Molecular Identification of Iron Oxidizing Bacteria Isolated from Acid Mine Drainages in Peru

2013 ◽  
Vol 825 ◽  
pp. 84-87 ◽  
Author(s):  
Michel Abanto ◽  
Nicolaza Pariona ◽  
Julio Calderon ◽  
Gregory Guerra ◽  
Rina Ramirez ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
Mine Drainage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Mine ◽  
The North ◽  
Acidophilic Bacteria ◽  
Iron Oxidizing Bacteria ◽  
Acid Mine Drainage Generation

Acidophilic iron-oxidizing microorganisms are important in both environmental and biotechnological applications. These microorganisms are known to accelerate the dissolution of sulfur minerals such as pyrite (FeS2), leading to the acid mine drainage generation , a serious pollution problem, that makes these microorganisms essential to the commercial processing of minerals and sulfur. In order to answer this question, diversity of native acidophilic bacteria isolated from acid mine drainage of Peru was evaluated. The samples were collected from Yanacocha mining (3000 m.a.s.l.) located in the North of Cajamarca region, Yanamina mining (4440 m.a.s.l.) located in the middle of Huancavelica region; finally, SPCC mining (2000 m.a.s.l.) located in the South of Moquegua region. We isolated 11 strains from which three were identified asAcidithiobacillus ferrooxidans, two asAt. ferrivorans, two asAt. ferridurans,three asLeptospirillum ferrooxidansand one asAcidiphilium sp.by comparative sequencing of PCR-amplified 16S rRNA genes. Phylogenetic analysis of the 16S rRNA genes revealed that some of the strains isolated are closely related to other already known, but there are some with similarities lower than < 95 percent. Our results provide the first study on the diversity of iron-oxidizing bacteria isolated from acid mine drainage of Peru.

scholarly journals Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales-Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes

2003 ◽  
Vol 69 (9) ◽  
pp. 5512-5518 ◽  
Author(s):  
Brett J. Baker ◽  
Philip Hugenholtz ◽  
Scott C. Dawson ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Mine Drainage ◽  
Close Association ◽  
Variable Region ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Acid Mine

ABSTRACT During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name “Candidatus Captivus acidiprotistae.” To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.

scholarly journals Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site

2000 ◽  
Vol 66 (9) ◽  
pp. 3842-3849 ◽  
Author(s):  
Philip L. Bond ◽  
Steven P. Smriga ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
New Genus ◽  
Mine Drainage ◽  
Iron Oxidation ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metal Reduction ◽  
Acid Mine ◽  
Metabolic Feature

ABSTRACT An unusually thick (∼1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif. The slime was studied over the period of 1 year. The subaerial form of the slime distinguished it from more typical submerged streamers. Phylogenetic analysis of 16S rRNA genes revealed a diversity of sequences that were mostly novel. Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime. The most abundant of the 16S rRNA genes detected were from organisms related toLeptospirillum species. The dominant sequence (71% of clones) may represent a new genus. Sequences within theArchaea of the Thermoplasmales lineage were detected. Most of these were only distantly related to known microorganisms. Also, sequences affiliating withAcidimicrobium were detected. Some of these were closely related to “Ferromicrobium acidophilus,” and others were affiliated with a lineage only represented by environmental clones. Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected. The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction. Thus, microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime. These results expand our knowledge of the biodiversity of acid mine drainage environments and extend our understanding of the ecology of extremely acidic systems.

scholarly journals Diversity of “Ca. Micrarchaeota” in Two Distinct Types of Acidic Environments and Their Associations with Thermoplasmatales

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 461 ◽  
Author(s):  
Olga V. Golyshina ◽  
Rafael Bargiela ◽  
Stepan V. Toshchakov ◽  
Nikolay A. Chernyh ◽  
Soshila Ramayah ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
Mine Drainage ◽  
Taxonomic Diversity ◽  
Kamchatka Peninsula ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Acid Mine ◽  
Acidic Environments

