Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

PubMed

Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

2013-08-01

This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings.

PubMed

Chen, Lin-Xing; Li, Jin-Tian; Chen, Ya-Ting; Huang, Li-Nan; Hua, Zheng-Shuang; Hu, Min; Shu, Wen-Sheng

2013-09-01

In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Methane oxidation and abundance of methane oxidizers in tropical agricultural soil (vertisol) in response to CuO and ZnO nanoparticles contamination.

PubMed

Mohanty, Santosh Ranjan; Rajput, Parul; Kollah, Bharati; Chourasiya, Dipanti; Tiwari, Archana; Singh, Muneshwar; Rao, A Subba

2014-06-01

There is worldwide concern over the increase use of nanoparticles (NPs) and their ecotoxicological effect. It is not known if the annual production of tons of industrial nanoparticles (NPs) has the potential to impact terrestrial microbial communities, which are so necessary for ecosystem functioning. Here, we have examined the consequences of adding the NPs particularly the metal oxide (CuO, ZnO) on CH4 oxidation activity in vertisol and the abundance of heterotrophs, methane oxidizers, and ammonium oxidizers. Soil samples collected from the agricultural field located at Madhya Pradesh, India, were incubated with either CuO and ZnO NPs or ionic heavy metals (CuCl2, ZnCl2) separately at 0, 10, and 20 μg g(-1) soil. CH4 oxidation activity in the soil samples was estimated at 60 and 100 % moisture holding capacity (MHC) in order to link soil moisture regime with impact of NPs. NPs amended to soil were highly toxic for the microbial-mediated CH4 oxidation, compared with the ionic form. The trend of inhibition was Zn 20 > Zn 10 > Cu 20 > Cu 10. NPs delayed the lag phase of CH4 oxidation to a maximum of 4-fold and also decreased the apparent rate constant k up to 50 % over control. ANOVA and Pearson correlation analysis (α = 0.01) revealed significant impact of NPs on the CH4 oxidation activity and microbial abundance (p < 0.0001, and high F statistics). Principal component analysis (PCA) revealed that PC1 (metal concentration) rendered 76.06 % of the total variance, while 18.17 % of variance accounted by second component (MHC). Biplot indicated negative impact of NPs on CH4 oxidation and microbial abundance. Our result also confirmed that higher soil moisture regime alleviates toxicity of NPs and opens new avenues of research to manage ecotoxicity and environmental hazard of NPs.

Rheological Enhancement of Pork Myofibrillar Protein-Lipid Emulsion Composite Gels via Glucose Oxidase Oxidation/Transglutaminase Cross-Linking Pathway.

PubMed

Wang, Xu; Xiong, Youling L; Sato, Hiroaki

2017-09-27

Porcine myofibrillar protein (MP) was modified with glucose oxidase (GluOx)-iron that produces hydroxyl radicals then subjected to microbial transglutaminase (TGase) cross-linking in 0.6 M NaCl at 4 °C. The resulting aggregation and gel formation of MP were examined. The GluOx-mediated oxidation promoted the formation of both soluble and insoluble protein aggregates via disulfide bonds and occlusions of hydrophobic groups. The subsequent TGase treatment converted protein aggregates into highly cross-linked polymers. MP-lipid emulsion composite gels formed with such polymers exhibited markedly enhanced gelling capacity: up to 4.4-fold increases in gel firmness and 3.5-fold increases in gel elasticity over nontreated protein. Microstructural examination showed small oil droplets dispersed in a densely packed gel matrix when MP was oxidatively modified, and the TGase treatment further contributed to such packing. The enzymatic GluOx oxidation/TGase treatment shows promise to improve the textural properties of emulsified meat products.

GEOCHEMICAL AND BIOLOGICAL ASPECTS OF SULFIDE MINERAL DISSOLUTION: LESSONS FROM IRON MOUNTAIN, CALIFORNIA. (R826189)

EPA Science Inventory

Abstract

The oxidative dissolution of sulfide minerals leading to acid mine drainage (AMD) involves a complex interplay between microorganisms, solutions, and mineral surfaces. Consequently, models that link molecular level reactions and the microbial communities that ...

In Vitro Anti-Oxidant and Anti-Microbial Potentiality Investigation of Different Fractions of Caryota urens Leaves

PubMed Central

Azam, Shofiul; Mahmud, Md. Kayes; Naquib, Md. Hamza; Hossain, Saad Mosharraf; Alam, Mohammad Nazmul; Uddin, Md. Josim; Sajid, Irfan; Hossain, Muhammad Sazzad; Karim, Md. Salimul; Hasan, Md. Ali

2016-01-01

Background: Caryota urens is a member of the Arecaceae family and a common plant in the Southeast Asian region. This plant has been reported as an anti-microbial agent in recent years. Thus, we aimed to find out the MIC (minimum inhibitory concentration) against different pathogenic microorganism. Methods: The leaves of C. urens were extracted and fractioned using different reagents (chloroform, n-hexane and carbon tetrachloride). Disc diffusion method was implemented for the assessment of in vitro anti-microbial potency (500 and 250 µg/disc). Result: The entire fraction showed good effect (with the zone of inhibition 19–25 mm) against both gram positive (Bacillus subtilis, Bacillus megaterium, Bacillus cereus, Sarina lutea) and gram negative (Vibrio mimicus, Shigella boydii, Escherichia coli, Pseudomonas aeruginosa) bacterial pathogens and fungal strains (Aspergillus niger, Saccharomyces cerevisiae). The plants also possess effective free radical scavenging potency with an IC50 of 130.32 µg/mL. Conclusion: This finding reflects a link between the presence of anti-oxidative material and a substantial anti-microbial activity, and substantiates all previous claims against C. urens. PMID:28536384

In Vitro Anti-Oxidant and Anti-Microbial Potentiality Investigation of Different Fractions of Caryota urens Leaves.

PubMed

Azam, Shofiul; Mahmud, Md Kayes; Naquib, Md Hamza; Hossain, Saad Mosharraf; Alam, Mohammad Nazmul; Uddin, Md Josim; Sajid, Irfan; Hossain, Muhammad Sazzad; Karim, Md Salimul; Hasan, Md Ali

2016-07-27

Caryota urens is a member of the Arecaceae family and a common plant in the Southeast Asian region. This plant has been reported as an anti-microbial agent in recent years. Thus, we aimed to find out the MIC (minimum inhibitory concentration) against different pathogenic microorganism. The leaves of C. urens were extracted and fractioned using different reagents (chloroform, n -hexane and carbon tetrachloride). Disc diffusion method was implemented for the assessment of in vitro anti-microbial potency (500 and 250 µg/disc). The entire fraction showed good effect (with the zone of inhibition 19-25 mm) against both gram positive ( Bacillus subtilis , Bacillus megaterium , Bacillus cereus , Sarina lutea ) and gram negative ( Vibrio mimicus , Shigella boydii , Escherichia coli , Pseudomonas aeruginosa ) bacterial pathogens and fungal strains ( Aspergillus niger , Saccharomyces cerevisiae ). The plants also possess effective free radical scavenging potency with an IC 50 of 130.32 µg/mL. This finding reflects a link between the presence of anti-oxidative material and a substantial anti-microbial activity, and substantiates all previous claims against C. urens .

A mechanism for bacterial transformation of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle.

PubMed

Lidbury, Ian; Kröber, Eileen; Zhang, Zhidong; Zhu, Yijun; Murrell, J Colin; Chen, Yin; Schäfer, Hendrik

2016-09-01

The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi, a model marine heterotrophic bacterium, can oxidize DMS to DMSO using trimethylamine monooxygenase (Tmm). Purified Tmm oxidizes DMS to DMSO at a 1:1 ratio. Mutagenesis of the tmm gene in R. pomeroyi completely abolished DMS oxidation and subsequent DMSO formation. Expression of Tmm and DMS oxidation in R. pomeroyi is methylamine-dependent and regulated at the post-transcriptional level. Considering that Tmm is present in approximately 20% of bacterial cells inhabiting marine surface waters, particularly the marine Roseobacter clade and the SAR11 clade, our observations contribute to a mechanistic understanding of biological DMSO production in surface seawater. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Lipids as paleomarkers to constrain the marine nitrogen cycle

PubMed Central

Rush, Darci

2017-01-01

Summary Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past. PMID:28142226

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

PubMed Central

Heidelberg, John F.

2016-01-01

ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. PMID:27208118

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

PubMed

Tully, Benjamin J; Heidelberg, John F

2016-07-15

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. Copyright © 2016 Tully and Heidelberg.

Formation of Deep Sea Umber Deposits Linked to Microbial Metal Oxidation at the South Atlantic Ridge

NASA Astrophysics Data System (ADS)

Peng, Xiaotong; Ta, Kaiwen; Chen, Shun; Zhang, Lijuan; Xu, Hengchao

2015-04-01

Umber deposits are important metalliferous deposits, which occur in off-axis half-graben structures at ancient and modern ocean floor. The genesis of umber deposits has remained controversial for several decades. Recently, microbial Fe(II) oxidation associated with low-temperature diffuse venting has been identified as a key process for the formation of umber deposits, but the exact biochemical mechanisms involved to the precipitation of Mn oxides and co-precipitation of Fe oxyhydroxides and Mn oxides in umber deposits still remain unknown. Here, we used nano secondary ion mass spectrometer, synchrotron-based X-ray absorption spectroscopy, electron microscopy, and molecular techniques to demonstrate the coexistence of two types of metal-oxidizing bacteria within deep-sea hydrothermal umber deposits at the South Atlantic Ridge, where we found unique spheroids composed of biogenic Fe oxyhydroxides and Mn oxides in the deposits. Our data suggest that Fe oxyhydroxides and Mn oxides are metabolic by-products of lithotrophic Fe(II)-oxidizing bacteria and heterotrophic Mn(II)-oxidizing bacteria, respectively. The hydrothermal vents fuel lithotrophic Fe(II)-oxidizing bacteria, which constitute a trophic base that may support the activities of heterotrophic Mn(II)-oxidizing bacteria. The biological origin of umber deposits underscore the importance of geomicrobiologcial interaction in triggering the formation of deep-sea deposits, with important implications for the generation of submarine Mn deposits and crusts.

Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches

NASA Astrophysics Data System (ADS)

Schwab, Valérie F.; Herrmann, Martina; Roth, Vanessa-Nina; Gleixner, Gerd; Lehmann, Robert; Pohnert, Georg; Trumbore, Susan; Küsel, Kirsten; Totsche, Kai U.

2017-05-01

Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physico-chemistry are still not well understood due to the complexity of interactions between surface and subsurface. Within the framework of Hainich (north-western Thuringia, central Germany) Critical Zone Exploratory of the Collaborative Research Centre AquaDiva, we used the relative abundances of phospholipid-derived fatty acids (PLFAs) to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physico-chemistry. The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite-oxidizing bacteria (11Me16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies bioavailable substrates. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulfate-reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3- concentrations, suggesting the occurrence of active iron reduction and the possible role of fungi in meditating iron solubilization and transport in those aquifer domains. In more NH4+-rich anoxic groundwaters, anammox bacteria and SRB-derived PLFAs increased with NH4+ concentration, further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA- and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which showed high predominance of nitrite-oxidizing bacteria Nitrospira, e.g. Nitrospira moscoviensis, in oxic aquifer zones and of anammox bacteria in more NH4+-rich anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based datasets affiliated with iron-reducing bacteria in more Fet-rich groundwater supported the occurrence of active dissimilatory iron reduction. The functional diversity of the microbial communities in the biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

PubMed

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-08-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H 2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H 2 , often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H 2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H 2 consumption and retardation of radionuclide migration.

Linking microbial heterotrophic activity and sediment lithology in oxic, oligotrophic sub-seafloor sediments of the north atlantic ocean.

PubMed

Picard, Aude; Ferdelman, Timothy G

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7-8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with (14)C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO(2) (with O(2) as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm(-3) d(-1)) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm(-3) d(-1)). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link.

Linking Microbial Heterotrophic Activity and Sediment Lithology in Oxic, Oligotrophic Sub-Seafloor Sediments of the North Atlantic Ocean

PubMed Central

Picard, Aude; Ferdelman, Timothy G.

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7–8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with 14C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO2 (with O2 as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm−3 d−1) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm−3 d−1). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link. PMID:22207869

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments.

PubMed

Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip J R; Boschker, Henricus T S

2015-09-01

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following (13)C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas (13)C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Microbial acceleration of aerobic pyrite oxidation at circumneutral pH.

PubMed

Percak-Dennett, E; He, S; Converse, B; Konishi, H; Xu, H; Corcoran, A; Noguera, D; Chan, C; Bhattacharyya, A; Borch, T; Boyd, E; Roden, E E

2017-09-01

Pyrite (FeS 2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO 2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals. © 2017 John Wiley & Sons Ltd.

Sources and Contributions of Oxygen During Microbial Pyrite Oxidation: the Triple Oxygen Isotopes of Sulfate

NASA Astrophysics Data System (ADS)

Ziegler, K.; Coleman, M. L.; Mielke, R. E.; Young, E. D.

2008-12-01

The triple isotopes of oxygen (Δ17O' = δ17O'-0.528 × δ18O' using logarithmic deltas) can trace the oxygen sources of sulfate produced during sulfide oxidation, an important biogeochemical process on Earth's surface and possibly also on Mars [1]. δ18OSO4 compositions are determined by the isotopic selectivity of the mechanism(s) responsible for their changes, and the δ18O value of the reactants (O2 vs. H2O). The relative proportional importance and contribution of each of those sources and mechanisms, as well as their associated isotopic fractionations, are not well understood. We are investigating the use of Δ 17O as a quantitative and qualitative tracer for the different processes and oxygen sources involved in sulfate production. Δ17O signatures are distinct fingerprints of these reservoirs, independent of fractionation factors that can be ambiguous. We conducted controlled abiotic and biotic (Acidithiobacillus ferrooxidans, A.f.) laboratory experiments in which water was spiked with 18O, allowing us to quantify the sources of sulfate oxygen and therefore the processes attending sulfate formation. Results of this Δ17O tracer study show that A.f. microbes initiate pyrite S-oxidation within hours of exposure, and that sulfate is produced from ~90% atmospheric oxygen. This initial lag-phase (< 3 days) is characterized by subtle and multiple changes in oxygen source and contribution that is likely due to the adjustment of the microbial metabolism from S to Fe2+-oxidation. A more detailed understanding of the microbial mechanisms and behavior in the initial lag-phase will aid in the understanding of the ecological conditions required for microbial populations to establish and survive. An exponential phase of growth, facilitated by microbial Fe2+-oxidation, follows. The source of sulfate rapidly switches to abiotic sulfide oxidation during exponential growth and the source of oxygen switches from atmospheric O2 to nearly ~100% water. Pending acquisition of complimentary chemistry data (in progress), we interpret our isotope data to indicate that the biotic fractionation factor ɛ18OSO4-O2 of at least ~ -25 to - 35‰ is augmented by microbially induced kinetic fractionation; it is larger than expected based on published equilibrium values [2,3,4]. Our inferred ɛ18OSO4-H2O of at least ~+10‰ is similar to some reported values. These new insights into the close links between microbial life cycle and sources of sulfate oxygen during sulfide oxidation, and their oxygen isotopic expressions, will help elucidate the role of microbial oxidation in natural systems. If microbial populations in natural systems remain in a perpetual lag-phase due to constrains of chemistry, atmospheric oxygen will imprint its isotopic signature onto sulfate deposits. Ultimately, such data could be used as biosignatures on Early Earth or Mars. [1] Brunner and Coleman (2008) EPSL 270, 63-72. [2] Balci et al. (2007) GCA 71, 3796-3811. [3] Pisapia et al. (2007) GCA 71, 2474-2490. [4] Taylor et al. (1984) GCA 48, 2669-2678.

Landscape topography structures the soil microbiome in arctic polygonal tundra.

PubMed

Taş, Neslihan; Prestat, Emmanuel; Wang, Shi; Wu, Yuxin; Ulrich, Craig; Kneafsey, Timothy; Tringe, Susannah G; Torn, Margaret S; Hubbard, Susan S; Jansson, Janet K

2018-02-22

In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH 4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N 2 O, reflecting low N 2 O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

PubMed

Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

2018-04-06

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Lipids as paleomarkers to constrain the marine nitrogen cycle.

PubMed

Rush, Darci; Sinninghe Damsté, Jaap S

2017-06-01

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio-available nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments

PubMed Central

Hernsdorf, Alex W; Amano, Yuki; Miyakawa, Kazuya; Ise, Kotaro; Suzuki, Yohey; Anantharaman, Karthik; Probst, Alexander; Burstein, David; Thomas, Brian C; Banfield, Jillian F

2017-01-01

Geological sequestration in deep underground repositories is the prevailing proposed route for radioactive waste disposal. After the disposal of radioactive waste in the subsurface, H2 may be produced by corrosion of steel and, ultimately, radionuclides will be exposed to the surrounding environment. To evaluate the potential for microbial activities to impact disposal systems, we explored the microbial community structure and metabolic functions of a sediment-hosted ecosystem at the Horonobe Underground Research Laboratory, Hokkaido, Japan. Overall, we found that the ecosystem hosted organisms from diverse lineages, including many from the phyla that lack isolated representatives. The majority of organisms can metabolize H2, often via oxidative [NiFe] hydrogenases or electron-bifurcating [FeFe] hydrogenases that enable ferredoxin-based pathways, including the ion motive Rnf complex. Many organisms implicated in H2 metabolism are also predicted to catalyze carbon, nitrogen, iron and sulfur transformations. Notably, iron-based metabolism is predicted in a novel lineage of Actinobacteria and in a putative methane-oxidizing ANME-2d archaeon. We infer an ecological model that links microorganisms to sediment-derived resources and predict potential impacts of microbial activity on H2 consumption and retardation of radionuclide migration. PMID:28350393

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

H2O2 from the oxidative burst orchestrates the plant hypersensitive disease resistance response.

PubMed

Levine, A; Tenhaken, R; Dixon, R; Lamb, C

1994-11-18

Microbial elicitors or attempted infection with an avirulent pathogen strain causes the rapid production of reactive oxygen intermediates. We report here that H2O2 from this oxidative burst not only drives the cross-linking of cell wall structural proteins, but also functions as a local trigger of programmed death in challenged cells and as a diffusible signal for the induction in adjacent cells of genes encoding cellular protectants such as glutathione S-transferase and glutathione peroxidase. Thus, H2O2 from the oxidative burst plays a key role in the orchestration of a localized hypersensitive response during the expression of plant disease resistance.

Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

PubMed

Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

1996-05-01

Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction.

Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

PubMed Central

Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

1996-01-01

Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction. PMID:8633860

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

NASA Astrophysics Data System (ADS)

Francis, C.

2015-12-01

Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention. Using a combination of molecular, biogeochemical, and 'omics' approaches, we have been examining how N-cycling microbial communities throughout the SFBD change in relation to environmental fluctuations—a critical step in understanding how microbial populations drive biogeochemical cycling in this estuary.

[Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

PubMed

Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

2012-01-01

Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Soil nitrogen cycling and availability are linked to ammonia oxidizer abundance across a tropical mean annual temperature gradient

NASA Astrophysics Data System (ADS)

Pierre, S.; Litton, C. M.; Giardina, C. P.; Sparks, J. P.; Groffman, P.; Hewson, I.; Fahey, T.

2016-12-01

Interactions among environmental variables can obfuscate the primary drivers linking soil microbial community function to ecosystem biogeochemistry. These connections are important to understand in order to predict ecosystem responses to global climate change. In particular, the role of mean annual temperature (MAT) in regulating carbon (C) and nitrogen (N) cycling via microbial communities remains unclear. To study these dynamics in situ, we used a a natural elevation gradient of tropical wet montane forest on Mauna Kea, Hawai'i with established permanent plots. Across the gradient, environmental variables besides MAT remain constant. We studied the abundance and activity of the amoA gene, which regulates the rate-limiting step of nitrification, in ammonia oxidizing archaea (AOA) and bacteria (AOB) with relation to N availability and cycling across increasing MAT. Our results show that the abundance of amoA is positively correlated with MAT (p<0.05; r2=0.34) and that MAT and amoA abundance are the primary predictors of nitrate (NO3-) bioavailability (p<0.05). We also found that the relative expression of amoA (cDNA/DNA) is not correlated with MAT or potential net nitrification rate. Our results indicate the direct role of MAT in ammonia oxidizer community structure and demonstrate feedbacks to nutrient availability in forest systems. These findings suggest that forest primary production and carbon cycling may be affected by AOA and AOB responses to rising MAT.

Coupled biotic-abiotic oxidation of organic matter by biogenic MnO_{2}

NASA Astrophysics Data System (ADS)

Gonzalez, Julia; Peña, Jasquelin

2016-04-01

Some reactive soil minerals are strongly implicated in stabilising organic matter. However, others can play an active role in the oxidation of organic molecules. In natural systems, layer-type manganese oxide minerals (MnO2) typically occur as biomineral assemblages consisting of mineral particles and microbial biomass. Both the mineral and biological fractions of the assemblage can be powerful oxidants of organic C. The biological compartment relies on a set of enzymes to drive oxidative transformations of reduced C-substrates, whereas MnO2 minerals are strong, less specific abiotic oxidants that are assumed to rely on interfacial interactions between C-substrates and the mineral surface. This project aims to understand the coupling between microbial C mineralization and abiotic C oxidation mediated by MnO2 in bacterial-MnO2 assemblages. Specifically, under conditions of high C turnover, microbial respiration can significantly alter local pH, dissolved oxygen and pool of available reductants, which may modify rates and mechanism of C oxidation by biotic and abiotic components. We first investigated changes in the solution chemistry of Pseudomonas putida suspensions exposed to varying concentrations of glucose, chosen to represent readily bioavailable substrates in soils. Glucose concentrations tested ranged between 0 and 5.5mM and changes in pH, dissolved oxygen and dissolved organic and inorganic carbon were tracked over 48h. We then combined literature review and wet-chemical experiments to compile the pH dependence of rates of organic substrate oxidation by MnO2, including glucose. Our results demonstrate a strong pH dependence for these abiotic reactions. In assemblages of P. putida - MnO2, kinetic limitations for abiotic C oxidation by MnO2 are overcome by changes in biogeochemical conditions that result from bacterial C metabolism. When extrapolated to a soil solution confronted to an input of fresh dissolved organic matter, bacterial C metabolism of the labile fraction may lower solution pH into a regime that favours abiotic oxidation of recalcitrant C by MnO2. This project demonstrates that the co-occurrence of mineral particles with metabolically active cells provides a direct link between the C and Mn cycles.

The development of Fe-nodules surrounding biological material mediated by microorganisms

NASA Astrophysics Data System (ADS)

Yoshida, Hidekazu; Yamamoto, Koshi; Murakami, Yuki; Katsuta, Nagayoshi; Hayashi, Toru; Naganuma, Takeshi

2008-09-01

Takashikozo is a phenomenon of Quaternary sediments in Japan. They are cylindrical Fe-oxyhydroxide nodules that form as plaques round plant roots, where Fe is preferentially concentrated to develop a solid wall. Structural features suggest that after the roots have decayed, the central space where the roots were situated acts as a flow path for oxidized water. Analysis of microbial 16S rDNA extracted from the nodules identified iron-oxidizing bacteria encrusted round the roots where they are the likely initiators of nodule formation. Direct microscopic observation revealed an accumulation of Fe-oxyhydroxides that fill the pore spaces and is also likely to be linked with the encrusting microbial colonies. Geological history and nanofossil evidence suggest that these Fe-nodules may have been buried at a depth of up to several tens of meters for at least 105 years in reducing Quaternary sediments. Thus Fe-oxyhydroxide nodules that have formed in a geological environment at the interfaces between water and rock by microbial mediation can persist under reducing conditions. If this is the case, the phenomenon is significant as an analogue of post-closure conditions in radioactive waste repositories, since it could influence nuclide migration.

Soil nitrate reducing processes – drivers, mechanisms for spatial variation, and significance for nitrous oxide production

PubMed Central

Giles, Madeline; Morley, Nicholas; Baggs, Elizabeth M.; Daniell, Tim J.

2012-01-01

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate (NO3−) and production of the potent greenhouse gas, nitrous oxide (N2O). A number of factors are known to control these processes, including O2 concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N2O production from soils. PMID:23264770

Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production.

PubMed

Giles, Madeline; Morley, Nicholas; Baggs, Elizabeth M; Daniell, Tim J

2012-01-01

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.

Increased electrical output when a bacterial ABTS oxidizer is used in a microbial fuel cell

USDA-ARS?s Scientific Manuscript database

Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. The present study examined the formation in culture of an unidentified bacterial oxidant and investigated the ...

Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

PubMed Central

Kozubal, Mark A.; Macur, Richard E.; Jay, Zackary J.; Beam, Jacob P.; Malfatti, Stephanie A.; Tringe, Susannah G.; Kocar, Benjamin D.; Borch, Thomas; Inskeep, William P.

2012-01-01

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats in Yellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C. PMID:22470372

HONO (nitrous acid) emissions from acidic northern soils

NASA Astrophysics Data System (ADS)

Maljanen, Marja; Yli-Pirilä, Pasi; Joutsensaari, Jorma; Sulassaari, Sirkka; Martikainen, Pertti J.

2014-05-01

The photolysis of HONO (nitrous acid) is an important source of OH radical, the key oxidizing agent in the atmosphere, contributing also to removal of atmospheric methane (CH4), the second most important greenhouse gas after carbon dioxide (CO2). There are missing sources of HONO when considering the chemical reactions in the atmosphere. Soil could be such a missing source. Emissions of HONO from soils studied in laboratory incubations have been recently reported. The soil-derived HONO has been connected to soil nitrite (NO2-) and a study with an ammonium oxidizing bacterium has shown that HONO could be produced in ammonium oxidation. Our hypothesis was that boreal acidic soils with high nitrification activity could be important sources of HONO. We selected a range of dominant northern acidic soils and showed in microcosm experiments that soils which have the highest nitrous oxide (N2O) and nitric oxide (NO) emissions (drained peatlands) also have the highest HONO production rates. The emissions of HONO are thus linked to nitrogen cycle processes. In contrast to drained peatlands, natural peatlands with high water table and boreal coniferous forests on mineral soils with low nitrification capacity had low HONO emissions. It is known that in natural peatlands with high water table and in boreal coniferous forest soils, low nitrification activity (microbial production of nitrite and nitrate) limits their N2O production. Low nitrification rate and low availability of nitrite in these soils are the likely reasons for their low HONO production rates. We studied the origin of HONO in one drained peat soil by inhibiting nitrification with acetylene. Acetylene blocked NO emissions but did not affect HONO or N2O emissions, thus ammonium oxidation is not the direct mechanism for the HONO emission in this soil. It is still an open question if HONO originates directly from some microbial process like ammonium oxidation or chemically from nitrite produced in microbial processes.

Microbial degradation of hydrochlorofluorocarbons (CHCl2F and CHCl2CF3) in soils and sediments

USGS Publications Warehouse

Oremland, R.S.; Lonergan, D.J.; Culbertson, C.W.; Lovley, D.R.

1996-01-01

The ability of microorganisms to degrade trace levels of the hydrochlorofluorocarbons HCFC-21 and HCFC-123 was investigated. Methanotroph- linked oxidation of HCFC-21 was observed in aerobic soils, and anaerobic degradation of HCFC-21 occurred in freshwater and salt marsh sediments. Microbial degradation of HCFC-123 was observed in anoxic freshwater and salt marsh sediments, and the recovery of 1,1,1-trifluoro-2-chloroethane indicated the involvement of reductive dechlorination. No degradation of HCFC-123 was observed in aerobic soils. In same experiments, HCFCs were degraded at low (parts per billion) concentrations, raising the possibility that bacteria in nature remove HCFCs from the atmosphere.

Formation of carbonate pipes in the northern Okinawa Trough linked to strong sulfate exhaustion and iron supply

NASA Astrophysics Data System (ADS)

Peng, Xiaotong; Guo, Zixiao; Chen, Shun; Sun, Zhilei; Xu, Hengchao; Ta, Kaiwen; Zhang, Jianchao; Zhang, Lijuan; Li, Jiwei; Du, Mengran

2017-05-01

The microbial anaerobic oxidation of methane (AOM), a key biogeochemical process that consumes substantial amounts of methane produced in seafloor sediments, can lead to the formation of carbonate deposits at or beneath the sea floor. Although Fe oxide-driven AOM has been identified in cold seep sediments, the exact mode by which it may influence the formation of carbonate deposits remains poorly understood. Here, we characterize the morphology, petrology and geochemistry of a methane-derived Fe-rich carbonate pipe in the northern Okinawa Trough (OT). We detect abundant authigenic pyrites, as well as widespread trace Fe, within microbial mat-like carbonate veins in the pipe. The in situ δ34S values of these pyrites range from -3.9 to 31.6‰ (VCDT), suggesting a strong consumption of seawater sulfate by sulfate-driven AOM at the bottom of sulfate reduction zone. The positive δ56Fe values of pyrite and notable enrichment of Fe in the OT pipe concurrently indicate that the pyrites are primarily derived from Fe oxides in deep sediments. We propose that the Fe-rich carbonate pipe formed at the bottom of sulfate reduction zone, below which Fe-driven AOM, rather than Fe-oxide reduction coupled to organic matter degradation, might be responsible for the abundantly available Fe2+ in the fluids from which pyrites precipitated. The Fe-rich carbonate pipe described in this study probably represents the first fossil example of carbonate deposits linked to Fe-driven AOM. Because Fe-rich carbonate deposits have also been found at other cold seeps worldwide, we infer that similar processes may play an essential role in biogeochemical cycling of sub-seafloor methane and Fe at continental margins.

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry.

PubMed

Liu, Shanshan; Wang, Feng; Xue, Kai; Sun, Bo; Zhang, Yuguang; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong; Yang, Yunfeng

2015-03-01

Soil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southern China (subtropical climate zone) to central (warm temperate climate zone) and northern China (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soil pH and NH4 (+) -N content as environmental attributes closely correlated with microbial functional structures. In addition, average abundances of amoA-AOA (ammonia-oxidizing archaea) and amoA-AOB (ammonia-oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence both AOA and AOB contributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Complete cobalt recovery from lithium cobalt oxide in self-driven microbial fuel cell - Microbial electrolysis cell systems

NASA Astrophysics Data System (ADS)

Huang, Liping; Yao, Binglin; Wu, Dan; Quan, Xie

2014-08-01

Complete cobalt recovery from lithium cobalt oxide requires to firstly leach cobalt from particles LiCoO2 and then recover cobalt from aqueous Co(II). A self-driven microbial fuel cell (MFC)-microbial electrolysis cell (MEC) system can completely carry out these two processes, in which Co(II) is firstly released from particles LiCoO2 on the cathodes of MFCs and then reduced on the cathodes of MECs which are powered by the cobalt leaching MFCs. A cobalt leaching rate of 46 ± 2 mg L-1 h-1 with yield of 1.5 ± 0.1 g Co g-1 COD (MFCs) and a Co(II) reduction rate of 7 ± 0 mg L-1 h-1 with yield of 0.8 ± 0.0 g Co g-1 COD (MECs), as well as a overall system cobalt yield of 0.15 ± 0.01 g Co g-1 Co can be achieved in this self-driven MFC-MEC system. Coulombic efficiencies reach 41 ± 1% (anodic MFCs), 75 ± 0% (anodic MECs), 100 ± 2% (cathodic MFCs), and 29 ± 1% (cathodic MECs) whereas overall system efficiency averages 34 ± 1%. These results provide a new process of linking MFCs to MECs for complete recovery of cobalt and recycle of spent lithium ion batteries with no external energy consumption.

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

Thousands of Viral Populations Recovered from Peatland Soil Metagenomes Reveal Viral Impacts on Carbon Cycling in Thawing Permafrost

NASA Astrophysics Data System (ADS)

Emerson, J. B.; Brum, J. R.; Roux, S.; Bolduc, B.; Woodcroft, B. J.; Singleton, C. M.; Boyd, J. A.; Hodgkins, S. B.; Wilson, R.; Trubl, G. G.; Jang, H. B.; Crill, P. M.; Chanton, J.; Saleska, S. R.; Rich, V. I.; Tyson, G. W.; Sullivan, M. B.

2016-12-01

Methane and carbon dioxide emissions, which are under significant microbial control, provide positive feedbacks to climate change in thawing permafrost peatlands. Although viruses in marine systems have been shown to impact microbial ecology and biogeochemical cycling through host cell lysis, horizontal gene transfer, and auxiliary metabolic gene expression, viral ecology in permafrost and other soils remains virtually unstudied due to methodological challenges. Here, we identified viral sequences in 208 assembled bulk soil metagenomes derived from a permafrost thaw gradient in Stordalen Mire, northern Sweden, from 2010-2012. 2,048 viral populations were recovered, which genome- and network-based classification revealed to be largely novel, increasing known viral genera globally by 40%. Ecologically, viral communities differed significantly across the thaw gradient and by soil depth. Co-occurring microbial community composition, soil moisture, and pH were predictors of viral community composition, indicative of biological and biogeochemical feedbacks as permafrost thaws. Host prediction—achieved through clustered regularly interspaced short palindromic repeats (CRISPRs), tetranucleotide frequency patterns, and other sequence similarities to binned microbial population genomes—was able to link 38% of the viral populations to a microbial host. 5% of the implicated hosts were archaea, predominantly methanogens and ammonia-oxidizing Nitrososphaera, 45% were Acidobacteria or Verrucomicrobia (mostly predicted heterotrophic complex carbon degraders), and 21% were Proteobacteria, including methane oxidizers. Recovered viral genome fragments also contained auxiliary metabolic genes involved in carbon and nitrogen cycling. Together, these data reveal multiple levels of previously unknown viral contributions to biogeochemical cycling, including to carbon gas emissions, in peatland soils undergoing and contributing to climate change. This work represents a significant step towards understanding viral roles in microbially-mediated biogeochemical cycling in soil.

Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk

PubMed Central

Zhu, Weifei; Gregory, Jill C.; Org, Elin; Buffa, Jennifer A.; Gupta, Nilaksh; Wang, Zeneng; Li, Lin; Fu, Xiaoming; Wu, Yuping; Mehrabian, Margarete; Sartor, R. Balfour; McIntyre, Thomas M.; Silverstein, Roy L.; Tang, W.H. Wilson; DiDonato, Joseph A.; Brown, J. Mark; Lusis, Aldons J.; Hazen, Stanley L.

2016-01-01

SUMMARY Normal platelet function is critical to blood hemostasis and maintenance of a closed circulatory system. Heightened platelet reactivity, however, is associated with cardiometabolic diseases and enhanced potential for thrombotic events. We now show gut microbes, through generation of trimethylamine N-oxide (TMAO), directly contribute to platelet hyperreactivity and enhanced thrombosis potential. Plasma TMAO levels in subjects (N>4000) independently predicted incident (3 yr) thrombosis (heart attack, stroke) risk. Direct exposure of platelets to TMAO enhanced submaximal stimulus-dependent platelet activation from multiple agonists through augmented Ca2+ release from intracellular stores. Animal model studies employing dietary choline or TMAO, germ-free mice, and microbial transplantation, collectively confirm a role for gut microbiota and TMAO in modulating platelet hyperresponsiveness and thrombosis potential, and identify microbial taxa associated with plasma TMAO and thrombosis potential. Collectively, the present results reveal a previously unrecognized mechanistic link between specific dietary nutrients, gut microbes, platelet function, and thrombosis risk. PMID:26972052

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orphan, Victoria; Tyson, Gene; Meile, Christof

The global biological CH4 cycle is largely controlled through coordinated and often intimate microbial interactions between archaea and bacteria, the majority of which are still unknown or have been only cursorily identified. Members of the methanotrophic archaea, aka ‘ANME’, are believed to play a major role in the cycling of methane in anoxic environments coupled to sulfate, nitrate, and possibly iron and manganese oxides, frequently forming diverse physical and metabolic partnerships with a range of bacteria. The thermodynamic challenges overcome by the ANME and their bacterial partners and corresponding slow rates of growth are common characteristics in anaerobic ecosystems, and,more » in stark contrast to most cultured microorganisms, this type of energy and resource limited microbial lifestyle is likely the norm in the environment. While we have gained an in-depth systems level understanding of fast-growing, energy-replete microorganisms, comparatively little is known about the dynamics of cell respiration, growth, protein turnover, gene expression, and energy storage in the slow-growing microbial majority. These fundamental properties, combined with the observed metabolic and symbiotic versatility of methanotrophic ANME, make these cooperative microbial systems a relevant (albeit challenging) system to study and for which to develop and optimize culture-independent methodologies, which enable a systems-level understanding of microbial interactions and metabolic networks. We used an integrative systems biology approach to study anaerobic sediment microcosms and methane-oxidizing bioreactors and expanded our understanding of the methanotrophic ANME archaea, their interactions with physically-associated bacteria, ecophysiological characteristics, and underlying genetic basis for cooperative microbial methane-oxidation linked with different terminal electron acceptors. Our approach is inherently multi-disciplinary and multi-scaled, combining transcriptional and proteomic analyses with high resolution microscopy techniques, and stable isotopic and chemical analyses that span community level ‘omics investigations (cm scale) to interspecies consortia (µm scale), to the individual cell and its subcellular components (nm scale). We have organized our methodological approach into three broad categories, RNA-based, Protein-targeted and Geochemical, each encompassing a range of scales, with many techniques and resulting datasets that are highly complementary with one another, and together, offer a unique systems-level perspective of methane-based microbial interactions.« less

Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orphan, Victoria Jeanne

2014-11-26

Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions betweenmore » microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of spatially structured microbial partnerships, including other syntrophic associations, microbial mats, biofilms, and plant-microbe or animal-microbe symbioses in nature.« less

New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

PubMed

Imhoff, Johannes F

2016-05-24

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.

Nitrification inhibition by hexavalent chromium Cr(VI)--Microbial ecology, gene expression and off-gas emissions.

