scholarly journals Isolation and Physiology of Bacteria from Contaminated Subsurface Sediments

2010 ◽  
Vol 76 (22) ◽  
pp. 7413-7419 ◽  
Author(s):  
Annette Bollmann ◽  
Anthony V. Palumbo ◽  
Kim Lewis ◽  
Slava S. Epstein
Keyword(s):  
Heavy Metals ◽  
Field Research ◽  
Diffusion Chamber ◽  
Stress Factors ◽  
Rrna Gene ◽  
Initial Growth ◽  
Diffusion Chambers ◽  
Oak Ridge ◽  
Subsurface Sediments ◽  
High Concentrations

ABSTRACT The majority of environmental microorganisms cannot be grown by traditional techniques. Here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. Using this approach, we isolated microorganisms from subsurface sediments from the Field Research Center (FRC) in Oak Ridge, TN. The sediments were acidic and highly contaminated with uranium, heavy metals, nitrate, and organic pollutants. Phylogenetic analysis of 16S rRNA gene sequences revealed clear differences between diversity of isolates obtained by the diffusion chamber approach and those obtained by conventional plating. The latter approach led to isolation of members of the Alpha- and Gammaproteobacteria, Actinobacteria, and Verrucomicrobia. Isolates obtained via the diffusion chamber approach represented the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Notably, one-third of the isolates obtained by the new method were closely related to species known from previous molecular surveys conducted in the FRC area. Since the initial growth of microorganisms inside diffusion chambers occurred in the presence of the environmental stress factors, we expected the isolates we obtained to be tolerant of these factors. We investigated the physiologies of selected isolates and discovered that the majority were indeed capable of growth under low pH and/or high concentrations of heavy metals and nitrate. This indicated that in contrast to conventional isolation, the diffusion chamber-based approach leads to isolation of species that are novel, exhibit tolerance to extant environmental conditions, and match some of the species previously discovered by molecular methods.

scholarly journals Denitrifying Bacteria Isolated from Terrestrial Subsurface Sediments Exposed to Mixed-Waste Contamination

2010 ◽  
Vol 76 (10) ◽  
pp. 3244-3254 ◽  
Author(s):  
Stefan J. Green ◽  
Om Prakash ◽  
Thomas M. Gihring ◽  
Denise M. Akob ◽  
Puja Jasrotia ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Field Research ◽  
Denitrifying Bacteria ◽  
Nitrate Contamination ◽  
Source Zone ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Oak Ridge ◽  
Subsurface Sediments ◽  
Terrestrial Subsurface

ABSTRACTIn terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the generaAfipiaandHyphomicrobium(Alphaproteobacteria),Rhodanobacter(Gammaproteobacteria),Intrasporangium(Actinobacteria), andBacillus(Firmicutes). Isolates from the phylumProteobacteriawere complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. rRNA gene analyses coupled with physiological and genomic analyses suggest that bacteria from the genusRhodanobacterare a diverse population of denitrifiers that are circumneutral to moderately acidophilic, with a high relative abundance in areas of the acidic source zone at the OR-IFRC site. Based on genome analysis,Rhodanobacterspecies contain two nitrite reductase genes and have not been detected in functional-gene surveys of denitrifying bacteria at the OR-IFRC site. Nitrite and nitrous oxide reductase gene sequences were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation and genomic and metagenomic data is essential to thein situcharacterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

scholarly journals Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation

2019 ◽  
Vol 85 (17) ◽  
Author(s):  
Michael P. Thorgersen ◽  
Xiaoxuan Ge ◽  
Farris L. Poole ◽  
Morgan N. Price ◽  
Adam P. Arkin ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Metal Contamination ◽  
Nitrate Removal ◽  
Nitrate Contamination ◽  
Contaminated Site ◽  
Sequence Variant ◽  
Oak Ridge ◽  
Global Issue ◽  
16S Rna ◽  
High Concentrations

ABSTRACTContamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCENitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.

scholarly journals Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium

2019 ◽  
Vol 8 (14) ◽  
Author(s):  
Ryann M. Brzoska ◽  
Marcel Huntemann ◽  
Alicia Clum ◽  
Amy Chen ◽  
Nikos Kyrpides ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Oak Ridge ◽  
Subsurface Sediments

Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.

scholarly journals Sulfide Ameliorates Metal Toxicity for Deep-Sea Hydrothermal Vent Archaea

