scholarly journals Guest commentary: The human microbiome and the promise of clinical ecology

2012 ◽  
Vol 33 (3) ◽  
pp. 90
Author(s):  
Phil Hugenholtz
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Environmental Samples ◽  
High Throughput Sequencing ◽  
Mine Drainage ◽  
Human Microbiome ◽  
Sargasso Sea ◽  
High Profile ◽  
Guest Commentary ◽  
Clinical Ecology

Metagenomics, the application of high-throughput sequencing to nucleic acids extracted directly from environmental samples, made its debut in 2004 through two high-profile papers in Science (Sargasso Sea) and Nature (acid mine drainage). A key strength of the approach is the ability to circumvent the well-known cultivation bottleneck and lay bare the genetic blueprints of ecologically important members of the microbial community, many of which cannot be easily obtained in culture.

scholarly journals Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients

2015 ◽  
Vol 81 (15) ◽  
pp. 4874-4884 ◽  
Author(s):  
Weimin Sun ◽  
Tangfu Xiao ◽  
Min Sun ◽  
Yiran Dong ◽  
Zengping Ning ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
High Throughput Sequencing ◽  
Southwest China ◽  
Mine Drainage ◽  
Redox Potentials ◽  
Content Type ◽  
Acid Mine ◽  
Abandoned Coal Mines ◽  
S Cycling

ABSTRACTLocated in southwest China, the Aha watershed is continually contaminated by acid mine drainage (AMD) produced from upstream abandoned coal mines. The watershed is fed by creeks with elevated concentrations of aqueous Fe (total Fe > 1 g/liter) and SO42−(>6 g/liter). AMD contamination gradually decreases throughout downstream rivers and reservoirs, creating an AMD pollution gradient which has led to a suite of biogeochemical processes along the watershed. In this study, sediment samples were collected along the AMD pollution sites for geochemical and microbial community analyses. High-throughput sequencing found various bacteria associated with microbial Fe and S cycling within the watershed and AMD-impacted creek. A large proportion of Fe- and S-metabolizing bacteria were detected in this watershed. The dominant Fe- and S-metabolizing bacteria were identified as microorganisms belonging to the generaMetallibacterium,Aciditerrimonas,Halomonas,Shewanella,Ferrovum,Alicyclobacillus, andSyntrophobacter. Among them,Halomonas,Aciditerrimonas,Metallibacterium, andShewanellahave previously only rarely been detected in AMD-contaminated environments. In addition, the microbial community structures changed along the watershed with different magnitudes of AMD pollution. Moreover, the canonical correspondence analysis suggested that temperature, pH, total Fe, sulfate, and redox potentials (Eh) were significant factors that structured the microbial community compositions along the Aha watershed.

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage

2018 ◽  
Vol 247 ◽  
pp. 624-632 ◽  
Author(s):  
Yaneth Vasquez ◽  
Maria C. Escobar ◽  
Johan S. Saenz ◽  
Maria F. Quiceno-Vallejo ◽  
Carmen M. Neculita ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Retention Time ◽  
Hydraulic Retention Time ◽  
Mine Drainage ◽  
Acid Mine

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

2020 ◽  
Vol 367 (15) ◽  
Author(s):  
Yang Li ◽  
Liang Yuan ◽  
Sheng Xue ◽  
Bingjun Liu ◽  
Gang Jin
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mine Drainage ◽  
Plant Root ◽  
Bacterial Community Composition ◽  
Cellular Processes ◽  
Acid Mine ◽  
Functional Bacteria ◽  
Plant Root System

ABSTRACT This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

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

<p>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<sup>-1</sup> and 10 mg L<sup>-1</sup>, 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.</p> <p>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 <em>in vivo</em> by enrichment cultivation and isolated strains were tested for their ability to perform arsenic redox transformation.</p> <p>Preliminary analyses indicated that the biofilm accumulated arsenic in the order of 6 · 10<sup>3</sup> mg kg<sup>-1</sup>, in contrast to 0.14 mg L<sup>-1</sup>, 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 <em>Cyanobacteria</em> belonging to the species <em>Tychonema</em> 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  oxidation.</p> <p>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.</p>

Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques

2013 ◽  
Vol 93 (2) ◽  
pp. 108-115 ◽  
Author(s):  
Ryan R. Auld ◽  
Maxine Myre ◽  
Nadia C.S. Mykytczuk ◽  
Leo G. Leduc ◽  
Thomas J.S. Merritt
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Direct Sequencing ◽  
Acid Mine

scholarly journals Fine-scale spatial patterns in microbial community composition in an acid mine drainage

2017 ◽  
Vol 93 (10) ◽  
Author(s):  
Jie-Liang Liang ◽  
Xiao-Jing Li ◽  
Hao-Yue Shu ◽  
Pandeng Wang ◽  
Jia-Liang Kuang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Community Composition ◽  
Spatial Patterns ◽  
Mine Drainage ◽  
Microbial Community Composition ◽  
Fine Scale ◽  
Acid Mine

scholarly journals Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage

2011 ◽  
Vol 77 (15) ◽  
pp. 5540-5544 ◽  
Author(s):  
Li-Nan Huang ◽  
Wen-Hua Zhou ◽  
Kevin B. Hallberg ◽  
Cai-Yun Wan ◽  
Jie Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Temporal Analysis ◽  
Temporal Variations ◽  
Microbial Populations ◽  
Content Type ◽  
Tailings Impoundment ◽  
Spatial And Temporal Analysis ◽  
Acidophilic Archaea

ABSTRACTAnalysis of spatial and temporal variations in the microbial community in the abandoned tailings impoundment of a Pb-Zn mine revealed distinct microbial populations associated with the different oxidation stages of the tailings. AlthoughAcidithiobacillus ferrooxidansandLeptospirillumspp. were consistently present in the acidic tailings, acidophilic archaea, mostlyFerroplasma acidiphilum, were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage.

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