Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia

Grönemeyer, Jann Lasse; Burbano, Claudia Sofía; Hurek, Thomas; Reinhold‐Hurek, Barbara

doi:10.1007/s11104-011-0798-7

Cited by 59 publications

(36 citation statements)

References 51 publications

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“…In one study, bacterial isolates from sorghum tissues were affiliated to the phyla Firmicutes, Actinobacteria, α-Proteobacteria and β-Proteobacteria, with no further characterisation (Grönemeyer et al, 2012). Ramond et al (2013) showed that the diversity of sorghum associated endophytic bacteria is lower than that of rhizospheric communities using t-RFLP and DGGE; however, the low resolution of the two fingerprinting techniques made it difficult to assign taxonomy for the recovered OTUs.…”

Section: Discussionmentioning

confidence: 99%

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Maropola

Ramond

Trindade

2015

Journal of Microbiological Methods

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Keywords:Metagenomic DNA extraction Endophytic bacteria Sorghum root and stem t-RFLP Pyrosequencing Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB-and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and stem microbiome diversities were analysed via 454 pyrosequencing, and this revealed that the two tissues harbour significantly different endophytic communities. Nevertheless, both communities are dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas; which have previously been shown to play a role in plant growth promotion. This study shows that DNA extraction protocols introduce biases in culture-independent studies of environmental microbial communities by influencing the mDNA quality, which impacts the microbial diversity analyses and evaluation. Using the broad-spectrum SDSbased DNA extraction protocol allows the recovery of the most diverse endophytic communities associated with sorghum tissues and, as such, establishes a reliable basis for future study of endophytic communities.

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Section: Discussionmentioning

confidence: 99%

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Maropola

Ramond

Trindade

2015

Journal of Microbiological Methods

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“…The ability to solubilize inorganic phosphate was tested by growing the bacterial isolates on Pikovskaya agar (Oxoid Ltd) dyed with bromophenol blue (Sigma-Aldrich Co.) [14] for 10 days at 30°C. The formation of more transparent zones around the bacterial colonies was indicative of inorganic phosphate solubilization on Pikovskaya agar.…”

Section: Inorganic Phosphate Solubilizationmentioning

confidence: 99%

“…The quantitative valuation of indole-3 acetic acid (IAA) was done according to [14], with slight modifications. Bacterial isolates were grown in VM-ethanol broth and adjusted to a concentration of OD 600 = 1.…”

Section: Quantitative Valuation Of Indole-3 Acetic Acid Productionmentioning

confidence: 99%

Isolation and Screening of Rhizosphere Bacteria from Grasses in East Kavango Region of Namibia for Plant Growth Promoting Characteristics

2015

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A diverse group of soil bacteria known as plant growth promoting rhizobacteria (PGPR) is able to inhabit the area close to plant roots and exert beneficial effects on plant growth. Beneficial interactions between rhizospheric bacteria and plants provide prospects for isolating culturable PGPR that can be used as bio-fertilizers for sustainable crop production in communities that cannot easily afford chemical fertilizers. This study was conducted with the aim of isolating rhizospheric bacteria from grasses along the Kavango River and screening the bacterial isolates for plant growth promoting characteristics. The bacteria were isolated from rhizospheres of Phragmites australis, Sporobolus sp., Vetiveria nigritana, Pennisetum glaucum and Sorghum bicolor. The isolates were screened for inorganic phosphate solubilization, siderophore production and indole-3-acetic acid (IAA) production. The nitrogen-fixing capability of the bacteria was determined by screening for the presence of the nifH gene. Up to 21 isolates were obtained from P. australis, Sporobolus sp., S. bicolor, P. glaucum and V. nigritana. The genera Bacillus, Enterobacter, Kocuria, Pseudomonas and Stenotrophomonas, identified via 16S rDNA were represented in the 13 PGPR strains isolated. The isolates exhibited more than one plant growth promoting trait and they were profiled as follows: three phosphate solubilizers, four siderophore producers, eight IAA producing isolates and five nitrogen-fixers. These bacteria can be used to develop bio-fertilizer inoculants for improved soil fertility management and sustainable production of local cereals.

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“…High concentration of copper (in the 500 μM range) was required to induce significant changes in the thermophilic bacterial community from the studied soils. (Table 3), including genera Massilia and Naxibacter, which contribute to plant growth promotion as identified in Massilia isolates [4]. Massilia sp.…”

Section: Characterization Of Soil Enrichmentsmentioning

confidence: 99%

Influence of Temperature and Copper on Oxalobacteraceae in Soil Enrichments

et al. 2015

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β-Proteobacteria is one of the most abundant phylum in soils, including autotrophic and heterotrophic ammonium-consumers with relevance in N circulation in soils. The effects of high-temperature events and phytosanitary treatments, such as copper amendments, on soil bacterial communities relevant to N-cycling remain to be studied. As an example, South Portugal soils are seasonally exposed to high-temperature periods, the temperature at the upper soil layers can reach over 40 °C. Here, we evaluated the dynamics of mesophilic and thermophilic bacteria from a temperate soil, in particular of heterotrophic β-Proteobacteria, regarding the ammonium equilibrium, as a function of temperature and copper treatment. Soil samples were collected from an olive orchard in southern Portugal. Selective enrichments were performed from samples under different conditions of temperature (30 and 50 °C) and copper supplementation (100 and 500 µM) in order to mime seasonal variations and phytosanitary treatments. Changes in the microbial communities under these conditions were examined by denaturing gradient gel electrophoresis, a molecular fingerprint technique. At moderate temperature--30 °C--either without or with copper addition, dominant members were identified as different strains belonging to genus Massilia, a genus of the Oxalobacteraceae (β-Proteobacteria), while at 50 °C, members of the Brevibacillus genus, phylum Firmicutes were also represented. Ammonium production during bacterial growth at moderate and high temperatures was not affected by copper addition. Results indicate that both copper and temperature selected specific tolerant bacterial strains with consequences for N-cycling in copper-treated orchards.

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Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia

Cited by 59 publications

References 51 publications

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Isolation and Screening of Rhizosphere Bacteria from Grasses in East Kavango Region of Namibia for Plant Growth Promoting Characteristics

Influence of Temperature and Copper on Oxalobacteraceae in Soil Enrichments

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