaga strains, which is recently described genus of rhizobia, as well as their ability to form nodules on any plants are under investigation.
Collapse
|
48
|
Chihaoui SA, Trabelsi D, Jdey A, Mhadhbi H, Mhamdi R. Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects richness and structure of rhizosphere bacterial communities and enhances nodulation and growth. Arch Microbiol 2015; 197:805-13. [PMID: 25967041 DOI: 10.1007/s00203-015-1118-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 11/25/2022]
Abstract
Agrobacterium sp. 10C2 is a nonpathogenic and non-symbiotic nodule-endophyte strain isolated from root nodules of Phaseolus vulgaris. The effect of this strain on nodulation, plant growth and rhizosphere bacterial communities of P. vulgaris is investigated under seminatural conditions. Inoculation with strain 10C2 induced an increase in nodule number (+54 %) and plant biomass (+16 %). Grains also showed a significant increase in phosphorus (+53 %), polyphenols (+217 %), flavonoids (+62 %) and total antioxidant capacity (+82 %). The effect of strain 10C2 on bacterial communities was monitored using terminal restriction fragment length polymorphism of PCR-amplified 16S rRNA genes. When the initial soil was inoculated with strain 10C2 and left 15 days, the Agrobacterium strain did not affect TRF richness but changed structure. When common bean was sown in these soils and cultivated during 75 days, both TRF richness and structure were affected by strain 10C2. TRF richness increased in the rhizosphere soil, while it decreased in the bulk soil (root free). The taxonomic assignation of TRFs induced by strain 10C2 in the bean rhizosphere revealed the presence of four phyla (Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria) with a relative preponderance of Firmicutes, represented mainly by Bacillus species. Some of these taxa (i.e., Bacillus licheniformis, Bacillus pumilus, Bacillus senegalensis, Bacillus subtilis, Bacillus firmus and Paenibacillus koreensis) are particularly known for their plant growth-promoting potentialities. These results suggest that the beneficial effects of strain 10C2 observed on plant growth and grain quality are explained at least in part by the indirect effect through the promotion of beneficial microorganisms.
Collapse
Affiliation(s)
- Saif-Allah Chihaoui
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, 2050, Hammam-Lif, Tunisia
| | | | | | | | | |
Collapse
|
49
|
Ezzakkioui F, El Mourabit N, Chahboune R, Castellano-Hinojosa A, Bedmar EJ, Barrijal S. Phenotypic and genetic characterization of rhizobia isolated from Hedysarum flexuosum in Northwest region of Morocco. J Basic Microbiol 2015; 55:830-7. [PMID: 25721451 DOI: 10.1002/jobm.201400790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/22/2015] [Indexed: 11/11/2022]
Abstract
Seventy bacterial strains were isolated from root nodules of the legume Hedysarum flexuosum grown wild in soils from Northwest Morocco. Repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) clustered the strains into 30 REP-PCR groups. The nearly complete sequence of the 16S rRNA gene from a representative strain of each REP-PCR pattern showed that 17 strains were closely related to members of the genus Rhizobium of the family Rhizobiaceae of the Alphaproteobacteria. Pairwise alignments between globally aligned sequences of the 16S rRNA gene indicated that the strains from H. flexuosum had 99.75-100% identity with Rhizobium sullae type strain IS123(T). The phenotypic characteristics analyzed allowed description of a wide physiological diversity among the isolates, where the carbohydrate assimilation test was the most discriminating. Analysis of the 16S rRNA gene of a representative strains from the remaining 13 REP-PCR groups showed they belong to a wide variety of phylogenetic groups being closely related to species of genera Stenotrophomonas, Serratia, Massilia, Acinetobacter, Achromobacter, and Pseudomonas from the Beta- and Gammaproteobacteria. The R. sullae strains identified in this study produced effective symbiosis with their original host plant. None of the other bacterial strains could form nodules on H. flexuosum.
Collapse
Affiliation(s)
- Fatima Ezzakkioui
- Lab. Valorisation Biotechnologique des Microorganismes, Faculty of Sciences and Techniques, University Abdelmalek Essaadi, Tanger, Morocco
| | | | - Rajaa Chahboune
- Lab. Valorisation Biotechnologique des Microorganismes, Faculty of Sciences and Techniques, University Abdelmalek Essaadi, Tanger, Morocco.,Faculté Polydisciplinaire de Nador, Morocco
| | - Antonio Castellano-Hinojosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia CSIC, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia CSIC, Granada, Spain
| | - Said Barrijal
- Lab. Valorisation Biotechnologique des Microorganismes, Faculty of Sciences and Techniques, University Abdelmalek Essaadi, Tanger, Morocco
| |
Collapse
|
50
|
Pandya M, Rajput M, Rajkumar S. Exploring plant growth promoting potential of non rhizobial root nodules endophytes of Vigna radiata. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715010105] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|