“Candidatus Micrarchaeota” are widely distributed in acidic environments; however, their cultivability and our understanding of their interactions with potential hosts are very limited. Their habitats were so far attributed with acidic sites, soils, peats, freshwater systems, and hypersaline mats. Using cultivation and culture-independent approaches (16S rRNA gene clonal libraries, high-throughput amplicon sequencing of V3-V4 region of 16S rRNA genes), we surveyed the occurrence of these archaea in geothermal areas on Kamchatka Peninsula and Kunashir Island and assessed their taxonomic diversity in relation with another type of low-pH environment, acid mine drainage stream (Wales, UK). We detected “Ca. Micrarchaeota” in thermophilic heterotrophic enrichment cultures of Kunashir and Kamchatka that appeared as two different phylotypes, namely “Ca. Mancarchaeum acidiphilum”-, and ARMAN-2-related, alongside their potential hosts, Cuniculiplasma spp. and other Thermoplasmatales archaea without defined taxonomic position. These clusters of “Ca. Micrarchaeota” together with three other groups were also present in mesophilic acid mine drainage community. Present work expands our knowledge on the diversity of “Ca. Micrarchaeota” in thermophilic and mesophilic acidic environments, suggests cultivability patterns of acidophilic archaea and establishes potential links between low-abundance species of thermophilic “Ca. Micrarchaeota” and certain Thermoplasmatales, such as Cuniculiplasma spp. in situ.

Assessing arsenic bioremediation potential of epilithic biofilms affected by acid-mine drainage

2020 ◽  
Author(s):  
Sarah Zecchin ◽  
Nicoletta Guerrieri ◽  
Evelien Jongepier ◽  
Leonardo Scaglioni ◽  
Gigliola Borgonovo ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Heterotrophic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sampling Point ◽  
Epilithic Biofilm ◽  
Acid Mine ◽  
Epilithic Biofilms

&lt;p&gt;Arsenic is a toxic but naturally abundant metalloid that globally leads to contamination in groundwater and soil, exposing millions of people to cancer and other arsenic-related diseases. In several areas in Northern Italy arsenic in soil and water exceeds law limits (20 mg kg&lt;sup&gt;-1&lt;/sup&gt; and 10 mg L&lt;sup&gt;-1&lt;/sup&gt;, respectively), due to both the mineralogy of bedrock and former mining activities. The Rio Rosso stream, located in the Anzasca Valley (Piedmont) is heavily affected by an acid mine drainage originated from an abandoned gold mine. Arsenic, together with other heavy metals, is transferred by the stream to the surrounding area. The stream is characterized by the presence of an extensive reddish epilithic biofilm at the opening of the mine and on the whole contaminated waterbed.&lt;/p&gt; &lt;p&gt;The aim of this study was to characterize the mechanisms allowing the biotic fraction of this biofilm to cope with extreme arsenic concentrations. The composition and functionality of the microbial communities constituting the epilithic biofilms sampled in the close proximity and downstream the mine were unraveled by 16S rRNA genes and shotgun Illumina sequencing in relation to the extreme physico-chemical parameters. In parallel, autotrophic and heterotrophic microbial populations were characterized &lt;em&gt;in vivo&lt;/em&gt; by enrichment cultivation and isolated strains were tested for their ability to perform arsenic redox transformation.&lt;/p&gt; &lt;p&gt;Preliminary analyses indicated that the biofilm accumulated arsenic in the order of 6 &amp;#183; 10&lt;sup&gt;3&lt;/sup&gt; mg kg&lt;sup&gt;-1&lt;/sup&gt;, in contrast to 0.14 mg L&lt;sup&gt;-1&lt;/sup&gt;, measured in the surrounding water. The main chemical parameter affecting the composition of the microbial community was the pH, being 2 next to the mine and 6.7 in the downstream sampling point. In both sampling sites iron- and sulfur-cycling microorganisms were retrieved by both cultivation and molecular methods. However, the diversity of the microbial community living next to the mine was significantly lower with respect to the community developed downstream. In the latter, autotrophic &lt;em&gt;Cyanobacteria&lt;/em&gt; belonging to the species &lt;em&gt;Tychonema&lt;/em&gt; were the dominant taxa. A complete arsenic cycle was shown to occur, with heterotrophic bacteria mainly responsible for arsenate reduction and autotrophic bacteria performing arsenite &amp;#160;oxidation.&lt;/p&gt; &lt;p&gt;These observations indicate that the epilithic biofilm living in the Rio Rosso stream represents a peculiar ecosystem where microorganisms cope with metalloid toxicity likely using diverse mechanisms. Such microbial metabolic properties might be exploited in bioremediation strategies applied in arsenic-contaminated environments.&lt;/p&gt;

scholarly journals Development and Application of Small-Subunit rRNA Probes for Assessment of Selected Thiobacillus Species and Members of the Genus Acidiphilium

