scholarly journals Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities

2009 ◽  
Vol 75 (7) ◽  
pp. 2192-2199 ◽  
Author(s):  
Brett J. Baker ◽  
Gene W. Tyson ◽  
Lindsey Goosherst ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
18S Rrna ◽  
Mine Drainage ◽  
Sequence Similarity ◽  
Extreme Environment ◽  
18S Rrna Gene ◽  
Trophic Levels ◽  
Ecosystem Functions ◽  
Rrna Gene ◽  
Acid Mine

ABSTRACT Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class Heterolobosea were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

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 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 16S rRNA Gene-Based Profiling of the Microbial Community in an Acid Mine Drainage Fe Precipitate at Libiola Mine (Liguria, Italy)

Minerals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1064
Author(s):  
Sirio Consani ◽  
Stefano Ghignone ◽  
Marina Pozzolini ◽  
Marco Giovine ◽  
Luigi Vezzulli ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Acid Mine ◽  
Starting Point ◽  
Wide Range ◽  
Libiola Mine

Acid mine drainage (AMD) is a common environmental problem in many sulphide mines worldwide, and it is widely accepted that the microbial community plays a major role in keeping the process of acid generation active. The aim of this work is to describe, for the first time, the microbial community thriving in goethite and jarosite Fe precipitates from the AMD of the Libiola mine. The observed association is dominated by Proteobacteria (>50%), followed by Bacteroidetes (22.75%), Actinobacteria (7.13%), Acidobacteria (5.79%), Firmicutes (2.56%), and Nitrospirae (1.88%). Primary producers seem to be limited to macroalgae, with chemiolithotrophic strains being almost absent. A phylogenetic analysis of bacterial sequences highlighted the presence of heterotrophic bacteria, including genera actively involved in the AMD Fe cycle and genera (such as Cytophaga and Flavobacterium) that are able to reduce cellulose. The Fe precipitates constitute a microaerobic and complex environment in which many ecological niches are present, as proved by the wide range of bacterial species observed. This study is the first attempt to quantitatively characterize the microbial community of the studied area and constitutes a starting point to learn more about the microorganisms thriving in the AMD of the Libiola mine, as well as their potential applications.

Roles of Oligotrophic Acidophiles (Alicyclobacillus) in Chalcopyrite Bioleaching System: Shake Flask Evaluation

2015 ◽  
Vol 1130 ◽  
pp. 410-413
Author(s):  
Xing Yu Liu ◽  
Ming Jiang Zhang ◽  
Wen Yan Liu ◽  
Bo Wei Chen ◽  
Chun Yu Meng ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Mine Drainage ◽  
Community Change ◽  
Rrna Gene ◽  
Acid Mine ◽  
Copper Leaching ◽  
Culture Independent ◽  
Different Temperatures ◽  
Two Temperatures

An oligotrophic culture of acidophiles (Alicyclobacillus) isolated from Dexin acid mine drainage was evaluated for its synergistic effect in chalcopyrite bioleaching. Bioleaching of chalcopyrite with and without theAlicyclobacillusculture was investigated at different temperatures (33°C, 45 °C and 65 °C) and a culture-independent approach based on 16S rRNA gene clone library was used to analyze changes in the microbial community change during the bioleaching process. For 33oC leaching tests, only the bacterial community was analyzed, but for the other two temperatures, both the bacterial community and archaea communities were analyzed. Results showed that at high leaching temperature (65°C),Alicyclobacillusculture could increase copper leaching recovery from 57.83% to 60.7%. While at relative low temperature (45°C and 33°C), addingAlicyclobacillusculture inhibited copper bioleaching, copper leaching recovery decreased from 36.10% to 31.52% and from 34.02% to 21.97% respectively at 45°C and 33°C. Clone libraries analysis showed thatAlicyclobacillushelps the growth of genusSulfobacillusat 45 °C while inhibiting the growth of genusLeptospillumat both 33°C and 45 °C. Furthermore, when addingAlicyclobacillusgrowth ofFerroplasmawas limited andAcidoplasmawas facilitated at 45°C. At 60°C, addingAlicyclobacillusculture facilitated the growth of genusMetallosphaerawhile limiting the growth ofLeptospillumandFerroplasma. The results showed potential application ofAlicyclobacillusin high temperature chalcopyrite bioleaching and bioremediation of acid mine drainage.

scholarly journals RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage

2013 ◽  
Vol 79 (6) ◽  
pp. 2019-2026 ◽  
Author(s):  
Xue Guo ◽  
Huaqun Yin ◽  
Jing Cong ◽  
Zhimin Dai ◽  
Yili Liang ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Gene Cluster ◽  
Molecular Phylogenetics ◽  
Mine Drainage ◽  
Calvin Cycle ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Bisphosphate Carboxylase ◽  
Acid Mine ◽  
Horizontal Transfers

ABSTRACTThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-sixcbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities ofcbbLand the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.

scholarly journals Diversity of Dissimilatory Sulfite Reductase Genes (dsrAB) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage

2010 ◽  
Vol 76 (14) ◽  
pp. 4819-4828 ◽  
Author(s):  
John W. Moreau ◽  
Robert A. Zierenberg ◽  
Jillian F. Banfield
Keyword(s):  
Salt Marsh ◽  
Acid Mine Drainage ◽  
Pore Water ◽  
Mine Drainage ◽  
Sequence Data ◽  
Rrna Gene ◽  
Ambient Conditions ◽  
Acid Mine ◽  
Dsrab Gene ◽  
Marsh Sediments

ABSTRACT Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered dsrAB sequences from three sites sampled along an AMD flow path indicated the dominance of a single Desulfovibrio species. Other major sequence clades were related most closely to Desulfosarcina, Desulfococcus, Desulfobulbus, and Desulfosporosinus species. The presence of metal sulfides with low δ34S values relative to δ34S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of ∼2), although possibly within less acidic microenvironments. Interestingly, δ34S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.

scholarly journals MORPHOLOGICAL AND MOLECULAR VARIATION OF FUSARIUM OXYSPORUM F.SP LYCOPERSICI ISOLATES CAUSING FUSARIUM WILT IN TOMATO

2020 ◽  
Vol 21 (supplement 1) ◽  
Author(s):  
K. Vignesh ◽  
K. Rajamohan ◽  
R. Anandan ◽  
R. Udhayakumar
Keyword(s):  
Fusarium Oxysporum ◽  
Fusarium Wilt ◽  
18S Rrna ◽  
Sequence Similarity ◽  
Fusarium Species ◽  
Critical Role ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Molecular Variation

Tomato (Solanum lycopersicum L.) is one of the most important, commercial and widely grown vegetable crop in the world. Tomato plays a critical role in nutritional food requirements, income and employment opportunities for the people. However, its production is threatened by the Fusarium wilt caused by Fusarium oxysporum f.sp. lycopersici and productionlossesbetween30%to40%. In the present investigation an attempt has been made to study the morphological and molecular variation of Fusarium oxysporum f.sp lycopersici isolates. Usual identification of Fusarium species based on their micro and macroscopic features and morphological characters alone may lead to incorrect designation. In order to identify the correct species, we amplified the 18S rRNA gene region by PCR, sequenced and analyzed for sequence similarity among the NCBI data through BLAST. Further, PCR amplification of ITS regions was performed using ITS primers. The amplified product of 18S rRNA gene was sequenced and deposited to Gen Bank with the accession numbers.

scholarly journals Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site

2019 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Jeff R. Havig ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
Gene Sequence ◽  
Mine Drainage ◽  
Metagenomic Data ◽  
National Forest ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Rrna Gene Sequence ◽  
Metabolic Diversity ◽  
Acid Mine

ABSTRACTBackgroundFerrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY.ResultsHere we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp.. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis.ConclusionsPreviously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.

scholarly journals Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site

2020 ◽  
Author(s):  
Christen Grettenberger ◽  
Jeff Havig ◽  
Trinity Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
Gene Sequence ◽  
Mine Drainage ◽  
Metagenomic Data ◽  
National Forest ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Rrna Gene Sequence ◽  
Metabolic Diversity ◽  
Acid Mine

Abstract Background Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY. Results Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp.. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis. Conclusions Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.

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

2007 ◽  
Vol 73 (19) ◽  
pp. 6001-6011 ◽  
Author(s):  
Salvador Mirete ◽  
Carolina G. de Figueras ◽  
Jose E. González-Pastor
Keyword(s):  
Acid Mine Drainage ◽  
Resistance Genes ◽  
Mine Drainage ◽  
Nickel Content ◽  
Metal Resistance ◽  
Rrna Gene ◽  
Nickel Resistance ◽  
Phylogenetic Groups ◽  
Resistance Determinants ◽  
Acid Mine

ABSTRACT Metal resistance determinants have traditionally been found in cultivated bacteria. To search for genes involved in nickel resistance, we analyzed the bacterial community of the rhizosphere of Erica andevalensis, an endemic heather which grows at the banks of the Tinto River, a naturally metal-enriched and extremely acidic environment in southwestern Spain. 16S rRNA gene sequence analysis of rhizosphere DNA revealed the presence of members of five phylogenetic groups of Bacteria and the two main groups of Archaea mostly associated with sites impacted by acid mine drainage (AMD). The diversity observed and the presence of heavy metals in the rhizosphere led us to construct and screen five different metagenomic libraries hosted in Escherichia coli for searching novel nickel resistance determinants. A total of 13 positive clones were detected and analyzed. Insights about their possible mechanisms of resistance were obtained from cellular nickel content and sequence similarities. Two clones encoded putative ABC transporter components, and a novel mechanism of metal efflux is suggested. In addition, a nickel hyperaccumulation mechanism is proposed for a clone encoding a serine O-acetyltransferase. Five clones encoded proteins similar to well-characterized proteins but not previously reported to be related to nickel resistance, and the remaining six clones encoded hypothetical or conserved hypothetical proteins of uncertain functions. This is the first report documenting nickel resistance genes recovered from the metagenome of an AMD environment.

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