Assessment of 16S rRNA gene-based phylogenetic diversity and promising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat

Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.

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Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria

Frontiers in Microbiology ◽

10.3389/fmicb.2021.642587 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tessa E. Reid ◽

Vanessa N. Kavamura ◽

Maïder Abadie ◽

Adriana Torres-Ballesteros ◽

Mark Pawlett ◽

...

Keyword(s):

16S Rrna ◽

Plant Growth ◽

16S Rrna Gene ◽

Fertilizer Application ◽

Chemical Fertilizer ◽

Rrna Gene ◽

Plant Growth Promoting ◽

Total Community ◽

Inorganic Chemical ◽

Growth Promoting

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.

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Isolation and characterization of bacteria from tomato and assessment of its plant growth-promoting traits in three economically important crops in Al-Ahsa region, Saudi Arabia

Journal of Environmental Biology ◽

10.22438/jeb/42/4/mrn-1758 ◽

2021 ◽

Vol 42 (4) ◽

pp. 973-981

Author(s):

M.F. Aldayel ◽

◽

A. Khalifa ◽

Keyword(s):

Saudi Arabia ◽

Salt Stress ◽

16S Rrna ◽

Plant Growth ◽

Rrna Gene ◽

Eruca Sativa ◽

Plant Growth Promoting ◽

Number Of Leaves ◽

Growth Promoting ◽

Plant Growth Promoting Traits

Aim: This study aimed to isolate, characterize and assess the plant growth-promoting traits of bacterial isolates inhabiting the rhizosphere of Solanum lycopersicum L. (tomato) against three plants—Eruca sativa, Lepidium sativum and Raphanus sativum—from Saudi Arabia's Al-Ahsa region. Methodology: bacterial isolate designated as SLK10 was obtained from the rhizosphere of tomato grown in the Al-Ahsa region, Saudi Arabia. SLK10 was further characterized morphologically, biochemically and genotypically using 16S rRNA gene sequencing. The roles in alleviating salt stress effects on three important economic crops were also assessed by implementing a cross-inoculation strategy. Results: SLK10 formed a circular, non-pigmented and raised colony with an entire margin. The cells were rod shaped and Gram negative. SLK10 displayed multiple plant growth-stimulating features, such as the solubilization of inorganic phosphate and the production of phytohormones and acetoin. Comparative sequence analysis of 16S rRNA gene revealed that SLK10 belonged to Pseudomonas monteilii, to which it exhibited 99.86% sequence homology. SLK10 significantly promoted the length of primary root, stem and number of leaves in Eruca sativa, Lepidium sativumand Raphanus sativus growing under 1000 ppm salt stress. The number of leaves in L. sativum and R. sativus growing under 2000 ppm salt stress was substantially enhanced by SLK10. Interpretation: SLK10 is a plant growth-promoting bacterium and can be used as a green fertilizer to increase soil fertility and plant productivity in the Eastern region of Saudi Arabia.

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Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

Microorganisms ◽

10.3390/microorganisms8091291 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1291

Author(s):

Ivete Sandra Maquia ◽

Paula Fareleira ◽

Isabel Videira e Castro ◽

Denise R. A. Brito ◽

Ricardo Soares ◽

...

Keyword(s):

16S Rrna ◽

Plant Growth ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Fire Regimes ◽

Rrna Gene ◽

Wide Range ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Culture Dependent

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.

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Assessing the Plant Growth-promoting Traits and Host Specificity of Endophytic Bacteria of Pulse Crops

Legume Research - An International Journal ◽

10.18805/lr-4491 ◽

2021 ◽

Author(s):

R. Thamizh Vendan ◽

D. Balachandar

Keyword(s):

Plant Growth ◽

Endophytic Bacteria ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Growth And Yield ◽

Rrna Gene ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Rrna Gene Sequencing ◽