2000 ◽  
Vol 66 (7) ◽  
pp. 3065-3072 ◽  
Author(s):  
Jordan Peccia ◽  
Eric A. Marchand ◽  
Joann Silverstein ◽  
Mark Hernandez
Keyword(s):  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Small Subunit ◽  
Rrna Genes ◽  
Ribosomal Database Project ◽  
Oligonucleotide Probes ◽  
Small Subunit Rrna ◽  
Variable Regions ◽  
Acid Mine ◽  
Acidophilic Bacteria

ABSTRACT Culture-dependent studies have implicated sulfur-oxidizing bacteria as the causative agents of acid mine drainage and concrete corrosion in sewers. Thiobacillus species are considered the major representatives of the acid-producing bacteria in these environments. Small-subunit rRNA genes from all of the Thiobacillus andAcidiphilium species catalogued by the Ribosomal Database Project were identified and used to design oligonucleotide DNA probes. Two oligonucleotide probes were synthesized to complement variable regions of 16S rRNA in the following acidophilic bacteria:Thiobacillus ferrooxidans and T. thiooxidans(probe Thio820) and members of the genus Acidiphilium(probe Acdp821). Using 32P radiolabels, probe specificity was characterized by hybridization dissociation temperature (Td ) with membrane-immobilized RNA extracted from a suite of 21 strains representing three groups of bacteria. Fluorochrome-conjugated probes were evaluated for use with fluorescent in situ hybridization (FISH) at the experimentally determinedTd s. FISH was used to identify and enumerate bacteria in laboratory reactors and environmental samples. Probing of laboratory reactors inoculated with a mixed culture of acidophilic bacteria validated the ability of the oligonucleotide probes to track specific cell numbers with time. Additionally, probing of sediments from an active acid mine drainage site in Colorado demonstrated the ability to identify numbers of active bacteria in natural environments that contain high concentrations of metals, associated precipitates, and other mineral debris.

Effects of remediation on the bacterial community of an acid mine drainage impacted stream

2012 ◽  
Vol 58 (11) ◽  
pp. 1316-1326 ◽  
Author(s):  
Suchismita Ghosh ◽  
Moumita Moitra ◽  
Christopher J. Woolverton ◽  
Laura G. Leff
Keyword(s):  
Community Structure ◽  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Environmental Conditions ◽  
Bacterial Community Structure ◽  
Mine Drainage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Mine ◽  
Reference Stream

Acid mine drainage (AMD) represents a global threat to water resources, and as such, remediation of AMD-impacted streams is a common practice. During this study, we examined bacterial community structure and environmental conditions in a low-order AMD-impacted stream before, during, and after remediation. Bacterial community structure was examined via polymerase chain reaction amplification of 16S rRNA genes followed by denaturing gradient gel electrophoresis. Also, bacterial abundance and physicochemical data (including metal concentrations) were collected and relationships to bacterial community structure were determined using BIO-ENV analysis. Remediation of the study stream altered environmental conditions, including pH and concentrations of some metals, and consequently, the bacterial community changed. However, remediation did not necessarily restore the stream to conditions found in the unimpacted reference stream; for example, bacterial abundances and concentrations of some elements, such as sulfur, magnesium, and manganese, were different in the remediated stream than in the reference stream. BIO-ENV analysis revealed that changes in pH and iron concentration, associated with remediation, primarily explained temporal alterations in bacterial community structure. Although the sites sampled in the remediated stream were in relatively close proximity to each other, spatial variation in community composition suggests that differences in local environmental conditions may have large impacts on the microbial assemblage.

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.

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