PubMed

Kim, Young Mo; Park, Hongkeun; Chandran, Kartik

2016-04-01

The goal of this study was to investigate the responses in the physiology, microbial ecology and gene expression of nitrifying bacteria to imposition of and recovery from Cr(VI) loading in a lab-scale nitrification bioreactor. Exposure to Cr(VI) in the reactor strongly inhibited nitrification performance resulting in a parallel decrease in nitrate production and ammonia consumption. Cr(VI) exposure also led to an overall decrease in total bacterial concentrations in the reactor. However, the fraction of ammonia oxidizing bacteria (AOB) decreased to a greater extent than the fraction of nitrite oxidizing bacteria (NOB). In terms of functional gene expression, a rapid decrease in the transcript concentrations of amoA gene coding for ammonia oxidation in AOB was observed in response to the Cr(VI) shock. In contrast, transcript concentrations of the nxrA gene coding for nitrite oxidation in NOB were relatively unchanged compared to Cr(VI) pre-exposure levels. Therefore, Cr(VI) exposure selectively and directly inhibited activity of AOB, which indirectly resulted in substrate (nitrite) limitation to NOB. Significantly, trends in amoA expression preceded performance trends both during imposition of and recovery from inhibition. During recovery from the Cr(VI) shock, the high ammonia concentrations in the bioreactor resulted in an irreversible shift towards AOB populations, which are expected to be more competitive in high ammonia environments. An inadvertent impact during recovery was increased emission of nitrous oxide (N2O) and nitric oxide (NO), consistent with recent findings linking AOB activity and the production of these gases. Therefore, Cr(VI) exposure elicited multiple responses on the microbial ecology, gene expression and both aqueous and gaseous nitrogenous conversion in a nitrification process. A complementary interrogation of these multiple responses facilitated an understanding of both direct and indirect inhibitory impacts on nitrification. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biomineralization of As(V)-hydrous ferric oxyhydroxide in microbial mats of an acid-sulfate-chloride geothermal spring, Yellowstone National Park

NASA Astrophysics Data System (ADS)

Inskeep, William P.; Macur, Richard E.; Harrison, Gregory; Bostick, Benjamin C.; Fendorf, Scott

2004-08-01

Acid-sulfate-chloride (pH˜3) geothermal springs in Yellowstone National Park (YNP) often contain Fe(II), As(III), and S(-II) at discharge, providing several electron donors for chemolithotrophic metabolism. The microbial populations inhabiting these environments are inextricably linked with geochemical processes controlling the behavior of As and Fe. Consequently, the objectives of the current study were to (i) characterize Fe-rich microbial mats of an ASC thermal spring, (ii) evaluate the composition and structure of As-rich hydrous ferric oxides (HFO) associated with these mats, and (iii) identify microorganisms that are potentially responsible for mat formation via the oxidation of Fe(II) and or As(III). Aqueous and solid phase mat samples obtained from a spring in Norris Basin, YNP (YNP Thermal Inventory NHSP35) were analyzed using a complement of chemical, microscopic and spectroscopic techniques. In addition, molecular analysis (16S rDNA) was used to identify potentially dominant microbial populations within different mat locations. The biomineralization of As-rich HFO occurs in the presence of nearly equimolar aqueous As(III) and As(V) (˜12 μM), and ˜ 48 μM Fe(II), forming sheaths external to microbial cell walls. These solid phases were found to be poorly ordered nanocrystalline HFO containing mole ratios of As(V):Fe(III) of 0.62 ± 0.02. The bonding environment of As(V) and Fe(III) is consistent with adsorption of arsenate on edge and corner positions of Fe(III)-OH octahedra. Numerous archaeal and bacterial sequences were identified (with no closely related cultured relatives), along with several 16S sequences that are closely related to Acidimicrobium, Thiomonas, Metallosphaera and Marinithermus isolates. Several of these cultured relatives have been implicated in Fe(II) and or As(III) oxidation in other low pH, high Fe, and high As environments (e.g. acid-mine drainage). The unique composition and morphologies of the biomineralized phases may be useful as modern-day analogs for identifying microbial life in past Fe-As rich environments.

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

PubMed Central

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

PubMed

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.

PubMed

Scharko, Nicole K; Schütte, Ursel M E; Berke, Andrew E; Banina, Lauren; Peel, Hannah R; Donaldson, Melissa A; Hemmerich, Chris; White, Jeffrey R; Raff, Jonathan D

2015-12-01

Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment.

Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment.

PubMed

Casciotti, Karen L; Buchwald, Carolyn; Santoro, Alyson E; Frame, Caitlin

2011-01-01

Nitrification is a microbially-catalyzed process whereby ammonia (NH(3)) is oxidized to nitrite (NO(2)(-)) and subsequently to nitrate (NO(3)(-)). It is also responsible for production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Because the microbes responsible for nitrification are primarily autotrophic, nitrification provides a unique link between the carbon and nitrogen cycles. Nitrogen and oxygen stable isotope ratios have provided insights into where nitrification contributes to the availability of NO(2)(-) and NO(3)(-), and where it constitutes a significant source of N(2)O. This chapter describes methods for determining kinetic isotope effects involved with ammonia oxidation and nitrite oxidation, the two independent steps in the nitrification process, and their expression in the marine environment. It also outlines some remaining questions and issues related to isotopic fractionation during nitrification. Copyright © 2011 Elsevier Inc. All rights reserved.

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils.

PubMed

Sutton, Nora B; Langenhoff, Alette A M; Lasso, Daniel Hidalgo; van der Zaan, Bas; van Gaans, Pauline; Maphosa, Farai; Smidt, Hauke; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-03-01

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids.

PubMed

Knief, Claudia; Altendorf, Karlheinz; Lipski, André

2003-11-01

A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur-oxidizing and iron-oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography-mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis-7-hexadecenoic acid (16:1 cis7) and 11-methyl hexadecanoic acid (16:0 11methyl), which are as-yet not known for any sulphide-oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide-oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.

Electricity production coupled to ammonium in a microbial fuel cell.

PubMed

He, Zhen; Kan, Jinjun; Wang, Yanbing; Huang, Yuelong; Mansfeld, Florian; Nealson, Kenneth H

2009-05-01

The production of electricity from ammonium was examined using a rotating-cathode microbial fuel cell (MFC). The addition of ammonium chloride, ammonium sulfate, or ammonium phosphate (monobasic) resulted in electricity generation, while adding sodium chloride, nitrate, or nitrite did not cause any increase in current production. The peak current increased with increasing amount of ammonium addition up to 62.3 mM of ammonium chloride, suggesting that ammonium was involved in electricity generation either directly as the anodic fuel or indirectly as substrates for nitrifiers to produce organic compounds for heterotrophs. Adding nitrate or nitrite with ammonium increased current production compared to solely ammonium addition. Using 16S rRNA-linked molecular analyses, we found ammonium-oxidizing bacteria and denitrifying bacteria on both the anode and cathode electrodes, whereas no anammox bacteria were detected. The dominant ammonium-oxidizing bacteria were closely related to Nitrosomonas europaea. The present MFC achieved an ammonium removal efficiency of 49.2 +/- 5.9 or 69.7 +/- 3.6%, depending on hydraulic retention time, but exhibited a very low Coulombic efficiency.

Analysis of in situ manganese(II) oxidation in the Columbia River and offshore plume: Linking microbial community structure to active biogeochemical cycles

PubMed Central

Anderson, C. R.; Davis, R. E.; Bandolin, N. S.; Baptista, A. M.; Tebo, B. M.

2017-01-01

The Columbia River is a major source of dissolved nutrients and trace metals for the west coast of North America. A large proportion of these nutrients are sourced from the Columbia River Estuary where coastal and terrestrial waters mix and resuspend particulate matter within the water column. As estuarine water is discharged off the coast it transports the particulate matter, dissolved nutrients and microorganisms forming nutrient rich and metabolically dynamic plumes. In this study, bacterial manganese oxidation within the plume and estuary was investigated during spring and neap tides. The microbial community proteome was fractionated and assayed for Mn oxidation activity. Proteins from the outer membrane and the loosely bound outer membrane fractions were separated using size exclusion chromatography and Mn(II)-oxidizing eluates were analyzed with tandem mass spectrometry to identify potential Mn oxidase protein targets. Multi-copper oxidase (MCO) and heme-peroxidase enzymes were identified in active fractions. T-RFLP cluster analysis indicates that the organisms oxidizing the most Mn(II) were sourced from the Columbia River estuary and nearshore coastal ocean. These organisms are producing up to 10 fM MnO2 cell−1 day−1. Evidence for the presence of Mn(II)-oxidizing bacterial isolates from the genera Aurantimonas, Rhodobacter, Bacillus, and Shewanella was found in T-RFLP profiles. Q-PCR was used to quantify the gene copies of the heme-peroxidase, Aurantimonas SSU rRNA and total bacterial SSU rRNA gene copies. The probes used suggested that Aurantimonas could only account for 1.7% of heme-peroxidase genes quantified suggesting that peroxidase driven manganese oxidation capabilities are widespread throughout other organisms in this environment. PMID:21418498

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.

PubMed

Pan, Yao; Abell, Guy C J; Bodelier, Paul L E; Meima-Franke, Marion; Sessitsch, Angela; Bodrossy, Levente

2014-08-01

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

Impact of temperature and substrate concentration on degradation rates of acetate, propionate and hydrogen and their links to microbial community structure.

PubMed

Zhao, Jing; Westerholm, Maria; Qiao, Wei; Yin, Dongmin; Bi, Shaojie; Jiang, Mengmeng; Dong, Renjie

2018-05-01

The present study investigates the conversion of acetate, propionate and hydrogen consumption linked to the microbial community structure and related to temperature and substrate concentration. Biogas reactors were continuously fed with coffee powder (20 g-COD/L) or acetate (20, 40, and 60 g-COD/L) and operated for 193 days at 37 °C or 55 °C conditions. Starting HRT was 23 days which was then reduced to 7 days. The kinetics of acetate and propionate degradation and hydrogen consumption rates were measured in batch assays. At HRT 7 days, the degradation rate of propionate was higher in thermophilic batches, while acetate degradation rate was higher at mesophilic conditions. The gaseous hydrogen consumption in acetate reactors increased proportionally with temperature and substrate concentration, while the dissolved hydrogen was not affected. The relative high abundance of hydrogentrophic methanogens indicated that the methanogenesis was directed towards the syntrophic acetate oxidation pathway at high acetate concentration and high temperature. Copyright © 2018 Elsevier Ltd. All rights reserved.

Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge.

PubMed

Schrenk, Matthew O; Kelley, Deborah S; Bolton, Sheryl A; Baross, John A

2004-10-01

The recently discovered Lost City Hydrothermal Field (LCHF) represents a new type of submarine hydrothermal system driven primarily by exothermic serpentinization reactions in ultramafic oceanic crust. Highly reducing, alkaline hydrothermal environments at the LCHF produce considerable quantities of hydrogen, methane and organic molecules through chemo- and biosynthetic reactions. Here, we report the first analyses of microbial communities inhabiting carbonate chimneys awash in warm, high pH fluids at the LCHF and the predominance of a single group of methane-metabolizing Archaea. The predominant phylotype, related to the Methanosarcinales, formed tens of micrometre-thick biofilms in regions adjacent to hydrothermal flow. Exterior portions of active structures harboured a diverse microbial community composed primarily of filamentous Eubacteria that resembled sulphide-oxidizing species. Inactive samples, away from regions of hydrothermal flow, contained phylotypes related to pelagic microorganisms. The abundance of organisms linked to the volatile chemistry at the LCHF hints that similar metabolic processes may operate in the subseafloor. These results expand the range of known geological settings that support biological activity to include submarine hydrothermal systems that are not dependent upon magmatic heat sources.

Microbial reduction of Fe(III) and turnover of acetate in Hawaiian soils.

PubMed

Küsel, Kirsten; Wagner, Christine; Trinkwalter, Tanja; Gössner, Anita S; Bäumler, Rupert; Drake, Harold L

2002-04-01

Soils contain anoxic microzones, and acetate is an intermediate during the turnover of soil organic carbon. Due to negligible methanogenic activities in well-drained soils, acetate accumulates under experimentally imposed short-term anoxic conditions. In contrast to forest, agricultural, and prairie soils, grassland soils from Hawaii rapidly consumed rather than formed acetate when incubated under anoxic conditions. Thus, alternative electron acceptors that might be linked to the anaerobic oxidation of soil organic carbon in Hawaiian soils were assessed. Under anoxic conditions, high amounts of Fe(II) were formed by Hawaiian soils as soon as soils were depleted of nitrate. Rates of Fe(II) formation for different soils ranged from 0.01 to 0.31 micromol (g dry weight soil)(-1) h(-1), but were not positively correlated to increasing amounts of poorly crystallized iron oxides. In general, sulfate-reducing and methanogenic activities were negligible. Supplemental acetate was rapidly oxidized to CO2 via the sequential reduction of nitrate and Fe(III) in grassland soil (obtained near Kaena State Park). Supplemental H2 stimulated the formation of Fe(II), but H2-utilizing acetogens appeared to also be involved in the consumption of H2. Approximately 270 micromol Fe(III) (g dry weight soil)(-1) was available for Fe(III)-reducing bacteria, and acetate became a stable end product when Fe(III) was depleted in long-term incubations. Most-probable-number estimates of H2- and acetate-utilizing Fe(III) reducers and of H2-utilizing acetogens were similar. These results indicate that (i) the microbial reduction of Fe(III) is an important electron-accepting process for the anaerobic oxidation of organic matter in Fe(III)-rich Hawaiian soils of volcanic origin, and (ii) acetate, formed by the combined activity of fermentative and acetogenic bacteria, is an important trophic link in anoxic microsites of these soils.

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center.

PubMed

Anantharaman, Karthik; Breier, John A; Dick, Gregory J

2016-01-01

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic 'bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy.

Oxidative Weathering and Microbial Diversity of an Inactive Seafloor Hydrothermal Sulfide Chimney

PubMed Central

Li, Jiangtao; Cui, Jiamei; Yang, Qunhui; Cui, Guojie; Wei, Bingbing; Wu, Zijun; Wang, Yong; Zhou, Huaiyang

2017-01-01

When its hydrothermal supply ceases, hydrothermal sulfide chimneys become inactive and commonly experience oxidative weathering on the seafloor. However, little is known about the oxidative weathering of inactive sulfide chimneys, nor about associated microbial community structures and their succession during this weathering process. In this work, an inactive sulfide chimney and a young chimney in the early sulfate stage of formation were collected from the Main Endeavor Field of the Juan de Fuca Ridge. To assess oxidative weathering, the ultrastructures of secondary alteration products accumulating on the chimney surface were examined and the presence of possible Fe-oxidizing bacteria (FeOB) was investigated. The results of ultrastructure observation revealed that FeOB-associated ultrastructures with indicative morphologies were abundantly present. Iron oxidizers primarily consisted of members closely related to Gallionella spp. and Mariprofundus spp., indicating Fe-oxidizing species likely promote the oxidative weathering of inactive sulfide chimneys. Abiotic accumulation of Fe-rich substances further indicates that oxidative weathering is a complex, dynamic process, alternately controlled by FeOB and by abiotic oxidization. Although hydrothermal fluid flow had ceased, inactive chimneys still accommodate an abundant and diverse microbiome whose microbial composition and metabolic potential dramatically differ from their counterparts at active vents. Bacterial lineages within current inactive chimney are dominated by members of α-, δ-, and γ-Proteobacteria and they are deduced to be closely involved in a diverse set of geochemical processes including iron oxidation, nitrogen fixation, ammonia oxidation and denitrification. At last, by examining microbial communities within hydrothermal chimneys at different formation stages, a general microbial community succession can be deduced from early formation stages of a sulfate chimney to actively mature sulfide structures, and then to the final inactive altered sulfide chimney. Our findings provide valuable insights into the microbe-involved oxidative weathering process and into microbial succession occurring at inactive hydrothermal sulfide chimney after high-temperature hydrothermal fluids have ceased venting. PMID:28785251

Quantitative X-ray photoelectron spectroscopy-based depth profiling of bioleached arsenopyrite surface by Acidithiobacillus ferrooxidans

NASA Astrophysics Data System (ADS)

Zhu, Tingting; Lu, Xiancai; Liu, Huan; Li, Juan; Zhu, Xiangyu; Lu, Jianjun; Wang, Rucheng

2014-02-01

In supergene environments, microbial activities significantly enhance sulfide oxidation and result in the release of heavy metals, causing serious contamination of soils and waters. As the most commonly encountered arsenic mineral in nature, arsenopyrite (FeAsS) accounts for arsenic contaminants in various environments. In order to investigate the geochemical behavior of arsenic during microbial oxidation of arsenopyrite, (2 3 0) surfaces of arsenopyrite slices were characterized after acidic (pH 2.00) and oxidative decomposition with or without an acidophilic microorganism Acidithiobacillus ferrooxidans. The morphology as well as chemical and elemental depth profiles of the oxidized arsenopyrite surface were investigated by scanning electron microscopy and X-ray photoelectron spectroscopy. With the mediation of bacteria, cell-shaped and acicular pits were observed on the reacted arsenopyrite surface, and the concentration of released arsenic species in solution was 50 times as high as that of the abiotic reaction after 10 days reaction. Fine-scale XPS depth profiles of the reacted arsenopyrite surfaces after both microbial and abiotic oxidation provided insights into the changes in chemical states of the elements in arsenopyrite surface layers. Within the 450 nm surface layer of abiotically oxidized arsenopyrite, Fe(III)-oxides appeared and gradually increased towards the surface, and detectable sulfite and monovalent arsenic appeared above 50 nm. In comparison, higher contents of ferric sulfate, sulfite, and arsenite were found in the surface layer of approximately 3 μm of the microbially oxidized arsenopyrite. Intermediates, such as Fe(III)-AsS and S0, were detectable in the presence of bacteria. Changes of oxidative species derived from XPS depth profiles show the oxidation sequence is Fe > As = S in abiotic oxidation, and Fe > S > As in microbial oxidation. Based on these results, a possible reaction path of microbial oxidation was proposed in a concept model.

Microbial ecology of soda lakes: investigating sulfur and nitrogen cycling at Mono Lake, CA, USA

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Phillips, A. A.; Wells, M.; Bao, R.; Fullerton, K. M.; Stamps, B. W.; Speth, D. R.; Johnson, H.; Sessions, A. L.

2017-12-01

Soda lakes represent unique ecosystems characterized by extremes of pH, salinity and distinct geochemical cycling. Despite these extreme conditions, soda lakes are important repositories of biological adaptation and have a highly functional microbial system. We investigated the biogeochemical cycling of sulfur and nitrogen compounds in Mono Lake, California, located east of the Sierra Nevada mountains. Mono lake is characterized by hyperalkaline, hypersaline and high sulfate concentrations and can enter prolonged periods of meromixis due to freshwater inflow. Typically, the microbial sulfur cycle is highly active in soda lakes with both oxidation and reduction of sulfur compounds. However, the biological sulfur cycle is connected to many other main elemental cycles such as carbon, nitrogen and metals. Here we investigated the interaction between sulfur and nitrogen cycling in Mono lake using a combination of molecular, isotopic, and geochemical observations to explore the links between microbial phylogenetic composition and functionality. Metagenomic and 16S rRNA gene amplicon sequencing were determined at two locations and five depths in May 2017. 16S rRNA gene amplicon sequencing analysis revealed organisms capable of both sulfur and nitrogen cycling. The relative abundance and distribution of functional genes (dsrA, soxAB, nifH, etc) were also determined. These genetic markers indicate the potential in situ relevance of specific carbon, nitrogen, and sulfur pathways in the water column prior to the transition to meromictic stratification. However, genes for sulfide oxidation, denitrification, and ammonification were present. Genome binning guided by the most abundant dsrA sequences, GC content, and abundance with depth identified a Thioalkalivibrio paradoxus bin containing genes capable of sulfur oxidation, denitrification, and nitrate reduction. The presence of a large number of sulfur and nitrogen cycling genes associated with Thioalkalivibrio paradoxus suggests thiosulfate oxidation may be coupled to nitrate reduction despite the extremely low level of nitrate in Mono Lake. Our results illustrate the centrality of living organisms in both shaping and responding to geochemical cycles, as well as future directions for exploring coupled biogeochemical cycles in Mono Lake.

Cultivating the Deep Subsurface Microbiome

NASA Astrophysics Data System (ADS)

Casar, C. P.; Osburn, M. R.; Flynn, T. M.; Masterson, A.; Kruger, B.

2017-12-01

Subterranean ecosystems are poorly understood because many microbes detected in metagenomic surveys are only distantly related to characterized isolates. Cultivating microorganisms from the deep subsurface is challenging due to its inaccessibility and potential for contamination. The Deep Mine Microbial Observatory (DeMMO) in Lead, SD however, offers access to deep microbial life via pristine fracture fluids in bedrock to a depth of 1478 m. The metabolic landscape of DeMMO was previously characterized via thermodynamic modeling coupled with genomic data, illustrating the potential for microbial inhabitants of DeMMO to utilize mineral substrates as energy sources. Here, we employ field and lab based cultivation approaches with pure minerals to link phylogeny to metabolism at DeMMO. Fracture fluids were directed through reactors filled with Fe3O4, Fe2O3, FeS2, MnO2, and FeCO3 at two sites (610 m and 1478 m) for 2 months prior to harvesting for subsequent analyses. We examined mineralogical, geochemical, and microbiological composition of the reactors via DNA sequencing, microscopy, lipid biomarker characterization, and bulk C and N isotope ratios to determine the influence of mineralogy on biofilm community development. Pre-characterized mineral chips were imaged via SEM to assay microbial growth; preliminary results suggest MnO2, Fe3O4, and Fe2O3 were most conducive to colonization. Solid materials from reactors were used as inoculum for batch cultivation experiments. Media designed to mimic fracture fluid chemistry was supplemented with mineral substrates targeting metal reducers. DNA sequences and microscopy of iron oxide-rich biofilms and fracture fluids suggest iron oxidation is a major energy source at redox transition zones where anaerobic fluids meet more oxidizing conditions. We utilized these biofilms and fluids as inoculum in gradient cultivation experiments targeting microaerophilic iron oxidizers. Cultivation of microbes endemic to DeMMO, a system locally dominated by unclassified and candidate phyla, has the potential to yield novel subsurface organisms with unique physiologies. We intend to further utilize subsurface isolates to probe the effects of geochemical perturbations on biosignatures in future studies, thus broadening our understanding of subterranean ecosystems.

Bacterial oxidation of methyl bromide in fumigated agricultural soils

USGS Publications Warehouse

Miller, L.G.; Connell, T.L.; Guidetti, J.R.; Oremland, R.S.

1997-01-01

The oxidation of [14C]methyl bromide ([14C]MeBr) to 14CO2 was measured in field experiments with soils collected from two strawberry plots fumigated with mixtures of MeBr and chloropicrin (CCI3NO2). Although these fumigants are considered potent biocides, we found that the highest rates of MeBr oxidation occurred 1 to 2 days after injection when the fields were tarped, rather than before or several days after injection. No oxidation of MeBr occurred in heat-killed soils, indicating that microbes were the causative agents of the oxidation. Degradation of MeBr by chemical and/or biological processes accounted for 20 to 50% of the loss of MeBr during fumigation, with evasion to the atmosphere inferred to comprise the remainder. In laboratory incubations, complete removal of [14C]MeBr occurred within a few days, with 47 to 67% of the added MeBr oxidized to 14CO2 and the remainder of counts associated with the solid phase. Chloropicrin inhibited the oxidation of MeBr, implying that use of this substance constrains the extent of microbial degradation of MeBr during fumigation. Oxidation was by direct bacterial attack of MeBr and not of methanol, a product of the chemical hydrolysis of MeBr. Neither nitrifying nor methane-oxidizing bacteria were sufficiently active in these soils to account for the observed oxidation of MeBr, nor could the microbial degradation of MeBr be linked to cooxidation with exogenously supplied electron donors. However, repeated addition of MeBr to live soils resulted in higher rates of its removal, suggesting that soil bacteria used MeBr as an electron donor for growth. To support this interpretation, we isolated a gram-negative, aerobic bacterium from these soils which grew with MeBr as a sole source of carbon and energy.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Hypersaline Microbial Mat Lipid Biomarkers

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

2002-01-01

Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

Microbial ecology of denitrification in biological wastewater treatment.

PubMed

Lu, Huijie; Chandran, Kartik; Stensel, David

2014-11-01

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Preserved Filamentous Microbial Biosignatures in the Brick Flat Gossan, Iron Mountain, California

PubMed Central

Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A.

2015-01-01

Abstract A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater as tentative possibilities. Key Words: Geobiology—Biosignatures—Filaments—Mars—Microbial fossils. Astrobiology 15, 637–668. PMID:26247371

Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio

PubMed Central

Dar, Shabir A.; Kleerebezem, Robbert; Stams, Alfons J. M.; Kuenen, J. Gijs

2008-01-01

The microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. The population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. At the influent lactate to sulfate molar ratio of 0.35 mol mol−1, i.e., electron donor limitation, lactate oxidation was mainly carried out by incompletely oxidizing sulfate-reducing bacteria, which formed 80–85% of the total bacterial population. Desulfomicrobium- and Desulfovibrio-like species were the most abundant sulfate-reducing bacteria. Acetogens and methanogenic Archaea were mostly outcompeted, although less than 2% of an acetogenic population could still be observed at this limiting concentration of lactate. In the near absence of sulfate (i.e., at very high lactate/sulfate ratio), acetogens and methanogenic Archaea were the dominant microbial communities. Acetogenic bacteria represented by Dendrosporobacter quercicolus-like species formed more than 70% of the population, while methanogenic bacteria related to uncultured Archaea comprising about 10–15% of the microbial community. At an influent lactate to sulfate molar ratio of 2 mol mol−1, i.e., under sulfate-limiting conditions, a different metabolic route was followed by the mixed anaerobic community. Apparently, lactate was fermented to acetate and propionate, while the majority of sulfidogenesis and methanogenesis were dependent on these fermentation products. This was consistent with the presence of significant levels (40–45% of total bacteria) of D. quercicolus-like heteroacetogens and a corresponding increase of propionate-oxidizing Desulfobulbus-like sulfate-reducing bacteria (20% of the total bacteria). Methanogenic Archaea accounted for 10% of the total microbial community. PMID:18305937

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Pilot scale application of nanosized iron oxides as electron acceptors for bioremediation

NASA Astrophysics Data System (ADS)

Bosch, Julian; Fritzsche, Andreas; Frank-Fahle, Beatrice; Lüders, Tilmann; Höss, Sebastian; Eisenmann, Heinrich; Held, Thomas; Totsche, Kai U.; Meckenstock, Rainer U.

2014-05-01

Microbial reduction of ferric iron is a major biogeochemical process in groundwater aquifer ecosystems and often associated with the degradation of organic contaminants, as bacteria couple iron reduction to the oxidation reduced carbon like e.g. BTEX. Yet in general the low bioavailability of natural iron oxides limits microbial reduction rates. However, nanosized iron oxides have an unequally enhanced bioavailability and reactivity compared to their respective bulk, macro-sized, and more crystalline materials. At the same time, nanosized iron oxides can be produced in stable colloidal suspensions, permitting efficient injections into contaminated aquifers. We examined the reactivity of nanosized synthetic colloidal iron oxides in microbial iron reduction. Application of colloidal nanoparticles led to a strong and sustainable enhancement of microbial reaction rates in batch experiments and sediment columns. Toluene oxidation was increased five-fold as compared to bulk, non-colloidal ferrihydrite as electron acceptor. Furthermore, we developed a unique approach for custom-tailoring the subsurface mobility of these particles after being injected into a contaminant plume. In a field pilot application, we injected 18 m3 of an iron oxide nanoparticle solution into a BTEX contaminated aquifer with a maximum excess pressure as low as 0.2 bar. The applied suspension showed a superior subsurface mobility, creating a reactive zone of 4 m height (corresponding to the height of the confined aquifer) and 6 m in diameter. Subsequent monitoring of BTEX, microbial BTEX degradation metabolites, ferrous iron generation, stable isotopes fractionation, microbial populations, and methanogenesis demonstrated the strong impact of our approach. Mathematic processed X-ray diffractograms and FTIR spectra provided a semi-quantitatively estimate of the long-term fate of the iron oxide colloids in the aquifer. Potential environmental risks of the injection itself were monitored with ecotoxicological investigations. Our data suggest that the injection of ferric iron nanoparticles as electron acceptors into contaminated aquifers for the enhancement of microbial contaminant degradation might develop into a novel bioremediation strategy.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

PubMed

Kantor, Rose S; Huddy, Robert J; Iyer, Ramsunder; Thomas, Brian C; Brown, Christopher T; Anantharaman, Karthik; Tringe, Susannah; Hettich, Robert L; Harrison, Susan T L; Banfield, Jillian F

2017-03-07

Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

Bacterial gene abundances as indicators of greenhouse gas emission in soils.

PubMed

Morales, Sergio E; Cosart, Theodore; Holben, William E

2010-06-01

Nitrogen fixing and denitrifying bacteria, respectively, control bulk inputs and outputs of nitrogen in soils, thereby mediating nitrogen-based greenhouse gas emissions in an ecosystem. Molecular techniques were used to evaluate the relative abundances of nitrogen fixing, denitrifying and two numerically dominant ribotypes (based on the > or =97% sequence similarity at the 16S rRNA gene) of bacteria in plots representing 10 agricultural and other land-use practices at the Kellogg biological station long-term ecological research site. Quantification of nitrogen-related functional genes (nitrite reductase, nirS; nitrous oxide reductase, nosZ; and nitrogenase, nifH) as well as two dominant 16S ribotypes (belonging to the phyla Acidobacteria, Thermomicrobia) allowed us to evaluate the hypothesis that microbial community differences are linked to greenhouse gas emissions under different land management practices. Our results suggest that the successional stages of the ecosystem are strongly linked to bacterial functional group abundance, and that the legacy of agricultural practices can be sustained over decades. We also link greenhouse gas emissions with specific compositional responses in the soil bacterial community and assess the use of denitrifying gene abundances as proxies for determining nitrous oxide emissions from soils.

Structural characterization of terrestrial microbial Mn oxides from Pinal Creek, AZ

USGS Publications Warehouse

Bargar, J.R.; Fuller, C.C.; Marcus, M.A.; Brearley, A.J.; Perez De la Rosa, M.; Webb, S.M.; Caldwell, W.A.

2009-01-01

The microbial catalysis of Mn(II) oxidation is believed to be a dominant source of abundant sorption- and redox-active Mn oxides in marine, freshwater, and subsurface aquatic environments. In spite of their importance, environmental oxides of known biogenic origin have generally not been characterized in detail from a structural perspective. Hyporheic zone Mn oxide grain coatings at Pinal Creek, Arizona, a metals-contaminated stream, have been identified as being dominantly microbial in origin and are well studied from bulk chemistry and contaminant hydrology perspectives. This site thus presents an excellent opportunity to study the structures of terrestrial microbial Mn oxides in detail. XRD and EXAFS measurements performed in this study indicate that the hydrated Pinal Creek Mn oxide grain coatings are layer-type Mn oxides with dominantly hexagonal or pseudo-hexagonal layer symmetry. XRD and TEM measurements suggest the oxides to be nanoparticulate plates with average dimensions on the order of 11 nm thick ?? 35 nm diameter, but with individual particles exhibiting thickness as small as a single layer and sheets as wide as 500 nm. The hydrated oxides exhibit a 10-?? basal-plane spacing and turbostratic disorder. EXAFS analyses suggest the oxides contain layer Mn(IV) site vacancy defects, and layer Mn(III) is inferred to be present, as deduced from Jahn-Teller distortion of the local structure. The physical geometry and structural details of the coatings suggest formation within microbial biofilms. The biogenic Mn oxides are stable with respect to transformation into thermodynamically more stable phases over a time scale of at least 5 months. The nanoparticulate layered structural motif, also observed in pure culture laboratory studies, appears to be characteristic of biogenic Mn oxides and may explain the common occurrence of this mineral habit in soils and sediments. ?? 2008 Elsevier Ltd.

Thermodynamic controls on the kinetics of microbial low-pH Fe(II) oxidation.

PubMed

Larson, Lance N; Sánchez-España, Javier; Kaley, Bradley; Sheng, Yizhi; Bibby, Kyle; Burgos, William D

2014-08-19

Acid mine drainage (AMD) is a major worldwide environmental threat to surface and groundwater quality. Microbial low-pH Fe(II) oxidation could be exploited for cost-effective AMD treatment; however, its use is limited because of uncertainties associated with its rate and ability to remove Fe from solution. We developed a thermodynamic-based framework to evaluate the kinetics of low-pH Fe(II) oxidation. We measured the kinetics of low-pH Fe(II) oxidation at five sites in the Appalachian Coal Basin in the US and three sites in the Iberian Pyrite Belt in Spain and found that the fastest rates of Fe(II) oxidation occurred at the sites with the lowest pH values. Thermodynamic calculations showed that the Gibbs free energy of Fe(II) oxidation (ΔG(oxidation)) was also most negative at the sites with the lowest pH values. We then conducted two series of microbial Fe(II) oxidation experiments in laboratory-scale chemostatic bioreactors operated through a series of pH values (2.1-4.2) and found the same relationships between Fe(II) oxidation kinetics, ΔG(oxidation), and pH. Conditions that favored the fastest rates of Fe(II) oxidation coincided with higher Fe(III) solubility. The solubility of Fe(III) minerals, thus plays an important role on Fe(II) oxidation kinetics. Methods to incorporate microbial low-pH Fe(II) oxidation into active and passive AMD treatment systems are discussed in the context of these findings. This study presents a simplified model that describes the relationship between free energy and microbial kinetics and should be broadly applicable to many biogeochemical systems.

Low Stress Mechanical Properties of Plasma-Treated Cotton Fabric Subjected to Zinc Oxide-Anti-Microbial Treatment.

PubMed

Kan, Chi-Wai; Lam, Yin-Ling

2013-01-22

Cotton fabrics are highly popular because of their excellent properties such as regeneration, bio-degradation, softness, affinity to skin and hygroscopic properties. When in contact with the human body, cotton fabrics offer an ideal environment for microbial growth due to their ability to retain oxygen, moisture and warmth, as well as nutrients from spillages and body sweat. Therefore, an anti-microbial coating formulation (Microfresh and Microban together with zinc oxide as catalyst) was developed for cotton fabrics to improve treatment effectiveness. In addition, plasma technology was employed in the study which roughened the surface of the materials, improving the loading of zinc oxides on the surface. In this study, the low stress mechanical properties of plasma pre-treated and/or anti-microbial-treated cotton fabric were studied. The overall results show that the specimens had improved bending properties when zinc oxides were added in the anti-microbial coating recipe. Also, without plasma pre-treatment, anti-microbial-treatment of cotton fabric had a positive effect only on tensile resilience, shear stress at 0.5° and compressional energy, while plasma-treated specimens had better overall tensile properties even after anti-microbial treatment.

Low Stress Mechanical Properties of Plasma-Treated Cotton Fabric Subjected to Zinc Oxide-Anti-Microbial Treatment

PubMed Central

Kan, Chi-Wai; Lam, Yin-Ling

2013-01-01

Cotton fabrics are highly popular because of their excellent properties such as regeneration, bio-degradation, softness, affinity to skin and hygroscopic properties. When in contact with the human body, cotton fabrics offer an ideal environment for microbial growth due to their ability to retain oxygen, moisture and warmth, as well as nutrients from spillages and body sweat. Therefore, an anti-microbial coating formulation (Microfresh and Microban together with zinc oxide as catalyst) was developed for cotton fabrics to improve treatment effectiveness. In addition, plasma technology was employed in the study which roughened the surface of the materials, improving the loading of zinc oxides on the surface. In this study, the low stress mechanical properties of plasma pre-treated and/or anti-microbial-treated cotton fabric were studied. The overall results show that the specimens had improved bending properties when zinc oxides were added in the anti-microbial coating recipe. Also, without plasma pre-treatment, anti-microbial-treatment of cotton fabric had a positive effect only on tensile resilience, shear stress at 0.5° and compressional energy, while plasma-treated specimens had better overall tensile properties even after anti-microbial treatment. PMID:28809311

Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System

PubMed Central

Cytryn, Eddie; van Rijn, Jaap; Schramm, Andreas; Gieseke, Armin; de Beer, Dirk; Minz, Dror

2005-01-01

Bacteria presumably involved in oxygen- or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus Thiomicrospira and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the Rhodobacteraceae (genera Roseobacter, Rhodobacter, and Rhodobium) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for Thauera-, Hydrogenophaga-, and Dethiosulfovibrio-like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet phylogenetically diverse microbial populations in nature. PMID:16204531

The influence of in situ chemical oxidation on microbial community composition in groundwater contaminated with chlorinated solvents.

PubMed

Sercu, Bram; Jones, Antony D G; Wu, Cindy H; Escobar, Mauricio H; Serlin, Carol L; Knapp, Timothy A; Andersen, Gary L; Holden, Patricia A

2013-01-01

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO(4)) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO(4) exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray-Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO(4) was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO(4) exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.

Development of microbial spoilage and lipid and protein oxidation in rabbit meat.

PubMed

Nakyinsige, K; Sazili, A Q; Aghwan, Z A; Zulkifli, I; Goh, Y M; Abu Bakar, F; Sarah, S A

2015-10-01

This experiment aimed to determine microbial spoilage and lipid and protein oxidation during aerobic refrigerated (4°C) storage of rabbit meat. Forty male New Zealand white rabbits were slaughtered according to the Halal slaughter procedure. The hind limbs were used for microbial analysis while the Longissimus lumborum m. was used for determination of lipid and protein oxidation. Bacterial counts generally increased with aging time and the limit for fresh meat (10(8)cfu/g) was reached at d 7 postmortem. Significant differences in malondialdehyde content were observed after 3d of storage. The thiol concentration significantly decreased with increase in aging time. The band intensities of myosin heavy chain and troponin T significantly reduced with increased refrigerated storage while actin remained relatively stable. This study thus proposes protein oxidation as a potential deteriorative change in refrigerated rabbit meat along with microbial spoilage and lipid oxidation. Copyright © 2015 Elsevier Ltd. All rights reserved.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Turbid Bottom Waters and Ammonium-Rich Freshwaters as Nitrification Hotspots in a Large Urban Estuary (San Francisco Bay, CA)

NASA Astrophysics Data System (ADS)

Damashek, J.; Casciotti, K. L.; Francis, C.

