Predicting the Metabolic Potential of the Novel Iron Oxidising Bacterium "Ferrovum" sp. JA12 Using Comparative Genomics

2013 ◽  
Vol 825 ◽  
pp. 153-156 ◽  
Author(s):  
Sophie Mosler ◽  
Anja Poehlein ◽  
Sonja Voget ◽  
Rolf Daniel ◽  
Judith Kipry ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Acid Mine Drainage ◽  
Pilot Plant ◽  
Mine Drainage ◽  
The Novel ◽  
Metabolic Potential ◽  
Essential Nutrients ◽  
Novel Genus ◽  
Acid Mine ◽  
Powerful Approach

Here we describe the potential uptake and assimilation pathways for the essential nutrients C, N, P, and S in the acidophilic iron oxidiser Ferrovum strain JA12, a member of a novel genus among the Betaproteobacteria. Comparative genomics proved to be a powerful approach to give first insights into the biochemical potential of this novel genus and to understand the reasons for the dominating abundance of Ferrovum spp. in a pilot plant to remediate acid mine drainage.

scholarly journals Metagenome assembled genomes of novel taxa from an acid mine drainage environment

2021 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
Acid Mine

Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

scholarly journals Treatment of acid mine drainage with coal fly ash in a jet loop reactor pilot plant

2020 ◽  
Vol 159 ◽  
pp. 106611 ◽  
Author(s):  
Rosicky Methode Kalombe ◽  
Tunde Victor Ojumu ◽  
Vinny Ndjate Katambwe ◽  
Michael Nzadi ◽  
Denzil Bent ◽  
...  
Keyword(s):  
Fly Ash ◽  
Acid Mine Drainage ◽  
Pilot Plant ◽  
Mine Drainage ◽  
Coal Fly Ash ◽  
Loop Reactor ◽  
Acid Mine

scholarly journals Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 485 ◽  
Author(s):  
Alexis P Yelton ◽  
Luis R Comolli ◽  
Nicholas B Justice ◽  
Cindy Castelle ◽  
Vincent J Denef ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Structural Differentiation ◽  
Acid Mine

scholarly journals Metagenome assembled genomes of novel taxa from an acid mine drainage environment

2020 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
Acid Mine

ABSTRACTAcid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and include one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies.IMPORTANCEBioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

scholarly journals Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Shu-ning Ou ◽  
Jie-Liang Liang ◽  
Xiao-min Jiang ◽  
Bin Liao ◽  
Pu Jia ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Acid Mine Drainage ◽  
Single Molecule ◽  
High Throughput Sequencing ◽  
Mine Drainage ◽  
Acid Stress ◽  
Sequencing Technology ◽  
Metabolic Potential ◽  
Acid Mine ◽  
Adaptation Mechanisms

Fungi in acid mine drainage (AMD) environments are of great concern due to their potentials of decomposing organic carbon, absorbing heavy metals and reducing AMD acidity. Based on morphological analysis and ITS/18S high-throughput sequencing technology, previous studies have provided deep insights into the diversity and community composition of fungi in AMD environments. However, knowledge about physiology, metabolic potential and transcriptome profiles of fungi inhabiting AMD environments is still scarce. Here, we reported the physiological, genomic, and transcriptomic characterization of Acidiella bohemica SYSU C17045 to improve our understanding of the physiological, genomic, and transcriptomic mechanisms underlying fungal adaptation to AMD environments. A. bohemica was isolated from an AMD environment, which has been proved to be an acidophilic fungus in this study. The surface of A. bohemica cultured in AMD solutions was covered with a large number of minerals such as jarosite. We thus inferred that the A. bohemica might have the potential of biologically induced mineralization. Taking advantage of PacBio single-molecule real-time sequencing, we obtained the high-quality genome sequences of A. bohemica (50 Mbp). To our knowledge, this was the first attempt to employ a third-generation sequencing technology to explore the genomic traits of fungi isolated from AMD environments. Moreover, our transcriptomic analysis revealed that a series of genes in the A. bohemica genome were related to its metabolic pathways of C, N, S, and Fe as well as its adaptation mechanisms, including the response to acid stress and the resistance to heavy metals. Overall, our physiological, genomic, and transcriptomic data provide a foundation for understanding the metabolic potential and adaptation mechanisms of fungi in AMD environments.

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