2004 ◽  
Vol 70 (4) ◽  
pp. 2551-2555 ◽  
Author(s):  
Virginia P. Edgcomb ◽  
Stephen J. Molyneaux ◽  
Mak A. Saito ◽  
Karen Lloyd ◽  
Simone Böer ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Metal Sulfide ◽  
Toxic Metal ◽  
Stress Factors ◽  
Microbial Life ◽  
High Concentrations ◽  
Free Metal

ABSTRACT The chemical stress factors for microbial life at deep-sea hydrothermal vents include high concentrations of heavy metals and sulfide. Three hyperthermophilic vent archaea, the sulfur-reducing heterotrophs Thermococcus fumicolans and Pyrococcus strain GB-D and the chemolithoautotrophic methanogen Methanocaldococcus jannaschii, were tested for survival tolerance to heavy metals (Zn, Co, and Cu) and sulfide. The sulfide addition consistently ameliorated the high toxicity of free metal cations by the formation of dissolved metal-sulfide complexes as well as solid precipitates. Thus, chemical speciation of heavy metals with sulfide allows hydrothermal vent archaea to tolerate otherwise toxic metal concentrations in their natural environment.

scholarly journals U(VI) Sequestration in Hydroxyapatite Produced by Microbial Glycerol 3-Phosphate Metabolism

2009 ◽  
Vol 75 (18) ◽  
pp. 5773-5778 ◽  
Author(s):  
Evgenya S. Shelobolina ◽  
Hiromi Konishi ◽  
Huifang Xu ◽  
Eric E. Roden
Keyword(s):  
National Laboratory ◽  
Field Research ◽  
Department Of Energy ◽  
Phosphate Metabolism ◽  
Glycerol Phosphate ◽  
Transmission Electron Microscopy Analysis ◽  
Energy Field ◽  
Oak Ridge ◽  
Electron Microscopy Analysis ◽  
High Concentrations

ABSTRACT Previous studies have demonstrated the potential for removal of U(VI) from solution via precipitation of U(VI)-bearing calcium-phosphate (Ca-P) minerals coupled to microbial hydrolysis of glycerol phosphate compounds. We evaluated this process in circumneutral-pH groundwater from Area 2 of the U.S. Department of Energy Field Research Center at Oak Ridge National Laboratory. Area 2 groundwater contains high concentrations of dissolved calcium (ca. 4 mM), and thus, release of phosphate during glycerol phosphate metabolism has the potential to create conditions favorable for U(VI) sequestration in Ca-P minerals. Microbial enumeration and isolation studies verified the presence of aerobic and nitrate-reducing glycerol 3-phosphate (G3P)-metabolizing microorganisms in Area 2 sediments. Coprecipitation of U(VI) with Ca-P minerals coupled to microbial G3P hydrolysis was demonstrated in artificial groundwater under aerobic and nitrate-reducing conditions. Transmission electron microscopy analysis and mineral-washing experiments demonstrated that U(VI) was incorporated into the structure of the insoluble Ca-P mineral hydroxyapatite [Ca5(PO4)3OH]. Our results support the idea that U(VI) can be effectively removed from solution in contaminated aquifers through stimulation of microbial organophosphate metabolism.

scholarly journals Sarcocornia neei as an Indicator of Environmental Pollution: A Comparative Study in Coastal Wetlands of Central Chile

Plants ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 66 ◽  
Author(s):  
Verónica Meza ◽  
Camilo Lillo ◽  
Daniela Rivera ◽  
Eva Soto ◽  
Rodrigo Figueroa
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Metal Pollution ◽  
Heavy Metal Pollution ◽  
Coastal Wetlands ◽  
Central Zone ◽  
Soil Samples ◽  
Stress Factors ◽  
Central Chile ◽  
High Concentrations