2015-12-01

Nitrification is the link between reduced and oxidized forms of inorganic nitrogen, and is therefore a crucial step in the estuarine nitrogen cycle. Ammonia-oxidizing microorganisms catalyze the rate-limiting step of ammonia oxidation to nitrite and thus play key roles in the biogeochemical cycling nutrient-rich estuaries. Yet, few studies have measured nitrification rates in tandem with ammonia oxidizer functional gene (amoA) expression, abundance, and diversity in estuary waters. Here, we present a multi-year data set on the microbial ecology and biogeochemistry of nitrification in the San Francisco Bay-Delta, the largest estuary on the North American west coast, collected throughout all regions of the estuary from 2012 to 2014. Data on microbial community distributions use functional gene-based PCR assays to assess the diversity, abundance, and mRNA expression of ammonia oxidizers, while stable isotope tracer experiments were used to measure nitrification rates. Ammonia-oxidizing archaea (AOA) typically outnumbered ammonia-oxidizing bacteria (AOB) throughout the sampled gradient, though the relative abundance of AOB was often greater in brackish regions. mRNA expression of amoA appeared to largely track DNA abundance, but suggested only a fraction of the ammonia-oxidizing community was typically active. AOA were always numerically dominant in the Sacramento River, where average nitrification rates were highest, suggesting the AOA communities in this river are responsible for a relatively constant nitrification hotspot. Additionally, depth profiles of nitrification rates suggested high biogeochemical activity near the sediment-water interface in samples with abnormally high turbidity, indicating similar but transient nitrification hotspots in bottom waters containing resuspended sediments. This work increases our knowledge of the ecology and dynamics of ammonia oxidizers in the San Francisco Bay-Delta, with time series data allowing for the putative identification of regions of persistent or transiently high nitrogen cycling rates.

Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor.

PubMed

Zhang, Xiaojing; Zhang, Nan; Fu, Haoqiang; Chen, Tao; Liu, Sa; Zheng, Shuhua; Zhang, Jie

2017-11-01

In this study, a membrane bioreactor (MBR) was adopted for completely autotrophic nitrogen removal over nitrite (CANON) process. Zinc oxide nanoparticles (ZnO NPs) was step-wise increased to analyze the influence on nitrogen removal, microbial activity and microbial communities. Finally ZnO NPs was removed to study its recovery capability. The bioactivities of ammonia-oxidizing bacteria (AOB), anaerobic ammonia-oxidizing bacteria (AAOB) and nitrite-oxidizing bacteria (NOB) were detected by batch experiments. Results showed that the ZnO NPs with low concentration (≤5mgL -1 ) was profitable for nitrogen removal while the high concentration performed inhibition, and it lowered the abundance of both AOB and NOB while enhanced that of AAOB. ZnO NPs with high concentration (≥10mgL -1 ) suppressed both AOB and AAOB, and long-term exposure within ZnO NPs led to microbial diversity decrease. The inhibition threshold of ZnO NPs on CANON process was 10mgL -1 , and the profitable concentration was 1mgL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

PubMed

Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

2013-10-01

The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Potential for microbial oxidation of ferrous iron in basaltic glass.

PubMed

Xiong, Mai Yia; Shelobolina, Evgenya S; Roden, Eric E

2015-05-01

Basaltic glass (BG) is an amorphous ferrous iron [Fe(II)]-containing material present in basaltic rocks, which are abundant on rocky planets such as Earth and Mars. Previous research has suggested that Fe(II) in BG can serve as an energy source for chemolithotrophic microbial metabolism, which has important ramifications for potential past and present microbial life on Mars. However, to date there has been no direct demonstration of microbially catalyzed oxidation of Fe(II) in BG. In this study, three different culture systems were used to investigate the potential for microbial oxidation of Fe(II) in BG, including (1) the chemolithoautotrophic Fe(II)-oxidizing, nitrate-reducing "Straub culture"; (2) the mixotrophic Fe(II)-oxidizing, nitrate-reducing organism Desulfitobacterium frappieri strain G2; and (3) indigenous microorganisms from a streambed Fe seep in Wisconsin. The BG employed consisted of clay and silt-sized particles of freshly quenched lava from the TEB flow in Kilauea, Hawaii. Soluble Fe(II) or chemically reduced NAu-2 smectite (RS) were employed as positive controls to verify Fe(II) oxidation activity in the culture systems. All three systems demonstrated oxidation of soluble Fe(II) and/or structural Fe(II) in RS, whereas no oxidation of Fe(II) in BG material was observed. The inability of the Straub culture to oxidize Fe(II) in BG was particularly surprising, as this culture can oxidize other insoluble Fe(II)-bearing minerals such as biotite, magnetite, and siderite. Although the reason for the resistance of the BG toward enzymatic oxidation remains unknown, it seems possible that the absence of distinct crystal faces or edge sites in the amorphous glass renders the material resistant to such attack. These findings have implications with regard to the idea that Fe(II)-Si-rich phases in basalt rocks could provide a basis for chemolithotrophic microbial life on Mars, specifically in neutral-pH environments where acid-promoted mineral dissolution and utilization of dissolved Fe(II) as an energy source is not likely to take place.

Combination of microbial oxidation and biogenic schwertmannite immobilization: A potential remediation for highly arsenic-contaminated soil.

PubMed

Yang, Zhihui; Wu, Zijian; Liao, Yingping; Liao, Qi; Yang, Weichun; Chai, Liyuan

2017-08-01

Here, a novel strategy that combines microbial oxidation by As(III)-oxidizing bacterium and biogenic schwertmannite (Bio-SCH) immobilization was first proposed and applied for treating the highly arsenic-contaminated soil. Brevibacterium sp. YZ-1 isolated from a highly As-contaminated soil was used to oxidize As(III) in contaminated soils. Under optimum culture condition for microbial oxidation, 92.3% of water-soluble As(III) and 84.4% of NaHCO 3 -extractable As(III) in soils were removed. Bio-SCH synthesized through the oxidation of ferrous sulfate by Acidithiobacillus ferrooxidans immobilize As(V) in the contaminated soil effectively. Consequently, the combination of microbial oxidation and Bio-SCH immobilization performed better in treating the highly As-contaminated soil with immobilization efficiencies of 99.3% and 82.6% for water-soluble and NaHCO 3 -extractable total As, respectively. Thus, the combination can be considered as a green remediation strategy for developing a novel and valuable solution for As-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of a Burkholderia cenocepacia ABTS Oxidizer in a Microbial Fuel Cell

USDA-ARS?s Scientific Manuscript database

Microbial fuel cells (MFCs) often use biological processes to generate electrons from organic material contained in the anode chamber and abiotic processes employing atmospheric oxygen as the oxidant in the cathode chamber. This study investigated the accumulation of an oxidant in bacterial cultures...

Preserved Filamentous Microbial Biosignatures in the Brick Flat Gossan, Iron Mountain, California.

PubMed

Williams, Amy J; Sumner, Dawn Y; Alpers, Charles N; Karunatillake, Suniti; Hofmann, Beda A

2015-08-01

A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater as tentative possibilities.

Preserved filamentous microbial biosignatures in the Brick Flat gossan, Iron Mountain, California

USGS Publications Warehouse

Williams, Amy J.; Sumner, Dawn Y.; Alpers, Charles N.; Karunatillake, Suniti; Hofmann, Beda A

2015-01-01

A variety of actively precipitating mineral environments preserve morphological evidence of microbial biosignatures. One such environment with preserved microbial biosignatures is the oxidized portion of a massive sulfide deposit, or gossan, such as that at Iron Mountain, California. This gossan may serve as a mineralogical analogue to some ancient martian environments due to the presence of oxidized iron and sulfate species, and minerals that only form in acidic aqueous conditions, in both environments. Evaluating the potential biogenicity of cryptic textures in such martian gossans requires an understanding of how microbial textures form biosignatures on Earth. The iron-oxide-dominated composition and morphology of terrestrial, nonbranching filamentous microbial biosignatures may be distinctive of the underlying formation and preservation processes. The Iron Mountain gossan consists primarily of ferric oxide (hematite), hydrous ferric oxide (HFO, predominantly goethite), and jarosite group minerals, categorized into in situ gossan, and remobilized iron deposits. We interpret HFO filaments, found in both gossan types, as HFO-mineralized microbial filaments based in part on (1) the presence of preserved central filament lumina in smooth HFO mineral filaments that are likely molds of microbial filaments, (2) mineral filament formation in actively precipitating iron-oxide environments, (3) high degrees of mineral filament bending consistent with a flexible microbial filament template, and (4) the presence of bare microbial filaments on gossan rocks. Individual HFO filaments are below the resolution of the Mars Curiosity and Mars 2020 rover cameras, but sinuous filaments forming macroscopic matlike textures are resolvable. If present on Mars, available cameras may resolve these features identified as similar to terrestrial HFO filaments and allow subsequent evaluation for their biogenicity by synthesizing geochemical, mineralogical, and morphological analyses. Sinuous biogenic filaments could be preserved on Mars in an iron-rich environment analogous to Iron Mountain, with the Pahrump Hills region and Hematite Ridge in Gale Crater astentative possibilities.

Large Fractions of CO2-Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds

PubMed Central

Herrmann, Martina; Rusznyák, Anna; Akob, Denise M.; Schulze, Isabel; Opitz, Sebastian; Totsche, Kai Uwe

2015-01-01

The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed—upper and lower—limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 103 to 6 × 106 genes liter−1 over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricella and Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds. PMID:25616797

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

PubMed Central

Huang, Li-Nan; Zhou, Wen-Hua; Hallberg, Kevin B.; Wan, Cai-Yun; Li, Jie; Shu, Wen-Sheng

2011-01-01

Analysis 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. Although Acidithiobacillus ferrooxidans and Leptospirillum spp. were consistently present in the acidic tailings, acidophilic archaea, mostly Ferroplasma acidiphilum, were predominant in the oxidized zones and the oxidation front, indicating their importance to generation of acid mine drainage. PMID:21705549

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center

PubMed Central

Anantharaman, Karthik; Breier, John A; Dick, Gregory J

2016-01-01

Microbial processes within deep-sea hydrothermal plumes affect ocean biogeochemistry on global scales. In rising hydrothermal plumes, a combination of microbial metabolism and particle formation processes initiate the transformation of reduced chemicals like hydrogen sulfide, hydrogen, methane, iron, manganese and ammonia that are abundant in hydrothermal vent fluids. Despite the biogeochemical importance of this rising portion of plumes, it is understudied in comparison to neutrally buoyant plumes. Here we use metagenomics and bioenergetic modeling to describe the abundance and genetic potential of microorganisms in relation to available electron donors in five different hydrothermal plumes and three associated background deep-sea waters from the Eastern Lau Spreading Center located in the Western Pacific Ocean. Three hundred and thirty one distinct genomic ‘bins' were identified, comprising an estimated 951 genomes of archaea, bacteria, eukarya and viruses. A significant proportion of these genomes is from novel microorganisms and thus reveals insights into the energy metabolism of heretofore unknown microbial groups. Community-wide analyses of genes encoding enzymes that oxidize inorganic energy sources showed that sulfur oxidation was the most abundant and diverse chemolithotrophic microbial metabolism in the community. Genes for sulfur oxidation were commonly present in genomic bins that also contained genes for oxidation of hydrogen and methane, suggesting metabolic versatility in these microbial groups. The relative diversity and abundance of genes encoding hydrogen oxidation was moderate, whereas that of genes for methane and ammonia oxidation was low in comparison to sulfur oxidation. Bioenergetic-thermodynamic modeling supports the metagenomic analyses, showing that oxidation of elemental sulfur with oxygen is the most dominant catabolic reaction in the hydrothermal plumes. We conclude that the energy metabolism of microbial communities inhabiting rising hydrothermal plumes is dictated by the underlying plume chemistry, with a dominant role for sulfur-based chemolithoautotrophy. PMID:26046257

In situ analysis of oxygen consumption and diffusive transport in high-temperature acidic iron-oxide microbial mats.

PubMed

Bernstein, Hans C; Beam, Jacob P; Kozubal, Mark A; Carlson, Ross P; Inskeep, William P

2013-08-01

The role of dissolved oxygen as a principal electron acceptor for microbial metabolism was investigated within Fe(III)-oxide microbial mats that form in acidic geothermal springs of Yellowstone National Park (USA). Specific goals of the study were to measure and model dissolved oxygen profiles within high-temperature (65-75°C) acidic (pH = 2.7-3.8) Fe(III)-oxide microbial mats, and correlate the abundance of aerobic, iron-oxidizing Metallosphaera yellowstonensis organisms and mRNA gene expression levels to Fe(II)-oxidizing habitats shown to consume oxygen. In situ oxygen microprofiles were obtained perpendicular to the direction of convective flow across the aqueous phase/Fe(III)-oxide microbial mat interface using oxygen microsensors. Dissolved oxygen concentrations dropped from ∼ 50-60 μM in the bulk-fluid/mat surface to below detection (< 0.3 μM) at a depth of ∼ 700 μm (∼ 10% of the total mat depth). Net areal oxygen fluxes into the microbial mats were estimated to range from 1.4-1.6 × 10(-4)  μmol cm(-2)  s(-1) . Dimensionless parameters were used to model dissolved oxygen profiles and establish that mass transfer rates limit the oxygen consumption. A zone of higher dissolved oxygen at the mat surface promotes Fe(III)-oxide biomineralization, which was supported using molecular analysis of Metallosphaera yellowstonensis 16S rRNA gene copy numbers and mRNA expression of haem Cu oxidases (FoxA) associated with Fe(II)-oxidation. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

PubMed

Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

2017-02-01

The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L -1 ) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L -1 . The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L -1 NiO NPs at the phyla, class and genus levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Iron-mediated anaerobic oxidation of methane in brackish coastal sediments.

PubMed

Egger, Matthias; Rasigraf, Olivia; Sapart, Célia J; Jilbert, Tom; Jetten, Mike S M; Röckmann, Thomas; van der Veen, Carina; Bândă, Narcisa; Kartal, Boran; Ettwig, Katharina F; Slomp, Caroline P

2015-01-06

Methane is a powerful greenhouse gas and its biological conversion in marine sediments, largely controlled by anaerobic oxidation of methane (AOM), is a crucial part of the global carbon cycle. However, little is known about the role of iron oxides as an oxidant for AOM. Here we provide the first field evidence for iron-dependent AOM in brackish coastal surface sediments and show that methane produced in Bothnian Sea sediments is oxidized in distinct zones of iron- and sulfate-dependent AOM. At our study site, anthropogenic eutrophication over recent decades has led to an upward migration of the sulfate/methane transition zone in the sediment. Abundant iron oxides and high dissolved ferrous iron indicate iron reduction in the methanogenic sediments below the newly established sulfate/methane transition. Laboratory incubation studies of these sediments strongly suggest that the in situ microbial community is capable of linking methane oxidation to iron oxide reduction. Eutrophication of coastal environments may therefore create geochemical conditions favorable for iron-mediated AOM and thus increase the relevance of iron-dependent methane oxidation in the future. Besides its role in mitigating methane emissions, iron-dependent AOM strongly impacts sedimentary iron cycling and related biogeochemical processes through the reduction of large quantities of iron oxides.

Iron oxide nanoparticles in geomicrobiology: from biogeochemistry to bioremediation.

PubMed

Braunschweig, Juliane; Bosch, Julian; Meckenstock, Rainer U

2013-09-25

Iron oxides are important constituents of soils and sediments and microbial iron reduction is considered to be a significant anaerobic respiration process in the subsurface, however low microbial reduction rates of macroparticulate Fe oxides in laboratory studies led to an underestimation of the role of Fe oxides in the global Fe redox cycle. Recent studies show the high potential of nano-sized Fe oxides in the environment as, for example, electron acceptor for microbial respiration, electron shuttle between different microorganisms, and scavenger for heavy metals. Biotic and abiotic reactivity of iron macroparticles differ significantly from nano-sized Fe oxides, which are usually much more reactive. Factors such as particle size, solubility, ferrous iron, crystal structure, and organic molecules were identified to influence the reactivity. This review discusses factors influencing the microbial reactivity of Fe oxides. It highlights the differences between natural and synthetic Fe oxides especially regarding the presence of organic molecules such as humic acids and natural organic matter. Attention is given to the transport behavior of Fe oxides in laboratory systems and in the environment, because of the high affinity of different contaminants to Fe oxide surfaces and associated co-transport of pollutants. The high reactivity of Fe oxides and their potential as adsorbents for different pollutants are discussed with respect to application and development of remediation technologies. Copyright © 2013. Published by Elsevier B.V.

Geomicrobiological cycling of antimony

NASA Astrophysics Data System (ADS)

Kulp, T. R.; Terry, L.; Dovick, M. A.; Braiotta, F.

2013-12-01

Microbiologically catalyzed oxidation and reduction of toxic metalloids (e.g., As, Se, and Te) generally proceeds much faster than corresponding abiotic reactions. These microbial transformations constitute biogeochemical cycles that control chemical speciation and environmental behavior of metalloids in aqueous environments. Particular progress has been made over the past two decades in documenting microbiological biotransformations of As, which include anaerobic respiratory reduction of As(V) to As(III), oxidation of As(III) to As(V) linked to chemoautotrophy or photoautotrophy, and cellular detoxification pathways. By contrast, microbial interactions with Sb, As's group 15 neighbor and a toxic element of emerging global concern, are poorly understood. Our work with sediment microcosms, enrichment cultures, and bacterial isolates suggests that prokaryotic metabolisms may be similarly important to environmental Sb cycling. Enrichment cultures and isolates from a Sb-contaminated mine site in Idaho exhibited Sb(V)-dependent heterotrophic respiration under anaerobic conditions and Sb(III)-dependent autotrophic growth in the presence of air. Live, anoxic cultures reduced 2 mM Sb(V) to Sb(III) within 5 d, while no activity occurred in killed controls. Sb(V) reduction was stimulated by lactate or acetate and was quantitatively coupled to the oxidation of lactate. The oxidation of radiolabeled 14C-acetate (monitored by GC-GPC) demonstrated Sb(V)-dependent oxidation to 14CO2, suggesting a dissimilatory process. Sb(V) dependent growth in cultures was demonstrated by direct counting. Microbiological reduction of Sb(V) also occurred in anerobic sediment microcosms from an uncontaminated suburban lake, but did not appear to be linked to growth and is interpreted as a mechanism of biological detoxification. Aerobic microcosms and cultures from the Idaho mine oxidized 2 mM Sb(III) to Sb(V) within 7 d and coupled this reaction to cell growth quantified by direct counting. An anoxygenic photosynthetic community of purple sulfur bacteria from Pyramid Lake, NV, however, that was capable of growth via anoxygenic photosynthesis using As(III) as an electron donor was not capable of similar growth using Sb(III). These results suggest that geomicrobiological Sb cycling is an important influence on the environmental speciation and behavior of Sb, and portend the presence of a global biogeochemical Sb cycle that is analogous to but distinct from that for As.

Two-Step Oxidation of Refractory Gold Concentrates with Different Microbial Communities.

PubMed

Wang, Guo-Hua; Xie, Jian-Ping; Li, Shou-Peng; Guo, Yu-Jie; Pan, Ying; Wu, Haiyan; Liu, Xin-Xing

2016-11-28

Bio-oxidation is an effective technology for treatment of refractory gold concentrates. However, the unsatisfactory oxidation rate and long residence time, which cause a lower cyanide leaching rate and gold recovery, are key factors that restrict the application of traditional bio-oxidation technology. In this study, the oxidation rate of refractory gold concentrates and the adaption of microorganisms were analyzed to evaluate a newly developed two-step pretreatment process, which includes a high temperature chemical oxidation step and a subsequent bio-oxidation step. The oxidation rate and recovery rate of gold were improved significantly after the two-step process. The results showed that the highest oxidation rate of sulfide sulfur could reach to 99.01 % with an extreme thermophile microbial community when the pulp density was 5%. Accordingly, the recovery rate of gold was elevated to 92.51%. Meanwhile, the results revealed that moderate thermophiles performed better than acidophilic mesophiles and extreme thermophiles, whose oxidation rates declined drastically when the pulp density was increased to 10% and 15%. The oxidation rates of sulfide sulfur with moderate thermophiles were 93.94% and 65.73% when the pulp density was increased to 10% and 15%, respectively. All these results indicated that the two-step pretreatment increased the oxidation rate of refractory gold concentrates and is a potential technology to pretreat the refractory sample. Meanwhile, owing to the sensitivity of the microbial community under different pulp density levels, the optimization of microbial community in bio-oxidation is necessary in industry.

Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments.

PubMed

Chen, Jing; Dick, Richard; Lin, Jih-Gaw; Gu, Ji-Dong

2016-12-01

Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.

Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment.

PubMed

Johnson, Sarah Stewart; Chevrette, Marc Gerard; Ehlmann, Bethany L; Benison, Kathleen Counter

2015-01-01

The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars.

Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier.

PubMed

Hoyles, Lesley; Snelling, Tom; Umlai, Umm-Kulthum; Nicholson, Jeremy K; Carding, Simon R; Glen, Robert C; McArthur, Simon

2018-03-21

Gut microbiota composition and function are symbiotically linked with host health and altered in metabolic, inflammatory and neurodegenerative disorders. Three recognised mechanisms exist by which the microbiome influences the gut-brain axis: modification of autonomic/sensorimotor connections, immune activation, and neuroendocrine pathway regulation. We hypothesised interactions between circulating gut-derived microbial metabolites, and the blood-brain barrier (BBB) also contribute to the gut-brain axis. Propionate, produced from dietary substrates by colonic bacteria, stimulates intestinal gluconeogenesis and is associated with reduced stress behaviours, but its potential endocrine role has not been addressed. After demonstrating expression of the propionate receptor FFAR3 on human brain endothelium, we examined the impact of a physiologically relevant propionate concentration (1 μM) on BBB properties in vitro. Propionate inhibited pathways associated with non-specific microbial infections via a CD14-dependent mechanism, suppressed expression of LRP-1 and protected the BBB from oxidative stress via NRF2 (NFE2L2) signalling. Together, these results suggest gut-derived microbial metabolites interact with the BBB, representing a fourth facet of the gut-brain axis that warrants further attention.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Methane fates in the benthos and water column at cold seep sites along the continental margin of Central and North America

NASA Astrophysics Data System (ADS)

Hansman, Roberta L.; Thurber, Andrew R.; Levin, Lisa A.; Aluwihare, Lihini I.

2017-02-01

The potential influence of methane seeps on carbon cycling is a key question for global assessments, but the study of carbon cycling in surface sediments and the water column of cold seep environments is complicated by the high temporal and spatial variability of fluid and gas fluxes at these sites. In this study we directly examined carbon sources supporting benthic and planktonic food webs at venting methane seeps using isotopic and molecular approaches that integrate this variability. At four seep environments located along North and Central America, microorganisms from two size fractions were collected over several days from 2800 to 9050 l of seawater to provide a time-integrated measure of key microbial groups and the carbon sources supporting the overall planktonic microbial community. In addition to water column measurements, the extent of seafloor methane release was estimated at two of the sites by examining the stable carbon isotopic signature (δ13C) of benthic metazoan infauna. This signature reveals carbon sources fueling the base of the food chain and thus provides a metric that represents a time-integrated view of the dominant microbial processes within the sediment. The stable carbon isotopic composition of microbial DNA (δ13C-DNA), which had values between -17.0 and -19.5‰, indicated that bulk planktonic microbial production was not ultimately linked to methane or other 13C-depleted seep-derived carbon sources. Instead these data support the importance of organic carbon derived from either photo- or chemoautotrophic CO2 fixation to the planktonic food web. Results of qPCR of microbial DNA sequences coding for a subunit of the particulate methane monooxygenase gene (pmoA) showed that only a small percentage of the planktonic microbial community were potential methane oxidizers possessing pmoA (<5% of 16S rRNA gene copies). There was an overall decrease of 13C-depleted carbon fueling the benthic metazoan community from 3 to 5 cm below the seafloor to the sediment surface, reflecting limited use of isotopically depleted carbon at the sediment surface. Rare methane emission as indicated by limited aerobic methane oxidation acts to corroborate our findings for the planktonic microbial community.

Something new from something old? Fracking stimulated microbial processes

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Soil-borne microbial functional structure across different land uses.

PubMed

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Application of RNA Stable Isotope Probing (SIP) to Link Community Activity with Microorganisms Responsible for Autotrophy in the Subseafloor at Axial Seamount

NASA Astrophysics Data System (ADS)

Huber, J. A.; Fortunato, C. S.

2014-12-01

The global ocean comprises the Earth's largest biome, with microorganisms playing a dominant biogeochemical role. However, the potential for production of new microbial biomass within the subseafloor is rarely considered in traditional oceanographic paradigms of carbon cycling or microbial food webs. In this study, we used RNA Stable Isotope Probing (RNA SIP) to determine the microbial community composition and genetic repertoire of active subseafloor autotrophs in warm venting fluids from Axial Seamount. RNA is a responsive biomarker because it is a reflection of cellular activity independent of replication, and RNA SIP thus provides access to both the function of a microbial community and the phylogeny of the organisms accountable for key functions. Diffuse fluids were incubated shipboard at 30°C, 55°C, and 80°C with 13DIC and H2. Metatranscriptomic sequencing of both the enriched and non-enriched RNA was carried out from 13C and 12C controls. In addition, filtered fluid samples were preserved in situ for comparative meta -transcriptomic and -genomic analyses. Diverse lineages of bacteria and archaea and accompanying metabolisms were detected in situ, but RNA SIP results show dominance of three different groups of autotrophs active under each experimental condition. At 30°C, members of the Sulfurimonas genus dominated, with genes for hydrogen oxidation, nitrate reduction, and carbon fixation via the rTCA cycle highly expressed. At 55°C, both Caminibacter and Nautilia transcripts were detected for rTCA cycle, hydrogen oxidation, and nitrate reduction. At 80°C, transcripts for hydrogenotrophic methanogenesis mediated by members of Methanocaldococcus were detected. These results suggest the subseafloor hosts various anaerobic chemolithoautotrophs that span a wide temperature range, with hydrogen playing a key role in microbial metabolism. Complementary experiments are currently being carried out on the seafloor with a novel in situ incubator unit to provide further insights to primary productivity in the subseafloor.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

PubMed Central

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer. PMID:29099490

Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

NASA Astrophysics Data System (ADS)

Andre, B. J.; Rajaram, H.; Silverstein, J.

2010-12-01

Acid mine drainage, AMD, results from the oxidation of metal sulfide minerals (e.g. pyrite), producing ferrous iron and sulfuric acid. Acidophilic autotrophic bacteria such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans obtain energy by oxidizing ferrous iron back to ferric iron, using oxygen as the electron acceptor. Most existing models of AMD do not account for microbial kinetics or iron geochemistry rigorously. Instead they assume that oxygen limitation controls pyrite oxidation and thus focus on oxygen transport. These models have been successfully used for simulating conditions where oxygen availability is a limiting factor (e.g. source prevention by capping), but have not been shown to effectively model acid generation and effluent chemistry under a wider range of conditions. The key reactions, oxidation of pyrite and oxidation of ferrous iron, are both slow kinetic processes. Despite being extensively studied for the last thirty years, there is still not a consensus in the literature about the basic mechanisms, limiting factors or rate expressions for microbially enhanced oxidation of metal sulfides. An indirect leaching mechanism (chemical oxidation of pyrite by ferric iron to produce ferrous iron, with regeneration of ferric iron by microbial oxidation of ferrous iron) is used as the foundation of a conceptual model for microbially enhanced oxidation of pyrite. Using literature data, a rate expression for microbial consumption of ferrous iron is developed that accounts for oxygen, ferrous iron and pH limitation. Reaction rate expressions for oxidation of pyrite and chemical oxidation of ferrous iron are selected from the literature. A completely mixed stirred tank reactor (CSTR) model is implemented coupling the kinetic rate expressions, speciation calculations and flow. The model simulates generation of AMD and effluent chemistry that qualitatively agrees with column reactor and single rock experiments. A one dimensional reaction diffusion model at the scale of a single rock is developed incorporating the proposed kinetic rate expressions. Simulations of initiation, washout and AMD flows are discussed to gain a better understanding of the role of porosity, effective diffusivity and reactive surface area in generating AMD. Simulations indicate that flow boundary conditions control generation of acid rock drainage as porosity increases.

High-resolution (SIMS) versus bulk sulfur isotope patterns of pyrite in Proterozoic microbialites with diverse mat textures

NASA Astrophysics Data System (ADS)

Gomes, M. L.; Fike, D. A.; Bergmann, K.; Knoll, A. H.

2015-12-01

Sulfur (S) isotope signatures of sedimentary pyrite preserved in marine rocks provide a rich suite of information about changes in biogeochemical cycling associated with the evolution of microbial metabolisms and oxygenation of Earth surface environments. Conventionally, these S isotope records are based on bulk rock measurements. Yet, in modern microbial mat environments, S isotope compositions of sulfide can vary by up to 40‰ over a spatial range of ~ 1 mm. Similar ranges of S isotope variability have been found in Archean pyrite grains using both Secondary Ion Mass Spectrometry and other micro-analytical techniques. These micron-scale patterns have been linked to changes in rates of microbial sulfate reduction and/or sulfide oxidation, isotopic distillation of the sulfate reservoir due to microbial sulfate reduction, and post-depositional alteration. Fine-scale mapping of S isotope compositions of pyrite can thus be used to differentiate primary environmental signals from post-depositional overprinting - improving our understanding of both. Here, we examine micron-scale S isotope patterns of pyrite in microbialites from the Mesoproterozoic-Neoproterozoic Sukhaya Tunguska Formation and Neoproterozoic Draken Formation in order to explore S isotope variability associated with different mat textures and pyrite grain morphologies. A primary goal is to link modern observations of how sulfide spatial isotope distributions reflect active microbial communities present at given depths in the mats to ancient processes driving fine-sale pyrite variability in microbialites. We find large (up to 60‰) S isotope variability within a spatial range of less than 2.5cm. The micron-scale S isotope measurements converge around the S isotope composition of pyrite extracted from bulk samples of the same microbialites. These micron-scale pyrite S isotope patterns have the potential to reveal important information about ancient biogeochemical cycling in Proterozoic mat environments with implications for interpreting S isotope signatures from the geological record.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China.

PubMed

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73-0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41-95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs.

Natural attenuation process via microbial oxidation of arsenic in a high Andean watershed.

PubMed

Leiva, Eduardo D; Rámila, Consuelo d P; Vargas, Ignacio T; Escauriaza, Cristian R; Bonilla, Carlos A; Pizarro, Gonzalo E; Regan, John M; Pasten, Pablo A

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and < 310 mm annual rainfall), which are conditions that have rarely been studied. Our model system was the upper Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Synthesis and characterization of anti-bacterial and anti-fungal citrate-based mussel-inspired bioadhesives

PubMed Central

Guo, Jinshan; Wang, Wei; Hu, Jianqing; Xie, Denghui; Gerhard, Ethan; Nisic, Merisa; Shan, Dingying; Qian, Guoying; Zheng, Siyang; Yang, Jian

2016-01-01

Bacterial and fungal infections in the use of surgical devices and medical implants remain a major concern. Traditional bioadhesives fail to incorporate anti-microbial properties, necessitating additional anti-microbial drug injection. Herein, by the introduction of the clinically used and inexpensive anti-fungal agent, 10-undecylenic acid (UA), into our recently developed injectable citrate-based mussel-inspired bioadhesives (iCMBAs), a new family of anti-bacterial and anti-fungal iCMBAs (AbAf iCs) was developed. AbAf iCs not only showed strong wet tissue adhesion strength, but also exhibited excellent in vitro cyto-compatibility, fast degradation, and strong initial and considerable long-term anti-bacterial and anti-fungal ability. For the first time, the biocompatibility and anti-microbial ability of sodium metaperiodate (PI), an oxidant used as a cross-linking initiator in the AbAf iCs system, was also thoroughly investigated. Our results suggest that the PI-based bioadhesives showed better anti-microbial properties compared to the unstable silver-based bioadhesive materials. In conclusion, AbAf iCs family can serve as excellent anti-bacterial and anti-fungal bioadhesive candidates for tissue/wound closure, wound dressing, and bone regeneration, especially when bacterial or fungal infections are a major concern. PMID:26874283

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

DOE PAGES

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder; ...

2017-01-31

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Synthesis and characterization of anti-bacterial and anti-fungal citrate-based mussel-inspired bioadhesives.

PubMed

Guo, Jinshan; Wang, Wei; Hu, Jianqing; Xie, Denghui; Gerhard, Ethan; Nisic, Merisa; Shan, Dingying; Qian, Guoying; Zheng, Siyang; Yang, Jian

2016-04-01

Bacterial and fungal infections in the use of surgical devices and medical implants remain a major concern. Traditional bioadhesives fail to incorporate anti-microbial properties, necessitating additional anti-microbial drug injection. Herein, by the introduction of the clinically used and inexpensive anti-fungal agent, 10-undecylenic acid (UA), into our recently developed injectable citrate-based mussel-inspired bioadhesives (iCMBAs), a new family of anti-bacterial and anti-fungal iCMBAs (AbAf iCs) was developed. AbAf iCs not only showed strong wet tissue adhesion strength, but also exhibited excellent in vitro cyto-compatibility, fast degradation, and strong initial and considerable long-term anti-bacterial and anti-fungal ability. For the first time, the biocompatibility and anti-microbial ability of sodium metaperiodate (PI), an oxidant used as a cross-linking initiator in the AbAf iCs system, was also thoroughly investigated. Our results suggest that the PI-based bioadhesives showed better anti-microbial properties compared to the unstable silver-based bioadhesive materials. In conclusion, AbAf iCs family can serve as excellent anti-bacterial and anti-fungal bioadhesive candidates for tissue/wound closure, wound dressing, and bone regeneration, especially when bacterial or fungal infections are a major concern. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

DOE PAGES

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

2016-04-18

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

PubMed

Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

2016-01-01

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.

The role of FeS(aq) molecular clusters in microbial redox cycling and iron mineralization.

NASA Astrophysics Data System (ADS)

Druschel, G.; Oduro, H.; Sperling, J.; Johnson, C.

2008-12-01

Iron sulfide molecular clusters, FeS(aq), are a group of polynuclear Fe-S complexes varying in size between a few and a few hundred molecules that occur in many environments and are critical parts of cycling between soluble iron and iron sulfide minerals. These clusters react uniquely with voltammetric Au-amalgam electrodes, and the signal for these molecules has now been observed in many terrestrial and marine aquatic settings. FeS(aq) clusters form when aqueous sulfide and iron(II) interact, but the source of those ions can come from abiotic or microbial sulfate and iron reduction or from the abiotic non-oxidative dissolution of iron sulfide minerals. Formation of iron sulfide minerals, principally mackinawite as the first solid nanocrystalline phase in many settings, is necessarily preceeded by formation and evolution of these molecular clusters as mineralization proceeds, and the clusters have been suggested to additionally be part of the pyritization process (Rickard and Luther, 1997; Luther and Rickard, 2005). In several systems, we have also observed FeS(aq) clusters to be the link between Fe-S mineral dissolution and oxidation of iron and sulfide, with important implications for changes to the overall oxidation pathway. Microorganisms can clearly be involved in the formation of FeS(aq) through iron and sulfate reduction, but it is not clear to date if organisms can utilize these clusters either as metabolic components or as anabolic 'building blocks' for enzyme production. Cycling of iron in the Fe-S system linked to FeS(aq) would clearly be a critical part of understanding iron isotope dynamics preserved in iron sulfide minerals. We will review ongoing work towards understanding the role of FeS(aq) in iron cycling and isotope fractionation as well as the measurement and characterization of this key class of iron complexes using environmental voltammetry.

Microbial Anaerobic Ammonium Oxidation Under Iron Reducing Conditions, Alternative Electron Acceptors

NASA Astrophysics Data System (ADS)

Ruiz-Urigüen, M.; Jaffe, P. R.

2015-12-01

Autotrophic Acidimicrobiaceae-bacterium named A6 (A6), part of the Actinobacteria phylum have been linked to anaerobic ammonium (NH4+) oxidation under iron reducing conditions. These organisms obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, the TEAs are iron oxides [Fe(III)], which are reduced to Fe(II), this process is known as Feammox. Our studies indicate that alternative forms of TEAs can be used by A6, e.g. iron rich clays (i.e. nontronite) and electrodes in bioelectrochemical systems such as Microbial Electrolysis Cells (MECs), which can sustain NH4+removal and A6 biomass production. Our results show that nontronite can support Feammox and promote bacterial cell production. A6 biomass increased from 4.7 x 104 to 3.9 x 105 cells/ml in 10 days. Incubations of A6 in nontronite resulted in up to 10 times more NH4+ removal and 3 times more biomass production than when ferrihydrite is used as the Fe(III) source. Additionally, Fe in nontronite can be reoxidized by aeration and A6 can reutilize it; however, Fe is still finite in the clay. In contrast, in MECs, A6 harvest electrons from NH4+ and use an anode as an unlimited TEA, as a result current is produced. We operated multiple MECs in parallel using a single external power source, as described by Call & Logan (2011). MECs were run with an applied voltage of 0.7V and different growing mediums always containing initial 5mM NH4+. Results show that current production is favored when anthraquinone-2,6-disulfonate (AQDS), an electron shuttled, is present in the medium as it facilitates the transfer of electrons from the bacterial cell to the anode. Additionally, A6 biomass increased from 1 x 104 to 9.77 x 105cells/ml in 14 days of operation. Due to Acidimicrobiaceae-bacterium A6's ability to use various TEAs, MECs represent an alternative, iron-free form, for optimized biomass production of A6 and its application in NH4+ oxidation, an essential process in water quality control. Future work seeks to scale up MECs in order to achieve rates of microbial NH4+ oxidation comparable to existing technologies.

