Effect of Genetically Modified Poplars on Soil Microbial Communities during the Phytoremediation of Waste Mine Tailings

Abstract

The application of transgenic plants to clean up environmental pollution caused by the wastes of heavy metal mining is a promising method for removing metal pollutants from soils. However, the effect of using genetically modified organisms for phytoremediation is a poorly researched topic in terms of microbial community structures, despite the important role of microorganisms in the health of soil. In this study, a comparative analysis of the bacterial and archaeal communities found in the rhizosphere of genetically modified (GM) versus wild-type (WT) poplar was conducted on trees at different growth stages (i.e., the rhizospheres of 1.5-, 2.5-, and 3-year-old poplars) that were cultivated on contaminated soils together with nonplanted control soil. Based on the results of DNA pyrosequencing, poplar type and growth stages were associated with directional changes in the structure of the microbial community. The rate of change was faster in GM poplars than in WT poplars, but the microbial communities were identical in the 3-year-old poplars. This phenomenon may arise because of a higher rate and greater extent of metal accumulation in GM poplars than in naturally occurring plants, which resulted in greater changes in soil environments and hence the microbial habitat.Heavy metal pollution threatening human health and the ecosystem is a growing concern worldwide (55). Excessive levels of heavy metals cause serious damage to living organisms that inhabit such environments (3). Furthermore, as a result of the bioaccumulation of heavy metals over time, organisms that do not inhabit contaminated areas may also be subject to higher exposure through the food chain (67). One of the main sources of heavy metal pollution in soil, water, and sediments is the metal purification procedure, which includes mining, smelting, and the tailings from these industries (55). In Korea, approximately 1,000 metal mines have been suspended or closed in the last 30 years, with metal mine tailings amounting to about 10 million tons (40a). The leftover mine tailings contain high concentrations of heavy metals and are a major source of environmental pollution; thus, a number of physicochemical methods have been developed to prevent pollution and/or restore the ecosystem of polluted sites (51).Phytoremediation, which is the use of plants to clean up environmental pollution, has received much attention as a promising method for the removal of metal pollutants in soils (6, 66). Phytoremediation is a cost-effective and environmentally friendly approach compared to other environmentally invasive, expensive, and inefficient cleanup technologies (66). A number of plant species are capable of high-level organic compound degradation or heavy metal hyperaccumulation. Viable candidates for metal phytoremediation include the alpine pennycress Thlaspi caerulescens, the Indian mustard Brassica juncea, the sunflower Helianthusannuus, the yellow poplar Liriodendrontulipifera, and the shrub tobacco Nicotianaglaucum (6). However, slow rates of removal and incomp...

Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food,gajami-sikhae

“…V1, V2, and V3 variable regions of 16S rRNA genes were amplified using barcoded a fusion primers. 24,25) DNA amplification was executed using a mixture of 1 μL template DNA, 2 μL each primer (20 pmol), 1 μL dNTP (100 mM for each dNTP), 5 μL 10 × PCR buffer, 0.25 μL Taq polymerase (Roche, Mannheim, Germany), and 40.7 μL H 2 O in a C1000 Touch thermal cycler (Bio-Rad, Herculres, CA, USA). The PCR conditions were as follow: 5 min at 94°C (initial denaturation); 30 cycles of 30 s at 94°C (denaturation), 30 s at 55°C (annealing), 30 s at 72°C (extension); and 72°C for 7 min (final extension).…”

Bacterial and fungal community composition across the soil depth profiles in a fallow field

“…Pyrosequencing data were analyzed following the descriptions in previous studies (Chun et al 2010, Hur et al 2011, Kim et al 2012a. Reads obtained were sorted according to unique barcodes of the PCR products.…”

Assessment of Soil Microbial Communities in Carotenoid-Biofortified Rice Ecosystem

“…Investigating the microbial community structure from soil where Bt-maize were cultivated for four years showed a yearly difference in the microorganism taxon distribution and ratio, but no significant difference between Bt and non-Bt maize (Barriuso et al, 2012). Also, it has been reported that although there was a difference in the microorganism population structure at the early stages of GM plant cultivation, this level was stabilized and returned to similar levels between GM and non-GM crop after several years (Hur et al, 2011). As such, it is suggested that analyzing the effect of cultivating GM crop on the soil microbiota should be carried by on a case by case basis and both short-term and long-term studies need to be carried out.…”

“…Pyrosequencing Analysis The extracted metagenomic DNA was used for pyrosequencing analysis as in previous reports by Hur et al(2011). PCR amplifications were performed using a C1000 Touch thermal cycler (Bio-Rad, CA, USA) and barcorded fusion primers (http://www.…”

“…Until now, study on how GM crop impact the soil microbiota was analyzed by cultivation, molecular biological techniques such as DGGE or temperature gradient gel electrophoresis (TGGE), or soil enzyme-substrate utilization analysis such as community level physiological profiling (CLPP) of soil microbial community. However development of pyrosequencing, a next-generation sequencing technique, has made it possible to analyze a wider range of microorganisms and is now being applied to study the effect of GM crops on the soil microbial community (Barriuso et al, 2012;Hur et al, 2011;Lee et al, 2011). Numerous studies have shown how transgenes from GM crops can persist within the soil for a prolonged period Hay et al, 2002;Lee et al, 2007).…”