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.

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 Comparison of Acid Mine Drainage Microbial Communities in Physically and Geochemically Distinct Ecosystems

2000 ◽  
Vol 66 (11) ◽  
pp. 4962-4971 ◽  
Author(s):  
Philip L. Bond ◽  
Greg K. Druschel ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Acid Leaching ◽  
Massive Sulfide ◽  
Molecular Data ◽  
Oligonucleotide Probes ◽  
Acid Mine ◽  
Ore Body ◽  
A Site

ABSTRACT This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of ∼0.5 to ∼1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. “Ferroplasma” spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength.Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated.Sulfobacillus spp. were detected as a prominent inhabitant in warmer (∼43°C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.

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 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.

New microbiological strategies that enable the selective recovery and recycling of metals from acid mine drainage and mine process waters

2012 ◽  
Vol 76 (7) ◽  
pp. 2683-2692 ◽  
Author(s):  
I. Ňancucheo ◽  
S. Hedrich ◽  
D. B. Johnson
Keyword(s):  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Environmental Pollutants ◽  
Microbial Oxidation ◽  
Mine Waters ◽  
Acid Mine ◽  
Acidophilic Bacteria ◽  
Active Chemical ◽  
Valuable Metals ◽  
Commercial Value

AbstractApproaches currently used for remediating acid mine drainage (chiefly active chemical treatment and passive bioremediation systems) have a number of major detractions, including their failure to recover potentially valuable metals from these waters. Bioremediation strategies that utilize reactor-housed microorganisms can circumvent this problem, but have tended not to be widely used due to their relatively high costs. We have devised innovative approaches for remediating mine waters that use acidophilic bacteria to remove metals either as oxidized or reduced phases, using modular bioreactors that are designed to operate at minimal cost and to generate products that have commercial value. A composite system is described that combines microbial oxidation of ferrous iron with abiotic precipitation of ferric iron as schwertmannite, a mineral that has commercial value as an absorbent of arsenate and other environmental pollutants, and as a pigment. Sulfidogenic bioreactors maintained at acidic pH values are used to selectively precipitate metal sulfides, such as CuS. Tests with synthetic mine drainage containing mixtures of soluble metals confirmed that these systems can generate relatively pure mineral deposits from complex acid waters. The units are designed to be configured differently, according to the nature of the mine water requiring treatment.

scholarly journals The small ribosomal subunit RNA isoforms in Plasmodium cynomolgi.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 857-865 ◽  
Author(s):  
V Corredor ◽  
V Enea
Keyword(s):  
Ribosomal Subunit ◽  
Plasmodium Species ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Genes ◽  
Last Common Ancestor ◽  
Small Subunit Rrna ◽  
Specific Sequence ◽  
Variable Regions ◽  
Plasmodium Cynomolgi

Abstract We report the isolation, characterization and analysis of the small subunit rRNA genes in Plasmodium cynomolgi (Ceylon). As in other Plasmodium species, these genes are present in low copy number, are unlinked and form two types that are distinct in sequence and are expressed stage specifically. The asexually expressed (type A) genes are present in four copies in the Ceylon- and in five copies in the Berok-strain. Surprisingly, the sexually expressed (type B) gene is present in a single copy. The vast majority of the differences between gene types is confined to the variable regions. The pattern of divergence is different from that observed in Plasmodium berghei or in Plasmodium falciparum. Analysis of the small subunit rRNA sequences of P. cynomolgi, P. berghei and P. falciparum, indicates that the two gene types do not evolve independently but rather interact (through gene conversion or some form of recombination) to such an extent as to erase whatever stage-specific sequence signatures they may have had in the last common ancestor.

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.

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