The queen's gut refines with age: longevity phenotypes in a social insect model.

PubMed

Anderson, Kirk E; Ricigliano, Vincent A; Mott, Brendon M; Copeland, Duan C; Floyd, Amy S; Maes, Patrick

2018-06-18

In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polarized by a suite of age-associated factors including hormones, nutrition, immune senescence, and oxidative stress. Similar to other model organisms, the aging gut microbiota of short-lived (worker) honey bees accrue Proteobacteria and are depleted of Lactobacillus and Bifidobacterium, consistent with a suite of host senescence markers. In contrast, long-lived (queen) honey bees maintain youthful cellular function with much lower expression of oxidative stress genes, suggesting a very different host environment for age-associated microbial succession. We sequenced the microbiota of 63 honey bee queens exploring two chronological ages and four alimentary tract niches. To control for genetic and environmental variation, we quantified carbonyl accumulation in queen fat body tissue as a proxy for biological aging. We compared our results to the age-specific microbial succession of worker guts. Accounting for queen source variation, two or more bacterial species per niche differed significantly by queen age. Biological aging in queens was correlated with microbiota composition highlighting the relationship of microbiota with oxidative stress. Queens and workers shared many major gut bacterial species, but differ markedly in community structure and age succession. In stark contrast to aging workers, carbonyl accumulation in queens was significantly associated with increased Lactobacillus and Bifidobacterium and depletion of various Proteobacteria. We present a model system linking changes in gut microbiota to diet and longevity, two of the most confounding variables in human microbiota research. The pattern of age-associated succession in the queen microbiota is largely the reverse of that demonstrated for workers. The guts of short-lived worker phenotypes are progressively dominated by three major Proteobacteria, but these same species were sparse or significantly depleted in long-lived queen phenotypes. More broadly, age-related changes in the honey bee microbiota reflect the regulatory anatomy of reproductive host metabolism. Our synthesis suggests that the evolution of colony-level reproductive physiology formed the context for host-microbial interactions and age-related succession of honey bee microbiota.

Biodegradation of organic matter and anodic microbial communities analysis in sediment microbial fuel cells with/without Fe(III) oxide addition.

PubMed

Xu, Xun; Zhao, Qingliang; Wu, Mingsong; Ding, Jing; Zhang, Weixian

2017-02-01

To enhance the biodegradation of organic matter in sediment microbial fuel cell (SMFC), Fe(III) oxide, as an alternative electron acceptor, was added into the sediment. Results showed that the SMFC with Fe(III) oxide addition obtained higher removal efficiencies for organics than the SMFC without Fe(III) oxide addition and open circuit bioreactor, and produced a maximum power density (P max ) of 87.85mW/m 2 with a corresponding maximum voltage (V max ) of 0.664V. The alteration of UV-254 and specific ultraviolet absorbance (SUVA) also demonstrated the organic matter in sediments can be effectively removed. High-throughput sequencing of anodic microbial communities indicated that bacteria from the genus Geobacter were predominantly detected (21.23%) in the biofilm formed on the anode of SMFCs, while Pseudomonas was the most predominant genus (18.12%) in the presence of Fe(III) oxide. Additionally, compared with the open circuit bioreactor, more electrogenic bacteria attached to the biofilm of anode in SMFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation

NASA Astrophysics Data System (ADS)

Jerez, Carlos A.

The microbial solubilization of metals using chemolithoautotrophic microorganisms has successfully been used in industrial processes called biomining to extract metals such as copper, gold, uranium and others. The most studied leaching bacteria are from the genus Acidithiobacillus belonging to the Gram-negative γ-proteobacteria. Acidithiobacillus spp. obtain their energy from the oxidation of ferrous iron, elemental sulfur, or partially oxidized sulfur compounds. Other thermophilic archaeons capable of oxidizing sulfur and iron (II) have also been known for many years, and they are mainly from the genera Sulfolobus, Acidianus, Metallosphaera and Sulfurisphaera. Recently, some mesophilic iron (II)-oxidizing archaeons such as Ferroplasma acidiphilium and F. acidarmanus belonging to the Thermoplasmales have also been isolated and characterized. Recent studies of microorganisms consider them in their consortia, integrating fundamental biological knowledge with metagenomics, metaproteomics, and other data to obtain a global picture of how a microbial community functions. The understanding of microbial growth and activities in oxidizing metal ions will be useful for improving applied microbial biotechnologies such as biomining, bioshrouding, biomonitoring and bioremediation of metals in acidic environments.

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although themore » contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.« less

Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

PubMed

Armitage, David W

2017-11-01

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.

Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea

PubMed Central

Horak, Rachel E A; Qin, Wei; Schauer, Andy J; Armbrust, E Virginia; Ingalls, Anitra E; Moffett, James W; Stahl, David A; Devol, Allan H

2013-01-01

Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis–Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l−1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15NH4+ dilution technique. PMID:23657360

Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea.

PubMed

Horak, Rachel E A; Qin, Wei; Schauer, Andy J; Armbrust, E Virginia; Ingalls, Anitra E; Moffett, James W; Stahl, David A; Devol, Allan H

2013-10-01

Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l(-1) was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used (15)NH4(+) dilution technique.

Microbial Fe biomineralization in mafic and ultramafic rocks

NASA Astrophysics Data System (ADS)

Templeton, A. S.; Mayhew, L.; McCollom, T.; Trainor, T.

2011-12-01

Fluid-filled microfractures within mafic and ultramafic rocks, such as basalt and peridotite, may be one of the most ubiquitous microbial habitats on the modern and ancient earth. In seafloor and subseafloor systems, one of the dominant energy sources is the oxidation of Fe by numerous potential oxidants under aerobic to anaerobic conditions. In particular, the oxidation of Fe may be directly catalyzed by microbial organisms, or result in the production of molecular hydrogen which can then fuel diverse lithotrophic metabolisms. However, it remains challenging to identify the dominant metabolic activities and unravel the microscale biogeochemical processes occuring within such rock-hosted systems. We are investigating the mechanisms of solid-state Fe-oxidation and biomineralization in basalt, olivine, pyroxenes and basalts, in the presence and absence of microbial organisms that can thrive across the full stability range of water. In this talk we will present synchrotron-based x-ray scattering and spectroscopic analyses of Fe speciation within secondary minerals formed during microbially-mediated vs. abiotic water-rock interactions. Determining the valence state and mineralogy of Fe-bearing phases is critical for determining the water-rock reaction pathways and identifying potential biominerals that may form; therefore, we will highlight new approaches for identifying key Fe transformations within complex geological media. In addition, many of our experimental studies involve the growth of lithotrophic biofilms on well-characterized mineral surfaces in order to determine the chemistry of the microbe-mineral interface during progressive electron-transfer reactions. By coupling x-ray spectroscopy, x-ray diffraction, and electron-microscopy measurements, we will also contrast the evolution of mineral surfaces that undergo microbially-mediated oxidative alteration against minerals surfaces that produce H2 to sustain anaerobic microbial communities.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

PubMed

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China

PubMed Central

Jiang, Zhou; Li, Ping; Jiang, Dawei; Dai, Xinyue; Zhang, Rui; Wang, Yanhong; Wang, Yanxin

2016-01-01

Arsenic biogeochemistry has been studied extensively in acid sulfate-chloride hot springs, but not in acid sulfate hot springs with low chloride. In this study, Zhenzhuquan in Tengchong geothermal area, a representative acid sulfate hot spring with low chloride, was chosen to study arsenic geochemistry and microbial community structure using Illumina MiSeq sequencing. Over 0.3 million 16S rRNA sequence reads were obtained from 6-paired parallel water and sediment samples along its outflow channel. Arsenic oxidation occurred in the Zhenxhuquan pool, with distinctly high ratios of arsenate to total dissolved arsenic (0.73–0.86). Coupled with iron and sulfur oxidation along the outflow channel, arsenic accumulated in downstream sediments with concentrations up to 16.44 g/kg and appeared to significantly constrain their microbial community diversity. These oxidations might be correlated with the appearance of some putative functional microbial populations, such as Aquificae and Pseudomonas (arsenic oxidation), Sulfolobus (sulfur and iron oxidation), Metallosphaera and Acidicaldus (iron oxidation). Temperature, total organic carbon and dissolved oxygen significantly shaped the microbial community structure of upstream and downstream samples. In the upstream outflow channel region, most microbial populations were microaerophilic/anaerobic thermophiles and hyperthermophiles, such as Sulfolobus, Nocardia, Fervidicoccus, Delftia, and Ralstonia. In the downstream region, aerobic heterotrophic mesophiles and thermophiles were identified, including Ktedonobacteria, Acidicaldus, Chthonomonas and Sphingobacteria. A total of 72.41–95.91% unassigned-genus sequences were derived from the downstream high arsenic sediments 16S rRNA clone libraries. This study could enable us to achieve an integrated understanding on arsenic biogeochemistry in acid hot springs. PMID:26761709

Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

PubMed

Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

2014-11-01

In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

PubMed

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

NASA Astrophysics Data System (ADS)

Musat, N.; Kuypers, M. M. M.

2009-04-01

Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

Microbial Transformations of Nitrogen, Sulfur, and Iron Dictate Vegetation Composition in Wetlands: A Review

PubMed Central

Lamers, Leon P. M.; van Diggelen, Josepha M. H.; Op den Camp, Huub J. M.; Visser, Eric J. W.; Lucassen, Esther C. H. E. T.; Vile, Melanie A.; Jetten, Mike S. M.; Smolders, Alfons J. P.; Roelofs, Jan G. M.

2012-01-01

The majority of studies on rhizospheric interactions focus on pathogens, mycorrhizal symbiosis, or carbon transformations. Although the biogeochemical transformations of N, S, and Fe have profound effects on vegetation, these effects have received far less attention. This review, meant for microbiologists, biogeochemists, and plant scientists includes a call for interdisciplinary research by providing a number of challenging topics for future ecosystem research. Firstly, all three elements are plant nutrients, and microbial activity significantly changes their availability. Secondly, microbial oxidation with oxygen supplied by radial oxygen loss from roots in wetlands causes acidification, while reduction using alternative electron acceptors leads to generation of alkalinity, affecting pH in the rhizosphere, and hence plant composition. Thirdly, reduced species of all three elements may become phytotoxic. In addition, Fe cycling is tightly linked to that of S and P. As water level fluctuations are very common in wetlands, rapid changes in the availability of oxygen and alternative terminal electron acceptors will result in strong changes in the prevalent microbial redox reactions, with significant effects on plant growth. Depending on geological and hydrological settings, these interacting microbial transformations change the conditions and resource availability for plants, which are both strong drivers of vegetation development and composition by changing relative competitive strengths. Conversely, microbial composition is strongly driven by vegetation composition. Therefore, the combination of microbiological and plant ecological knowledge is essential to understand the biogeochemical and biological key factors driving heterogeneity and total (i.e., microorganisms and vegetation) community composition at different spatial and temporal scales. PMID:22539932

Arsenite and Ferrous Iron Oxidation Linked to Chemolithotrophic Denitrification for the Immobilization of Arsenic in Anoxic Environments

PubMed Central

Sun, Wenjie; Sierra-Alvarez, Reyes; Milner, Lily; Oremland, Ron; Field, Jim A.

2014-01-01

The objective of this study was to explore a bioremediation strategy based on injecting NO3− to support the anoxic oxidation of ferrous iron (Fe(II)) and arsenite (As(III)) in the subsurface as a means to immobilize As in the form of arsenate (As(V)) adsorbed onto biogenic ferric (Fe(III)) (hydr)oxides. Continuous flow sand filled columns were used to simulate a natural anaerobic groundwater and sediment system with co-occurring As(III) and Fe(II) in the presence (SF1) or absence (SF2) of nitrate, respectively. During operation for 250 days, the average influent arsenic concentration of 567 µg l−1 was reduced to 10.6 (±9.6) µg l−1 in the effluent of column SF1. The cumulative removal of Fe(II) and As(III) in SF1 was 6.5–10-fold higher than that in SF2. Extraction and measurement of the mass of iron and arsenic immobilized on the sand packing of the columns was close to the iron and arsenic removed from the aqueous phase during column operation. The dominant speciation of the immobilized iron and arsenic was Fe(III) and As(V) in SF1, compared with Fe(II) and As(III) in SF2. The speciation was confirmed by XRD and XPS. The results indicate that microbial oxidation of As(III) and Fe(II) linked to denitrification resulted in the enhanced immobilization of aqueous arsenic in anaerobic environments by forming Fe(III) (hydr)oxides coated sands with adsorbed As(V). PMID:19764221

Microbial oxidation of pyrrhotites in coal chars

USGS Publications Warehouse

Miller, K.W.; Risatti, J.B.

1988-01-01

The ability of Thiobacillus ferrooxidans to oxidize pyrrhotite minerals occurring in coal chars was investigated, to evaluate the feasibility of microbial char desulphurization. Bio-oxidation of pyrrhotites in chars produced by two different processes was demonstrated conclusively. Microbial removal of sulphur from a char and its parent coal proceeded at the rate of 3.5% and 12% day-1, respectively with a total of 48% and 81% removal after 27 days. The pH of shake flask cultures containing the coal dropped naturally to a final value of 2.2, while the pH of cultures containing the corresponding char rose and had to be lowered artificially with additional acid. Amending char cultures with elemental sulphur to increase acidity upon bio-oxidation and prevent precipitation of ferric iron was successful; however, the extent of pyrrhotite removal, as demonstated by X-ray diffraction analysis, was not improved. As yet, there is no explanation for the failure of microbial removal of pyrrhotitic sulphur to go to completion. ?? 1988.

Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater

PubMed Central

Mailloux, Brian J.; Trembath-Reichert, Elizabeth; Cheung, Jennifer; Watson, Marlena; Stute, Martin; Freyer, Greg A.; Ferguson, Andrew S.; Ahmed, Kazi Matin; Alam, Md. Jahangir; Buchholz, Bruce A.; Thomas, James; Layton, Alice C.; Zheng, Yan; Bostick, Benjamin C.; van Geen, Alexander

2013-01-01

Chronic exposure to arsenic (As) by drinking shallow groundwater causes widespread disease in Bangladesh and neighboring countries. The release of As naturally present in sediment to groundwater has been linked to the reductive dissolution of iron oxides coupled to the microbial respiration of organic carbon (OC). The source of OC driving this microbial reduction—carbon deposited with the sediments or exogenous carbon transported by groundwater—is still debated despite its importance in regulating aquifer redox status and groundwater As levels. Here, we used the radiocarbon (14C) signature of microbial DNA isolated from groundwater samples to determine the relative importance of surface and sediment-derived OC. Three DNA samples collected from the shallow, high-As aquifer and one sample from the underlying, low-As aquifer were consistently younger than the total sediment carbon, by as much as several thousand years. This difference and the dominance of heterotrophic microorganisms implies that younger, surface-derived OC is advected within the aquifer, albeit more slowly than groundwater, and represents a critical pool of OC for aquifer microbial communities. The vertical profile shows that downward transport of dissolved OC is occurring on anthropogenic timescales, but bomb 14C-labeled dissolved OC has not yet accumulated in DNA and is not fueling reduction. These results indicate that advected OC controls aquifer redox status and confirm that As release is a natural process that predates human perturbations to groundwater flow. Anthropogenic perturbations, however, could affect groundwater redox conditions and As levels in the future. PMID:23487743

HONO (nitrous acid) emissions from acidic northern soils

NASA Astrophysics Data System (ADS)

Maljanen, Marja; Yli-Pirilä, Pasi; Joutsensaari, Jorma; Martikainen, Pertti J.

2015-04-01

The photolysis of HONO (nitrous acid) is an important source of OH radical, the key oxidizing agent in the atmosphere, contributing also to removal of atmospheric methane (CH4), the second most important greenhouse gas after carbon dioxide (CO2). The emissions of HONO from soils have been recently reported in few studies. Soil HONO emissions are regarded as missing sources of HONO when considering the chemical reactions in the atmosphere. The soil-derived HONO has been connected to soil nitrite (NO2-) and also directly to the activity of ammonia oxidizing bacteria, which has been studied with one pure culture. Our hypothesis was that boreal acidic soils with high nitrification activity could be also sources of HONO and the emissions of HONO are connected with nitrification. We selected a range of dominant northern acidic soils and showed in microcosm experiments that soils which have the highest nitrous oxide (N2O) and nitric oxide (NO) emissions (drained peatlands) also have the highest HONO production rates. The emissions of HONO are thus linked to nitrogen cycle and also NO and N2O emissions. Natural peatlands and boreal coniferous forests on mineral soils had the lowest HONO emissions. It is known that in natural peatlands with high water table and in boreal coniferous forest soils, low nitrification activity (microbial production of nitrite and nitrate) limits their N2O production. Low availability of nitrite in these soils is the likely reason also for their low HONO production rates. We also studied the origin of HONO in one peat soil with acetylene and other nitrification inhibitors and we found that HONO production is not closely connected to ammonium oxidation (nitrification). Acetylene blocked NO emissions but did not affect HONO or N2O emissions, thus there is another source behind HONO emission from these soils than ammonium oxidation. It is still an open question if this process is microbial or chemical origin.

Physical and Biological Carbon Isotope Fractionation in Methane During Gas-Push-Pull-Tests

NASA Astrophysics Data System (ADS)

Gonzalez-Gil, G.; Schroth, M. H.; Gomez, K.; Zeyer, J.

2005-12-01

Stable isotope analyses have become a common tool to assess microbially-mediated processes in subsurface environments. We investigated if stable carbon isotope analysis can be used as a tool to complement gas push-pull tests (GPPTs), a novel technique that was recently developed and tested for the in-situ quantification of CH4 oxidation in soils. During a GPPT a gas mixture containing CH4, O2 and nonreactive tracer gases is injected into the soil, where CH4 is oxidized by indigenous microorganisms. Thereafter, a blend of injected gas mixture and soil air is extracted from the same location, and CH4 oxidation is quantified from an analysis of extracted CH4 and tracer gases. To assess the magnitude of physical isotope fractionation due to molecular diffusion during GPPTs, we conducted laboratory experiments in the absence of microbial activity in a 1m-high, 1m-diameter tank filled with dry sand. During the GPPTs' extraction phase, the isotopic composition of methane was analyzed. Results indicated strong carbon isotope fractionation (>20 per mil) during GPPTs. To assess the combined effect of physical and biological isotope fractionation, numerical simulations of GPPTs were conducted in which microbial CH4 isotope fractionation was simulated using first-order rate constants and microbial kinetic isotope fractionation factors previously reported for methane oxidation in landfill environments. Results of these simulations indicated that for small CH4 oxidation rates, overall isotope fractionation in CH4 is dominated by physical fractionation. Conversely, for high CH4 oxidation rates, overall fractionation is dominated by biological fractionation. Thus, CH4 isotope fractionation data alone from a single GPPT cannot be used to assess microbial CH4 oxidation. However, biological fractionation may be quantified if physical fractionation due to diffusion is known. This can be achieved by conducting two sequential GPPTs, with microbial activity being inhibited in the second test.

Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

PubMed

Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

2016-06-27

Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO 3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

Long-distance electron transport occurs globally in marine sediments

NASA Astrophysics Data System (ADS)

Burdorf, Laurine D. W.; Tramper, Anton; Seitaj, Dorina; Meire, Lorenz; Hidalgo-Martinez, Silvia; Zetsche, Eva-Maria; Boschker, Henricus T. S.; Meysman, Filip J. R.

2017-02-01

Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

PubMed Central

Hawley, Alyse K.; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P.; Kheirandish, Sam; Michiels, Céline C.; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A.; Hallam, Steven J.

2016-01-01

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet—a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite “leakage” during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales. PMID:27655888

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone.

PubMed

Louca, Stilianos; Hawley, Alyse K; Katsev, Sergei; Torres-Beltran, Monica; Bhatia, Maya P; Kheirandish, Sam; Michiels, Céline C; Capelle, David; Lavik, Gaute; Doebeli, Michael; Crowe, Sean A; Hallam, Steven J

2016-10-04

Microorganisms are the most abundant lifeform on Earth, mediating global fluxes of matter and energy. Over the past decade, high-throughput molecular techniques generating multiomic sequence information (DNA, mRNA, and protein) have transformed our perception of this microcosmos, conceptually linking microorganisms at the individual, population, and community levels to a wide range of ecosystem functions and services. Here, we develop a biogeochemical model that describes metabolic coupling along the redox gradient in Saanich Inlet-a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones (OMZs). The model reproduces measured biogeochemical process rates as well as DNA, mRNA, and protein concentration profiles across the redox gradient. Simulations make predictions about the role of ubiquitous OMZ microorganisms in mediating carbon, nitrogen, and sulfur cycling. For example, nitrite "leakage" during incomplete sulfide-driven denitrification by SUP05 Gammaproteobacteria is predicted to support inorganic carbon fixation and intense nitrogen loss via anaerobic ammonium oxidation. This coupling creates a metabolic niche for nitrous oxide reduction that completes denitrification by currently unidentified community members. These results quantitatively improve previous conceptual models describing microbial metabolic networks in OMZs. Beyond OMZ-specific predictions, model results indicate that geochemical fluxes are robust indicators of microbial community structure and reciprocally, that gene abundances and geochemical conditions largely determine gene expression patterns. The integration of real observational data, including geochemical profiles and process rate measurements as well as metagenomic, metatranscriptomic and metaproteomic sequence data, into a biogeochemical model, as shown here, enables holistic insight into the microbial metabolic network driving nutrient and energy flow at ecosystem scales.

Production and early preservation of lipid biomarkers in iron hot springs.

PubMed

Parenteau, Mary N; Jahnke, Linda L; Farmer, Jack D; Cady, Sherry L

2014-06-01

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51-54°C, pH 5.5-6.0, and are very high in dissolved Fe(II) at 5.8-5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs--environmental conditions that have been previously identified as highly relevant for Mars exploration.

Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parenteau, Mary N.; Jahnke, Linda L.; Farmer, Jack D.

2014-06-01

The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fattymore » acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. Finally, this study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration.« less

The fate of nitrogen is linked to iron(II) availability in a freshwater lake sediment

NASA Astrophysics Data System (ADS)

Robertson, Elizabeth K.; Thamdrup, Bo

2017-05-01

The fate of nitrogen in natural environments is controlled by anaerobic nitrate-reducing processes by which nitrogen is removed as N2 or retained as NH4+. These processes can potentially be driven by oxidation of reduced inorganic compounds at oxic-anoxic interfaces. Several studies have investigated the use of Fe2+ as an electron donor in nitrate reduction in bacterial cultures, however current information on this process in the environment is sparse. We aimed to determine whether nitrate-reducing processes in the freshwater Lake Almind (Silkeborg, Denmark) were linked to Fe2+ oxidation. Anaerobic sediment slurries were supplemented with 15N-substrates and electron donors (Fe2+ and/or acetate) to characterize nitrate-reducing processes under environmentally relevant substrate concentrations and at higher concentrations traditionally used in microbial enrichment studies. Dissimilatory nitrate reduction to ammonium, DNRA, was stimulated by Fe2+ addition in 7 of 10 slurry experiments and in some cases, denitrification was concomitantly reduced. The determined kinetic parameters (Vmax and Km) for Fe2+-driven DNRA were 4.7 μmol N L-1 d-1 and 33.8 μmol Fe2+ L-1, respectively and reaction stoichiometry for Fe2+:NH4+ (8.2:1) was consistent with that of predicted stoichiometry (8:1). Conversely, under enrichment conditions, denitrification was greatly increased while DNRA rates remained unchanged. Increased Fe2+ concentrations may be exploited by DNRA organisms and have an inhibitory effect on denitrification, thus Fe2+ may play a role in regulating N transformations in Lake Almind. Furthermore, we suggest enrichment conditions may promote the adaptation or change of microbial communities to optimally utilize the available high substrate concentrations; misrepresenting metabolisms occurring in situ.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Insights from the Metagenome of an Acid Salt Lake: The Role of Biology in an Extreme Depositional Environment

PubMed Central

Johnson, Sarah Stewart; Chevrette, Marc Gerard; Ehlmann, Bethany L.; Benison, Kathleen Counter

2015-01-01

The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars. PMID:25923206

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

DOE PAGES

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; ...

2018-01-29

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. Amore » nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.« less

Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms.

PubMed

Araújo, Ademir Sérgio Ferreira; Lima, Luciano Moura; Santos, Vilma Maria; Schmidt, Radomir

2016-10-01

Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.

Microbial removal of no.sub.x from gases

DOEpatents

Sublette, Kerry L.

1991-01-01

Disclosed is a process by which a gas containing nitric oxide is contacted with an anaerobic microbial culture of denitrifying bacteria to effect the chemical reduction of the nitric oxide to elemental nitrogen. The process is particularly suited to the removal of nitric oxide from flue gas streams and gas streams from nitric acid plants. Thiobacillus dentrificians as well as other bacteria are disclosed for use in the process.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrash, Daniel A.; Lalonde, Stefan V.; González-Arismendi, Gabriela

The formation of dolomite in modern peritidal environments is linked to the degradation of buried microbial mats, with complexation of Ca and Mg by extracellular polymeric substances (EPSs) and alkalinity generation through organic carbon respiration facilitating the nucleation of dolomite precursors. In the past two decades, microbial sulfate reduction, methanogenesis, and methanotrophy have all been considered as potential drivers of the nucleation process, but it remains unclear why dolomite formation could not also occur in suboxic sediments where abundant alkalinity is produced by processes linked to Mn(IV) and/or Fe(III) reduction coupled with the diffusion and reoxidation of reduced sulfur species.more » Here we report the interstitial occurrence of spheroidal aggregates of nanometer-scale Ca-rich dolomite rhombohedra within suboxic sediments associated with remnant microbial mats that developed in the peritidal zone of the Archipelago Los Roques, Venezuela. Multiple analytical tools, including EPMA, ICP-MS, synchrotron-based XRF and XRD, and spatially resolved XANES microanalyses, show that the dolomite-cemented interval exhibits depleted bulk iron concentrations, but is interstitially enriched in Mn and elemental sulfur (S⁰). Manganese occurs in several oxidation states, indicating that the dolomite-cemented interval was the locus of complex biological redox transformations characterized by coupled Mn and S cycling. The tight correspondence between sedimentary Mn and MgCO₃ concentrations further hints at a direct role for Mn during dolomitization. While additional studies are required to confirm its relevance in natural settings, we propose a model by which coupled Mn–S redox cycling may promote alkalinity generation and thus dolomite formation in manner similar to, or even more efficiently, than bacterial sulfate reduction alone.« less

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

PubMed Central

Wilmes, Paul; Wexler, Margaret; Bond, Philip L.

2008-01-01

Background Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced biological phosphorus removal (EBPR). Methodology/Principal Findings A laboratory-scale sequencing batch reactor was successfully operated for different levels of EBPR, removing around 25, 40 and 55 mg/l P. The microbial communities were dominated by the uncultured polyphosphate-accumulating organism “Candidatus Accumulibacter phosphatis”. When EBPR failed, the sludge was dominated by tetrad-forming α-Proteobacteria. Representative and reproducible 2D gel protein separations were obtained for all sludge samples. 638 protein spots were matched across gels generated from the phosphate removing sludges. 111 of these were excised and 46 proteins were identified using recently available sludge metagenomic sequences. Many of these closely match proteins from “Candidatus Accumulibacter phosphatis” and could be directly linked to the EBPR process. They included enzymes involved in energy generation, polyhydroxyalkanoate synthesis, glycolysis, gluconeogenesis, glycogen synthesis, glyoxylate/TCA cycle, fatty acid β oxidation, fatty acid synthesis and phosphate transport. Several proteins involved in cellular stress response were detected. Conclusions/Significance Importantly, this study provides direct evidence linking the metabolic activities of “Accumulibacter” to the chemical transformations observed in EBPR. Finally, the results are discussed in relation to current EBPR metabolic models. PMID:18392150

MICROBIAL RESPONSES TO IN SITU CHEMICAL OXIDATION, SIX-PHASE HEATING, AND STEAM INJECTION REMEDIATION TECHNOLOGIES IN GROUND WATER

EPA Science Inventory

The evaluation of microbial responses to three in situ source removal remedial technologies including permanganate-based in-situ chemical oxidation (ISCO), six-phase heating (SPH), and steam injection (SI) was performed at Cape Canaveral Air Station in Florida. The investigatio...

Assessment of anti-oxidant activity of plant extracts using microbial test systems.

PubMed

Oktyabrsky, O; Vysochina, G; Muzyka, N; Samoilova, Z; Kukushkina, T; Smirnova, G

2009-04-01

To evaluate the anti-oxidant properties of extracts from 20 medicinal herbs growing in western Siberia using microbial test systems and different in vitro methods. In vivo anti-oxidant activity of extracts was evaluated for their capacity to protect bacteria, Escherichia coli, against bacteriostatic and bactericidal effects of H(2)O(2) and menadione, and action on anti-oxidant gene expression. In vitro anti-oxidant activity has been examined by a number of methods including: the 1,1-diphenyl-2-picrylhydrazyl radical (DPPH(*))-scavenging assay, chelating activity and capacity to protect plasmid DNA against oxidative damage. In addition, total polyphenol content was determined. The extracts of Fragaria vesca, Rosa majalis, Pentaphylloides fruticosa, Alchemilla vulgaris and Pulmonaria mollis possessed the highest levels of anti-oxidant activity in vivo and in vitro. The protective properties were more closely related to the DPPH(*) radical-scavenging activity, tannin content and action on anti-oxidant gene expression than to other parameters. The extracts of medicinal plants may have anti-oxidant effects on bacteria simultaneously through several different pathways, including direct inhibition of reactive oxygen species, iron chelation and anti-oxidant genes induction. Using microbial test systems, we revealed herbs that may be used as potential sources of natural anti-oxidants.

Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds

USGS Publications Warehouse

Herrmann, Martina; Rusznyák, Anna; Akob, Denise M.; Schulze, Isabel; Opitz, Sebastian; Totsche, Kai Uwe; Küsel, Kirsten

2015-01-01

The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed—upper and lower—limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 103 to 6 × 106 genes liter−1 over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricellaand Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.

Oxidation of aromatic contaminants coupled to microbial iron reduction

USGS Publications Warehouse

Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

1989-01-01

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

USGS Publications Warehouse

Dowdle, P.R.; Oremland, R.S.

1998-01-01

The microbial oxidation of elemental selenium [Se(O)] was studied by employing 75Se(O) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.The microbial oxidation of elemental selenium [Se(0)] was studied by employing 75Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Colloidal Nanomolybdenum Influence upon the Antioxidative Reaction of Chickpea Plants ( Cicer arietinum L.)

NASA Astrophysics Data System (ADS)

Taran, Nataliya; Batsmanova, Ludmila; Kosyk, Oksana; Smirnov, Oleksandr; Kovalenko, Mariia; Honchar, Liubov; Okanenko, Alexander

2016-10-01

The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops. The purpose of the study was a comparative evaluation of presowing treatment with nanomolybdenum and microbiological preparation impact upon the development of adaptive responses in chickpea plants. Oxidative processes did not develop in all variants of the experiment but in variants treated with microbial preparation, and joint action of microbial and nanopreparations even declined, as evidenced by the reduction of thiobarbituric acid reactive substances in photosynthetic tissues by 15 %. The activity of superoxide dismutase increased (by 15 %) in variant "nanomolybdenum" and joint action "microbial + nanomolybdenum," but it decreased by 20 % in variants with microbial preparation treatment. The same dependence was observed in changes of catalase activity. Antioxidant status factor, which takes into account the ratio of antioxidant to pro-oxidant, was the highest in variants with joint action of microbial preparation and nanomolybdenum (0.7), the lowest in variants with microbial treatment only (0.1). Thus, the results show that the action of nanoparticles of molybdenum activated antioxidant enzymes and decreased oxidative processes, thus promoting adaptation of plants.

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs

DOE PAGES

Beam, Jacob P.; Bernstein, Hans C.; Jay, Zackary J.; ...

2016-02-15

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3-3.5; temperature = 68-75°C) inmore » YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4-40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14-30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1-2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day -1 , and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.« less

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs

PubMed Central

Beam, Jacob P.; Bernstein, Hans C.; Jay, Zackary J.; Kozubal, Mark A.; Jennings, Ryan deM.; Tringe, Susannah G.; Inskeep, William P.

2016-01-01

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3–3.5; temperature = 68–75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4–40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14–30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1–2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day−1, and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems. PMID:26913020

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.

PubMed

Beam, Jacob P; Bernstein, Hans C; Jay, Zackary J; Kozubal, Mark A; Jennings, Ryan deM; Tringe, Susannah G; Inskeep, William P

2016-01-01

Biomineralized ferric oxide microbial mats are ubiquitous features on Earth, are common in hot springs of Yellowstone National Park (YNP, WY, USA), and form due to direct interaction between microbial and physicochemical processes. The overall goal of this study was to determine the contribution of different community members to the assembly and succession of acidic high-temperature Fe(III)-oxide mat ecosystems. Spatial and temporal changes in Fe(III)-oxide accretion and the abundance of relevant community members were monitored over 70 days using sterile glass microscope slides incubated in the outflow channels of two acidic geothermal springs (pH = 3-3.5; temperature = 68-75°C) in YNP. Hydrogenobaculum spp. were the most abundant taxon identified during early successional stages (4-40 days), and have been shown to oxidize arsenite, sulfide, and hydrogen coupled to oxygen reduction. Iron-oxidizing populations of Metallosphaera yellowstonensis were detected within 4 days, and reached steady-state levels within 14-30 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized near 30 days, and emerged as the dominant functional guild after 70 days and in mature Fe(III)-oxide mats (1-2 cm thick). First-order rate constants of Fe(III)-oxide accretion ranged from 0.046 to 0.05 day(-1), and in situ microelectrode measurements showed that the oxidation of Fe(II) is limited by the diffusion of O2 into the Fe(III)-oxide mat. The formation of microterracettes also implicated O2 as a major variable controlling microbial growth and subsequent mat morphology. The assembly and succession of Fe(III)-oxide mat communities follows a repeatable pattern of colonization by lithoautotrophic organisms, and the subsequent growth of diverse organoheterotrophs. The unique geochemical signatures and micromorphology of extant biomineralized Fe(III)-oxide mats are also useful for understanding other Fe(II)-oxidizing systems.

The nitrogen cycle in anaerobic methanotrophic mats of the Black Sea is linked to sulfate reduction and biomass decomposition.

PubMed

Siegert, Michael; Taubert, Martin; Seifert, Jana; von Bergen-Tomm, Martin; Basen, Mirko; Bastida, Felipe; Gehre, Matthias; Richnow, Hans-Hermann; Krüger, Martin

2013-11-01

Anaerobic methanotrophic (ANME) mats host methane-oxidizing archaea and sulfate-reducing prokaryotes. Little is known about the nitrogen cycle in these communities. Here, we link the anaerobic oxidation of methane (AOM) to the nitrogen cycle in microbial mats of the Black Sea by using stable isotope probing. We used four different (15)N-labeled sources of nitrogen: dinitrogen, nitrate, nitrite and ammonium. We estimated the nitrogen incorporation rates into the total biomass and the methyl coenzyme M reductase (MCR). Dinitrogen played an insignificant role as nitrogen source. Assimilatory and dissimilatory nitrate reduction occurred. High rates of nitrate reduction to dinitrogen were stimulated by methane and sulfate, suggesting that oxidation of reduced sulfur compounds such as sulfides was necessary for AOM with nitrate as electron acceptor. Nitrate reduction to dinitrogen occurred also in the absence of methane as electron donor but at six times slower rates. Dissimilatory nitrate reduction to ammonium was independent of AOM. Ammonium was used for biomass synthesis under all conditions. The pivotal enzyme in AOM coupled to sulfate reduction, MCR, was synthesized from nitrate and ammonium. Results show that AOM coupled to sulfate reduction along with biomass decomposition drive the nitrogen cycle in the ANME mats of the Black Sea and that MCR enzymes are involved in this process. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Epsilonproteobacterial hydroxylamine oxidoreductase (εHao): characterization of a 'missing link' in the multihaem cytochrome c family.

PubMed

Haase, Doreen; Hermann, Bianca; Einsle, Oliver; Simon, Jörg

2017-07-01

Members of the multihaem cytochrome c family such as pentahaem cytochrome c nitrite reductase (NrfA) or octahaem hydroxylamine oxidoreductase (Hao) are involved in various microbial respiratory electron transport chains. Some members of the Hao subfamily, here called εHao proteins, have been predicted from the genomes of nitrate/nitrite-ammonifying bacteria that usually lack NrfA. Here, εHao proteins from the host-associated Epsilonproteobacteria Campylobacter fetus and Campylobacter curvus and the deep-sea hydrothermal vent bacteria Caminibacter mediatlanticus and Nautilia profundicola were purified as εHao-maltose binding protein fusions produced in Wolinella succinogenes. All four proteins were able to catalyze reduction of nitrite (yielding ammonium) and hydroxylamine whereas hydroxylamine oxidation was negligible. The introduction of a tyrosine residue at a position known to cause covalent trimerization of Hao proteins did neither stimulate hydroxylamine oxidation nor generate the Hao-typical absorbance maximum at 460 nm. In most cases, the εHao-encoding gene haoA was situated downstream of haoC, which predicts a tetrahaem cytochrome c of the NapC/NrfH family. This suggested the formation of a membrane-bound HaoCA assembly reminiscent of the menaquinol-oxidizing NrfHA complex. The results indicate that εHao proteins form a subfamily of ammonifying cytochrome c nitrite reductases that represents a 'missing link' in the evolution of NrfA and Hao enzymes. © 2017 John Wiley & Sons Ltd.

