scholarly journals Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

2014 ◽  
Vol 80 (12) ◽  
pp. 3677-3686 ◽  
Author(s):  
Jun Liu ◽  
Zheng-Shuang Hua ◽  
Lin-Xing Chen ◽  
Jia-Liang Kuang ◽  
Sheng-Jin Li ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Community Composition ◽  
Environmental Conditions ◽  
Mine Tailings ◽  
Large Scale ◽  
Hot Springs ◽  
Mine Drainage ◽  
Rrna Gene ◽  
Content Type ◽  
Geochemical Parameters

ABSTRACTRecent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within theAlphaproteobacteria,Deltaproteobacteria, andFirmicuteswere attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

scholarly journals Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1473
Author(s):  
Ani Saghatelyan ◽  
Armine Margaryan ◽  
Hovik Panosyan ◽  
Nils-Kåre Birkeland
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
High Altitude ◽  
Hot Springs ◽  
Hot Spring ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Geothermal Springs ◽  
Bacterial Phyla ◽  
Terrestrial Hot Springs

The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.

scholarly journals Microbial Diversity Analysis of Sediment from Nakdong River Estuary in the Republic of Korea Using 16S rRNA Gene Amplicon Sequencing

2018 ◽  
Vol 7 (14) ◽  
Author(s):  
Kyunghoi Kim
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Large Scale ◽  
Sediment Quality ◽  
River Estuary ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Nakdong River ◽  
The Republic

Deterioration of sediment quality has been found in the Nakdong River Estuary after large-scale reclamations. Here, I report microbial diversity in sediments of Nakdong River Estuary in the Republic of Korea based on 16S rRNA gene sequencing by next-generation sequencing (NGS) techniques.

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals A New Fungal Isolate, Penidiella sp. Strain T9, Accumulates the Rare Earth Element Dysprosium

2015 ◽  
Vol 81 (9) ◽  
pp. 3062-3068 ◽  
Author(s):  
Takumi Horiike ◽  
Mitsuo Yamashita
Keyword(s):  
Rare Earth ◽  
Mine Drainage ◽  
Liquid Waste ◽  
Morphological Characterization ◽  
Rrna Gene ◽  
Content Type ◽  
Cell Pellet ◽  
Acidic Conditions ◽  
High Concentrations ◽  
Rrna Gene Sequencing

ABSTRACTWith an aim to develop a highly efficient method for the recovery of rare earth elements (REEs) by using microorganisms, we attempted to isolate dysprosium (Dy)-accumulating microorganisms that grow under acidic conditions from environmental samples containing high concentrations of heavy metals. One acidophilic strain, T9, which was isolated from an abandoned mine, decreased the concentration of Dy in medium that contained 100 mg/liter Dy to 53 mg/liter Dy after 3 days of cultivation at pH 2.5. The Dy content in the cell pellet of the T9 strain was 910 μg/mg of dry cells. The T9 strain also accumulated other REEs. Based on the results of 28S-D1/D2 rRNA gene sequencing and morphological characterization, we designated this fungal strainPenidiellasp. T9. Bioaccumulation of Dy was observed on the cell surface of the T9 strain by elemental mapping using scanning electron microscopy-energy dispersive X-ray spectroscopy. Our results indicate thatPenidiellasp. T9 has the potential to recover REEs such as Dy from mine drainage and industrial liquid waste under acidic conditions.

Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4149-4157 ◽  
Author(s):  
Nathaniel A. Losey ◽  
Bradley S. Stevenson ◽  
Hans-Jürgen Busse ◽  
Jaap S. Sinninghe Damsté ◽  
W. Irene C. Rijpstra ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Hot Springs ◽  
Hot Spring ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Novel Bacterium ◽  
Fermentative Growth ◽  
Novel Genus And Species ◽  
The 16S Rrna Gene

