Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage

Mirete, Salvador; Figueras, Carolina G. de; González-Pastor, José Eduardo

doi:10.1128/aem.00048-07

Cited by 111 publications

(81 citation statements)

References 58 publications

(57 reference statements)

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“…Among them were members of the archaeal phylum Crenarchaeota, including clones from Origin sites 1 and 2 (OR1, OR2) related to sequences derived from an acidmine drainage study from the Chinese Tong ShanKou mine (96% similar to DQ901270). These were phylogenetically distinct from the crenarchaeal clones found in an RT rhizosphere study (Mirete et al, 2007) that branched among the South African gold mine crenarchaeal group-1. We further detected a singleton crenarchaeal clone from Berrocal site 2 (BE2) related to an archaeal sequence from a subsurface acid-mine drainage system (99% similar to AY082452).…”

Section: Resultsmentioning

confidence: 61%

Microbial community structure across the tree of life in the extreme Río Tinto

et al. 2010

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Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidencebased methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.

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Section: Resultsmentioning

confidence: 61%

Microbial community structure across the tree of life in the extreme Río Tinto

et al. 2010

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“…The other newly detected bacterial indicators of metal contamination identified here are Planctomyceteceae DQ906072 and Xanthomonadales FJ228294. The clone sequences of accession numbers DQ906072 and FJ228294 originate from the rhizosphere of plants adapted to acid mine drainage (50) and acidic mine pit lakes (www.ncbi.nlm.hih.gov), respectively. This supports our results, implying the presence of two unknown bacterial species that predominantly inhabit metal-contaminated acidic soils.…”

Section: Discussionmentioning

confidence: 99%

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

Hur

Kim

Song

et al. 2011

Appl Environ Microbiol

147

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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...

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“…In a recent metagenomic analysis of the rhizosphere of plants growing in the banks of Rio Tinto (Mirete et al 2007), new genetic systems conferring nickel resistance have been identified by screening an E. coli library: these include ABC transporters and enzymes, as serine acetyltransferase (SAT), which are known to play similar roles in hyperaccumulating plants (Freeman et al 2004). From these data an emerging hypothesis is that for bacteria several independent mechanisms may operate to confer metal resistance, emphasizing the role of the species' (and community's) gene pool and horizontal gene transfer other than that of single genes.…”

Section: Genes For Metal Resistance: Single Operons or Genome Adaptatmentioning

confidence: 99%

Plants as extreme environments? Ni-resistant bacteria and Ni-hyperaccumulators of serpentine flora

2009

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During recent years there has been an increasing interest in the bacterial communities occurring in unusual, often extreme, environments. On serpentine outcrops around the world, a high diversity of plant species showing the peculiar features of metal hyperaccumulation is present. These metal hyperaccumulators have received much attention for their potential biotechnological exploitation in phytoremediation processes, but also as unusual, extreme habitats for the associated bacterial flora, which could reveal novel details concerning bacterial adaptation. This paper will briefly focus on the research topics that have been addressed to date on bacteria associated with serpentine plants and aims to provide a state of the art and to present possible future directions for research which could lead to new insights on microbial adaptation and evolution, and potentially applied in technologies for sustainable use and remediation of contaminated land.

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Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage

Cited by 111 publications

References 58 publications

Microbial community structure across the tree of life in the extreme Río Tinto

Microbial community structure across the tree of life in the extreme Río Tinto

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

Plants as extreme environments? Ni-resistant bacteria and Ni-hyperaccumulators of serpentine flora

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