Fishing for biodiversity: Novel methanopterin-linked C1 transfergenes deduced from the Sargasso Sea metagenome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kalyuzhnaya, Marina G.; Nercessian, Olivier; Lapidus, Alla

2004-07-01

The recently generated database of microbial genes from anoligotrophic environment populated by a calculated 1,800 of major phylotypes (the Sargasso Sea metagenome) presents a great source for expanding local databases of genes indicative of a specific function. In this paper we analyze the Sargasso Sea metagenome in terms of the presence of methanopterin-linked C1 transfer genes that are signature for methylotrophy. We conclude that more than 10 phylotypes possessing genes of interest are present in this environment, and a few of these are relatively abundant species. The sequences representative of the major phylotypes do not appear to belong to anymore » known microbial group capable of methanopterin-linked C1 transfer. Instead, they separate from all known sequences on phylogenetic trees, pointing towards their affiliation with a novel microbial phylum. These data imply a broader distribution of methanopterin-linked functions in the microbial world than previously known.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beam, Jake; Bernstein, Hans C.; Jay, Z.

Iron oxide microbial mats are ubiquitous geobiological features on Earth and occur in extant acidic hot springs of Yellowstone National Park (YNP), WY, USA, and form as a result of microbial processes. The relative contribution of different organisms to the development of these mat ecosystems is of specific interest. We hypothesized that chemolithoautotrophic organisms contribute to the early development and production of Fe(III)-oxide mats, which could support later-colonizing heterotrophic microorganisms. Sterile glass slides were incubated in the outflow channels of two acidic geothermal springs in YNP, and spatiotemporal changes in Fe(III)-oxide accretion and abundance of relevant community members were measured.more » Lithoautotrophic Hydrogenobaculum spp. were first colonizers and the most abundant taxa identified during early successional stages (7 – 40 days). Populations of M. yellowstonensis colonized after ~ 7 days, corresponding to visible Fe(III)-oxide accretion. Heterotrophic archaea colonized after 30 days, and emerge as the dominant functional guild in mature iron oxide mats (1 – 2 cm thick) that form after 70 – 120 days. First-order rate constants of iron oxide accretion ranged from 0.05 – 0.046 day-1, and reflected the absolute amount of iron accreted. Micro- and macroscale microterracettes were identified during iron oxide mat development, and suggest that the mass transfer of oxygen limits microbial growth. This was also demonstrated using microelectrode measurements of oxygen as a function of mat depth, which showed steep gradients in oxygen from the aqueous mat interface to ~ 1 mm. The formation and succession of amorphous Fe(III)-oxide mat communities follows a predictable pattern of distinct stages and growth. The successional stages and microbial signatures observed in these extant Fe(III)-oxide mat communities may be relevant to other past or present Fe(III)-oxide mineralizing systems.« less

Identification of Antimony- and Arsenic-Oxidizing Bacteria Associated with Antimony Mine Tailing

PubMed Central

Hamamura, Natsuko; Fukushima, Koh; Itai, Takaaki

2013-01-01

Antimony (Sb) is a naturally occurring toxic element commonly associated with arsenic (As) in the environment and both elements have similar chemistry and toxicity. Increasing numbers of studies have focused on microbial As transformations, while microbial Sb interactions are still not well understood. To gain insight into microbial roles in the geochemical cycling of Sb and As, soils from Sb mine tailing were examined for the presence of Sb- and As-oxidizing bacteria. After aerobic enrichment culturing with AsIII (10 mM) or SbIII (100 μM), pure cultures of Pseudomonas- and Stenotrophomonas-related isolates with SbIII oxidation activities and a Sinorhizobium-related isolate capable of AsIII oxidation were obtained. The AsIII-oxidizing Sinorhizobium isolate possessed the aerobic arsenite oxidase gene (aioA), the expression of which was induced in the presence of AsIII or SbIII. However, no SbIII oxidation activity was detected from the Sinorhizobium-related isolate, suggesting the involvement of different mechanisms for Sb and As oxidation. These results demonstrate that indigenous microorganisms associated with Sb mine soils are capable of Sb and As oxidation, and potentially contribute to the speciation and mobility of Sb and As in situ. PMID:23666539

[Effect of temperature on the rate of oxidation of pyrrhotite-rich sulfide ore flotation concentrate and the structure of the acidophilic chemolithoautotrophic microbial community].

PubMed

Moshchanetskii, P V; Pivovarova, T A; Belyi, A V; Kondrat'eva, T F

2014-01-01

Oxidation of flotation concentrate of a pyrrhotite-rich sulfide ore by acidophilic chemolithoautotrophic microbial communities at 35, 40, and 45 degrees C was investigated. According to the physicochemical parameters of the liquid phase of the pulp, as well as the results of analysis of the solid residue after biooxidation and cyanidation, the community developed at 40 degrees C exhibited the highest rate of oxidation. The degree of gold recovery at 35, 40, and 45 degrees C was 89.34, 94.59, and 83.25%, respectively. At 40 degrees C, the highest number of microbial cells (6.01 x 10(9) cells/mL) was observed. While temperature had very little effect on the species composition of microbial communities, except for the absence of Leptospirillum ferriphilum at 35 degrees C, the shares of individual species in the communities varied with temperature. Relatively high numbers of Sulfobacillus thermosulfidooxidans, the organism oxidizing iron and elemental sulfur at higher rates than other acidophilic chemolithotrophic species, were observed at 40 degrees C.

Tracking Spatial and Temporal Changes in Microbial Metabolic Potential and Gene Expression Patterns Across Geochemical Gradients at Axial Seamount

NASA Astrophysics Data System (ADS)

Fortunato, C. S.; Butterfield, D. A.; Larson, B.; Algar, C. K.; Huber, J. A.

2016-12-01

Microbial communities living both near and within the subseafloor are important players in the biogeochemical cycling of the deep ocean. To better understand the metabolic and gene expression patterns of these understudied communities, we collected low-temperature diffuse fluids for metagenomic, metatranscriptomic, and geochemical analyses from Axial Seamount, an active submarine volcano off the coast of Oregon, USA in 2013-2015. In April of 2015 Axial Seamount erupted along its north rift, five months before the 2015 samples were collected. This study thus provides both spatial and temporal analysis of subseafloor microbial communities pre and post eruption. The time series for this study focused on three vents at the south end of the caldera: Anemone, Marker 33, and Marker 113. Chemistry data shows that at each vent there are different geochemical conditions and thus a potentially different microbial metabolic profile. Anemone has the most oxidizing conditions and the highest abundance and expression of sulfur oxidation genes, attributed to both SUP05 and Epsilonproteobacteria. The most reducing conditions were observed at Marker 113, the site with the lowest oxygen concentration and where methanogenesis was the dominant metabolism, with 18.5% of all annotated transcripts attributed to methanogenesis. Although individual vents were metabolically distinct, there was very little variation in the overall taxonomic and metabolic profiles of each vent across years, even after the 2015 eruption. A diffuse fluid sample taken from the North Rift Zone post eruption showed similar community taxonomy to both Anemone and Marker 33; analyses of the metabolic potential and gene expression at this site is ongoing and will act as a comparison between the communities of the time series vents and those that were closer to the eruption site. Together, these chemical and `omic datasets reveal a dynamic microbial community at each vent, taxonomically diverse and involved in a wide array of biogeochemical transformations. Results are being used to model the functional dynamics and fluxes of vent communities to more closely link microbiological productivity at hydrothermal systems to deep-sea biogeochemical processes and will be also used to inform future projects using instrumentation on the cabled array at Axial Seamount.

Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run.

PubMed

Grettenberger, Christen L; Pearce, Alexandra R; Bibby, Kyle J; Jones, Daniel S; Burgos, William D; Macalady, Jennifer L

2017-04-01

Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens , a species that is associated with high rates of Fe(II) oxidation in laboratory studies. IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121-1123, 1970, https://doi.org/10.1126/science.167.3921.1121). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens , a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation. Copyright © 2017 American Society for Microbiology.

Engineering redox homeostasis to develop efficient alcohol-producing microbial cell factories.

PubMed

Zhao, Chunhua; Zhao, Qiuwei; Li, Yin; Zhang, Yanping

2017-06-24

The biosynthetic pathways of most alcohols are linked to intracellular redox homeostasis, which is crucial for life. This crucial balance is primarily controlled by the generation of reducing equivalents, as well as the (reduction)-oxidation metabolic cycle and the thiol redox homeostasis system. As a main oxidation pathway of reducing equivalents, the biosynthesis of most alcohols includes redox reactions, which are dependent on cofactors such as NADH or NADPH. Thus, when engineering alcohol-producing strains, the availability of cofactors and redox homeostasis must be considered. In this review, recent advances on the engineering of cellular redox homeostasis systems to accelerate alcohol biosynthesis are summarized. Recent approaches include improving cofactor availability, manipulating the affinity of redox enzymes to specific cofactors, as well as globally controlling redox reactions, indicating the power of these approaches, and opening a path towards improving the production of a number of different industrially-relevant alcohols in the near future.

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

NASA Astrophysics Data System (ADS)

Dekas, Anne E.; Poretsky, Rachel S.; Orphan, Victoria J.

2009-10-01

Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell-resolution nanometer secondary ion mass spectrometry images of 15N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N2, as well as structurally similar CN-, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

DOE PAGES

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; ...

2017-01-09

Microbial phototrophs, key primary producers on Earth, use H 2O, H 2, H 2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis’. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii doesmore » not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. Lastly, this process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities.« less

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

PubMed Central

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; Dohnalkova, Alice C.; Fredrickson, James K.; Madigan, Michael T.; Beyenal, Haluk

2017-01-01

Microbial phototrophs, key primary producers on Earth, use H2O, H2, H2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis'. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii does not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. This process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities. PMID:28067226

Real-time monitoring of subsurface microbial metabolism with graphite electrodes

DOE PAGES

Wardman, Colin; Nevin, Kelly P.; Lovley, Derek R.

2014-11-21

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μ M range. In ordermore » to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2- 14C]-acetate metabolism. There was a direct correlation between current production and the rate that [2- 14C]-acetate was metabolized to 14CO 2 and 14CH 4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. In conclusion, the results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.« less

Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

NASA Astrophysics Data System (ADS)

Davis, R.; Tebo, B. M.

2013-12-01

Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn oxidases McoA and MopA. The greater diversity of Mn oxidase pathways in this metagenome suggests a more diverse Mn oxidizing microbial community in the cold pumice sample. Key enzymes for four of the six known carbon fixation pathways (the Calvin Cycle, the reductive TCA cycle, the Wood-Ljungdahl pathway, and the 3-hydroxypropionate/4-hydroxybutyrate Cycle) were also identified in both samples indicating primary production occurs via a diverse community of carbon fixing organisms. Together, these samples contain active, diverse populations of Mn oxidizing bacteria living in association with microbial communities supported by chemoautotrophic carbon fixation.

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

The effect of coal bed dewatering and partial oxidation on biogenic methane potential

USGS Publications Warehouse

Jones, Elizabeth J.P.; Harris, Steve H.; Barnhart, Elliott P.; Orem, William H.; Clark, Arthur C.; Corum, Margo D.; Kirshtein, Julie D.; Varonka, Matthew S.; Voytek, Mary A.

2013-01-01

Coal formation dewatering at a site in the Powder River Basin was associated with enhanced potential for secondary biogenic methane determined by using a bioassay. We hypothesized that dewatering can stimulate microbial activity and increase the bioavailability of coal. We analyzed one dewatered and two water-saturated coals to examine possible ways in which dewatering influences coal bed natural gas biogenesis by looking at differences with respect to the native coal microbial community, coal-methane organic intermediates, and residual coal oxidation potential. Microbial biomass did not increase in response to dewatering. Small Subunit rRNA sequences retrieved from all coals sampled represented members from genera known to be aerobic, anaerobic and facultatively anaerobic. A Bray Curtis similarity analysis indicated that the microbial communities in water-saturated coals were more similar to each other than to the dewatered coal, suggesting an effect of dewatering. There was a higher incidence of long chain and volatile fatty acid intermediates in incubations of the dewatered coal compared to the water-saturated coals, and this could either be due to differences in microbial enzymatic activities or to chemical oxidation of the coal associated with O2 exposure. Dilute H2O2 treatment of two fractions of structural coal (kerogen and bitumen + kerogen) was used as a proxy for chemical oxidation by O2. The dewatered coal had a low residual oxidation potential compared to the water-saturated coals. Oxidation with 5% H2O2 did increase the bioavailability of structural coal, and the increase in residual oxidation potential in the water saturated coals was approximately equivalent to the higher methanogenic potential measured in the dewatered coal. Evidence from this study supports the idea that coal bed dewatering could stimulate biogenic methanogenesis through partial oxidation of the structural organics in coal once anaerobic conditions are restored.

Acetogenic microbial degradation of vinyl chloride

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

2000-01-01

Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C- acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries, respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and humic acids- reducing conditions.Under methanogenic conditions, microbial degradation of [1,2-14C]vinyl chloride (VC) resulted in significant (14 ?? 3% maximum recovery) but transient recovery of radioactivity as 14C-acetate. Subsequently, 14C-acetate was degraded to 14CH4 and 14CO2 (18 ?? 2% and 54 ?? 3% final recoveries respectively). In contrast, under 2-bromoethanesulfonic acid (BES) amended conditions, 14C-acetate recovery remained high (27 ?? 1% maximum recovery) throughout the study, no 14CH4 was produced, and the final recovery of 14CO2 was only 35 ?? 4%. These results demonstrate that oxidative acetogenesis may be an important mechanism for anaerobic VC biodegradation. Moreover, these results (1) demonstrate that microbial degradation of VC to CH4 and CO2 may involve oxidative acetogenesis followed by acetotrophic methanogenesis and (2) suggest that oxidative acetogenesis may be the initial step in the net oxidation of VC to CO2 reported previously under Fe(III)-reducing, SO4-reducing, and humic acids-reducing conditions.

A microbial functional group-based module for simulating methane production and consumption: Application to an incubated permafrost soil

DOE PAGES

Xu, Xiaofeng; Elias, Dwayne A.; Graham, David E.; ...

2015-07-23

In this study, accurately estimating methane (CH 4) flux is critically important for investigating and predicting the biogeochemistry-climate feedback. Better simulating CH 4 flux requires explicit representations of microbial processes on CH 4 dynamics because all processes for CH 4 production and consumption are actually carried out by microbes. A microbial functional group based module was developed and tested against an incubation experiment. The module considers four key mechanisms for CH 4 production and consumption: methanogenesis from acetate or single-carbon compounds and CH 4 oxidation using molecular oxygen or other inorganic electron acceptors. These four processes were carried out bymore » four microbial functional groups: acetoclastic methanogens, hydrogenotrophic methanogens, aerobic methanotrophs, and anaerobic methanotrophs. This module was then linked with the decomposition subroutine of the Community Land Model, and was further used to simulate dynamics of carbon dioxide (CO 2) and CH 4 concentrations from an incubation experiment with permafrost soils. The results show that the model could capture the dynamics of CO 2 and CH 4 concentrations in microcosms with top soils, mineral layer soils and permafrost soils under natural and saturated moisture conditions and a temperature gradient of -2°C, 3°C, and 5°C. Sensitivity analysis confirmed the importance of acetic acid's direct contribution as substrate and indirect effects through pH feedback on CO 2 and CH 4 production and consumption. This study suggests that representing the microbial mechanisms is critical for modeling CH 4 production and consumption; it is urgent to incorporate microbial mechanisms into Earth system models for better predicting the behavior of the climate system.« less

Transmission of Atherosclerosis Susceptibility with Gut Microbial Transplantation*

PubMed Central

Gregory, Jill C.; Buffa, Jennifer A.; Org, Elin; Wang, Zeneng; Levison, Bruce S.; Zhu, Weifei; Wagner, Matthew A.; Bennett, Brian J.; Li, Lin; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2015-01-01

Recent studies indicate both clinical and mechanistic links between atherosclerotic heart disease and intestinal microbial metabolism of certain dietary nutrients producing trimethylamine N-oxide (TMAO). Here we test the hypothesis that gut microbial transplantation can transmit choline diet-induced TMAO production and atherosclerosis susceptibility. First, a strong association was noted between atherosclerotic plaque and plasma TMAO levels in a mouse diversity panel (n = 22 strains, r = 0.38; p = 0.0001). An atherosclerosis-prone and high TMAO-producing strain, C57BL/6J, and an atherosclerosis-resistant and low TMAO-producing strain, NZW/LacJ, were selected as donors for cecal microbial transplantation into apolipoprotein e null mice in which resident intestinal microbes were first suppressed with antibiotics. Trimethylamine (TMA) and TMAO levels were initially higher in recipients on choline diet that received cecal microbes from C57BL/6J inbred mice; however, durability of choline diet-dependent differences in TMA/TMAO levels was not maintained to the end of the study. Mice receiving C57BL/6J cecal microbes demonstrated choline diet-dependent enhancement in atherosclerotic plaque burden as compared with recipients of NZW/LacJ microbes. Microbial DNA analyses in feces and cecum revealed transplantation of donor microbial community features into recipients with differences in taxa proportions between donor strains that were transmissible to recipients and that tended to show coincident proportions with TMAO levels. Proportions of specific taxa were also identified that correlated with plasma TMAO levels in donors and recipients and with atherosclerotic lesion area in recipients. Atherosclerosis susceptibility may be transmitted via transplantation of gut microbiota. Gut microbes may thus represent a novel therapeutic target for modulating atherosclerosis susceptibility. PMID:25550161

Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruhn, D F; Thompson, D N; Noah, K S

1999-06-01

Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, Leptospirillum, Ferromicrobium, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. Aftermore » acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.« less

Arsenite and ferrous iron oxidation linked to chemolithotrophic denitrification for the immobilization of arsenic in anoxic environments

USGS Publications Warehouse

Sun, W.; Sierra-Alvarez, R.; Milner, L.; Oremland, R.; Field, J.A.

2009-01-01

The objective of this study was to explore a bioremediation strategy based on injecting NO3- to support the anoxic oxidation of ferrous iron (Fe(II)) and arsenite (As(III)) in the subsurface as a means to immobilize As in the form of arsenate (As(V)) adsorbed onto biogenic ferric (Fe(III)) (hydr)oxides. Continuous flows and filled columns were used to simulate a natural anaerobic groundwater and sediment system with co-occurring As(III) and Fe(II) in the presence (column SF1) or absence (column SF2) of nitrate, respectively. During operation for 250 days, the average influent arsenic concentration of 567 ??g L-1 was reduced to 10.6 (??9.6) ??g L-1 in the effluent of column SF1. The cumulative removal of Fe(II) and As(III) in SF1 was 6.5 to 10-fold higher than that in SF2. Extraction and measurement of the mass of iron and arsenic immobilized on the sand packing of the columns were close to the iron and arsenic removed from the aqueous phase during column operation. The dominant speciation of the immobilized iron and arsenic was Fe(III) and As(V) in SF1, compared with Fe(II) and As(III) in SF2. The speciation was confirmed by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The results indicate that microbial oxidation of As(III) and Fe(II) linked to denitrification resulted in the enhanced immobilization of aqueous arsenic in anaerobic environments by forming Fe(III) (hydr)oxide coated sands with adsorbed As(V). ?? 2009 American Chemical Society.

Microbial production and oxidation of methane in deep subsurface

NASA Astrophysics Data System (ADS)

Kotelnikova, Svetlana

2002-10-01

The goal of this review is to summarize present studies on microbial production and oxidation of methane in the deep subterranean environments. Methane is a long-living gas causing the "greenhouse" effect in the planet's atmosphere. Earlier, the deep "organic carbon poor" subsurface was not considered as a source of "biogenic" methane. Evidence of active methanogenesis and presence of viable methanogens including autotrophic organisms were obtained for some subsurface environments including water-flooded oil-fields, deep sandy aquifers, deep sea hydrothermal vents, the deep sediments and granitic groundwater at depths of 10 to 2000 m below sea level. As a rule, the deep subterranean microbial populations dwell at more or less oligotrophic conditions. Molecular hydrogen has been found in a variety of subsurface environments, where its concentrations were significantly higher than in the tested surface aquatic environments. Chemolithoautotrophic microorganisms from deep aquifers that could grow on hydrogen and carbon dioxide can act as primary producers of organic carbon, initiating heterotrophic food chains in the deep subterranean environments independent of photosynthesis. "Biogenic" methane has been found all over the world. On the basis of documented occurrences, gases in reservoirs and older sediments are similar and have the isotopic character of methane derived from CO 2 reduction. Groundwater representing the methanogenic end member are characterized by a relative depletion of dissolved organic carbon (DOC) in combination with an enrichment in 13C in inorganic carbon, which is consistent with the preferential reduction of 12CO 2 by autotrophic methanogens or acetogens. The isotopic composition of methane formed via CO 2 reduction is controlled by the δ13C of the original CO 2 substrate. Literature data shows that CH 4 as heavy as -40‰ or -50‰ can be produced by the microbial reduction of isotopically heavy CO 2. Produced methane may be oxidized microbially to carbon dioxide. Microbial methane oxidation is a biogeochemical process that limits the release of methane, a greenhouse gas from anaerobic environments. Anaerobic methane oxidation plays an important role in marine sediments. Similar processes may take place in deep subsurface and thus fuel the deep microbial community. Organisms or consortia responsible for anaerobic methane oxidation have not yet been cultured, although diverse aerobic methanotrophs have been isolated from a variety of underground niches. The presence of aerobic methanotrophs in the anoxic subsurface remains to be explained. The presence of methane in the deep subsurface have been shown all over the world. The flux of gases between the deep subsurface and the atmosphere is driven by the concentration gradient from depth to the atmosphere. However, methane is consumed by methanotrophs on the way of its evolution in oxidized environments and is transformed to organic form, available for further microbial processing. When the impact of subsurface environments to global warming is estimated, it is necessary to take into account the activity of methane-producing Archaea and methane-oxidizing biofilters in groundwater. Microbial production and oxidation of methane is involved in the carbon cycle in the deep subsurface environments.

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

GIBBs: A new soil biology index to quantify beneficial bacteria in the soil

USDA-ARS?s Scientific Manuscript database

Microbial diversity has been linked to soil resilience and health but few microbial indices explicitly link diversity to function. Many of the thousands of bacteria species present in soils enhance plant nutrition, confer stress tolerance, and promote plant growth and productivity through specific m...

Electrodes as Terminal Electron Acceptors in Anaerobic Ammonium Oxidation

NASA Astrophysics Data System (ADS)

Ruiz-Urigüen, M.; Jaffe, P. R.

2017-12-01

Anaerobic ammonium (NH4+) oxidation under iron (Fe) reducing conditions is a microbial- mediated process known as Feammox. This is a novel pathway in the nitrogen cycle, and a key process for alleviating NH4+ accumulation in anoxic soils, wetlands, and wastewater. Acidimicrobiaceae-bacterium A6, phylum Actinobacteria, are one type of autotrophic bacteria linked to this process. The Feammox-bacteria obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, iron oxides are the TEAs. However, in this study we show that electrodes in Microbial Electrolysis Cells (MECs) or electrodes set in the field can be used as TEAs by Feammox-bacteria. The potential difference between electrodes is the driving force for electron transfer, making the reaction energetically feasible. Our results show that MECs containing Feammox cultures can remove NH4+ up to 3.5 mg/L in less than 4 hours, compared to an average of 9 mg/L in 2 weeks when cultured under traditional conditions. Concomitantly, MECs produce an average current of 30.5 A/m3 whilst dead bacteria produced low (<2.7 A/m3) or no current. Furthermore, we have measured that A6 biomass increased from 5E4 cells/ml to 9.77E5 cells/ml in 2 weeks of operation, indicating the feasibility of growing A6 in MECs. Results from the electrodes in the field show higher percentage of electrogenic bacteria, including Acidimicrobiaceae-bacterium, on the more reducing electrode, compared to the more oxidized one. Our initial results also suggest that electrodes contained more Actinobacteria when compared to bulk soil. Electrodes as TEAs enhance electrogenic bacteria recovery and culturing. The use of MECs for the productions of Feammox-bacteria eliminates the dependence of Fe, a finite electron acceptor, therefore, allowing for continuous NH4+ removal. Finally, Fe-free Feammox-bacteria can be applied to reduce other metals of environmental concern; therefore, opening the range of possible application of Feammox-bacteria.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Tao; Kukkadapu, Ravi K.; Griffin, Aron M.

Fe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies of microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area goethite. Cryogenic (12K) 57Fe Mössbauermore » spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate) in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl22H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicatesilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26-87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe(II) addition and system redox potential may account for the microbial and abiotic reaction systems. Our experiments provide new insight into pathways for Fe(III) reduction in mixed Fe(III)-oxide/Fe(III)-phyllosilicate assemblages, and provide key mechanistic insight for interpreting microbial reduction experiments and field data from complex natural soils and sediments.« less

Textural and mineralogical characteristics of microbial fossils associated with modern and ancient iron (oxyhydr)oxides: terrestrial analogue for sediments in Gale Crater.

PubMed

Potter-McIntyre, Sally L; Chan, Marjorie A; McPherson, Brian J

2014-01-01

Iron (oxyhydr)oxide microbial mats in modern to ∼100 ka tufa terraces are present in a cold spring system along Ten Mile Graben, southeastern Utah, USA. Mats exhibit morphological, chemical, and textural biosignatures and show diagenetic changes that occur over millennial scales. The Jurassic Brushy Basin Member of the Morrison Formation in the Four Corners region of the USA also exhibits comparable microbial fossils and iron (oxyhydr)oxide biosignatures in the lacustrine unit. Both the modern spring system and Brushy Basin Member represent alkaline, saline, groundwater-fed systems and preserve diatoms and other similar algal forms with cellular elaboration. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se, P) are associated with microbial fossils in modern and ancient iron (oxyhydr)oxides and may be potential markers for biosignatures. The presence of ferrihydrite in ∼100 ka fossil microbial mats and Jurassic rocks suggests that this thermodynamically unstable mineral may also be a potential biomarker. One of the most extensive sedimentary records on Mars is exposed in Gale Crater and consists of non-acidic clays and sulfates possibly of lacustrine origin. These terrestrial iron (oxyhydr)oxide examples are a valuable analogue because of similar iron- and clay-rich host rock compositions and will help (1) understand diagenetic processes in a non-acidic, saline lacustrine environment such as the sedimentary rocks in Gale Crater, (2) document specific biomediated textures, (3) demonstrate how biomediated textures might persist or respond to diagenesis over time, and (4) provide a ground truth library of textures to explore and compare in extraterrestrial iron (oxyhydr)oxides, where future explorations hope to detect past evidence of life.

Filamentous hydrous ferric oxide biosignatures in a pipeline carrying acid mine drainage at Iron Mountain Mine, California

USGS Publications Warehouse

Williams, Amy J.; Alpers, Charles N.; Sumner, Dawn Y.; Campbell, Kate M.

2017-01-01

A pipeline carrying acidic mine effluent at Iron Mountain, CA, developed Fe(III)-rich precipitate caused by oxidation of Fe(II)aq. The native microbial community in the pipe included filamentous microbes. The pipe scale consisted of microbial filaments, and schwertmannite (ferric oxyhydroxysulfate, FOHS) mineral spheres and filaments. FOHS filaments contained central lumina with diameters similar to those of microbial filaments. FOHS filament geometry, the geochemical environment, and the presence of filamentous microbes suggest that FOHS filaments are mineralized microbial filaments. This formation of textural biosignatures provides the basis for a conceptual model for the development and preservation of biosignatures in other environments.

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake

PubMed Central

Yau, Sheree; Lauro, Federico M; Williams, Timothy J; DeMaere, Matthew Z; Brown, Mark V; Rich, John; Gibson, John AE; Cavicchioli, Ricardo

2013-01-01

Organic Lake is a shallow, marine-derived hypersaline lake in the Vestfold Hills, Antarctica that has the highest reported concentration of dimethylsulfide (DMS) in a natural body of water. To determine the composition and functional potential of the microbial community and learn about the unusual sulfur chemistry in Organic Lake, shotgun metagenomics was performed on size-fractionated samples collected along a depth profile. Eucaryal phytoflagellates were the main photosynthetic organisms. Bacteria were dominated by the globally distributed heterotrophic taxa Marinobacter, Roseovarius and Psychroflexus. The dominance of heterotrophic degradation, coupled with low fixation potential, indicates possible net carbon loss. However, abundant marker genes for aerobic anoxygenic phototrophy, sulfur oxidation, rhodopsins and CO oxidation were also linked to the dominant heterotrophic bacteria, and indicate the use of photo- and lithoheterotrophy as mechanisms for conserving organic carbon. Similarly, a high genetic potential for the recycling of nitrogen compounds likely functions to retain fixed nitrogen in the lake. Dimethylsulfoniopropionate (DMSP) lyase genes were abundant, indicating that DMSP is a significant carbon and energy source. Unlike marine environments, DMSP demethylases were less abundant, indicating that DMSP cleavage is the likely source of high DMS concentration. DMSP cleavage, carbon mixotrophy (photoheterotrophy and lithoheterotrophy) and nitrogen remineralization by dominant Organic Lake bacteria are potentially important adaptations to nutrient constraints. In particular, carbon mixotrophy relieves the extent of carbon oxidation for energy production, allowing more carbon to be used for biosynthetic processes. The study sheds light on how the microbial community has adapted to this unique Antarctic lake environment. PMID:23619305

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

NASA Astrophysics Data System (ADS)

Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

2013-07-01

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations) was nearly constant (250 μM) throughout the stream. Based on the level of detectable dissolved molecular oxygen (O2) of the stream water (⩾38 μM) along with metabolic measurements, it was predicted that nitrification by thermophilic AOA and NOB components in the microbial mats that were exposed to the stream water would constrain the concentrations and isotopic ratios of ΣNH3, NO2- and NO3- of the stream water. The δ15N value of ΣNH3 increased from 0‰ to 7‰ with decreasing concentration, which was consistent with the previously reported isotopic fractionation for microbial ΣNH3 oxidation. In contrast, the δ15N value of NO2- was 22‰ lighter than that of NO3- in the steam water at the same site, indicating an inverse isotopic fractionation for microbial NO2- oxidation. The variation in concentrations and δ15N values of ΣNH3, NO2- and NO3- was largely explained using a two-step nitrification model, and the apparent nitrogen isotopic fractionations of ΣNH3 oxidation and NO2- oxidation were estimated to be 0.986 and 1.020, respectively. In the interstitial water within the microbial mats, the compositional and isotopic properties of TIN at the downstream site indicated potential denitrification by the anaerobic microbial components. The geochemically deduced transition of microbial nitrogen metabolism was substantiated through cultivation-independent microbiological analyses.

Flume experiments elucidate relationships between microbial genetics, nitrogen species and hydraulics in controlling nitrous oxide production in the hyporheic zone

NASA Astrophysics Data System (ADS)

Quick, A. M.; Farrell, T. B.; Reeder, W. J.; Feris, K. P.; Tonina, D.; Benner, S. G.

2014-12-01

The hyporheic zone is a potentially important producer of nitrous oxide, a powerful greenhouse gas. The location and magnitude of nitrous oxide generation within the hyporheic zone involves complex interactions between multiple nitrogen species, redox conditions, microbial communities, and hydraulics. To better understand nitrous oxide generation and emissions from streams, we conducted large-scale flume experiments in which we monitored pore waters along hyporheic flow paths within stream dune structures. Measured dissolved oxygen, ammonia, nitrate, nitrite, and dissolved nitrous oxide showed distinct spatial relationships reflecting redox changes along flow paths. Denitrifying genes (nosZ, nirS, and nirK), determined using qPCR, were spatially associated with abundances of nitrogen species. Using residence times along a flow path, clear trends in oxygen conditions, genes encoding for microbial catalysis, and nitrogen species were observed. Hotspots of targeted genes correlated with hotspots for conversion of nitrogen species, including nitrous oxide production and conversion to dinitrogen. Trends were apparent regardless of dune size, allowing for the possibility to apply observed relationships to multiple streambed morphologies. Relating streambed morphology and loading of nitrogen species allows for prediction of nitrous oxide production in the hyporheic zone.

Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction

PubMed Central

Hansel, Colleen M.; Zeiner, Carolyn A.; Santelli, Cara M.; Webb, Samuel M.

2012-01-01

Manganese (Mn) oxides are among the most reactive minerals within the environment, where they control the bioavailability of carbon, nutrients, and numerous metals. Although the ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides is scattered throughout the bacterial and fungal domains of life, the mechanism and physiological basis for Mn(II) oxidation remains an enigma. Here, we use a combination of compound-specific chemical assays, microspectroscopy, and electron microscopy to show that a common Ascomycete filamentous fungus, Stilbella aciculosa, oxidizes Mn(II) to Mn oxides by producing extracellular superoxide during cell differentiation. The reactive Mn oxide phase birnessite and the reactive oxygen species superoxide and hydrogen peroxide are colocalized at the base of asexual reproductive structures. Mn oxide formation is not observed in the presence of superoxide scavengers (e.g., Cu) and inhibitors of NADPH oxidases (e.g., diphenylene iodonium chloride), enzymes responsible for superoxide production and cell differentiation in fungi. Considering the recent identification of Mn(II) oxidation by NADH oxidase-based superoxide production by a common marine bacterium (Roseobacter sp.), these results introduce a surprising homology between some prokaryotic and eukaryotic organisms in the mechanisms responsible for Mn(II) oxidation, where oxidation appears to be a side reaction of extracellular superoxide production. Given the versatility of superoxide as a redox reactant and the widespread ability of fungi to produce superoxide, this microbial extracellular superoxide production may play a central role in the cycling and bioavailability of metals (e.g., Hg, Fe, Mn) and carbon in natural systems. PMID:22802654

Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction.

PubMed

Hansel, Colleen M; Zeiner, Carolyn A; Santelli, Cara M; Webb, Samuel M

2012-07-31

Manganese (Mn) oxides are among the most reactive minerals within the environment, where they control the bioavailability of carbon, nutrients, and numerous metals. Although the ability of microorganisms to oxidize Mn(II) to Mn(III/IV) oxides is scattered throughout the bacterial and fungal domains of life, the mechanism and physiological basis for Mn(II) oxidation remains an enigma. Here, we use a combination of compound-specific chemical assays, microspectroscopy, and electron microscopy to show that a common Ascomycete filamentous fungus, Stilbella aciculosa, oxidizes Mn(II) to Mn oxides by producing extracellular superoxide during cell differentiation. The reactive Mn oxide phase birnessite and the reactive oxygen species superoxide and hydrogen peroxide are colocalized at the base of asexual reproductive structures. Mn oxide formation is not observed in the presence of superoxide scavengers (e.g., Cu) and inhibitors of NADPH oxidases (e.g., diphenylene iodonium chloride), enzymes responsible for superoxide production and cell differentiation in fungi. Considering the recent identification of Mn(II) oxidation by NADH oxidase-based superoxide production by a common marine bacterium (Roseobacter sp.), these results introduce a surprising homology between some prokaryotic and eukaryotic organisms in the mechanisms responsible for Mn(II) oxidation, where oxidation appears to be a side reaction of extracellular superoxide production. Given the versatility of superoxide as a redox reactant and the widespread ability of fungi to produce superoxide, this microbial extracellular superoxide production may play a central role in the cycling and bioavailability of metals (e.g., Hg, Fe, Mn) and carbon in natural systems.

A microbial-mineralization approach for syntheses of iron oxides with a high specific surface area.

PubMed

Yagita, Naoki; Oaki, Yuya; Imai, Hiroaki

2013-04-02

Of minerals and microbes: A microbial-mineralization-inspired approach was used to facilitate the syntheses of iron oxides with a high specific surface area, such as 253 m(2)g(-1) for maghemite (γ-Fe(2)O(3)) and 148 m(2)g(-1) for hematite (α-Fe(2)O(3)). These iron oxides can be applied to electrode material of lithium-ion batteries, adsorbents, and catalysts. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

PubMed Central

Jahnke, Linda L.; Farmer, Jack D.; Cady, Sherry L.

2014-01-01

Abstract The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521. PMID:24886100

The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.

PubMed

Vieira, A; Ribera-Guardia, A; Marques, R; Barreto Crespo, M T; Oehmen, A; Carvalho, G

2018-06-02

The emission of the greenhouse gas nitrous oxide (N 2 O) can occur during biological nutrient removal. Denitrifying enhanced biological phosphorus removal (d-EBPR) systems are an efficient means of removing phosphate and nitrogen, performed by denitrifying polyphosphate-accumulating organisms (d-PAOs). The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO 3 - ), nitrite (NO 2 - ), and N 2 O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. Reverse transcriptase-qPCR (RT-qPCR) and high-throughput sequencing, combined with chemical analysis, were used to study gene expression, microbial diversity, and denitrification kinetics. The potential for N 2 O production was greater than the potential for its reduction in most tests. A strong correlation was observed between the N 2 O reduction rate and the relative gene expression of nitrous oxide reductase per nitrite reductase (nosZ/(nirS + nirK)), suggesting that the expression of denitrifying marker genes is a strong predictor of the N 2 O reduction rate. The d-EBPR community maintained a core population with low variations throughout the study. Furthermore, phylogenetic analyses of the studied marker genes revealed that the organisms actively involved in denitrification were closely related to Thauera sp., Candidatus Accumulibacter phosphatis, and Candidatus Competibacter denitrificans. Moreover, Competibacter-related OTUs seem to be important contributors to the N 2 O reduction capacity of the system, likely scavenging the N 2 O produced by other organisms. Overall, this study contributes to a better understanding of the microbial biochemistry and the genetics involving biological denitrification removal, important to minimize N 2 O emissions in wastewater treatment plants.

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

In-Situ Quantification of Microbial Processes Controlling Methane Emissions From Rice Plants

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Cho, R.; Zeyer, J. A.