A novel bacterium was isolated from a freshwater hot spring, the Hale House Spring, located at Hot Springs National Park, Hot Springs, AR, USA. Cells of strain MP-01T stained Gram-negative, were rod-shaped, non-motile, strictly anaerobic and chemo-organotrophic and did not form spores. Growth occurred at 50–65 °C, with an optimum at 60 °C, at pH 6.0–8.0, with an optimum at pH 6.5–7.0, and at NaCl concentrations up to 0.5 % (w/v), with optimum growth in the absence of NaCl. Strain MP-01T was capable of fermentative growth on pyruvate or proteinaceous substrates as well as reducing Fe(III) and Mn(IV). Major fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and the major isoprenoid quinone was MK-10. In the polyamine pattern, sym-homospermidine was the predominant compound. The DNA G+C content was 62.7 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that strain MP-01T represents the first reported cultivated member of subdivision 23 of the Acidobacteria . It is proposed that strain MP-01T represents a novel genus and species, for which the name Thermoanaerobaculum aquaticum gen. nov., sp. nov. is proposed. The type strain of Thermoanaerobaculum aquaticum is MP-01T ( = DSM 24856T = JCM 18256T).

scholarly journals Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4027-4032 ◽  
Author(s):  
Zhiyong Ruan ◽  
Yanwei Wang ◽  
Chi Zhang ◽  
Jinlong Song ◽  
Yi Zhai ◽  
...  
Keyword(s):  
Type Species ◽  
Large Scale ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acetogenic Bacterium ◽  
Clostridium Subterminale ◽  
The 16S Rrna Gene

A Gram-staining-positive, spore-forming, obligately anaerobic, acetogenic bacterium, designated LAM1030T, was isolated from methanogenic consortia enriched from biogas slurry collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM1030T were motile, straight or spiral-rod-shaped. Strain LAM1030T could utilize glucose, fructose, maltose, galactose, lactose, sucrose, cellobiose, mannitol, pyruvate, succinic acid and tryptophan as the sole carbon source. Acetic acid, isovaleric acid and butanoic acid were the main products of glucose fermentation. Sodium sulfite was used as an electron acceptor. Growth of strain LAM1030T was completely inhibited by the addition of ampicillin, tetracycline, gentamicin or erythromycin at a concentration of 20 µg ml−1. The main polar lipids of strain LAM1030T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, 11 unknown glycolipids and two unknown phospholipids. No respiratory quinone was detected. The major fatty acids of strain LAM1030T were C16 : 0 (21.1 %), C14 : 0 (10.3 %), summed feature 9 (including C16:0 10-methyl and/or iso-C17:1 ω9c) (11.3% ), summed feature 3 (including C16:1 ω7c and/or C16:1 ω6c) (10.6% ) and iso-C15 : 0 (6.6 %). Analysis of the 16S rRNA gene sequence indicated that strain LAM1030T belonged to the genus Clostridium and was most closely related to Clostridium subterminale DSM 6970T, Clostridium thiosulfatireducens DSM 13105T and Clostridium sulfidigenes DSM 18982T, with 97.0, 96.9 and 96.8 % similarity, respectively. The G+C content of the genomic DNA of strain LAM1030T was 31.2±0.3 mol%. On the basis of its phenotypic, phylogenetic and chemotaxonomic characterization, strain LAM1030T is suggested to represent a novel species of the genus Clostridium , for which the name Clostridium huakuii sp. nov. is proposed. The type strain is LAM1030T ( = ACCC 00698T = JCM 19186T).

scholarly journals Geochemical Niches of Iron-Oxidizing Acidophiles in Acidic Coal Mine Drainage

2014 ◽  
Vol 81 (4) ◽  
pp. 1242-1250 ◽  
Author(s):  
Daniel S. Jones ◽  
Courtney Kohl ◽  
Christen Grettenberger ◽  
Lance N. Larson ◽  
William D. Burgos ◽  
...  
Keyword(s):  
Mine Drainage ◽  
Stream Water ◽  
Subsequent Treatment ◽  
Ecological Niches ◽  
Content Type ◽  
Somerset County ◽  
Dissolved Iron ◽  
Geochemical Parameters ◽  
Low Levels ◽  
Red Eyes