Being adapted to saline environments, halophytes are plant species that have received considerable attention due to their ability to cope with environmental stress factors, such as high concentrations of soluble salts and heavy metals. In this work, we focused on determining if the Sarcocornia neei (S. neei) plant can be considered as an indicator of heavy metal pollution in soil. This was done by analyzing the concentration of cadmium (Cd), lead (Pb), copper (Cu), and arsenic (As) in plants and soil sampled from two wetlands in the central zone of Chile: a wetland contaminated by industrial activities and a wetland protected by the Chilean government. In addition, 14 fertility parameters (pH, electrical conductivity, organic matter, nitrogen (N), phosphorus (P), potassium (K), sodium (Na), Pb, calcium (Ca), magnesium (Mg), Manganese (Mn), zinc (Zn), iron (Fe), and boron (B)) were analyzed for soil samples in both wetlands. This was done to differentiate between available elements and contamination by heavy metals. Plant and soil samples in the contaminated wetland exhibited significantly higher heavy metal concentrations in comparison to samples analyzed from the protected wetland. This indicates that the S. neei plant can be further researched as an indicator of heavy metal pollution in saline soils and possibly for phytoremediation purposes.

scholarly journals Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination

2010 ◽  
Vol 60 (3) ◽  
pp. 546-553 ◽  
Author(s):  
Om Prakash ◽  
Thomas M. Gihring ◽  
Dava D. Dalton ◽  
Kuk-Jeong Chin ◽  
Stefan J. Green ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Citrate Synthase ◽  
Sequence Similarity ◽  
Field Research ◽  
Department Of Energy ◽  
Hydrocarbon Contamination ◽  
Rrna Gene ◽  
Oak Ridge

An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32T, was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the Geobacteraceae-specific citrate synthase (gltA) mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus Geobacter and shared 92–98 % 16S rRNA gene and 75–81 % rpoB gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Geobacter uraniireducens Rf4T, according to 16S rRNA gene sequence similarity, strain FRC-32T showed a DNA–DNA relatedness value of 21 %. Cells of strain FRC-32T were Gram-negative, non-spore-forming, curved rods, 1.0–1.5 μm long and 0.3–0.5 μm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus Geobacter. The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 °C and pH 6.7–7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the Geobacter group, strain FRC-32T conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32T was metabolically versatile and, unlike its closest relative, G. uraniireducens, was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with fumarate as the electron acceptor. Thus, based on genotypic, phylogenetic and phenotypic differences, strain FRC-32T is considered to represent a novel species of the genus Geobacter, for which the name Geobacter daltonii sp. nov. is proposed. The type strain is FRC-32T (=DSM 22248T=JCM 15807T).

scholarly journals Characterization of the 12S rRNA Gene Sequences of the Harvester Termite Anacanthotermes ochraceus (Blattodea: Hodotermitidae) and Its Role as A Bioindicator of Heavy Metal Accumulation Risks in Saudi Arabia

Insects ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 51
Author(s):  
Reem Alajmi ◽  
Rewaida Abdel-Gaber ◽  
Noura AlOtaibi
Keyword(s):  
Heavy Metals ◽  
Metal Accumulation ◽  
Heavy Metal Accumulation ◽  
12S Rrna ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Termite Species ◽  
12S Rrna Gene ◽  
The Mean ◽  
High Concentrations

Termites are social insects of economic importance that have a worldwide distribution. Identifying termite species has traditionally relied on morphometric characters. Recently, several mitochondrial genes have been used as genetic markers to determine the correlation between different species. Heavy metal accumulation causes serious health problems in humans and animals. Being involved in the food chain, insects are used as bioindicators of heavy metals. In the present study, 100 termite individuals of Anacanthotermes ochraceus were collected from two Saudi Arabian localities with different geoclimatic conditions (Riyadh and Taif). These individuals were subjected to morphological identification followed by molecular analysis using mitochondrial 12S rRNA gene sequence, thus confirming the morphological identification of A. ochraceus. Furthermore, a phylogenetic analysis was conducted to determine the genetic relationship between the acquired species and other termite species with sequences previously submitted in the GenBank database. Several heavy metals including Ca, Al, Mg, Zn, Fe, Cu, Mn, Ba, Cr, Co, Be, Ni, V, Pb, Cd, and Mo were measured in both collected termites and soil samples from both study sites. All examined samples (termite and soil) showed high concentrations of metals with different concentrations and ratios. Generally, most measured metals had a significantly high concentration in soil and termites at Taif, except for Ca, Cd, Co, Cr, Cu, Mg, and Ni showing significantly high concentrations at Riyadh. Furthermore, termites accumulated higher amounts of heavy metals than the soil at both locations. The mean concentrations of the measured metals in soil samples were found to be in the descending order Ca ˃ Al ˃ Mg ˃ Zn ˃ Fe ˃ Cu ˃ Mn ˃ Ba ˃ Cr ˃ Co ˃ Be ˃ Ni ˃ V ˃ Pb ˃ Cd ˃ Mo, while it was Ca ˃ Mg ˃ Al ˃ Fe ˃ Zn ˃ Cu ˃ Mn ˃ Be ˃ Ba ˃ Pb ˃ Cr ˃ V ˃ Ni ˃ Cd ˃ Mo ˃ Co in termite specimens. The mean concentrations of the studied metals were determined in the soil and termite specimens at both locations. In addition, the contamination factor, pollution load index (PLI) and degree of contamination were calculated for all studied metals in different samples, indicating that both studied sites were polluted. However, Taif showed a significantly higher degree of pollution. Thus, the accurate identification of economically important insects, such as termites, is of crucial importance to plan for appropriate control strategies. In addition, termites are a good bioindicator to study land pollution.