2011-12-01

Methane is an important greenhouse gas contributing to global warming. Among other sources, rice (paddy) soils represent a major nonpoint source of biogenic methane. In flooded paddy soils methane is produced under anaerobic conditions. Conversely, methanotrophic microorganisms oxidize methane to carbon dioxide in the root zone of rice plants, thus reducing overall methane emissions to the atmosphere. We present a novel combination of methods to quantify methanogenesis and methane oxidation in paddy soils and to link methane turnover to net emissions of rice plants. To quantify methane turnover in the presence of high methane background concentrations, small-scale push-pull tests (PPTs) were conducted in paddy soils using stable isotope-labeled substrates. Deuterated acetate and 13-C bicarbonate were employed to discern and quantify acetoclastic and hydrogenotrophic methanogenesis, while 13-C methane was employed to quantify methane oxidation. During 2.5 hr-long PPTs, 140 mL of a test solution containing labeled substrates and nonreactive tracers (Ar, Br-) was injected into paddy soils of potted rice plants. After a short rest period, 480 mL of test solution/pore water mixture was extracted from the same location. Methane turnover was then computed from extraction-phase breakthrough curves of substrates and/or products, and nonreactive tracers. To link methane turnover to net emissions, methane emissions from paddy soils and rice plants were individually determined immediately preceding PPTs using static flux chambers. We will present results of a series of experiments conducted in four different potted rice plants. Preliminary results indicate substantial variability in methane turnover and net emission between different rice plants. The employed combination of methods appears to provide a robust means to quantitatively link methane turnover in paddy soils to net emissions from rice plants.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.

PubMed

Scholten, Johannes C M; Culley, David E; Nie, Lei; Munn, Kyle J; Chow, Lely; Brockman, Fred J; Zhang, Weiwen

2007-06-29

The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.

Electron transfer properties of peat organic matter: from electrochemical analysis to redox processes in peatlands

NASA Astrophysics Data System (ADS)

Sander, Michael; Getzinger, Gordon; Walpen, Nicolas

2017-04-01

Peat organic matter contains redox-active functional groups that can accept and/or donate electrons from and to biotic and abiotic reaction partners present in peatlands. Several studies have provided evidence that electron accepting quinone moieties in the peat organic matter may act as terminal electron acceptors for anaerobic microbial respiration. This respiration pathway may competitively suppress methanogenesis and thereby lead to excess carbon dioxide to methane formation in peatlands. Electron donating phenolic moieties in peat organic matter have long been considered to inhibit microbial and enzymatic activities in peatlands, thereby contributing to carbon stabilization and accumulation in these systems. Phenols are expected to be comparatively stable in anoxic parts of the peats as phenoloxidases, a class of enzymes capable of oxidatively degrading phenols, require molecular oxygen as co-substrate. Despite the general recognition of the importance of redox-active moieties in peat organic matter, the abundance, redox properties and reactivities of these moieties remain poorly studied and understood, in large part due to analytical challenges. This contribution will, in a first part, summarize recent advances in our research group on the analytical chemistry of redox-active moieties in peat organic matter. We will show how mediated electrochemical analysis can be used to quantify the capacities of electron accepting and donating moieties in both dissolved and particulate peat organic matter. We will link these capacities to the physicochemical properties of peat organic matter and provide evidence for quinones and phenols as major electron accepting and donating moieties, respectively. The second part of this contribution will highlight how these electroanalytical techniques can be utilized to advance a more fundamental understanding of electron transfer processes involving peat organic matter. These processes include the redox cycling (i.e., repeated reduction and re-oxidation) of peat organic matter under alternating anoxic-oxic conditions as well as the oxidation of phenolic moieties in peat organic matter by phenol oxidases in the presence of molecular oxygen. Overall, this contribution will attempt to link molecular-level insights into the redox properties of peat organic matter to larger scale redox processes that are important to carbon cycling in peatlands.

Proteomic Characterization of Central Pacific Oxygen Minimum Zone Microbial Communities

NASA Astrophysics Data System (ADS)

Saunders, J. K.; McIlvin, M. M.; Moran, D.; Held, N.; Futrelle, J.; Webb, E.; Santoro, A.; Dupont, C.; Saito, M.

2018-05-01

Microbial proteomic profiles are excellent for surveying vast expanses of pelagic ecosystems for links between microbial communities and the biogeochemical cycles they mediate. Data from the ProteOMZ expedition supports the utility of this method.

Textural and Mineralogical Characteristics of Microbial Fossils Associated with Modern and Ancient Iron (Oxyhydr)Oxides: Terrestrial Analogue for Sediments in Gale Crater

PubMed Central

Chan, Marjorie A.; McPherson, Brian J.

2014-01-01

Abstract Iron (oxyhydr)oxide microbial mats in modern to ∼100 ka tufa terraces are present in a cold spring system along Ten Mile Graben, southeastern Utah, USA. Mats exhibit morphological, chemical, and textural biosignatures and show diagenetic changes that occur over millennial scales. The Jurassic Brushy Basin Member of the Morrison Formation in the Four Corners region of the USA also exhibits comparable microbial fossils and iron (oxyhydr)oxide biosignatures in the lacustrine unit. Both the modern spring system and Brushy Basin Member represent alkaline, saline, groundwater-fed systems and preserve diatoms and other similar algal forms with cellular elaboration. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se, P) are associated with microbial fossils in modern and ancient iron (oxyhydr)oxides and may be potential markers for biosignatures. The presence of ferrihydrite in ∼100 ka fossil microbial mats and Jurassic rocks suggests that this thermodynamically unstable mineral may also be a potential biomarker. One of the most extensive sedimentary records on Mars is exposed in Gale Crater and consists of non-acidic clays and sulfates possibly of lacustrine origin. These terrestrial iron (oxyhydr)oxide examples are a valuable analogue because of similar iron- and clay-rich host rock compositions and will help (1) understand diagenetic processes in a non-acidic, saline lacustrine environment such as the sedimentary rocks in Gale Crater, (2) document specific biomediated textures, (3) demonstrate how biomediated textures might persist or respond to diagenesis over time, and (4) provide a ground truth library of textures to explore and compare in extraterrestrial iron (oxyhydr)oxides, where future explorations hope to detect past evidence of life. Key Words: Biogeochemistry—Mars—Biosignatures—Diagenesis—Iron oxides. Astrobiology 14, 1–14. PMID:24380534

Nitrous oxide emissions and denitrification rates: A blueprint for smart management and remediation of agricultural landscapes.

NASA Astrophysics Data System (ADS)

Tomasek, A.; Hondzo, M.; Kozarek, J. L.

2015-12-01

Anthropogenic activities have greatly altered the global nitrogen cycle, especially in the agriculturally dominated Midwest, with severe consequences on human and aquatic health. Complete microbial denitrification can be viewed as a nitrogen sink, converting soluble nitrate into inert nitrogen gas. This research aims to quantify and correlate the driving parameters in microbial denitrification and explore the relationship to the abundance of denitrifying genes and the microbial communities at these sites. Denitrifying genes for each step in the denitrification process have been quantified. Data from a field site in Southern Minnesota has been collected throughout the season for two years enabling investigation into the temporal variability of denitrification. Data was collected at two cross-sections across the channel to determine the effect of bank location and moisture content on denitrification. Data were collected in an experimental basin in the summer of 2015 to determine the effect of flooding and benthic organic matter content and quality on microbial denitrification and nitrous oxide production. Four sediment types were investigated in three different flood regimes. After each raising or lowering of the water level, soil cores were taken to determine soil characteristics, the potential denitrification using the denitrification enzyme activity method, nitrous oxide production using a static core method, and the denitrifying gene abundance. Chambers were also deployed over each soil amendment in each flood regime to determine the nitrous oxide production over time. Results from these studies will convey a more complete explanation of denitrification and nitrous oxide production under varying environmental conditions. By determining the driving parameters for microbial denitrification, denitrification hot spots and hot moments can be created and enhanced. One potential consequence of increased denitrification is the possibility of incomplete denitrification resulting in the release of nitrous oxide, a greenhouse gas with 300 times the warming potential of carbon dioxide. The investigation of nitrous oxide emissions and correlation to denitrification rates will facilitate smart management and remediation efforts of agricultural landscapes.

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation.

PubMed

Sutton, Nora B; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H M

2015-01-01

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2-4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation.

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

PubMed Central

Sutton, Nora B.; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H. M.

2015-01-01

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation. PMID:26244346

Perchlorate bioreduction linked to methane oxidation in a membrane biofilm reactor: Performance and microbial community structure.

PubMed

Xie, Ting; Yang, Qi; Winkler, Mari K H; Wang, Dongbo; Zhong, Yu; An, Hongxue; Chen, Fei; Yao, Fubin; Wang, Xiaolin; Wu, Jiawei; Li, Xiaoming

2018-06-05

Perchlorate bioreduction coupled to methane oxidation was successfully achieved without the addition of nitrate or nitrite in a membrane biofilm reactor (MBfR) inoculated with a mixture of freshwater sediments and anaerobic digester sludge as well as return activated sludge. The reactor was operated at different methane pressures (60, 40 and 20 Kpa) and influent perchlorate concentrations (1, 5 and 10 mg/L) to evaluate the biochemical process of perchlorate bioreduction coupled to methane oxidation. Perchlorate was completely reduced with a higher removal flux of 92.75 mg/m 2 ·d using methane as the sole carbon source and electron donor, other than hydrogen or other limiting organics. Quantitative real-time PCR showed that bacteria prevailed over archaea and the abundances of mcrA, pMMO, pcrA, and nirS genes were correlated with the influent perchlorate flux. High-throughput sequencing of 16S rRNA genes demonstrated that the functional community consisted of methanotrophs, methylotrophs, perchlorate-reducing bacteria, as well as various denitrifiers. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruhn, Debby Fox; Thompson, David Neal; Noah, Karl Scott

1999-06-01

Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, “Leptospirillum”, “Ferromicrobium”, and Acidiphilium. Two temperatures (30°C and 45°C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. Aftermore » acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to low the pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.« less

Connecting the Dots: Could Microbial Translocation Explain Commonly Reported Symptoms in HIV Disease?

PubMed Central

Wilson, Natalie L.; Vance, David E.; Moneyham, Linda D.; Raper, James L.; Mugavero, Michael J.; Heath, Sonya L.; Kempf, Mirjam-Colette

2017-01-01

Microbial translocation within the context of HIV disease has been described as one of the contributing causes of inflammation and disease progression in HIV infection. HIV-associated symptoms have been related to inflammatory markers and sCD14, a surrogate marker for microbial translocation, suggesting a plausible link between microbial translocation and symptom burden in HIV disease. Similar pathophysiological responses and symptoms have been reported in inflammatory bowel disease. We provide a comprehensive review of microbial translocation, HIV-associated symptoms, and symptoms connected with inflammation. We identify studies showing a relationship among inflammatory markers, sCD14, and symptoms reported in HIV disease. A conceptual framework and rationale to investigate the link between microbial translocation and symptoms is presented. The impact of inflammation on symptoms supports recommendations to reduce inflammation as part of HIV symptom management. Research in reducing microbial translocation-induced inflammation is limited, but needed, to further promote positive health outcomes among HIV-infected patients. PMID:25305025

Connecting the dots: could microbial translocation explain commonly reported symptoms in HIV disease?

PubMed

Wilson, Natalie L; Vance, David E; Moneyham, Linda D; Raper, James L; Mugavero, Michael J; Heath, Sonya L; Kempf, Mirjam-Colette

2014-01-01

Microbial translocation within the context of HIV disease has been described as one of the contributing causes of inflammation and disease progression in HIV infection. HIV-associated symptoms have been related to inflammatory markers and sCD14, a surrogate marker for microbial translocation, suggesting a plausible link between microbial translocation and symptom burden in HIV disease. Similar pathophysiological responses and symptoms have been reported in inflammatory bowel disease. We provide a comprehensive review of microbial translocation, HIV-associated symptoms, and symptoms connected with inflammation. We identify studies showing a relationship among inflammatory markers, sCD14, and symptoms reported in HIV disease. A conceptual framework and rationale to investigate the link between microbial translocation and symptoms is presented. The impact of inflammation on symptoms supports recommendations to reduce inflammation as part of HIV symptom management. Research in reducing microbial translocation-induced inflammation is limited, but needed, to further promote positive health outcomes among HIV-infected patients. Published by Elsevier Inc.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

PubMed

Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Ter Horst, Rob; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J

2016-11-03

Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input.

PubMed

Xu, Xi-jun; Chen, Chuan; Wang, Ai-jie; Yu, Hao; Zhou, Xu; Guo, Hong-liang; Yuan, Ye; Lee, Duu-jong; Zhou, Jizhong; Ren, Nan-qi

2014-08-15

Limited-oxygen mediated synergistic relationships between sulfate-reducing bacteria (SRB), nitrate-reducing bacteria (NRB) and sulfide-oxidizing bacteria (SOB, including nitrate-reducing, sulfide-oxidizing bacteria NR-SOB) were predicted to simultaneously remove contaminants of nitrate, sulfate and high COD, and eliminate sulfide generation. A lab-scale experiment was conducted to examine the impact of limited oxygen on these oxy-anions degradation, sulfide oxidation and associated microbial functional responses. In all scenarios tested, the reduction of both nitrate and sulfate was almost complete. When limited-oxygen was fed into bioreactors, S(0) formation was significantly improved up to ∼ 70%. GeoChip 4.0, a functional gene microarray, was used to determine the microbial gene diversity and functional potential for nitrate and sulfate reduction, and sulfide oxidation. The diversity of the microbial community in bioreactors was increased with the feeding of limited oxygen. Whereas the intensities of the functional genes involved in sulfate reduction did not show a significant difference, the abundance of the detected denitrification genes decreased in limited oxygen samples. More importantly, sulfide-oxidizing bacteria may alter their populations/genes in response to limited oxygen potentially to function more effectively in sulfide oxidation, especially to elemental sulfur. The genes fccA/fccB from nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB), such as Paracoccus denitrificans, Thiobacillus denitrificans, Beggiatoa sp., Thiomicrospira sp., and Thioalkalivibrio sp., were more abundant under limited-oxygen condition. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Electricity generation coupled with wastewater treatment using a microbial fuel cell composed of a modified cathode with a ceramic membrane and cellulose acetate film.

PubMed

Seo, Ha Na; Lee, Woo Jin; Hwang, Tae Sik; Park, Doo Hyun

2009-09-01

A noncompartmented microbial fuel cell (NCMFC) composed of a Mn(IV)-carbon plate and a Fe(III)-carbon plate was used for electricity generation from organic wastewater without consumption of external energy. The Fe(III)-carbon plate, coated with a porous ceramic membrane and a semipermeable cellulose acetate film, was used as a cathode, which substituted for the catholyte and cathode. The Mn(IV)-carbon plate was used as an anode without a membrane or film coating. A solar cell connected to the NCMFC activated electricity generation and bacterial consumption of organic matter contained in the wastewater. More than 99 degrees of the organic matter was biochemically oxidized during wastewater flow through the four NCMFC units. A predominant bacterium isolated from the anode surface in both the conventional and the solar cell-linked NCMFC was found to be more than 99 degrees similar to a Mn(II)-oxidizing bacterium and Burkeholderia sp., based on 16S rDNA sequence analysis. The isolate reacted electrochemically with the Mn(IV)-modified anode and produced electricity in the NCMFC. After 90 days of incubation, a bacterial species that was enriched on the Mn(IV)-modified anode surface in all of the NCMFC units was found to be very similar to the initially isolated predominant species by comparing 16S rDNA sequences.

The activated sludge ecosystem contains a core community of abundant organisms

PubMed Central

Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

2016-01-01

Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

Quantification of nitrous oxide (N2O) emissions and soluble microbial product (SMP) production by a modified AOB-NOB-N2O-SMP model.

PubMed

Kim, MinJeong; Wu, Guangxue; Yoo, ChangKyoo

2017-03-01

A modified AOB-NOB-N 2 O-SMP model able to quantify nitrous oxide (N 2 O) emissions and soluble microbial product (SMP) production during wastewater treatment is proposed. The modified AOB-NOB-N 2 O-SMP model takes into account: (1) two-step nitrification by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), (2) N 2 O production by AOB denitrification under oxygen-limited conditions and (3) SMP production by microbial growth and endogenous respiration. Validity of the modified model is demonstrated by comparing the simulation results with experimental data from lab-scale sequencing batch reactors (SBRs). To reliably implement the modified model, a model calibration that adjusts model parameters to fit the model outputs to the experimental data is conducted. The results of this study showed that the modeling accuracy of the modified AOB-NOB-N 2 O-SMP model increases by 19.7% (NH 4 ), 51.0% (NO 2 ), 57.8% (N 2 O) and 16.7% (SMP) compared to the conventional model which does not consider the two-step nitrification and SMP production by microbial endogenous respiration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular characterization of anaerobic sulfur-oxidizing microbial communities in up-flow anaerobic sludge blanket reactor treating municipal sewage.

PubMed

Aida, Azrina A; Hatamoto, Masashi; Yamamoto, Masamitsu; Ono, Shinya; Nakamura, Akinobu; Takahashi, Masanobu; Yamaguchi, Takashi

2014-11-01

A novel wastewater treatment system consisting of an up-flow anaerobic sludge blanket (UASB) reactor and a down-flow hanging sponge (DHS) reactor with sulfur-redox reaction was developed for treatment of municipal sewage under low-temperature conditions. In the UASB reactor, a novel phenomenon of anaerobic sulfur oxidation occurred in the absence of oxygen, nitrite and nitrate as electron acceptors. The microorganisms involved in anaerobic sulfur oxidation have not been elucidated. Therefore, in this study, we studied the microbial communities existing in the UASB reactor that probably enhanced anaerobic sulfur oxidation. Sludge samples collected from the UASB reactor before and after sulfur oxidation were used for cloning and terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes of the bacterial and archaeal domains. The microbial community structures of bacteria and archaea indicated that the genus Smithella and uncultured bacteria within the phylum Caldiserica were the dominant bacteria groups. Methanosaeta spp. was the dominant group of the domain archaea. The T-RFLP analysis, which was consistent with the cloning results, also yielded characteristic fingerprints for bacterial communities, whereas the archaeal community structure yielded stable microbial community. From these results, it can be presumed that these major bacteria groups, genus Smithella and uncultured bacteria within the phylum Caldiserica, probably play an important role in sulfur oxidation in UASB reactors. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

PubMed

Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

2016-08-01

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

Microbial catabolic activities are naturally selected by metabolic energy harvest rate.

PubMed

González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

2015-12-01

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

USGS Publications Warehouse

Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

2011-01-01

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

The impact of biofumigation and chemical fumigation methods on the structure and function of the soil microbial community.

PubMed

Omirou, Michalis; Rousidou, Constantina; Bekris, Fotios; Papadopoulou, Kalliope K; Menkissoglou-Spiroudi, Urania; Ehaliotis, Constantinos; Karpouzas, Dimitrios G

2011-01-01

Biofumigation (BIOF) is carried out mainly by the incorporation of brassica plant parts into the soil, and this fumigation activity has been linked to their high glucosinolate (GSL) content. GSLs are hydrolyzed by the endogenous enzyme myrosinase to release isothiocyanates (ITCs). A microcosm study was conducted to investigate the effects induced on the soil microbial community by the incorporation of broccoli residues into soil either with (BM) or without (B) added myrosinase and of chemical fumigation, either as soil application of 2-phenylethyl ITC (PITC) or metham sodium (MS). Soil microbial activity was evaluated by measuring fluorescein diacetate hydrolysis and soil respiration. Effects on the structure of the total microbial community were assessed by phospholipid fatty acid analysis, while the impact on important fungal (ascomycetes (ASC)) and bacterial (ammonia-oxidizing bacteria (AOB)) guilds was evaluated by denaturating gradient gel electrophoresis (DGGE). Overall, B, and to a lesser extent BM, stimulated microbial activity and biomass. The diminished effect of BM compared to B was particularly evident in fungi and Gram-negative bacteria and was attributed to rapid ITC release following the myrosinase treatment. PITC did not have a significant effect, whereas an inhibitory effect was observed in the MS-treated soil. DGGE analysis showed that the ASC community was temporarily altered by BIOF treatments and more persistently by the MS treatment, while the structure of the AOB community was not affected by the treatments. Cloning of the ASC community showed that MS application had a deleterious effect on potential plant pathogens like Fusarium, Nectria, and Cladosporium compared to BIOF treatments which did not appear to inhibit them. Our findings indicate that BIOF induces changes on the structure and function of the soil microbial community that are mostly related to microbial substrate availability changes derived from the soil amendment with fresh organic materials.

Microbial Communities Associated with Biogenic Iron Oxide Mineralization in Circumneutral pH Environments

NASA Astrophysics Data System (ADS)

Chan, C. S.; Banfield, J. F.

2002-12-01

Lithotrophic growth on iron is a metabolism that has been found in a variety of neutral pH environments and is likely important in sustaining life in microaerophilic solutions, especially those low in organics. The composition of the microbial communities, especially the organisms that are responsible for iron oxidation, and carbon and nitrogen fixation, are not known, yet the ability to recognize these contributions is vital to our understanding of iron cycling in natural environments. Our approach has been to study the microbial community structure, mineralogy, and geochemistry of ~20 cm thick, 100's meters long, fluffy iron oxide-encrusted biological mats growing in the Piquette Mine tunnel, and to compare the results to those from geochemically similar environments. In situ measurements (Hydrolab) and geochemical characterization of bulk water samples and peepers (dialysis sampling vials) indicate that the environment is microaerobic, with micromolar levels of iron, high carbonate and sulfate, and typical groundwater nitrate and nitrite concentrations. 16S rDNA clone libraries show that the microbial mat and water contain communities with considerable diversity within the Bacterial domain, a large proportion of Nitrospira and Betaproteobacteria, and no Archaea. Because clone library data are not necessarily indicative of actual abundance, fluorescence in-situ hybridization (FISH) was performed on water, mat, and sediment samples from the Piquette mine and two circumneutral iron- and carbonate-rich springs in the Oregon Cascade Range. Domain- and phylum-level probes were chosen based on the clone library results (Nitrospira, Beta- and Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Planctomyces). FISH data reveal spatial associations between specific microbial groups and mineralized structures. The organisms responsible for making the mineralized sheaths that compose the bulk of the iron oxide mat are Betaproteobacteria (probably Leptothrix spp.). However, only a small proportion of the cells in the mat reside within the sheaths. Most are located on or around the sheaths, which provide a physical framework for the community. Preliminary results from FISH experiments on the iron-rich spring samples show some similarities, including an abundance of Betaproteobacteria. Enrichment and isolation experiments are being performed to identify the iron-oxidizing organisms. Iron-oxidizers have been enriched from all sites. In some cultures it has been difficult to isolate the iron-oxidizing organisms from a non-iron-oxidizing heterotroph, possibly indicating co-dependence. Knowledge of the microbial community structure and the metabolic activities of key members will enable us to better understand the processes and chemical conditions which generate iron oxide deposits found in the geologic record on Earth and possibly extraterrestrial habitats.

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

NASA Astrophysics Data System (ADS)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (<60 °C), Fe-rich and H2S-depleted hydrothermal fluids yielded δ56Fe values near +0.1‰, indistinguishable from basalt values. Suspended particles in the vent fluids and FeOx deposits recovered nearby active vents yielded systematically positive δ56Fe values. The enrichment in heavy Fe isotopes between +1.05‰ and +1.43‰ relative to Fe(II) in vent fluids suggest partial oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where they form, and are less sensitive to abiotic versus biotic origins. It follows that FeOx deposits at Loihi Seamount provides important modern analogues for ancient seafloor Fe-rich deposits allowing for testing hypotheses about the biogeochemical cycling of Fe isotopes on early Earth.

Possibilities for extremophilic microorganisms in microbial electrochemical systems

PubMed Central

Dopson, Mark; Ni, Gaofeng; Sleutels, Tom HJA

2015-01-01

Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems. PMID:26474966

Microbial diversity and community structure in an antimony-rich tailings dump.

PubMed

Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

2016-09-01

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation.

PubMed

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-11-17

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES.

Graphene oxide and H2 production from bioelectrochemical graphite oxidation

PubMed Central

Lu, Lu; Zeng, Cuiping; Wang, Luda; Yin, Xiaobo; Jin, Song; Lu, Anhuai; Jason Ren, Zhiyong

2015-01-01

Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES. PMID:26573014

[Acclimatization and characteristics of microbial community in sulphate-dependent anaerobic methane oxidation].

PubMed

Xi, Jing-Ru; Liu, Su-Qin; Li, Lin; Liu, Jun-Xin

2014-12-01

The greenhouse effect of methane is 26 times worse than that of carbon dioxide, and wastewater containing high concentrations of sulfate is harmful to water, soil and plants. Therefore, anaerobic oxidation of methane driven by sulfate is one of the effective ways for methane reduction. In this paper, with sulfate as the electron accepter, a microbial consortium capable of oxidating methane under anaerobic condition was cultured. The diversity and characteristics of bacterial and archaeal community were investigated by PCR-DGGE, and phylogenetic analysis of the dominant microorganisms was also carried out. The DGGE fingerprints showed that microbial community structure changed distinctly, and the abundance of methane-oxidizing archea and sulfate-reducing bacteria increased in the acclimatization system added sulfate. After acclimatization, the bacterial diversity increased, while archaea diversity decreased slightly. The representative bands in the DGGE profiles were excised and sequenced. Results indicated that the dominant species in the acclimatization system were Spirochaetes, Desulfuromonadales, Methanosarcinales, Methanosaeta. Methane converted into carbon dioxide while sulfate transformed into hydrogen sulfide and sulfur in the process of anaerobic methane oxidation accompanied by sulphate reduction.

Microbial content of household dust associated with exhaled NO in asthmatic children.

EPA Science Inventory

Exhaled nitric oxide (eNO) is increasingly used as a non-invasive measure of airway inflammation. Despite this, little information exists regarding the potential effects of indoor microbial components on eNO. We determined the influence of microbial contaminants in house dust and...

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea.

PubMed

Wu, Yuzhi; Qiu, Jian-Wen; Qian, Pei-Yuan; Wang, Yong

2018-05-01

In deep-sea cold seeps, microbial communities are shaped by geochemical components in seepage solutions. In the present study, we report the composition of microbial communities and potential metabolic activities in the surface sediment of Jiaolong cold seep at the northern South China Sea. Pyrosequencing of 16S rRNA gene amplicons revealed that a majority of the microbial inhabitants of the surface layers (0-6 cm) were sulfur oxidizer bacteria Sulfurimonas and archaeal methane consumer ANME-1, while sulfate reducer bacteria SEEP-SRB1, ANME-1 and ANME-2 dominated the bottom layers (8-14 cm). The potential ecological roles of the microorganisms were further supported by the presence of functional genes for methane oxidation, sulfur oxidation, sulfur reduction and nitrate reduction in the metagenomes. Metagenomic analysis revealed a significant correlation between coverage of 16S rRNA gene of sulfur oxidizer bacteria, functional genes involved in sulfur oxidation and nitrate reduction in different layers, indicating that sulfur oxidizing may be coupled to nitrate reducing at the surface layers of Jiaolong seeping site. This is probably related to the sulfur oxidizers of Sulfurimonas and Sulfurovum, which may be the capacity of nitrate reduction or associated with unidentified syntrophic nitrate-reducing microbes in the surface of the cold seep.

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Treesearch

Jennifer M. Fraterrigo; Teri C. Balser; Monica g. Turner

2006-01-01

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid...

Linking genes to ecosystem trace gas fluxes in a large-scale model system

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Cueva, A.; Volkmann, T. H. M.; Sengupta, A.; Troch, P. A.

2017-12-01

Soil microorganisms mediate biogeochemical cycles through biosphere-atmosphere gas exchange with significant impact on atmospheric trace gas composition. Improving process-based understanding of these microbial populations and linking their genomic potential to the ecosystem-scale is a challenge, particularly in soil systems, which are heterogeneous in biodiversity, chemistry, and structure. In oligotrophic systems, such as the Landscape Evolution Observatory (LEO) at Biosphere 2, atmospheric trace gas scavenging may supply critical metabolic needs to microbial communities, thereby promoting tight linkages between microbial genomics and trace gas utilization. This large-scale model system of three initially homogenous and highly instrumented hillslopes facilitates high temporal resolution characterization of subsurface trace gas fluxes at hundreds of sampling points, making LEO an ideal location to study microbe-mediated trace gas fluxes from the gene to ecosystem scales. Specifically, we focus on the metabolism of ubiquitous atmospheric reduced trace gases hydrogen (H2), carbon monoxide (CO), and methane (CH4), which may have wide-reaching impacts on microbial community establishment, survival, and function. Additionally, microbial activity on LEO may facilitate weathering of the basalt matrix, which can be studied with trace gas measurements of carbonyl sulfide (COS/OCS) and carbon dioxide (O-isotopes in CO2), and presents an additional opportunity for gene to ecosystem study. This work will present initial measurements of this suite of trace gases to characterize soil microbial metabolic activity, as well as links between spatial and temporal variability of microbe-mediated trace gas fluxes in LEO and their relation to genomic-based characterization of microbial community structure (phylogenetic amplicons) and genetic potential (metagenomics). Results from the LEO model system will help build understanding of the importance of atmospheric inputs to microorganisms pioneering fresh mineral matrix. Additionally, the measurement and modeling techniques that will be developed at LEO will be relevant for other investigators linking microbial genomics to ecosystem function in more well-developed soils with greater complexity.

Gaining electricity from in situ oxidation of hydrogen produced by fermentative cellulose degradation.

PubMed

Niessen, J; Schröder, U; Harnisch, F; Scholz, F

2005-01-01

To exploit the fermentative hydrogen generation and direct hydrogen oxidation for the generation of electric current from the degradation of cellulose. Utilizing the metabolic activity of the mesophilic anaerobe Clostridium cellulolyticum and the thermophilic Clostridium thermocellum we show that electricity generation is possible from cellulose fermentation. The current generation is based on an in situ oxidation of microbially synthesized hydrogen at platinum-poly(tetrafluoroaniline) (Pt-PTFA) composite electrodes. Current densities of 130 mA l(-1) (with 3 g cellulose per litre medium) were achieved in poised potential experiments under batch and semi-batch conditions. The presented results show that electricity generation is possible by the in situ oxidation of hydrogen, product of the anaerobic degradation of cellulose by cellulolytic bacteria. For the first time, it is shown that an insoluble complex carbohydrate like cellulose can be used for electricity generation in a microbial fuel cell. The concept represents a first step to the utilization of macromolecular biomass components for microbial electricity generation.

Enhancement of electricity production by graphene oxide in soil microbial fuel cells and plant microbial fuel cells.

PubMed

Goto, Yuko; Yoshida, Naoko; Umeyama, Yuto; Yamada, Takeshi; Tero, Ryugo; Hiraishi, Akira

2015-01-01

The effects of graphene oxide (GO) on electricity generation in soil microbial fuel cells (SMFCs) and plant microbial fuel cell (PMFCs) were investigated. GO at concentrations ranging from 0 to 1.9 g⋅kg(-1) was added to soil and reduced for 10 days under anaerobic incubation. All SMFCs (GO-SMFCs) utilizing the soils incubated with GO produced electricity at a greater rate and in higher quantities than the SMFCs which did not contain GO. In fed-batch operations, the overall average electricity generation in GO-SMFCs containing 1.0 g⋅kg(-1) of GO was 40 ± 19 mW⋅m(-2), which was significantly higher than the value of 6.6 ± 8.9 mW⋅m(-2) generated from GO-free SMFCs (p < 0.05). The increase in catalytic current at the oxidative potential was observed by cyclic voltammetry (CV) for GO-SMFC, with the CV curve suggesting the enhancement of electron transfer from oxidation of organic substances in the soil by the reduced form of GO. The GO-containing PMFC also displayed a greater generation of electricity compared to the PMFC with no added GO, with GO-PMFC producing 49 mW⋅m(-2) of electricity after 27 days of operation. Collectively, this study demonstrates that GO added to soil can be microbially reduced in soil, and facilitates electron transfer to the anode in both SMFCs and PMFCs.

Enhancement of Electricity Production by Graphene Oxide in Soil Microbial Fuel Cells and Plant Microbial Fuel Cells

PubMed Central

Goto, Yuko; Yoshida, Naoko; Umeyama, Yuto; Yamada, Takeshi; Tero, Ryugo; Hiraishi, Akira

2015-01-01

The effects of graphene oxide (GO) on electricity generation in soil microbial fuel cells (SMFCs) and plant microbial fuel cell (PMFCs) were investigated. GO at concentrations ranging from 0 to 1.9 g⋅kg−1 was added to soil and reduced for 10 days under anaerobic incubation. All SMFCs (GO-SMFCs) utilizing the soils incubated with GO produced electricity at a greater rate and in higher quantities than the SMFCs which did not contain GO. In fed-batch operations, the overall average electricity generation in GO-SMFCs containing 1.0 g⋅kg−1 of GO was 40 ± 19 mW⋅m−2, which was significantly higher than the value of 6.6 ± 8.9 mW⋅m−2 generated from GO-free SMFCs (p < 0.05). The increase in catalytic current at the oxidative potential was observed by cyclic voltammetry (CV) for GO-SMFC, with the CV curve suggesting the enhancement of electron transfer from oxidation of organic substances in the soil by the reduced form of GO. The GO-containing PMFC also displayed a greater generation of electricity compared to the PMFC with no added GO, with GO-PMFC producing 49 mW⋅m−2 of electricity after 27 days of operation. Collectively, this study demonstrates that GO added to soil can be microbially reduced in soil, and facilitates electron transfer to the anode in both SMFCs and PMFCs. PMID:25883931

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

PubMed Central

Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

2008-01-01

The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

The configuration of 2,6-diamino-3-hydroxypimelic acid in microbial cell walls

PubMed Central

Perkins, H. R.

1969-01-01

β-Hydroxydiaminopimelic acid, together with some diaminopimelic acid, occurs in the cell-wall mucopeptide of certain Actinomycetales. These components were converted into their di-DNP derivatives and separated by chromatography. Hence the relative proportions present in the cell walls of a number of species were measured. The problem of acid-induced inversion of configuration was studied. Of the diaminohydroxypimelic acids isomer B (see Scheme 2; amino groups meso, hydroxy group threo to its neighbouring amino group) always predominated but a small proportion of isomer D (amino groups l, hydroxy group erythro) also occurred. The configuration of the diaminohydroxypimelic acids was determined by periodate oxidation to glutamic γ-semialdehyde, which underwent spontaneous ring-closure. Reduction with sodium borohydride produced optically active proline, the configuration of which was determined by direct measurement of the optical rotation of DNP-proline. Un-cross-linked diaminohydroxypimelic acid in the cell wall was oxidized with periodate in the presence of ammonia. Since the remaining amino group was bound in peptide linkage, ring-closure was prevented and borohydride reduction of the aldehyde–ammonia presumed to be present resulted in the formation of ornithine. The quantity of ornithine was used as a measure of the degree of cross-linking. PMID:4311441

Geobiology: A Conceptual Framework for Understanding Earth's Surface

NASA Astrophysics Data System (ADS)

Sumner, D. Y.

2016-12-01

A topic of study becomes a new field when it provides a useful conceptual framework for understanding suites of important processes. Geobiology integrates microbial biology with Earth sciences in a way that allows us to ask - and answer - deeper questions about Earth and the life on it. Recent studies of the oxidation of Earth's surface exemplify the impact of Geobiology as a new field. For decades, scientists have understood that Earth's surface was oxidized by photosynthesis. Geochemical records indicate dramatic redox changes both globally, e.g. the loss of MIF sulfur signatures due to formation of an ozone layer, and locally, as preserved in sedimentary rocks. However, these records depend critically on the dynamics of both the global biosphere and local microbial ecology. For example, an increase in global redox due to photosynthetic iron oxidation has different biogeochemical implications than an increase from oxygenic photosynthesis; O2 reacts very differently with organic matter and minerals than iron oxyhydroxides do, influencing microbial ecology as well as potential geochemical signatures in sedimentary rocks. Thus, studies of modern microbial communities provide insights into the interactions among metabolisms and geochemical gradients that have shaped Earth's redox history. For example, the ability of cyanobacteria to create O2 oases in benthic mats and soils on land provides a new framework for evaluating redox-sensitive elemental fluxes to the ocean. Similarly, genomic studies of Cyanobacteria have revealed close relatives, Melainabacteria, that are mostly obligate anaerobes. The evolutionary relationships between these two groups, as preserved in their genomes, reflect important microbial processes that led to oxidation of Earth's surface. By combining insights from microbial biology and sedimentary geochemistry, geobiologists will develop significantly more accurate models of the interactions between life and Earth.

Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

2015-12-01

Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

PubMed

Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

2012-12-01

Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

Biogeochemistry of Fe(II) oxidation in a photosynthetic microbial mat: Implications for Precambrian Fe(II) oxidation

NASA Astrophysics Data System (ADS)

Trouwborst, Robert E.; Johnston, Anne; Koch, Gretchen; Luther, George W.; Pierson, Beverly K.

2007-10-01

We studied the role of microbial photosynthesis in the oxidation of Fe(II) to Fe(III) in a high Fe(II) and high Mn(II) hot spring devoid of sulfide and atmospheric oxygen in the source waters. In situ light and dark microelectrode measurements of Fe(II), Mn(II) and O 2 were made in the microbial mat consisting of cyanobacteria and anoxygenic photosynthetic Chloroflexus sp. We show that Fe(II) oxidation occurred when the mat was exposed to varying intensities of sunlight but not near infrared light. We did not observe any Mn(II) oxidation under any light or dark condition over the pH range 5-7. We observed the impact of oxygenic photosynthesis on Fe(II) oxidation, distinct from the influence of atmospheric O 2 and anoxygenic photosynthesis. In situ Fe(II) oxidation rates in the mats and cell suspensions exposed to light are consistent with abiotic oxidation by O 2. The oxidation of Fe(II) to form primary Fe(III) phases contributed to banded iron-formations (BIFs) during the Precambrian. Both oxygenic photosynthesis, which produces O 2 as an oxidizing waste product, and anoxygenic photosynthesis in which Fe(II) is used to fix CO 2 have been proposed as Fe(II) oxidation mechanisms. Although we do not know the specific mechanisms responsible for all Precambrian Fe(II) oxidation, we assessed the relative importance of both mechanisms in this modern hot spring environment. In this environment, cyanobacterial oxygen production accounted for all the observed Fe(II) oxidation. The rate data indicate that a modest population of cyanobacteria could have mediated sufficient Fe(II) oxidation for some BIFs.