ABSTRACTA legacy of coal mining in the Appalachians has provided a unique opportunity to study the ecological niches of iron-oxidizing microorganisms. Mine-impacted, anoxic groundwater with high dissolved-metal concentrations emerges at springs and seeps associated with iron oxide mounds and deposits. These deposits are colonized by iron-oxidizing microorganisms that in some cases efficiently remove most of the dissolved iron at low pH, making subsequent treatment of the polluted stream water less expensive. We used full-cycle rRNA methods to describe the composition of sediment communities at two geochemically similar acidic discharges, Upper and Lower Red Eyes in Somerset County, PA, USA. The dominant microorganisms at both discharges were acidophilicGallionella-like organisms, “Ferrovum” spp., andAcidithiobacillusspp.ArchaeaandLeptospirillumspp. accounted for less than 2% of cells. The distribution of microorganisms at the two sites could be best explained by a combination of iron(II) concentration and pH. Populations of theGallionella-like organisms were restricted to locations with pH >3 and iron(II) concentration of >4 mM, whileAcidithiobacillusspp. were restricted to pH <3 and iron(II) concentration of <4 mM.Ferrovumspp. were present at low levels in most samples but dominated sediment communities at pH <3 and iron(II) concentration of >4 mM. Our findings offer a predictive framework that could prove useful for describing the distribution of microorganisms in acid mine drainage, based on readily accessible geochemical parameters.

scholarly journals Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan

2020 ◽  
Vol 70 (11) ◽  
pp. 5701-5710 ◽  
Author(s):  
Mohit Kumar Saini ◽  
Weng ChihChe ◽  
Nathan Soulier ◽  
Aswathy Sebastian ◽  
Istvan Albert ◽  
...  
Keyword(s):  
Type Species ◽  
Microbial Mats ◽  
Hot Springs ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Circular Chromosome ◽  
Content Type ◽  
Link Type ◽  
Purple Sulphur Bacterium

A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40–56 °C) and pH 7.2 (range, pH 7–8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum . The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae . The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).

scholarly journals Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota

2020 ◽  
Vol 9 (5) ◽  
pp. 1589
Author(s):  
Kyung Eun Yun ◽  
Jimin Kim ◽  
Mi-hyun Kim ◽  
Eunkyo Park ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Large Scale ◽  
Blood Lipids ◽  
Density Lipoprotein ◽  
Lipoprotein Cholesterol ◽  
Control Group ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Lipid Markers

The gut microbiota has been linked to blood lipids. However, the relationship between the gut microbiome and other lipid markers like apolipoproteins A1 (apoA1) and B (apoB) as well as classical lipid markers in Asians remain unclear. Here, we examined the associations between gut microbial diversity and taxonomic compositions with both apolipoproteins and lipid markers in a large number of Korean patients. The fecal 16S rRNA gene sequencing data from 1141 subjects were analyzed and subjects were categorized into control group (G0) or abnormal group (G1) according to blood lipid measurements. The microbial diversity and several taxa of the gut microbiota were significantly associated with triglyceride, apoA1, and apoB levels, but not with total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol levels. The alpha diversity of the gut microbiota was inversely associated with high triglyceride level. Interestingly, G1 of apoA1 showed increased microbial richness and distinct microbial community compared with G0 of apoA1. A high abundance of Fusobacteria and low abundance of Oscillospira were found in the hypertriglyceridemia group. In this large-scale study, we identified associations of gut microbiota with apolipoproteins and classical lipid markers, indicating that the gut microbiota may be an important target for regulating blood lipids.

Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Inna A. Panova ◽  
Olga Ikkert ◽  
Marat R. Avakyan ◽  
Dmitry S. Kopitsyn ◽  
Andrey V. Mardanov ◽  
...  
Keyword(s):  
Mine Drainage ◽  
Sequence Similarity ◽  
Cell Structure ◽  
Draft Genome ◽  
Electron Acceptors ◽  
Rrna Gene ◽  
Protein Coding ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0–3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0–7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum Firmicutes , class Clostridia , family Peptococcaceae , genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus Desulfosporosinus , for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В−3021T).

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