Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review

Cárdenas, Juan Pablo; Quatrini, Raquel; Holmes, David S.

doi:10.1016/j.resmic.2016.06.007

Cited by 62 publications

(29 citation statements)

References 98 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In our study, we could not exclude the possibility that putative chitinases only present in S. thermosulfidooxidans might endow them with an additional ability to degrade the lysates of fungi in bioleaching systems. This scenario might be reasonable as fungi were found in several acidic environments, such as AMD ecosystems (Mosier et al, 2016), although their functional roles in bioleaching heaps remain elusive (Cárdenas et al, 2016). …”

Section: Discussionmentioning

confidence: 98%

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

et al. 2017

View full text Add to dashboard Cite

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.

show abstract

Section: Discussionmentioning

confidence: 98%

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

et al. 2017

View full text Add to dashboard Cite

show abstract

“…are also capable of sulfur oxidation in the presence of organic carbon (Hallberg et al, 2001). The current knowledge of ISCs oxidations by sewer acidophiles is drawn from pure culture studies, proven evidence of enzyme activities, and from speculative inferences through bioinformatic genome and metagenome analyses (Mangold et al, 2011; Cárdenas et al, 2016). …”

Section: Physiology Of Acidophilic Microorganisms In Sewer Corrosionmentioning

confidence: 99%

The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment

Kappler

Jiang

et al. 2017

Front. Microbiol.

View full text Add to dashboard Cite

Concrete corrosion is one of the most significant problems affecting valuable sewer infrastructure on a global scale. This problem occurs in the aerobic zone of the sewer, where a layer of surface corrosion develops on the exposed concrete and the surface pH is typically lowered from around 11–10 (pristine concrete) to pH 2–4. Acidophilic microorganisms become established as biofilms within the concrete corrosion layer and enhance the loss of concrete mass. Until recently, the acidophilic community was considered to comprise relatively few species of microorganisms, however, the biodiversity of the corrosion community is now recognized as being extensive and varying from different sewer environmental conditions. The diversity of acidophiles in the corrosion communities includes chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs. The activity of these microorganisms is strongly affected by H2S levels in the sewer gas phase, although CO2, organic matter, and iron in the corrosion layer influence this acidic ecosystem. This paper briefly presents the conditions within the sewer that lead to the development of concrete corrosion in that environment. The review focuses on the acidophilic microorganisms detected in sewer corrosion environments, and then summarizes their proposed functions and physiology, especially in relation to the corrosion process. To our knowledge, this is the first review of acidophilic corrosion microbial communities, in which, the ecology and the environmental conditions (when available) are considered. Ecological studies of sewer corrosion are limited, however, where possible, we summarize the important metabolic functions of the different acidophilic species detected in sewer concrete corrosion layers. It is evident that microbial functions in the acidic sewer corrosion environment can be linked to those occurring in the analogous acidic environments of acid mine drainage and bioleaching.

show abstract

“…They comprise culture-dependent (plating, MPN counts) and biomolecular approaches such as the genetic fingerprinting techniques, terminal restriction fragment length polymorphism (T-RLFP; Wakeman et al, 2008), capillary electrophoresis single-strand conformation polymorphism (CE-SSCP; Foucher et al, 2003), denaturating gradient gel electrophoresis (DGGE; Demergasso et al, 2005; Halinen et al, 2009), microscopic methods like fluorescence in situ hybridization (FISH and CARD-FISH, Schippers et al, 2008), microarray approaches (e.g., Garrido et al, 2008; Remonsellez et al, 2009), quantitative real-time PCR (qPCR; Liu et al, 2006; Zhang et al, 2009), and next generation sequencing techniques (e.g., Cardenas et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

et al. 2016

View full text Add to dashboard Cite

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.

show abstract

Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review

Cited by 62 publications

References 98 publications

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

Contact Info

Product

Resources

About