A Culture-Independent and Culture-Dependent Study of the Bacterial Community from the Bedrock Soil Interface

Olsson-Francis, Karen; Boardman, Carl; Pearson, Victoria K.; Schofield, P. F.; Oliver, Anna; Summers, Stephen

doi:10.4236/aim.2015.513089

Cited by 12 publications

(23 citation statements)

References 69 publications

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“…Therefore, by combining culturing and non‐culture methods, the micro‐ecological effects of the addition of microbial inocula to soil can be determined with accuracy. Many studies suggested the significance of combining culture‐dependent and culture‐independent methods to gain deeper insights into population structure and diversity of complex microbial communities (Liu et al., ; Lü et al., ; Olsson‐Francis et al., ; Zhang et al., ).…”

Section: Introductionmentioning

confidence: 99%

Effects of genetically modified Burkholderia pyrrocinia JK‐SH007E1 on soil microbial community in poplar rhizosphere

et al. 2018

Forest Pathology

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Summary It is important to assess the biosafety of genetically engineered bacteria before release into the environment. In a previous study, the genetically engineered bacterium Burkholderia pyrrocinia JK‐SH007E1 was developed, showing biological control activity against a poplar canker disease. In the present work, the potential effects of B. pyrrocinia JK‐SH007E1 on soil microbial diversity and population structure in the poplar rhizosphere were assessed. The micro‐ecological effects of JK‐SH007E1 on soil microbial communities were investigated using substrate utilization assays (Biolog EcoPlate), enzyme activity assays and 16S rRNA sequencing to research species diversity and population structure of soil microbial communities. The genetically engineered isolate JK‐SH007E1 improved the functional diversity, soil enzyme activities and alpha diversity of soil microbial communities. However, the positive effects after inoculation attenuated with time, except for soil enzyme activities. Treatments with JK‐SH007 or JK‐SH007E1 were not different in impacts on soil enzyme activity and functional diversity of soil microbial communities. The results demonstrated that inoculation of JK‐SH007E1 into the poplar rhizosphere posed little or no threat to soil microbial communities in the long term. This work provides an additional insight into the effects of genetically engineered JK‐SH007E1 on the environment during long‐term use as biological control against poplar canker diseases.

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Section: Introductionmentioning

confidence: 99%

Effects of genetically modified Burkholderia pyrrocinia JK‐SH007E1 on soil microbial community in poplar rhizosphere

et al. 2018

Forest Pathology

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“…The mechanisms employed by microorganisms in basaltic environments are variable and range from the production of excess protons, to the production of low molecular weight organic acids and siderophores (highly specific Fe (III) ligands), and, in some cases, and the production of extracellular polysaccharides and enzymes (Welch and Ullman, 1993 ; Vandevivere et al, 1994 ; Barker et al, 1998 ; Bennett et al, 2001 ; Wu et al, 2007 ; Olsson-Francis et al, 2015 ). These mechanisms may occur in the bulk phase or in local microenvironments, where concentrations would be much higher (Bennett et al, 2001 ).…”

Section: Introductionmentioning

confidence: 99%

Determination of Geochemical Bio-Signatures in Mars-Like Basaltic Environments

et al. 2017

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Bio-signatures play a central role in determining whether life existed on early Mars. Using a terrestrial basalt as a compositional analog for the martian surface, we applied a combination of experimental microbiology and thermochemical modeling techniques to identify potential geochemical bio-signatures for life on early Mars. Laboratory experiments were used to determine the short-term effects of biota on the dissolution of terrestrial basalt, and the formation of secondary alteration minerals. The chemoorganoheterotrophic bacterium, Burkholderia sp. strain B_33, was grown in a minimal growth medium with and without terrestrial basalt as the sole nutrient source. No growth was detected in the absence of the basalt. In the presence of basalt, during exponential growth, the pH decreased rapidly from pH 7.0 to 3.6 and then gradually increased to a steady-state of equilibrium of between 6.8 and 7.1. Microbial growth coincided with an increase in key elements in the growth medium (Si, K, Ca, Mg, and Fe). Experimental results were compared with theoretical thermochemical modeling to predict growth of secondary alteration minerals, which can be used as bio-signatures, over a geological timescale. We thermochemically modeled the dissolution of the basalt (in the absence of biota) in very dilute brine at 25°C, 1 bar; the pH was buffered by the mineral dissolution and precipitation reactions. Preliminary results suggested that at the water to rock ratio of 1 × 107, zeolite, hematite, chlorite, kaolinite, and apatite formed abiotically. The biotic weathering processes were modeled by varying the pH conditions within the model to adjust for biologic influence. The results suggested that, for a basaltic system, the microbially-mediated dissolution of basalt would result in “simpler” secondary alteration, consisting of Fe-hydroxide and kaolinite, under conditions where the abiotic system would also form chlorite. The results from this study demonstrate that, by using laboratory-based experiments and thermochemical modeling, it is possible to identify secondary alteration minerals that could potentially be used to distinguish between abiotic and biotic weathering processes on early Mars. This work will contribute to the interpretation of data from past, present, and future life detection missions to Mars.