Plant Growth Promoting Traits

Background: Symbiotic associations between legumes and Rhizobia are ancient and fundamental. However, the plant growth-promoting endophytes other than Rhizobia are not yet fully explored for pulses productivity. The present study was aimed to isolate efficient endophytic bacteria from pulses, assess their diversity, screen their plant growth-promoting activities and to test their potential as bio inoculants for pulses.Methods: We have isolated several endophytic bacteria from pulse crops more specifically from blackgram (Vigna mungo) and greengram (Vigna radiata). After careful screening, 15 promising endophytic isolates were selected for this study. The identification of endophytic bacterial isolates was performed by 16S rRNA gene sequencing. The isolates were tested for their potential for the plant growth-promoting traits such as nitrogen fixation, phosphate solubilization, indole-3-acetic acid production, siderophore secretion and antifungal activity. Pot culture experiments were conducted with the screened potential endophytic cultures.Result: The 16S rRNA gene sequencing revealed that species of Enterobacter, Bacillus, Pantoea, Pseudomonas, Acromobacter, Ocrobacterium were found as endophytes in blackgram and greengram. The in vitro screening identified Bacillus pumilus (BG-E6), Pseudomonas fluorescens (BG-E5) and Bacillus licheniformis (BG-E3) from blackgram and Pseudomonas chlororaphis (GG-E2) and Bacillus thuringiensis (GG-E7) from greengram as potential plant growth-promoting endophytes. These strains showed antagonism against plant pathogenic fungi. Upon inoculation of these endophytic PGPR strains, the blackgram and greengram growth and yield got increased. Among the strains, BG-E6 recorded 14.7% increased yield in blackgram and GG-E2 accounted for a 19.5% yield increase in greengram compared to respective uninoculated control. The experimental results showed that there was a host specificity found among the endophytic bacterial cultures with pulses. The cross inoculation of endophytic strains did not perform well to enhance the growth and yield of their alternate hosts.

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Biofilm Producing Rhizobacteria With Multiple Plant Growth-Promoting Traits Promote Growth of Tomato Under Water-Deficit Stress

Frontiers in Microbiology ◽

10.3389/fmicb.2020.542053 ◽

2020 ◽

Vol 11 ◽

Author(s):

Md. Manjurul Haque ◽

Md Khaled Mosharaf ◽

Moriom Khatun ◽

Md. Amdadul Haque ◽

Md. Sanaullah Biswas ◽

...

Keyword(s):

Plant Growth ◽

Water Deficit ◽

Xanthomonas Campestris ◽

Plant Pathogens ◽

Water Deficit Stress ◽

Rrna Gene ◽

Growth Promoters ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Plant Growth Promoting Traits

Plant growth-promoting rhizobacteria (PGPR) not only enhance plant growth but also control phytopathogens and mitigate abiotic stresses, including water-deficit stress. In this study, 21 (26.9%) rhizobacterial strains isolated from drought-prone ecosystems of Bangladesh were able to form air–liquid (AL) biofilms in the glass test tubes containing salt-optimized broth plus glycerol (SOBG) medium. Based on 16S rRNA gene sequencing, Pseudomonas chlororaphis (ESR3 and ESR15), P. azotoformans ESR4, P. poae ESR6, P. fluorescens (ESR7 and ESR25), P. gessardii ESR9, P. cedrina (ESR12, ESR16, and ESR23), P. veronii (ESR13 and ESR21), P. parafulva ESB18, Stenotrophomonas maltophilia ESR20, Bacillus cereus (ESD3, ESD21, and ESB22), B. horikoshii ESD16, B. aryabhattai ESB6, B. megaterium ESB9, and Staphylococcus saprophyticus ESD8 were identified. Fourier transform infrared spectroscopy studies showed that the biofilm matrices contain proteins, polysaccharides, nucleic acids, and lipids. Congo red binding results indicated that these bacteria produced curli fimbriae and nanocellulose-rich polysaccharides. Expression of nanocellulose was also confirmed by Calcofluor binding assays and scanning electron microscopy. In vitro studies revealed that all these rhizobacterial strains expressed multiple plant growth-promoting traits including N2 fixation, production of indole-3-acetic acid, solubilization of nutrients (P, K, and Zn), and production of ammonia, siderophores, ACC deaminase, catalases, lipases, cellulases, and proteases. Several bacteria were also tolerant to multifarious stresses such as drought, high temperature, extreme pH, and salinity. Among these rhizobacteria, P. cedrina ESR12, P. chlororaphis ESR15, and B. cereus ESD3 impeded the growth of Xanthomonas campestris pv. campestris ATCC 33913, while P. chlororaphis ESR15 and B. cereus ESD21 prevented the progression of Ralstonia solanacearum ATCC® 11696TM. In a pot experiment, tomato plants inoculated with P. azotoformans ESR4, P. poae ESR6, P. gessardii ESR9, P. cedrina ESR12, P. chlororaphis ESR15, S. maltophilia ESR20, P. veronii ESR21, and B. aryabhattai ESB6 exhibited an increased plant growth compared to the non-inoculated plants under water deficit-stressed conditions. Accordingly, the bacterial-treated plants showed a higher antioxidant defense system and a fewer tissue damages than non-inoculated plants under water-limiting conditions. Therefore, biofilm-producing PGPR can be utilized as plant growth promoters, suppressors of plant pathogens, and alleviators of water-deficit stress.

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