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

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.

scholarly journals Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules

2021 ◽  
Vol 12 ◽  
Author(s):  
Faten Ghodhbane-Gtari ◽  
Timothy D’Angelo ◽  
Abdellatif Gueddou ◽  
Sabrine Ghazouani ◽  
Maher Gtari ◽  
...  
Keyword(s):  
16S Rrna ◽  
Plant Growth ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Actinorhizal Plants ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Metagenomic Sequencing ◽  
Plant Growth Promoting ◽  
Growth Promoting

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.

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

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.

scholarly journals Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 42 ◽  
Author(s):  
Clarisse Brígido ◽  
Sakshi Singh ◽  
Esther Menéndez ◽  
Maria Tavares ◽  
Bernard Glick ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Endophytic Bacteria ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Mn Toxicity ◽  
Rhizobial Inoculation ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Different Soils

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate’s genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates’ plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

scholarly journals Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis

2018 ◽  
Vol 83 (5) ◽  
pp. 1333-1341 ◽  
Author(s):  
Maria Teresa P. Gonçalves ◽  
María José Benito ◽  
María de Guía Córdoba ◽  
Conceição Egas ◽  
Almudena V. Merchán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

scholarly journals 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

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.

scholarly journals Influence of Filter Pore Size on Composition and Relative Abundance of Bacterial Communities and Select Host-Specific MST Markers in Coastal Waters of Southern Lake Michigan

2021 ◽  
Vol 12 ◽  
Author(s):  
Muruleedhara N. Byappanahalli ◽  
Meredith B. Nevers ◽  
Dawn Shively ◽  
Cindy H. Nakatsu ◽  
Julie L. Kinzelman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pore Size ◽  
Coastal Waters ◽  
Bacterial Communities ◽  
Lake Michigan ◽  
Relative Proportion ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Wide Range

Water clarity is often the primary guiding factor in determining whether a prefiltration step is needed to increase volumes processed for a range of microbial endpoints. In this study, we evaluate the effect of filter pore size on the bacterial communities detected by 16S rRNA gene sequencing and incidence of two host-specific microbial source tracking (MST) markers in a range of coastal waters from southern Lake Michigan, using two independent data sets collected in 2015 (bacterial communities) and 2016–2017 (MST markers). Water samples were collected from river, shoreline, and offshore areas. For bacterial communities, each sample was filtered through a 5.0-μm filter, followed by filtration through a 0.22-μm filter, resulting in 70 and 143 filter pairs for bacterial communities and MST markers, respectively. Following DNA extraction, the bacterial communities were compared using 16S rRNA gene amplicons of the V3–V4 region sequenced on a MiSeq Illumina platform. Presence of human (Bacteroides HF183) and gull (Gull2, Catellicoccus marimammalium) host-specific MST markers were detected by qPCR. Actinobacteriota, Bacteroidota, and Proteobacteria, collectively represented 96.9% and 93.9% of the relative proportion of all phyla in the 0.22- and 5.0-μm pore size filters, respectively. There were more families detected in the 5.0-μm pore size filter (368) than the 0.22-μm (228). There were significant differences in the number of taxa between the two filter sizes at all levels of taxonomic classification according to linear discriminant analysis (LDA) effect size (LEfSe) with as many as 986 taxa from both filter sizes at LDA effect sizes greater than 2.0. Overall, the Gull2 marker was found in higher abundance on the 5.0-μm filter than 0.22 μm with the reverse pattern for the HF183 marker. This discrepancy could lead to problems with identifying microbial sources of contamination. Collectively, these results highlight the importance of analyzing pre- and final filters for a wide range of microbial endpoints, including host-specific MST markers routinely used in water quality monitoring programs. Analysis of both filters may increase costs but provides more complete genomic data via increased sample volume for characterizing microbial communities in coastal waters.

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

2021 ◽  
pp. 126729
Author(s):  
Luis Guillermo Teheran-Sierra ◽  
Michelli Inácio Gonçalves Funnicelli ◽  
Lucas Amoroso Lopes de Carvalho ◽  
Maria Inês Tiraboschi Ferro ◽  
Marcos Antônio Soares ◽  
...  
Keyword(s):  
Plant Growth ◽  
Synergistic Effect ◽  
Bacterial Communities ◽  
Agricultural Management ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Plant Growth Promoting Traits
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