scholarly journals A Novel Microbial Zearalenone Transformation through Phosphorylation

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 294
Author(s):  
Yan Zhu ◽  
Pascal Drouin ◽  
Dion Lepp ◽  
Xiu-Zhen Li ◽  
Honghui Zhu ◽  
...  
Keyword(s):  
Microbial Transformation ◽  
Acid Tolerance ◽  
Transformation Product ◽  
The United States ◽  
Corn Silage ◽  
Rrna Gene ◽  
Bacillus Spp ◽  
High Concentrations ◽  
The 16S Rrna Gene ◽  
Bacillus Strains

Zearalenone (ZEA) is a mycotoxin widely occurring in many agricultural commodities. In this study, a purified bacterial isolate, Bacillus sp. S62-W, obtained from one of 104 corn silage samples from various silos located in the United States, exhibited activity to transform the mycotoxin ZEA. A novel microbial transformation product, ZEA-14-phosphate, was detected, purified, and identified by HPLC, LC-MS, and NMR analyses. The isolate has been identified as belonging to the genus Bacillus according to phylogenetic analysis of the 16S rRNA gene and whole genome alignments. The isolate showed high efficacy in transforming ZEA to ZEA-14-phosphate (100% transformation within 24 h) and possessed advantages of acid tolerance (work at pH = 4.0), working under a broad range of temperatures (22–42 °C), and a capability of transforming ZEA at high concentrations (up to 200 µg/mL). In addition, 23 Bacillus strains of various species were tested for their ZEA phosphorylation activity. Thirteen of the Bacillus strains showed phosphorylation functionality at an efficacy of between 20.3% and 99.4% after 24 h incubation, suggesting the metabolism pathway is widely conserved in Bacillus spp. This study established a new transformation system for potential application of controlling ZEA although the metabolism and toxicity of ZEA-14-phosphate requires further investigation.

scholarly journals Spatial Variation of Water Chemistry in Aries River Catchment Western Romania

2021 ◽  
Vol 11 (14) ◽  
pp. 6592
Author(s):  
Ana Moldovan ◽  
Maria-Alexandra Hoaghia ◽  
Anamaria Iulia Török ◽  
Marius Roman ◽  
Ionut Cornel Mirea ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Water Quality ◽  
Water Chemistry ◽  
Water Samples ◽  
Mine Drainage ◽  
Pollution Indices ◽  
Mining Activities ◽  
River Catchment ◽  
High Concentrations ◽  
The Impact

This study aims to investigate the quality and vulnerability of surface water (Aries River catchment) in order to identify the impact of past mining activities. For this purpose, the pollution and water quality indices, Piper and Durov plots, as well vulnerability modeling maps were used. The obtained results indicate that the water samples were contaminated with As, Fe, Mn, Pb and have relatively high concentrations of SO42−, HCO3−, TDS, Ca, K, Mg and high values for the electrical conductivity. Possible sources of the high content of chemicals could be the natural processes or the inputs of the mine drainage. Generally, according to the pollution indices, which were correlated to high concentrations of heavy metals, especially with Pb, Fe and Mn, the water samples were characterized by heavy metals pollution. The water quality index classified the studied water samples into five different classes of quality, namely: unsuitable for drinking, poor, medium, good and excellent quality. Similarly, medium, high and very high vulnerability classes were observed. The Durov and Piper plots classified the waters into Mg-HCO3− and Ca-Cl− types. The past and present mining activities clearly change the water chemistry and alter the quality of the Aries River, with the water requiring specific treatments before use.

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