Impact of organic carbon and nutrients mobilized during chemical oxidation on subsequent bioremediation of a diesel-contaminated soil.

PubMed

Sutton, Nora B; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-02-01

Remediation with in situ chemical oxidation (ISCO) impacts soil organic matter (SOM) and the microbial community, with deleterious effects on the latter being a major hurdle to coupling ISCO with in situ bioremediation (ISB). We investigate treatment of a diesel-contaminated soil with Fenton's reagent and modified Fenton's reagent coupled with a subsequent bioremediation phase of 187d, both with and without nutrient amendment. Chemical oxidation mobilized SOM into the liquid phase, producing dissolved organic carbon (DOC) concentrations 8-16 times higher than the untreated field sample. Higher aqueous concentrations of nitrogen and phosphorous species were also observed following oxidation; NH4(+) increased 14-172 times. During the bioremediation phase, dissolved carbon and nutrient species were utilized for microbial growth-yielding DOC concentrations similar to field sample levels within 56d of incubation. In the absence of nutrient amendment, the highest microbial respiration rates were correlated with higher availability of nitrogen and phosphorus species mobilized by oxidation. Significant diesel degradation was only observed following nutrient amendment, implying that nutrients mobilized by chemical oxidation can increase microbial activity but are insufficient for bioremediation. While all bioremediation occurred in the first 28d of incubation in the biotic control microcosm with nutrient amendment, biodegradation continued throughout 187d of incubation following chemical oxidation, suggesting that chemical treatment also affects the desorption of organic contaminants from SOM. Overall, results indicate that biodegradation of DOC, as an alternative substrate to diesel, and biological utilization of mobilized nutrients have implications for the success of coupled ISCO and ISB treatments. Copyright © 2013 Elsevier Ltd. All rights reserved.

Elucidating microbial community adaptation to anaerobic co-digestion of fats, oils, and grease and food waste.

PubMed

Amha, Yamrot M; Sinha, Pooja; Lagman, Jewls; Gregori, Matt; Smith, Adam L

2017-10-15

Despite growing interest in co-digestion and demonstrated process improvements (e.g., enhanced stability and biogas production), few studies have evaluated how co-digestion impacts the anaerobic digestion (AD) microbiome. Three sequential bench-scale respirometry experiments were conducted at thermophilic temperature (50 °C) with various combinations of primary sludge (PS); thickened waste activated sludge (TWAS); fats, oils, and grease (FOG); and food waste (FW). Two additional runs were then performed to evaluate microbial inhibition at higher organic fractions of FOG (30-60% volatile solids loading (VSL; v/v)). Co-digestion of PS, TWAS, FOG, and FW resulted in a 26% increase in methane production relative to digestion of PS and TWAS. A substantial lag time was observed in biogas production for vessels with FOG addition that decreased by more than half in later runs, likely due to adaptation of the microbial community. 30% FOG with 10% FW showed the highest increase in methane production, increasing 53% compared to digestion of PS and TWAS. FOG addition above 50% VSL was found to be inhibitory with and without FW addition and resulted in volatile fatty acid (VFA) accumulation. Methane production was linked with high relative activity and abundance of syntrophic fatty-acid oxidizers alongside hydrogenotrophic methanogens, signaling the importance of interspecies interactions in AD. Specifically, relative activity of Syntrophomonas was significantly correlated with methane production. Further, methane production increased over subsequent runs along with methyl coenzyme M reductase (mcrA) gene expression, a functional gene in methanogens, suggesting temporal adaptation of the microbial community to co-digestion substrate mixtures. The study demonstrated the benefits of co-digestion in terms of performance enhancement and enrichment of key active microbial populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

PubMed Central

Mills, Heath J.; Martinez, Robert J.; Story, Sandra; Sobecky, Patricia A.

2005-01-01

The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate. PMID:15933026

Manganese Driven Carbon Oxidation along Oxic-Anoxic Interfaces in Forest Soils

NASA Astrophysics Data System (ADS)

Jones, M. E.; Keiluweit, M.

2017-12-01

Soils are the largest and most dynamic terrestrial carbon pool, storing a total of 3000 Pg of C - more than the atmosphere and biosphere combined. Because microbial oxidation determines the proportion of carbon that is either stored in the soil or emitted as climate active CO2, its rate directly impacts the global carbon cycle. Recently, a strong correlation between oxidation rates and manganese (Mn) content has been observed in forest soils globally, leading researchers conclude that Mn "is the single main factor governing" the oxidation of plant-derived particulate organic carbon (POC). Many soils are characterized by steep oxygen gradients, forming oxic-anoxic transitions that enable rapid redox cycling of Mn. Oxic-anoxic interfaces have been shown to promote fungal Mn oxidation and the formation of ligand-stabilized Mn(III), which ranks second only to superoxide as the most powerful oxidizing agent in the environment. Here we examined fungal Mn(III) formation along redox gradients in forest soils and their impact on POC oxidation rates. In both field and laboratory settings, oxic-anoxic transition zones showed the greatest Mn(III) concentrations, along with enhanced fungal growth, oxidative potential, production of soluble oxidation products, and CO2 production. Additional electrochemical and X-ray (micro)spectroscopic analyses indicated that oxic-anoxic interfaces represent ideal niches for fungal Mn(III) formation, owing to the ready supply of Mn(II), ligands and O2. Combined, our results suggest that POC oxidation relies on fungal Mn cycling across oxic-anoxic interfaces to produce Mn(III) based oxidants. Because predicted changes in the frequency and timing of precipitation dramatically alter soil moisture regimes in forest soils, understanding the mechanistic link between Mn cycling and carbon oxidation along oxic-anoxic interfaces is becoming increasingly important.

Lack of electricity production by Pelobacter carbinolicus indicates that the capacity for Fe(III) oxide reduction does not necessarily confer electron transfer ability to fuel cell anodes.

PubMed

Richter, Hanno; Lanthier, Martin; Nevin, Kelly P; Lovley, Derek R

2007-08-01

The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize ethanol, suggesting that P. carbinolicus grew in the fuel cell by converting ethanol to hydrogen and acetate, which G. sulfurreducens oxidized with electron transfer to the anode. Up to 83% of the electrons available in ethanol were recovered as electricity and in the metabolic intermediate acetate. Hydrogen consumption by G. sulfurreducens was important for ethanol metabolism by P. carbinolicus. Confocal microscopy and analysis of 16S rRNA genes revealed that half of the cells growing on the anode surface were P. carbinolicus, but there was a nearly equal number of planktonic cells of P. carbinolicus. In contrast, G. sulfurreducens was primarily attached to the anode. P. carbinolicus represents the first Fe(III) oxide-reducing microorganism found to be unable to produce current in a microbial fuel cell, providing the first suggestion that the mechanisms for extracellular electron transfer to Fe(III) oxides and fuel cell anodes may be different.

A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat.

PubMed

Xu, Rong; Wang, QuanQiu; Li, Li

2015-01-01

Dietary intakes of red meat and fat are established risk factors for both colorectal cancer (CRC) and cardiovascular disease (CVDs). Recent studies have shown a mechanistic link between TMAO, an intestinal microbial metabolite of red meat and fat, and risk of CVDs. Data linking TMAO directly to CRC is, however, lacking. Here, we present an unbiased data-driven network-based systems approach to uncover a potential genetic relationship between TMAO and CRC. We constructed two different epigenetic interaction networks (EINs) using chemical-gene, disease-gene and protein-protein interaction data from multiple large-scale data resources. We developed a network-based ranking algorithm to ascertain TMAO-related diseases from EINs. We systematically analyzed disease categories among TMAO-related diseases at different ranking cutoffs. We then determined which genetic pathways were associated with both TMAO and CRC. We show that CVDs and their major risk factors were ranked highly among TMAO-related diseases, confirming the newly discovered mechanistic link between CVDs and TMAO, and thus validating our algorithms. CRC was ranked highly among TMAO-related disease retrieved from both EINs (top 0.02%, #1 out of 4,372 diseases retrieved based on Mendelian genetics and top 10.9% among 882 diseases based on genome-wide association genetics), providing strong supporting evidence for our hypothesis that TMAO is genetically related to CRC. We have also identified putative genetic pathways that may link TMAO to CRC, which warrants further investigation. Through systematic disease enrichment analysis, we also demonstrated that TMAO is related to metabolic syndromes and cancers in general. Our genome-wide analysis demonstrates that systems approaches to studying the epigenetic interactions among diet, microbiome metabolisms, and disease genetics hold promise for understanding disease pathogenesis. Our results show that TMAO is genetically associated with CRC. This study suggests that TMAO may be an important intermediate marker linking dietary meat and fat and gut microbiota metabolism to risk of CRC, underscoring opportunities for the development of new gut microbiome-dependent diagnostic tests and therapeutics for CRC.

Distribution of microbial arsenic reduction, oxidation and extrusion genes along a wide range of environmental arsenic concentrations.

PubMed

Escudero, Lorena V; Casamayor, Emilio O; Chong, Guillermo; Pedrós-Alió, Carles; Demergasso, Cecilia

2013-01-01

The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

PubMed

Delgado-Baquerizo, Manuel; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Singh, Brajesh K; Maestre, Fernando T

2017-10-01

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide. © 2017 John Wiley & Sons Ltd/CNRS.

Simultaneous oxidation of arsenic and antimony at low and circumneutral pH, with and without microbial catalysis

USGS Publications Warehouse

Asta, Maria P.; Nordstrom, D. Kirk; McCleskey, R. Blaine

2012-01-01

Arsenic and Sb are common mine-water pollutants and their toxicity and fate are strongly influenced by redox processes. In this study, simultaneous Fe(II), As(III) and Sb(III) oxidation experiments were conducted to obtain rates under laboratory conditions similar to those found in the field for mine waters of both low and circumneutral pH. Additional experiments were performed under abiotic sterile conditions to determine the biotic and abiotic contributions to the oxidation processes. The results showed that under abiotic conditions in aerated Fe(III)–H2SO4 solutions, Sb(III) oxidizes slightly faster than As(III). The oxidation rates of both elements were accelerated by increasing As(III), Sb(III), Fe(III), and Cl− concentrations in the presence of light. For unfiltered circumneutral water from the Giant Mine (Yellowknife, NWT, Canada), As(III) oxidized at 15–78 μmol/L/h whereas Sb(III) oxidized at 0.03–0.05 μmol/L/h during microbial exponential growth. In contrast, As(III) and Sb(III) oxidation rates of 0.01–0.03 and 0.01–0.02 μmol/L/h, respectively, were obtained in experiments performed with acid unfiltered mine waters from the Iberian Pyritic Belt (SW Spain). These results suggest that the Fe(III) formed from microbial oxidation abiotically oxidized As(III) and Sb(III). After sterile filtration of both mine water samples, neither As(III), Sb(III), nor Fe(II) oxidation was observed. Hence, under the experimental conditions, bacteria were catalyzing As and Sb oxidation in the Giant Mine waters and Fe oxidation in the acid waters of the Iberian Pyrite Belt.

Electron microscopy study of microbial mat in the North Fiji basin hydrothermal vent

NASA Astrophysics Data System (ADS)

Park, H.; Kim, J. W.; Lee, J. W.

2017-12-01

Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that the hydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. In the present study multiline of analytical methods (X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM)) were utilized to investigate the mineralogy/chemistry of microbe-mineral interaction in hydrothermal microbial mat. Microbial mat samples were recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602. XRD analysis showed that red-colored microbial mat contains Fe-oxides and Fe-oxyhydroxides. Various morphologies of minerals in the red-colored microbial mat observed by SEM are mainly showed sheath shaped, resembled with Leptothrix microbial structure, stalks shaped, similar with Marioprofundus microbial structure and globule shaped microbial structures. They are also detected with DNA analysis. The cross sectional observation of microbial structures encrusted with Fe-oxide and Fe-oxyhydroxide at a nano scale by Transmission Electron Microscopy (TEM) and Focused Ion Beam (FIB) technique was developed to verify the structural/biogeochemical properties in the microbe-mineral interaction. Systematic nano-scale measurements on the biomineralization in the microbial mat leads the understandings of biogeochemical environments around the hydrothermal vent.

Microbial Synthesis of the Forskolin Precursor Manoyl Oxide in an Enantiomerically Pure Form.

PubMed

Nielsen, Morten T; Ranberg, Johan Andersen; Christensen, Ulla; Christensen, Hanne Bjerre; Harrison, Scott J; Olsen, Carl Erik; Hamberger, Björn; Møller, Birger Lindberg; Nørholm, Morten H H

2014-12-01

Forskolin is a promising medicinal compound belonging to a plethora of specialized plant metabolites that constitute a rich source of bioactive high-value compounds. A major obstacle for exploitation of plant metabolites is that they often are produced in small amounts and in plants difficult to cultivate. This may result in insufficient and unreliable supply leading to fluctuating and high sales prices. Hence, substantial efforts and resources have been invested in developing sustainable and reliable supply routes based on microbial cell factories. Here, we report microbial synthesis of (13R)-manoyl oxide, a proposed intermediate in the biosynthesis of forskolin and other medically important labdane-type terpenoids. Process optimization enabled synthesis of enantiomerically pure (13R)-manoyl oxide as the sole metabolite, providing a pure compound in just two steps with a yield of 10 mg/liter. The work presented here demonstrates the value of a standardized bioengineering pipeline and the large potential of microbial cell factories as sources for sustainable synthesis of complex biochemicals. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

2012 Gordon Research Conference on Mutagenesis - Formal Schedule and Speaker/Poster Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Demple, Bruce

2012-08-24

The delicate balance among cellular pathways that control mutagenic changes in DNA will be the focus of the 2012 Mutagenesis Gordon Research Conference. Mutagenesis is essential for evolution, while genetic stability maintains cellular functions in all organisms from microbes to metazoans. Different systems handle DNA lesions at various times of the cell cycle and in different places within the nucleus, and inappropriate actions can lead to mutations. While mutation in humans is closely linked to disease, notably cancers, mutational systems can also be beneficial. The conference will highlight topics of beneficial mutagenesis, including full establishment of the immune system, cellmore » survival mechanisms, and evolution and adaptation in microbial systems. Equal prominence will be given to detrimental mutation processes, especially those involved in driving cancer, neurological diseases, premature aging, and other threats to human health. Provisional session titles include Branching Pathways in Mutagenesis; Oxidative Stress and Endogenous DNA Damage; DNA Maintenance Pathways; Recombination, Good and Bad; Problematic DNA Structures; Localized Mutagenesis; Hypermutation in the Microbial World; and Mutation and Disease.« less

High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

PubMed Central

Ling, Alison L.; Robertson, Charles E.; Harris, J. Kirk; Frank, Daniel N.; Kotter, Cassandra V.; Stevens, Mark J.; Pace, Norman R.; Hernandez, Mark T.

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024

High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

PubMed

Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

2015-01-01

Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

PubMed Central

Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J.; Orcutt, Beth N.; Wang, Fengping

2016-01-01

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement. PMID:27199959

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions.

PubMed

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

LABORATORY AND FIELD RESULTS LINKING HIGH BULK CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

Diesel contaminated layer (i.e. 32-45 cm) was the most geoelectrically conductive and showed the peak microbial activity. Below the saturated zone microbial enhanced mineral weathering increases the ionic concentration of pore fluids, leading to increased bulk electrical conducit...

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

USDA-ARS?s Scientific Manuscript database

Exposure to environmental pollutants can alter gut microbial populations. Short-chain fatty acids (SCFAs), produced from gut microbial fermentation of dietary fibers such as inulin, exert numerous effects on host energy metabolism. SCFAs are also linked to health promoting effects, including a red...

EAG Eminent Speaker: Cold war biogeochemistry: Microbes as architects for metal attenuation

NASA Astrophysics Data System (ADS)

Küsel, K.

2012-04-01

Legacy uranium mining in the area of Ronneburg, Germany, has resulted in extensive outflow of highly heavy metal contaminated ground and upcoming mine waters. Mine water flows along a grassland into a small creek and forms iron-rich precipitates yielding rust-colored terraces at the creek bank. These iron oxyhydroxides could have been formed by iron oxidizing bacteria (FeOB) or by chemical oxidation. Precipitates may serve as important biogeochemical interfaces, because heavy metals can adsorb or co-precipitate with Fe(II) or Fe(III) minerals. Thus, microbial Fe(II) oxidation but also the reductive dissolution of iron oxides can be important processes affecting the stability of metal contaminants. Here we present a study on the potential for iron cycling processes and on indigenous bacterial communities in this acidic creek. Oxic and anoxic in vitro sediment incubations revealed iron oxidation and reduction rates of same magnitude, indicating active iron cycling regardless of pH. XRD and TEM comparing the suspended particle load of water samples with fresh creek sediment showed that amorphous particles likely formed first, then aged to become more crystalline iron oxyhydroxides, such as akaganeite and goethite. During this aging process some of the initially smooth, 50-300 nm spherical particles may have formed nano-sized needles, which could potentially provide high reactive surface area for chemical and biological reactions. Surprisingly, total and dissolved metal concentrations in creek water and sediment revealed that elements such as Mn, Si, Ni, or Zn stayed mostly in solution. Only some metals such as Cu, Cr, and U seemed to be particle-associated in the water, likely co-precipitated with or adsorbed onto freshly-precipitating minerals. Pelagic and particle-associated organisms from water as well as fresh sediments were used for 16S rRNA gene cloning and sequencing and showed that members of the Proteobacteria (mainly Betaproteobacteria and Deltaproteobacteria) dominated bacterial communities. The relative fraction of FeOB-related clones was especially high in upcoming underground water and sediment of the adjacent creek site. Up to 80% of clones in sediment microbial 16S rRNA gene clone libraries had ≥97% sequence similarity to reported FeOM or FeRM, demonstrating a strong link to function, even on RNA level. Three novel moderately acidophilic FeOM strains, Thiomonas sp. FB-Cd and FB-6 and Bordetella sp. FB-8, were isolated from pH 6.3 sediment. FB-6 is likely involved in in situ iron oxidation as it has high similarity to a RNA-derived clone from this sediment. Our results demonstrated active microbial iron cycling in heavy metal contaminated creeks, which have important implications for understanding natural attenuation.

Fluidized-bed bioreactor system for the microbial solubilization of coal

DOEpatents

Scott, C.D.; Strandberg, G.W.

1987-09-14

A fluidized-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fluidized-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fluidized-bed bioreactor. 2 figs.

Microbial denitrogenation of fossil fuels.

PubMed

Benedik, M J; Gibbs, P R; Riddle, R R; Willson, R C

1998-09-01

The microbial degradation of nitrogen compounds from fossil fuels is important because of the contribution these contaminants make to the formation of nitrogen oxides (NOx) and hence to air pollution and acid rain. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing process yields. We review the current status of microbial degradation of aromatic nitrogen compounds and discuss the potential of microbial processes to alleviate these problems.

Fluidized-bed bioreactor process for the microbial solubiliztion of coal

DOEpatents

Scott, Charles D.; Strandberg, Gerald W.

1989-01-01

A fluidized-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fluidized-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fluidized-bed bioreactor.

Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stegen, James C.; Konopka, Allan; McKinely, Jim

Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number ofmore » microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.« less

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park.

PubMed

Moran, James J; Whitmore, Laura M; Isern, Nancy G; Romine, Margaret F; Riha, Krystin M; Inskeep, William P; Kreuzer, Helen W

2016-05-01

The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonensis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with (13)C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilated by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moran, James J.; Whitmore, Laura M.; Isern, Nancy G.

The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonesis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with 13C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilatedmore » by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.« less

Anti-oxidant and anti-microbial properties of some ethno-therapeutically important medicinal plants of Indian Himalayan Region.

PubMed

Rawat, Sandeep; Jugran, Arun K; Bahukhandi, Amit; Bahuguna, Asutosh; Bhatt, Indra D; Rawal, Ranbeer S; Dhar, Uppeandra

2016-12-01

Therapeutic potential of medicinal plants as a source of noble natural anti-oxidants and anti-microbial agents has been well recognised all across the globe. In this study, phenolic compounds, in vitro anti-oxidant activity and anti-microbial properties have been investigated in five Himalayan medicinal plants, (e.g., Acorus calamus, Habenaria intermedia, Hedychium spicatum, Roscoea procera and Valeriana jatamansi) in different solvent systems. R. procera exhibited significantly (p < 0.05) higher phenolics; while H. spicatum was rich in flavonoids and V. jatamansi in anti-oxidant activity. Also, R. procera and H. spicatum were found rich in gallic acid; V. jatamansi in catechin, hydroxylbenzoic acid and caffeic acid and H. intermedia in hydroxyl benzoic acid. Solvent systems showed species specific response for extraction of total flavonoids and anti-oxidant activity. All the extracts were found effective against different bacterial and fungal strains in a dose dependent manner and maximum antimicrobial activity was found in R. procera as compared to other species. All the plant extracts showed greater activity against bacterial strains as compared to fungal strains. The results of this study suggest that extract of these species can be used as natural anti-oxidant to reduce free radical mediated disorders and as natural alternative for food preservation.

Effects of Potassium Permanganate Oxidation on Subsurface Microbial Activity

NASA Technical Reports Server (NTRS)

Rowland, Martin A.; Brubaker, Gaylen R.; Westray, Mark; Morris, Damon; Kohler, Keisha; McCool, Alex (Technical Monitor)

2001-01-01

In situ chemical oxidation has the potential for degrading large quantities of organic contaminants and can be more effective and timely than traditional ex situ treatment methods. However, there is a need to better characterize the potential effects of this treatment on natural processes. This study focuses on potential inhibition to anaerobic dechlorination of trichloroethene (TCE) in soils from a large manufacturing facility as a result of in situ oxidation using potassium permanganate (KMn04)Previous microcosm studies established that natural attenuation occurs on-site and that it is enhanced by the addition of ethanol to the system. A potential remediation scheme for the site involves the use of potassium permanganate to reduce levels of TCE in heavily contaminated areas, then to inject ethanol into the system to "neutralize" excess oxidant and enhance microbial degradation. However, it is currently unknown whether the exposure of indigenous microbial populations to potassium permanganate may adversely affect biological reductive dechlorination by these microorganisms. Consequently, additional microcosm studies were conducted to evaluate this remediation scheme and assess the effect of potassium permanganate addition on biological reductive dechlorination of TCE. Samples of subsurface soil and groundwater were collected from a TCE-impacted area of the site. A portion of the soil was pretreated with nutrients and ethanol to stimulate microbial activity, while the remainder of the soil was left unamended. Soil/groundwater microcosms were prepared in sealed vials using the nutrient-amended and unamended soils, and the effects of potassium permanganate addition were evaluated using two permanganate concentrations (0.8 and 2.4 percent) and two contact times (1 and 3 weeks). TCE was then re-added to each microcosm and TCE and dichloroethene (DCE) concentrations were monitored to determine the degree to which microbial dechlorination occurred following chemical oxidation. Evidence of microbial degradation was generally detected within four weeks after TCE addition. Increases in DCE concentrations were consistent with decreases in TCE. The concentration of TCE in the nutrient-amended samples exposed to 2.4% KMnO4 for one week degraded somewhat more slowly than the samples exposed to the 0.8% KMnO4. The rates of degradation did not correlate with the length of KMn04 exposure for the nutrient-amended microcosms. Microbial degradation of TCE in the unamended microcosms was generally similar to that observed in the nutrient-amended microcosms. One treatment condition (unamended, one week exposure, 2.4% KMnO4) was exposed to elevated levels of ethanol and showed little evidence of degradation. It is suspected that the high levels of ethanol were toxic to the microorganisms. The results of the study indicate that exposure of indigenous soil and groundwater microbial populations to KMnO4 at concentrations of 0.8 to 2.4% do not impair the ability of the microbial populations to dechlorinate TCE. Consequently, the combination of chemical oxidation followed by enhanced biological reductive dechlorination appears to be a viable remedial strategy for highly-impacted subsurface areas of the site.

Depth distribution of microbial production and oxidation of methane in northern boreal peatlands.

PubMed

Sundh, I; Nilsson, M; Granberg, G; Svensson, B H

1994-05-01

The depth distributions of anaerobic microbial methane production and potential aerobic microbial methane oxidation were assessed at several sites in both Sphagnum- and sedge-dominated boreal peatlands in Sweden, and compared with net methane emissions from the same sites. Production and oxidation of methane were measured in peat slurries, and emissions were measured with the closed-chamber technique. Over all eleven sites sampled, production was, on average, highest 12 cm below the depth of the average water table. On the other hand, highest potential oxidation of methane coincided with the depth of the average water table. The integrated production rate in the 0-60 cm interval ranged between 0.05 and 1.7 g CH4 m (-2) day(-) and was negatively correlated with the depth of the average water table (linear regression: r (2) = 0.50, P = 0.015). The depth-integrated potential CH4-oxidation rate ranged between 3.0 and 22.1 g CH4 m(-2) day(-1) and was unrelated to the depth of the average water table. A larger fraction of the methane was oxidized at sites with low average water tables; hence, our results show that low net emission rates in these environments are caused not only by lower methane production rates, but also by conditions more favorable for the development of CH4-oxidizing bacteria in these environments.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

PubMed

Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

2018-01-01

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

Mechanisms of Arsenic Mobilization and Attenuation in Subsurface Sediments

NASA Astrophysics Data System (ADS)

O'Day, P. A.; Illera, V.; Root, R.; Choi, S.; Vlassopoulos, D.

2007-12-01

This talk will review molecular mechanisms of As mobilization and attenuation in subsurface sediments using examples from recent field studies that represent a range in oxidation-redox (redox) potential. As a ubiquitous trace element in sediments, As speciation and fate is linked to the abundance and biogeochemical behavior of the generally more abundant redox-active elements Fe, S, and Mn. All four elements are subject to oxidation, reduction, and pH-dependent processes such as sorption, desorption, precipitation, and dissolution, and which may include both biotic and abiotic reaction steps. We have used spectroscopic interrogation and geochemical modeling to characterize As speciation in subsurface sediments in several contrasting environments, including high and low S and Fe settings. Aquifers most at risk for contamination by As include those that are rich in organic matter and nutrients, stimulating high rates of microbial reduction and creating anoxic conditions, but limited in labile or available S and/or Fe that remove As by precipitation or adsorption. In subsurface sediments with low labile S and Fe, laboratory experiments and spectroscopic studies suggest that sediment Mn minerals are important in the oxidation of sorbed As(III) to As(V), but that they have a limited oxidation capacity. Arsenic attenuation and mobilization in the subsurface are affected by seasonal variations when hydraulic conditions are influenced by surface infiltration, which may induce transitions from oxidized to reduced conditions (or vice versa) in porewater.

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

PubMed Central

Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified. PMID:27065954

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

PubMed

Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified.

Microbial degradation of [C14C]polystyrene and 1,3-diphenylbutane.

PubMed

Sielicki, M; Focht, D D; Martin, J P

1978-07-01

Microbial degradation of [beta-14C]polystyrene and 1,3-diphenylbutane, a compound structurally representing the smallest repeating unit of styrene (dimer), was investigated in soil and liquid enrichment cultures. Degradation rates in soil, as determined by 14CO2 evolution from applied [14C]polystyrene, varied from 1.5 to 3.0% for a 4-month period. Although relatively low, these percentages were 15 to 30 times greater than values previously reported. Enrichment cultures, containing 1,3-diphenylbutane as the only carbon souce, were used to determine the mechanisms of microbial oxidation of the polymer chain ends. Metabolism of 1,3-diphenylbutane appeared to involve the attack by a monooxygenease to form 2-phenyl-4-hydroxyphenylbutane followed by a further oxidation and subsequent fission of the benzene ring to yield 4-phenylvaleric acid and an unidentified 5-carbon fragment via the classic meta-fission pathway. Phenylacetic acid was probably formed from 4-phenylvaleric acid by subsequent beta-oxidation of the side chain, methyl-oxidation and decarboxylation. An initial examination of the population of microorganisms in the diphenylbutane enrichment cultures indicated that these oxidative reactions are carried out by common soil microorganism of the genera Bacillus, Pseudomonas, Micrococcus, and Nocardia.

Anaerobic Redox Cycling of Iron by Freshwater Sediment Microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Urrutia, Matilde M.; Churchill, Perry F.

2006-01-01

The potential for microbially-mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. MPN enumerations revealed the presence of significant populations of Fe(III)-reducing (ca. 108 cells mL-1) and Fe(II)-oxidizing, nitrate-reducing organisms (ca. 105 cells mL-1) in the sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (ca. 1 mM) medium with a small quantity (1% vol/vol) of wetland sediment, and resulted in the transient accumulation of NO2- and production of a mixture of end-products including NH4+. Fe(III) oxide (high surface area goethite) reduction took placemore » - after NO3- was depleted and continued until all the acetate was utilized. Addition of NO3 after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of + NO3-to NH4 . No significant NO2- accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by DGGE analysis of PCR amplified 16s rDNA and RT-PCR amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (= 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both + dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3-reduction to NH4 . Our findings suggest that microbially-catalyzed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic anaerobic Fe redox cycle in freshwater sediments.« less

[Thermoacidophilic micirobial community oxidizing the gold-bearing flotation concentrate of a pyrite-arsenopyrite ore].

PubMed

Paniushkina, A E; Tsaplina, I A; Grigor'eva, N V; Kondrat'eva, T F

2014-01-01

An aboriginal community of thermophilic acidophilic chemolithotrophic microorganisms (ACM) was isolated from a sample of pyrite gold-bearing flotation concentrateat 45-47 degrees C and pH 1.8-2.0. Compared to an experimental thermoacidophilic microbial consortium formed in the course of cultivation in parallel bioreactors, it had lower rates of iron leaching and oxidation, while its rate of sulfur oxidation was higher. A new thermophilic acidophilic microbial community was obtained by mutual enrichment with the micioorganisms from thie experimental and aboriginal communities during oxidation of sulfide ore flotation concentrate at 47 degrees C. The dominant bacteria of this new ACM community were Acidithiobacillus caldus strains (the most active sulfur oxidizers) and Sulfobacillus thermotolerans strains (active oxidizers of both iron and sulfur), while iron-oxidizing archaea of the family Ferroplasmaceae and heterotrophic bacteria Alicyclobacillus tolerans were the minor components. The new ACM community showed promise for leaching/oxidation of sulfides from flotation concentrates at high pulp density (S:L = 1:4).

Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

NASA Astrophysics Data System (ADS)

Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

2014-12-01

The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass pool suggests a diversity of processes that should be considered for inclusion in reactive transport models that aim to predict carbon turnover, nutrient flux, and redox reactions in natural and stimulated subsurface systems.

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

NASA Astrophysics Data System (ADS)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

Microbially catalyzed nitrate-dependent metal/radionuclide oxidation in shallow subsurface sediments

NASA Astrophysics Data System (ADS)

Weber, K.; Healy, O.; Spanbauer, T. L.; Snow, D. D.

2011-12-01

Anaerobic, microbially catalyzed nitrate-dependent metal/radionuclide oxidation has been demonstrated in a variety of sediments, soils, and groundwater. To date, studies evaluating U bio-oxidation and mobilization have primarily focused on anthropogenically U contaminated sites. In the Platte River Basin U originating from weathering of uranium-rich igneous rocks in the Rocky Mountains was deposited in shallow alluvial sediments as insoluble reduced uranium minerals. These reduced U minerals are subject to reoxidation by available oxidants, such nitrate, in situ. Soluble uranium (U) from natural sources is a recognized contaminant in public water supplies throughout the state of Nebraska and Colorado. Here we evaluate the potential of anaerobic, nitrate-dependent microbially catalyzed metal/radionuclide oxidation in subsurface sediments near Alda, NE. Subsurface sediments and groundwater (20-64ft.) were collected from a shallow aquifer containing nitrate (from fertilizer) and natural iron and uranium. The reduction potential revealed a reduced environment and was confirmed by the presence of Fe(II) and U(IV) in sediments. Although sediments were reduced, nitrate persisted in the groundwater. Nitrate concentrations decreased, 38 mg/L to 30 mg/L, with increasing concentrations of Fe(II) and U(IV). Dissolved U, primarily as U(VI), increased with depth, 30.3 μg/L to 302 μg/L. Analysis of sequentially extracted U(VI) and U(IV) revealed that virtually all U in sediments existed as U(IV). The presence of U(IV) is consistent with reduced Fe (Fe(II)) and low reduction potential. The increase in aqueous U concentrations with depth suggests active U cycling may occur at this site. Tetravalent U (U(IV)) phases are stable in reduced environments, however the input of an oxidant such as oxygen or nitrate into these systems would result in oxidation. Thus co-occurrence of nitrate suggests that nitrate could be used by bacteria as a U(IV) oxidant. Most probable number enumeration of nitrate-dependent U(IV) oxidizing microorganisms demonstrated an abundant community ranging from 1.61x104 to 2.74x104 cells g-1 sediment. Enrichments initiated verified microbial U reduction and U oxidation coupled to nitrate reduction. Sediment slurries were serially diluted and incubated over a period of eight weeks and compared to uninoculated controls. Oxidation (0-4,554 μg/L) and reduction (0-55 μg/L) of U exceeded uninoculated controls further providing evidence of a U biogeochemical cycling in these subsurface sediments. The oxidation of U(IV) could contribute to U mobilization in the groundwater and result in decreased water quality. Not only could nitrate serve as an oxidant, but Fe(III) could also contribute to U mobilization. Nitrate-dependent Fe(II) oxidation is an environmentally ubiquitous process facilitated by a diversity of microorganisms. Additional research is necessary in order to establish a role of biogenic Fe(III) oxides in U geochemical cycling at this site. These microbially mediated processes could also have a confounding effect on uranium mobility in subsurface environments.

Microbial interference mitigates Meloidogyne incognita mediated oxidative stress and augments bacoside content in Bacopa monnieri L.

PubMed

Gupta, Rupali; Singh, Akanksha; Ajayakumar, P V; Pandey, Rakesh

2017-06-01

Microbial interference plays an imperative role in plant development and response to various stresses. However, its involvement in mitigation of oxidative stress generated by plant parasitic nematode in plants remains elusive. In the present investigation, the efficacy of microbe's viz., Chitiniphilus sp. MTN22 and Streptomyces sp. MTN14 single and in combinations was examined to mitigate oxidative stress generated by M. incognita in medicinal plant, Bacopa monnieri. Microbial combination with and without pathogen also enhanced the growth parameters along with secondary metabolites (bacoside) of B. monnieri than the pathogen inoculated control. The study showed that initially the production of hydrogen peroxide (H 2 O 2 ) was higher in dual microbes infected with pathogen which further declined over M. incognita inoculated control plants. Superoxide dismutase and free radical scavenging activity were also highest in the same treatment which was linearly related with least lipid peroxidation and root gall formation in B. monnieri under the biotic stress. Microscopic visualization of total reactive oxygen species (ROS), H 2 O 2 , superoxide radical and programmed cell death in host plant further extended our knowledge and corroborated well with the above findings. Furthermore, scanning electron microscopy confirmed good microbial colonization on the host root surface around nematode penetration sites in plants treated with dual microbes under pathogenic stress. The findings offer novel insight into the mechanism adopted by the synergistic microbial strains in mitigating oxidative stress and simultaneously stimulating bacoside production under pathogenic stress. Copyright © 2017 Elsevier GmbH. All rights reserved.

Neutrophil-mediated oxidative burst and host defense are controlled by a Vav-PLCγ2 signaling axis in mice

PubMed Central

Graham, Daniel B.; Robertson, Charles M.; Bautista, Jhoanne; Mascarenhas, Francesca; Diacovo, M. Julia; Montgrain, Vivianne; Lam, Siu Kit; Cremasco, Viviana; Dunne, W. Michael; Faccio, Roberta; Coopersmith, Craig M.; Swat, Wojciech

2007-01-01

Oxidative burst, a critical antimicrobial mechanism of neutrophils, involves the rapid generation and release of reactive oxygen intermediates (ROIs) by the NADPH oxidase complex. Genetic mutations in an NADPH oxidase subunit, gp91 (also referred to as NOX2), are associated with chronic granulomatous disease (CGD), which is characterized by recurrent and life-threatening microbial infections. To combat such infections, ROIs are produced by neutrophils after stimulation by integrin-dependent adhesion to the ECM in conjunction with stimulation from inflammatory mediators, or microbial components containing pathogen-associated molecular patterns. In this report, we provide genetic evidence that both the Vav family of Rho GTPase guanine nucleotide exchange factors (GEFs) and phospholipase C–γ2 (PLC-γ2) are critical mediators of adhesion-dependent ROI production by neutrophils in mice. We also demonstrated that Vav was critically required for neutrophil-dependent host defense against systemic infection by Staphylococcus aureus and Pseudomonas aeruginosa, 2 common pathogens associated with fatal cases of hospital-acquired pneumonia. We identified a molecular pathway in which Vav GEFs linked integrin-mediated signaling with PLC-γ2 activation, release of intracellular Ca2+ cations, and generation of diacylglycerol to control assembly of the NADPH oxidase complex and ROI production by neutrophils. Taken together, our data indicate that integrin-dependent signals generated during neutrophil adhesion contribute to the activation of NADPH oxidase by a variety of distinct effector pathways, all of which require Vav. PMID:17932569

Evidence of Sulfate-Dependent Anaerobic Methane Oxidation within an Area Impacted by Coalbed Methane-Related Gas Migration

NASA Astrophysics Data System (ADS)

Wolfe, A. L.; Wikin, R. T.