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“…The local vegetation at all sites was dominated by Nardus and Moliniagrasses. Samples were collected aseptically in March 2013 using corers and stored as previously described [25]. X-ray diffraction (XRD) and X-ray fluorescence (XRF) analysis confirmed the composition of the bedrock was granite.…”

Section: Sample Collectionmentioning

confidence: 99%

“…Reads were removed from further analysis if one of the following criteria were met: 1) the read length was shorter than 150 bp, (2) number of ambiguous bases was greater than zero. The sequences were processed as previously described [25]. Rarefaction curves were generated using MG-RAST [30] and all sequences obtained in this study were submitted to MG-RAST [30] …”

Section: Bioinformatic Analysismentioning

confidence: 99%

“…Total nucleic acids were extracted from the isolates using the Phe: Chl: Iaa bead beating protocol described by [26]. The 16S rRNA gene was amplified using two sets of primers: 27f-Com2 and Com1-1541r, as previously described [25]. BioEdit software (v.7.1.3.0) was used to align the sequences and the resulting contigs were approximately 1500 bp in length.…”

Section: Isolation Of Bacteriamentioning

confidence: 99%

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A Study of the Microbial Community at the Interface between Granite Bedrock and Soil Using a Culture-Independent and Culture-Dependent Approach

Olsson-Francis¹,

Pearson²,

Schofield³

et al. 2016

AiM

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The dissolution of minerals plays an important role in the formation of soils and sediments. In nutrient limiting soils, minerals constitute a major reservoir of bio-essential cations. Of particular interest is granite as it is the major rock type of the continental land mass. Although certain bacteria have been shown to enhance weathering of granite-forming minerals, little is known about the dissolution of granite, at the whole rock scale, and the microbial community involved. In this study, both culture-independent and culture-dependent approaches were used to study the bacterial community at the interface between granite bedrock and nutrient limiting soil in Dartmoor National Park, United Kingdom. High throughput sequencing demonstrated that over 70% of the bacterial population consisted of the bacterial classes Bacilli, Beta-proteobacteria and Gamma-proteobacteria. Bacteria belonging to the genera Serratia, Pseudomonas, Bacillus, Paenibacillus, Chromobacterium and Burkholderia were isolated from the sample site. All of the isolates were able to grow in a minimal growth medium, which contained glucose and ammonium chloride, with granite as the sole source of bio-essential elements. Sixty six percent of the isolates significantly enhanced basalt dissolution (p < 0.05). Dissolution of Si, K, Ca and Mg correlated with production of oxalic acid and acidification. The results of this study suggest that microorganisms in nutrient limiting soils can enhance the rate of granite dissolution, which is an important part of the biogeo-* Corresponding author. K. Olsson-Francis et al. 234chemical cycle.

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A Culture-Independent and Culture-Dependent Study of the Bacterial Community from the Bedrock Soil Interface

Cited by 12 publications

References 69 publications

Effects of genetically modified Burkholderia pyrrocinia JK‐SH007E1 on soil microbial community in poplar rhizosphere

Effects of genetically modified Burkholderia pyrrocinia JK‐SH007E1 on soil microbial community in poplar rhizosphere

Determination of Geochemical Bio-Signatures in Mars-Like Basaltic Environments

A Study of the Microbial Community at the Interface between Granite Bedrock and Soil Using a Culture-Independent and Culture-Dependent Approach

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