2017-12-01

We evaluated water quality characteristics in the northern Raton Basin of Colorado and documented the response of the Poison Canyon aquifer system several years after upward migration of methane gas occurred from the deeper Vermejo Formation coalbed production zone. Over a 17-month study period, water samples were obtained from domestic water wells and monitoring wells located within the impacted area, and analyzed for 245 constituents, including organic compounds, nutrients, major and trace elements, dissolved gases, and isotopic tracers for carbon, sulfur, oxygen, and hydrogen. Multiple lines of evidence suggest that sulfate-dependent methane biodegradation, which involves the oxidation of methane (CH4) to carbon dioxide (CO2) using sulfate (SO42-) as the terminal electron acceptor, is occurring: (i) consumption of methane and sulfate and production of sulfide and bicarbonate, (ii) methane loss coupled to production of higher molecular weight (C2+) gaseous hydrocarbons, (iii) patterns of 13C enrichment and depletion in methane and dissolved inorganic carbon, and (iv) a systematic shift in sulfur and oxygen isotope ratios of sulfate, indicative of microbial sulfate reduction. Groundwater-methane attenuation is linked to the production of dissolved sulfide, and elevated dissolved sulfide concentrations represent an undesirable secondary water quality impact. The biogeochemical response of the aquifer system has not mobilized naturally occurring trace metals, including arsenic, chromium, cobalt, nickel, and lead, likely due to the microbial production of hydrogen sulfide, which favors stabilization of metals in aquifer solids.

Graphite oxide incorporated crosslinked polyvinyl alcohol and sulfonated styrene nanocomposite membrane as separating barrier in single chambered microbial fuel cell

NASA Astrophysics Data System (ADS)

Rudra, Ruchira; Kumar, Vikash; Pramanik, Nilkamal; Kundu, Patit Paban

2017-02-01

Different membranes with varied molar concentrations of graphite oxide (GO), 'in situ' polymerized sulfonated polystyrene (SS) and glutaraldehyde (GA) cross linked polyvinyl alcohol (PVA), have been analyzed as an effective and low cost nanocomposite barrier in single chambered microbial fuel cells (MFCs). The synthesized composite membranes, namely GO0.2, GO0.4 and GO0.6 exhibited comparatively better results with reduced water uptake (WU) and swelling ratios (SR) over the native PVA. The variation in properties is illustrated with membrane analyses, where GO0.4 showed an increased proton conductivity (PC) and ion exchange capacity (IEC) of 0.128 S cm-1 and 0.33 meq g-1 amongst all of the used membranes. In comparison, reduced oxygen diffusivity with lower water uptake showed a two-fold decrease in GO0.4 over pure PVA membrane (∼2.09 × 10-4 cm s-1). A maximum power density of 193.6 mW m-2 (773.33 mW m-3) with a current density of 803.33 mA m-2 were observed with GO0.4 fitted MFC, where ∼81.89% of chemical oxygen demand (COD) was removed using mixed firmicutes, as biocatalyst, in 25 days operation. In effect, the efficacy of GO incorporated crosslinked PVA and SS nanocomposite membrane has been evaluated as a polymer electrolyte membrane for harnessing bio-energy from single chambered MFCs.

Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania.

PubMed

Alain, Karine; Holler, Thomas; Musat, Florin; Elvert, Marcus; Treude, Tina; Krüger, Martin

2006-04-01

Paclele Mici is a terrestrial mud volcano field located in the Carpathian Mountains (Romania), where thermal alteration of sedimentary organic compounds leads to methane, higher hydrocarbons and other petroleum compounds that are continuously released into the environment. The hydrocarbons represent potential substrates for microorganisms. We studied lipid biomarkers, stable isotope ratios, the effect of substrate (methane, other organic compounds) addition and 16S rRNA genes to gain insights into the hitherto unknown microbial community at this site. Quantitative real-time polymerase chain reaction analysis demonstrated that bacteria were much more abundant than archaea. Phylogenetic analyses of 16S rDNA clone sequences indicated the presence of bacterial and archaeal lineages generally associated with the methane cycle (methanogens, aerobic and anaerobic methanotrophs), the sulfur cycle (sulfate reducers), and groups linked to the anaerobic degradation of alkanes or aromatic hydrocarbons. The presence of sulfate reducers, methanogens and methanotrophs in this habitat was also confirmed by concurrent surveys of lipid biomarkers and their isotopic signatures. Incubation experiments with several common and complex substrates revealed the potential of the indigenous microbial community for sulfate reduction, methanogenesis and aerobic methanotrophy. Additionally, consistently to the detection of methane-oxidizing archaea (ANME) and 13C-depleted archaeal lipids, a weak but significant activity of anaerobic methane oxidation was measured by radiotracer techniques and in vitro. This survey is the first to report the presence and activity of ANME in a terrestrial environment.

Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

PubMed Central

Headd, Brendan; Engel, Annette S.

2014-01-01

Terrestrial sulfidic springs support diverse microbial communities by serving as stable conduits for geochemically diverse and nutrient-rich subsurface waters. Microorganisms that colonize terrestrial springs likely originate from groundwater, but may also be sourced from the surface. As such, the biogeographic distribution of microbial communities inhabiting sulfidic springs should be controlled by a combination of spring geochemistry and surface and subsurface transport mechanisms, and not necessarily geographic proximity to other springs. We examined the bacterial diversity of seven springs to test the hypothesis that occurrence of taxonomically similar microbes, important to the sulfur cycle, at each spring is controlled by geochemistry. Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. Among the putative sulfide-oxidizing groups (Epsilonproteobacteria and Gammaproteobacteria), up to 83% of the sequences from geochemically similar springs clustered together. Abundant populations of Hydrogenimonas-like or Sulfurovum-like spp. (Epsilonproteobacteria) occurred with abundant Thiothrix and Thiofaba spp. (Gammaproteobacteria), but Arcobacter-like and Sulfurimonas spp. (Epsilonproteobacteria) occurred with less abundant gammaproteobacterial populations. These distribution patterns confirmed that geochemistry rather than biogeography regulates bacterial dominance at each spring. Potential biogeographic controls were related to paleogeologic sedimentation patterns that could control long-term microbial transport mechanisms that link surface and subsurface environments. Knowing the composition of a core sulfidic spring microbial community could provide a way to monitor diversity changes if a system is threatened by anthropogenic processes or climate change. PMID:25250021

Interactions between ammonia and nitrite oxidizing bacteria in co-cultures: Is there evidence for mutualism, commensalism, or competition?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayavedra-Soto, Luis; Arp, Daniel

Nitrification is a two-step environmental microbial process in the nitrogen cycle in which ammonia is oxidized to nitrate. Ammonia-oxidizing bacteria and archaea oxidize ammonia to nitrite and nitrite is oxidized to nitrate by nitrite-oxidizing bacteria. These microorganisms, which likely act in concert in a microbial community, play critical roles in the movement of inorganic N in soils, sediments and waters and are essential to the balance of the nitrogen cycle. Anthropogenic activity has altered the balance of the nitrogen cycle through agriculture practices and organic waste byproducts. Through their influence on available N for plant growth, nitrifying microorganisms influence plantmore » productivity for food and fiber production and the associated carbon sequestration. N Fertilizer production, primarily as ammonia, requires large inputs of natural gas and hydrogen. In croplands fertilized with ammonia-based fertilizers, nitrifiers contribute to the mobilization of this N by producing nitrate (NO3-), wasting the energy used in the production and application of ammonia-based fertilizer. The resulting nitrate is readily leached from these soils, oxidized to gaseous N oxides (greenhouse gases), and denitrified to N2 (which is no longer available as a plant N source). Still, ammonia oxidizers are beneficial in the treatment of wastewater and they also show potential to contribute to microbial bioremediation strategies for clean up of environments contaminated with chlorinated hydrocarbons. Mitigation of the negative effects and exploitation of the beneficial effects of nitrifiers will be facilitated by a systems-level understanding of the interactions of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria with the environment and with each other.« less

Influence of Oxygen and Nitrate on Fe (Hydr)oxide Mineral Transformation and Soil Microbial Communities during Redox Cycling.

PubMed

Mejia, Jacqueline; Roden, Eric E; Ginder-Vogel, Matthew

2016-04-05

Oscillations between reducing and oxidizing conditions are observed at the interface of anaerobic/oxic and anaerobic/anoxic environments, and are often stimulated by an alternating flux of electron donors (e.g., organic carbon) and electron acceptors (e.g., O2 and NO3(-)). In iron (Fe) rich soils and sediments, these oscillations may stimulate the growth of both Fe-reducing bacteria (FeRB) and Fe-oxidizing bacteria (FeOB), and their metabolism may induce cycling between Fe(II) and Fe(III), promoting the transformation of Fe (hydr)oxide minerals. Here, we examine the mineralogical evolution of lepidocrocite and ferrihydrite, and the adaptation of a natural microbial community to alternating Fe-reducing (anaerobic with addition of glucose) and Fe-oxidizing (with addition of nitrate or air) conditions. The growth of FeRB (e.g., Geobacter) is stimulated under anaerobic conditions in the presence of glucose. However, the abundance of these organisms depends on the availability of Fe(III) (hydr)oxides. Redox cycling with nitrate results in decreased Fe(II) oxidation thereby decreasing the availability of Fe(III) for FeRB. Additionally, magnetite is detected as the main product of both lepidocrocite and ferrihydrite reduction. In contrast, introduction of air results in increased Fe(II) oxidation, increasing the availability of Fe(III) and the abundance of Geobacter. In the lepidocrocite reactors, Fe(II) oxidation by dissolved O2 promotes the formation of ferrihydrite and lepidocrocite, whereas in the ferrihydrite reactors we observe a decrease in magnetite stoichiometry (e.g., oxidation). Understanding Fe (hydr)oxide transformation under environmentally relevant redox cycling conditions provides insight into nutrient availability and transport, contaminant mobility, and microbial metabolism in soils and sediments.

Mechanisms of Mineral Substrate Acquisition in a Thermoacidophile.

PubMed

Amenabar, Maximiliano J; Boyd, Eric S

2018-06-15

The thermoacidophile Acidianus is widely distributed in Yellowstone National Park hot springs that span large gradients in pH (1.60 to 4.84), temperature (42 to 90°C), and mineralogical composition. To characterize the potential role of flexibility in mineral-dependent energy metabolism in contributing to the widespread ecological distribution of this organism, we characterized the spectrum of minerals capable of supporting metabolism and the mechanisms that it uses to access these minerals. The energy metabolism of Acidianus strain DS80 was supported by elemental sulfur (S 0 ), a variety of iron (hydr)oxides, and arsenic sulfide. Strain DS80 reduced, oxidized, and disproportionated S 0 Cells growing via S 0 reduction and disproportionation did not require direct access to the mineral to reduce it, whereas cells growing via S 0 oxidation did require direct access, observations that are attributable to the role of H 2 S produced by S 0 reduction/disproportionation in solubilizing and increasing the bioavailability of S 0 Cells growing via iron (hydr)oxide reduction did not require access to the mineral, suggesting that the cells reduce Fe(III) that is being leached by the acidic growth medium. Cells growing via oxidation of arsenic sulfide with Fe(III) did not require access to the mineral to grow. The stoichiometry of reactants to products indicates that cells oxidize soluble As(III) released from oxidation of arsenic sulfide by aqueous Fe(III). Taken together, these observations underscore the importance of feedbacks between abiotic and biotic reactions in influencing the bioavailability of mineral substrates and defining ecological niches capable of supporting microbial metabolism. IMPORTANCE Mineral sources of electron donor and acceptor that support microbial metabolism are abundant in the natural environment. However, the spectrum of minerals capable of supporting a given microbial strain and the mechanisms that are used to access these minerals in support of microbial energy metabolism are often unknown, in particular among thermoacidophiles. Here, we show that the thermoacidophile Acidianus strain DS80 is adapted to use a variety of iron (hydro)oxide minerals, elemental sulfur, and arsenic sulfide to support growth. Cells rely on a complex interplay of abiologically and biologically catalyzed reactions that increase the solubility or bioavailability of minerals, thereby enabling their use in microbial metabolism. Copyright © 2018 American Society for Microbiology.

Fixed-bed bioreactor system for the microbial solubilization of coal

DOEpatents

Scott, C.D.; Strandberg, G.W.

1987-09-14

A fixed-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fixed-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the large scale production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fixed-bed bioreactor. 1 fig., 1 tab.

Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes.

PubMed

Dick, Gregory J; Lee, Yifan E; Tebo, Bradley M

2006-05-01

Microbial oxidation and precipitation of manganese at deep-sea hydrothermal vents are important oceanic biogeochemical processes, yet nothing is known about the types of microorganisms or mechanisms involved. Here we report isolation of a number of diverse spore-forming Mn(II)-oxidizing Bacillus species from Guaymas Basin, a deep-sea hydrothermal vent environment in the Gulf of California, where rapid microbially mediated Mn(II) oxidation was previously observed. mnxG multicopper oxidase genes involved in Mn(II) oxidation were amplified from all Mn(II)-oxidizing Bacillus spores isolated, suggesting that a copper-mediated mechanism of Mn(II) oxidation could be important at deep-sea hydrothermal vents. Phylogenetic analysis of 16S rRNA and mnxG genes revealed that while many of the deep-sea Mn(II)-oxidizing Bacillus species are very closely related to previously recognized isolates from coastal sediments, other organisms represent novel strains and clusters. The growth and Mn(II) oxidation properties of these Bacillus species suggest that in hydrothermal sediments they are likely present as spores that are active in oxidizing Mn(II) as it emerges from the seafloor.

Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments

PubMed Central

2013-01-01

This study introduces a newly isolated, genetically tractable bacterium (Pseudogulbenkiania sp. strain MAI-1) and explores the extent to which its nitrate-dependent iron-oxidation activity is directly biologically catalyzed. Specifically, we focused on the role of iron chelating ligands in promoting chemical oxidation of Fe(II) by nitrite under anoxic conditions. Strong organic ligands such as nitrilotriacetate and citrate can substantially enhance chemical oxidation of Fe(II) by nitrite at circumneutral pH. We show that strain MAI-1 exhibits unambiguous biological Fe(II) oxidation despite a significant contribution (∼30–35%) from ligand-enhanced chemical oxidation. Our work with the model denitrifying strain Paracoccus denitrificans further shows that ligand-enhanced chemical oxidation of Fe(II) by microbially produced nitrite can be an important general side effect of biological denitrification. Our assessment of reaction rates derived from literature reports of anaerobic Fe(II) oxidation, both chemical and biological, highlights the potential competition and likely co-occurrence of chemical Fe(II) oxidation (mediated by microbial production of nitrite) and truly biological Fe(II) oxidation. PMID:23402562

Chromite oxidation by manganese oxides in subseafloor basalts and the presence of putative fossilized microorganisms.

PubMed

Ivarsson, Magnus; Broman, Curt; Holm, Nils G

2011-06-03

Chromite is a mineral with low solubility and is thus resistant to dissolution. The exception is when manganese oxides are available, since they are the only known naturally occurring oxidants for chromite. In the presence of Mn(IV) oxides, Cr(III) will oxidise to Cr(VI), which is more soluble than Cr(III), and thus easier to be removed. Here we report of chromite phenocrysts that are replaced by rhodochrosite (Mn(II) carbonate) in subseafloor basalts from the Koko Seamount, Pacific Ocean, that were drilled and collected during the Ocean Drilling Program (ODP) Leg 197. The mineral succession chromite-rhodochrosite-saponite in the phenocrysts is interpreted as the result of chromite oxidation by manganese oxides. Putative fossilized microorganisms are abundant in the rhodochrosite and we suggest that the oxidation of chromite has been mediated by microbial activity. It has previously been shown in soils and in laboratory experiments that chromium oxidation is indirectly mediated by microbial formation of manganese oxides. Here we suggest a similar process in subseafloor basalts.

Chromite oxidation by manganese oxides in subseafloor basalts and the presence of putative fossilized microorganisms

PubMed Central

2011-01-01

Chromite is a mineral with low solubility and is thus resistant to dissolution. The exception is when manganese oxides are available, since they are the only known naturally occurring oxidants for chromite. In the presence of Mn(IV) oxides, Cr(III) will oxidise to Cr(VI), which is more soluble than Cr(III), and thus easier to be removed. Here we report of chromite phenocrysts that are replaced by rhodochrosite (Mn(II) carbonate) in subseafloor basalts from the Koko Seamount, Pacific Ocean, that were drilled and collected during the Ocean Drilling Program (ODP) Leg 197. The mineral succession chromite-rhodochrosite-saponite in the phenocrysts is interpreted as the result of chromite oxidation by manganese oxides. Putative fossilized microorganisms are abundant in the rhodochrosite and we suggest that the oxidation of chromite has been mediated by microbial activity. It has previously been shown in soils and in laboratory experiments that chromium oxidation is indirectly mediated by microbial formation of manganese oxides. Here we suggest a similar process in subseafloor basalts. PMID:21639896

An investigation of anaerobic methane oxidation by consortia of methanotrophic archaea and bacterial partners using nanoSIMS and process-based modeling

NASA Astrophysics Data System (ADS)

Shi, Y.; Kempes, C.; Chadwick, G.; McGlynn, S.; He, X.; Orphan, V. J.; Meile, C. D.

2016-02-01

The anaerobic oxidation of methane in marine sediments plays an important role in the global methane cycle. Mediated by a microbial consortium consisting of archaea and bacteria, it is estimated that almost 80% of all the methane that arises from marine sediments is oxidized anaerobically by this process (Reeburgh 2007, Chemical Reviews 107, 486-513). We used reactive transport modeling to compare and contrast potential mechanisms of methane oxidation. This included acetate, hydrogen, formate, and disulfide acting as intermediates that are exchanged between archaea and bacteria. Moreover, we investigated electron transport through nanowires, facilitating the electron exchange between the microbial partners. It was shown that reaction kinetics, transport intensities, and energetic considerations all could decisively impact the overall rate of methane consumption. Informed by observed microbial cell distribution, we applied the model to a range of spatial distribution patterns of archaea and bacteria. We found that a consortium with evenly distributed archaeal and bacterial cells has the potential to more efficiently oxidize methane, because the vicinity of bacteria and archaea counteracts the build up of products and therefore prevents the thermodynamic shutdown of microbial metabolism. Single cell stable isotope enrichment in archaeal-bacterial consortia observed by nanoSIMS revealed rather uniform levels of anabolic activity within consortia with different spatial distribution patterns. Comparison to model simulation illustrates that efficient exchange is necessary to reproduce such observations and prevent conditions that are energetically unfavorable for methane oxidation to take place. Model simulations indicate that a recently described mechanism of direct interspecies electron transport between the methanotrophic archaea and its bacterial partner through a conductive matrix (McGlynn et al. 2015, Nature, 10.1038/nature15512) is consistent with observations.

Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

PubMed Central

Scott, Jarrod J.; Benes, Joshua; Bowden, William B.

2015-01-01

The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long −149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. PMID:26386054

Lipid biomarker and microbial community of 49.6°E hydrothermal field at Southwest Indian Ocean Ridge

NASA Astrophysics Data System (ADS)

Lei, J.; Chu, F.; Yu, X.; Li, X.; Tao, C.

2012-12-01

In 2007, Chinese Research Cruises Discovered the First Active Hydrothermal Vent Field at the Ultraslow Spreading Southwest Indian Ridge. This study intent to get composition, evolution and origin information of lipid compounds in SWIR, and recognize the style of lipid biomarkers which have obviously indicative significance for community structure.Soluble organic matter were extracted from geological samples (including chimney sulfide, oxide, around hydrothermal vents) in Southwest Indian Ridge (SWIR), and divided into hydrocarbon, fatty acid component by column chromatography. GC, GC-MS, HPLC-MS were applied for composition and abundance analysis. Lipid in hydrothermal sulfide contains obvious isoprenoidal hydrocarbon biomarkers (Sq, IS40) and GDGTs (m/z=653) that associated with methanogenic archaea which belongs to Euryarchaeota, and iso /anti-iso fatty acid (iC15:0, aiC15:0, iC17:0, aiC17:0)which may originated from sulfate reducing bacteria (SRB).Lipids extracted from hydrothermal oxide lack isoprenoidal hydrocarbon, and Ph/C18 (0.57) is much lower than sulfide (1.22). Fatty acid compound of oxide include abundant saturated fatty (C16:0, C18:0) acid and mono-unsaturated fatty acids (C16:1n7, C18:1n7), but much less iso/anti-iso was detected. Lipid composition of hydrothermal oxide showed that archaea activity was seldom in hydrothermal oxide, and sulfur-oxidizing bacteria was the main microbial community.Study of Jaeschke (2010) showed that high temperature hydrothermal venting encompassed different microbial community from low temperature hydrothermal venting. Our study showed that in different stage of hydrothermal, microbial community structure may be distinct.

Secretome-based Manganese(II) Oxidation by Filamentous Ascomycete Fungi

NASA Astrophysics Data System (ADS)

Zeiner, C. A.; Purvine, S.; Zink, E.; Paša-Tolić, L.; Chaput, D.; Wu, S.; Santelli, C. M.; Hansel, C. M.

2017-12-01

Manganese (Mn) oxides are among the strongest oxidants in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and Mn peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Through a combination of chemical and in-gel assays, bulk mass spectrometry, and iTRAQ proteomics, we demonstrate enzymatic Mn(II) oxidation in the secretomes of three phylogenetically diverse Ascomycetes that were isolated from Mn-laden sediments. Candidate Mn(II)-oxidizing enzymes were species-specific and included bilirubin oxidase and tyrosinase in Stagonospora sp. SRC1lsM3a, GMC oxidoreductase in Paraconiothyrium sporulosum AP3s5-JAC2a, and FAD-binding oxidoreductases in Pyrenochaeta sp. DS3sAY3a. These findings were supported by full proteomic characterization of the secretomes, which revealed a lack of Mn, lignin, and versatile peroxidases in these Ascomycetes but a substantially higher proportion of LMCOs and GMC oxidoreductases compared to wood-rot Basidiomycetes. We also identified the potential for indirect enzymatic Mn(II) oxidation by hydroxyl radical, as the secretomes were rich in diverse lignocellulose-degrading enzymes that could participate in Fenton chemistry. A link between Mn(II) oxidation and carbon oxidation analogous to white-rot Basidiomycetes remains unknown in these Ascomycetes. Interestingly, growth rates on rich medium were unaffected by the presence of Mn(II), and the production of Mn(II)-oxidizing proteins in the secretome was constitutive and not inducible by Mn(II). Thus, no physiological benefit of Mn(II) oxidation in these Ascomycetes has yet been identified, and Mn(II) oxidation appears to be a side reaction. Future work will explore the lignin-degrading capacity of these fungi and any associated role of Mn(II) oxidation.

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

PubMed Central

Hagen, Live H.; Frank, Jeremy A.; Zamanzadeh, Mirzaman; Eijsink, Vincent G. H.; Pope, Phillip B.; Arntzen, Magnus Ø.

2016-01-01

ABSTRACT In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH3-N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum “Atribacteria.” These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. IMPORTANCE Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane. PMID:27815274

HORSE SPECIES SYMPOSIUM: Canine intestinal microbiology and metagenomics: From phylogeny to function.

PubMed

Guard, B C; Suchodolski, J S

2016-06-01

Recent molecular studies have revealed a complex microbiota in the dog intestine. Convincing evidence has been reported linking changes in microbial communities to acute and chronic gastrointestinal inflammation, especially in canine inflammatory bowel disease (IBD). The most common microbial changes observed in intestinal inflammation are decreases in the bacterial phyla Firmicutes (i.e., Lachnospiraceae, Ruminococcaceae, and ) and Bacteroidetes, with concurrent increases in Proteobacteria (i.e., ). Due to the important role of microbial-derived metabolites for host health, it is important to elucidate the metabolic consequences of gastrointestinal dysbiosis and physiological pathways implicated in specific disease phenotypes. Metagenomic studies have used shotgun sequencing of DNA as well as phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) to characterize functional changes in the bacterial metagenome in gastrointestinal disease. Furthermore, wide-scale and untargeted measurements of metabolic products derived by the host and the microbiota in intestinal samples allow a better understanding of the functional alterations that occur in gastrointestinal disease. For example, changes in bile acid metabolism and tryptophan catabolism recently have been reported in humans and dogs. Also, metabolites associated with the pentose phosphate pathway were significantly altered in chronic gastrointestinal inflammation and indicate the presence of oxidative stress in dogs with IBD. This review focuses on the advancements made in canine metagenomics and metabolomics and their implications in understanding gastrointestinal disease as well as the development of better treatment approaches.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Responses of soil ammonia-oxidizing microorganisms to repeated exposure of single-walled and multi-walled carbon nanotubes.

PubMed

Chen, Qinglin; Wang, Hui; Yang, Baoshan; He, Fei; Han, Xuemei; Song, Ziheng

2015-02-01

The impacts of carbon nanotubes (CNTs) including single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs) on soil microbial biomass and microbial community composition (especially on ammonium oxidizing microorganisms) have been evaluated. The first exposure of CNTs lowered the microbial biomass immediately, but the values recovered to the level of the control at the end of the experiment despite the repeated addition of CNTs. The abundance and diversity of ammonium-oxidizing archaea (AOA) were higher than that of ammonium-oxidizing bacteria (AOB) under the exposure of CNTs. The addition of CNTs decreased Shannon-Wiener diversity index of AOB and AOA. Two-way ANOVA analysis showed that CNTs had significant effects on the abundance and diversity of AOB and AOA. Dominant terminal restriction fragments (TRFs) of AOB exhibited a positive relationship with NH4(+), while AOA was on the contrary. It implied that AOB prefer for high-NH4(+) soils whereas AOA is favored in low NH4(+) soils in the CNT-contaminated soil. Copyright © 2014 Elsevier B.V. All rights reserved.

Mercury mobilization and speciation linked to bacterial iron oxide and sulfate reduction: A column study to mimic reactive transfer in an anoxic aquifer.

PubMed

Hellal, Jennifer; Guédron, Stéphane; Huguet, Lucie; Schäfer, Jörg; Laperche, Valérie; Joulian, Catherine; Lanceleur, Laurent; Burnol, André; Ghestem, Jean-Philippe; Garrido, Francis; Battaglia-Brunet, Fabienne

2015-09-01

Mercury (Hg) mobility and speciation in subsurface aquifers is directly linked to its surrounding geochemical and microbial environment. The role of bacteria on Hg speciation (i.e., methylation, demethylation and reduction) is well documented, however little data is available on their impact on Hg mobility. The aim of this study was to test if (i) Hg mobility is due to either direct iron oxide reduction by iron reducing bacteria (IRB) or indirect iron reduction by sulfide produced by sulfate reducing bacteria (SRB), and (ii) to investigate its subsequent fate and speciation. Experiments were carried out in an original column setup combining geochemical and microbiological approaches that mimic an aquifer including an interface of iron-rich and iron depleted zones. Two identical glass columns containing iron oxides spiked with Hg(II) were submitted to (i) direct iron reduction by IRB and (ii) to indirect iron reduction by sulfides produced by SRB. Results show that in both columns Hg was leached and methylated during the height of bacterial activity. In the column where IRB are dominant, Hg methylation and leaching from the column was directly correlated to bacterial iron reduction (i.e., Fe(II) release). In opposition, when SRB are dominant, produced sulfide induced indirect iron oxide reduction and rapid adsorption of leached Hg (or produced methylmercury) on neoformed iron sulfides (e.g., Mackinawite) or its precipitation as HgS. At the end of the SRB column experiment, when iron-oxide reduction was complete, filtered Hg and Fe concentrations increased at the outlet suggesting a leaching of Hg bound to FeS colloids that may be a dominant mechanism of Hg transport in aquifer environments. These experimental results highlight different biogeochemical mechanisms that can occur in stratified sub-surface aquifers where bacterial activities play a major role on Hg mobility and changes in speciation. Copyright © 2015 Elsevier B.V. All rights reserved.

Theagalloflavic Acid, a New Pigment Derived from Hexahydroxydiphenoyl Group, and Lignan Oxidation Products Produced by Aerobic Microbial Fermentation of Green Tea.

PubMed

Matsuo, Yosuke; Matsuda, Tomoko; Sugihara, Keisuke; Saito, Yoshinori; Zhang, Ying-Jun; Yang, Chong-Ren; Tanaka, Takashi

2016-01-01

Chinese ripe pu-erh tea is produced by aerobic microbial fermentation of green tea. To clarify the microbial degradation of tea polyphenols, Japanese commercial green tea was mixed with Chinese ripe pu-erh tea, which retains microorganisms, and fermented for 5 d. Chromatographic separation yielded a novel water-soluble yellow pigment termed theagalloflavic acid. Spectroscopic and chemical evidence suggested that this pigment was produced by oxidative ring cleavage of hexahydroxydiphenoyl esters. In addition, two new oxygenated lignin metabolites, (+)-5,5'-dihydroxypinoresinol and 5-hydroxydihydrodehydrodiconiferyl alcohol, were also isolated together with known degradation products of quercetin and tea catechins.

Microbial fuel cell treatment of fuel process wastewater

DOEpatents

Borole, Abhijeet P; Tsouris, Constantino

2013-12-03

The present invention is directed to a method for cleansing fuel processing effluent containing carbonaceous compounds and inorganic salts, the method comprising contacting the fuel processing effluent with an anode of a microbial fuel ell, the anode containing microbes thereon which oxidatively degrade one or more of the carbonaceous compounds while producing electrical energy from the oxidative degradation, and directing the produced electrical energy to drive an electrosorption mechanism that operates to reduce the concentration of one or more inorganic salts in the fuel processing effluent, wherein the anode is in electrical communication with a cathode of the microbial fuel cell. The invention is also directed to an apparatus for practicing the method.

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa.

PubMed

Muratova, Anna; Dubrovskaya, Ekaterina; Golubev, Sergey; Grinev, Vyacheslav; Chernyshova, Marina; Turkovskaya, Olga

2015-09-01

We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere. Copyright © 2015 Elsevier GmbH. All rights reserved.

Metabolite recycling and bidirectional C fluxes: Revolutionizing our view on microbial C cycling in soils

NASA Astrophysics Data System (ADS)

Dippold, M. A.; Apostel, C.; Kuzyakov, Y.

2016-12-01

Biogeochemists' view on microbial C transformation in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the anabolism. However, life in a C limited environment as challenging as soil requires microbial adaptation strategies at all levels of metabolism. By coupling of position-specific labeling of core metabolites with compound-specific isotope analysis we demonstrated that catabolic oxidation of these metabolites exists in parallel to reductive, energy consuming pathways, reducing them for anabolic purposes. Up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in the citric acid cycle. Furthermore, position-specific labeling of rather `cost-intensive' biomass compounds such as fatty acids revealed that intact recycling of metabolites is a crucial microbial adaptation to C scarcity in soils. Both processes are unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. To understand how microorganisms catalyze the biogeochemical fluxes in soil, a profound understanding of their metabolic adaptation strategies such as recycling or switching between bidirectional fluxes is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

Short-chain alkane cycling in deep Gulf of Mexico cold-seep sediments

NASA Astrophysics Data System (ADS)

Sibert, R.; Joye, S. B.; Hunter, K.

2015-12-01

Mixtures of light hydrocarbon gases are common in deep Gulf of Mexico cold-seep sediments, and are typically dissolved in pore fluids, adsorbed to sediment particles, trapped in methane ice, or as free gas. The dominant component in these natural gas mixtures is usually methane (>80% C1), but ethane (C2) and propane (C3) are nearly always present in trace amounts (<1% total). The processes that control the concentration and isotopic signature of these gases in sediments are well explained for methane, but the controls for C2/C3 cycling are still a relative mystery. Methane production proceeds in deep anoxic sediments by either 1) thermocatalytic cracking of fossil organic matter, or 2) as a direct product of microbial metabolism, i.e. methanogenesis. In surface sediments, it appears that both microbial consumption and chemical deposition of methane (i.e. as methane clathrate) ensures that >95% of the methane produced at depth never reaches the water column. Production of C1 and C2 in deep-sea sediments has been historically attributed only to thermocatalytic processes, though limited data suggests production of C2/C3 compounds through the activity of archaea at depth. Furthermore, carbon isotopic data on ethane and propane from deep cores of Gulf of Mexico sediments suggest alkanogenesis at >3 m depth in the sediment column and alkane oxidation in uppermost oxidant-rich sediments. Additional studies have also isolated microorganisms capable of oxidizing ethane and propane in the laboratory, but field studies of microbial-driven dynamics of C2/C3 gases in cold-seep sediments are rare. Here, we present the results of a series of incubation experiments using sediment slurries culled from surface sediments from one of the most prolific natural oil and gas seeps in the Gulf of Mexico. Rates of alkane oxidation were measured under a variety of conditions to assess the surface-driven microbial controls on C2/C3 cycling in cold-seep environments. Such microbial processes are important in terms of the possible 'oxidative overprinting' of alkane isotopic signatures produced at depth, possibly obscuring typical microbial isotopic signals.

Biological versus mineralogical chromium reduction: potential for reoxidation by manganese oxide.

PubMed

Butler, Elizabeth C; Chen, Lixia; Hansel, Colleen M; Krumholz, Lee R; Elwood Madden, Andrew S; Lan, Ying

2015-11-01

Hexavalent chromium (Cr(vi), present predominantly as CrO4(2-) in water at neutral pH) is a common ground water pollutant, and reductive immobilization is a frequent remediation alternative. The Cr(iii) that forms upon microbial or abiotic reduction often co-precipitates with naturally present or added iron (Fe), and the stability of the resulting Fe-Cr precipitate is a function of its mineral properties. In this study, Fe-Cr solids were formed by microbial Cr(vi) reduction using Desulfovibrio vulgaris strain RCH1 in the presence of the Fe-bearing minerals hematite, aluminum substituted goethite (Al-goethite), and nontronite (NAu-2, Clay Minerals Society), or by abiotic Cr(vi) reduction by dithionite reduced NAu-2 or iron sulfide (FeS). The properties of the resulting Fe-Cr solids and their behavior upon exposure to the oxidant manganese (Mn) oxide (birnessite) differed significantly. In microcosms containing strain RCH1 and hematite or Al-goethite, there was significant initial loss of Cr(vi) in a pattern consistent with adsorption, and significant Cr(vi) was found in the resulting solids. The solid formed when Cr(vi) was reduced by FeS contained a high proportion of Cr(iii) and was poorly crystalline. In microcosms with strain RCH1 and hematite, Cr precipitates appeared to be concentrated in organic biofilms. Reaction between birnessite and the abiotically formed Cr(iii) solids led to production of significant dissolved Cr(vi) compared to the no-birnessite controls. This pattern was not observed in the solids generated by microbial Cr(vi) reduction, possibly due to re-reduction of any Cr(vi) generated upon oxidation by birnessite by active bacteria or microbial enzymes. The results of this study suggest that Fe-Cr precipitates formed in groundwater remediation may remain stable only in the presence of active anaerobic microbial reduction. If exposed to environmentally common Mn oxides such as birnessite in the absence of microbial activity, there is the potential for rapid (re)formation of dissolved Cr(vi) above regulatory levels.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, T.; Griffin, A. M.; Gorski, C. A.

Dissimilatory microbial reduction of solid-phase Fe(III)-oxides and Fe(III)-bearing phyllosilicates (Fe(III)-phyllosilicates) is an important process in anoxic soils, sediments, and subsurface materials. Although various studies have documented the relative extent of microbial reduction of single-phase Fe(III)-oxides and Fe(III)-phyllosilicates, detailed information is not available on interaction between these two processes in situations where both phases are available for microbial reduction. The goal of this research was to use the model dissimilatory iron-reducing bacterium (DIRB) Geobacter sulfurreducens to study Fe(III)-oxide vs. Fe(III)-phyllosilicate reduction in a range of subsurface materials and Fe(III)-oxide stripped versions of the materials. Low temperature (12K) Mossbauer spectroscopy was usedmore » to infer changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate). A Fe partitioning model was employed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The results showed that in most cases Fe(III)- oxide utilization dominated (70-100 %) bulk Fe(III) reduction activity, and that electron transfer from oxide-derived Fe(II) played only a minor role (ca. 10-20 %) in Fe partitioning. In addition, the extent of Fe(III)-oxide reduction was positively correlated to surface area-normalized cation exchange capacity and the phyllosilicate-Fe(III)/total Fe(III) ratio, which suggests that the phyllosilicates in the natural sediments promoted Fe(III)-oxide reduction by binding of oxide-derived Fe(II), thereby enhancing Fe(III)-oxide reduction by reducing or delaying the inhibitory effect that Fe(II) accumulation on oxide and DIRB cell surfaces has on Fe(III)-oxide reduction. In general our results suggest that although Fe(III)-oxide reduction is likely to dominate bulk Fe(III) reduction in most subsurface sediments, Fe(II) binding by phyllosilicates is likely to play a key role in controlling the long-term kinetics of Fe(III)-oxide reduction.« less

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

PubMed Central

Hall, E. K.; Besemer, K.; Kohl, L.; Preiler, C.; Riedel, K.; Schneider, T.; Wanek, W.; Battin, T. J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems. PMID:22347877

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Role of microbial processes in linking sandstone diagenesis with organic-rich clays

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.; Falls, W.F.; Bradley, P.M.

1992-01-01

Shows that the processes of microbial organic-acid production (via fermentation) in clays and microbial organic-acid consumption (via sulfate reduction) in sands effectively link organic-rich clays to sandstone diagenesis in the Black Creek Formation of South Carolina. Diagenetic processes have resulted in the formation of 10 volume percent calcite cement, 0.1 volume percent authigenic pyrite, and 1.5 volume percent secondary porosity in Black Creek sands. However, the distribution of these diagenetic processes is not uniform, resulting in net destruction of porosity in some parts of the sand and net porosity enchancement in other parts. -from Authors

Purification system

NASA Technical Reports Server (NTRS)

Flanagan, David T. (Inventor); Gibbons, Randall E. (Inventor)

1992-01-01

A system for prolonging the life of a granulated activated charcoal (GAC) water treatment device is disclosed in which an ultraviolet light transparent material is used to constrain water to flow over carbon surfaces. It is configured to receive maximum flux from a UV radiation source for the purpose of preventing microbial proliferation on the carbon surfaces; oxidizing organic contaminants adsorbed from the water onto the carbon surfaces and from biodegradation of adsorbed microbial forms; disinfecting water; and oxidizing organic contaminants in the water.

Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control

Treesearch

Matt D. Busse; Samual E. Beattie; Robert F. Powers; Felipe G. Sanchez; Allan E. Tiarks

2006-01-01

We tested three disturbance hypotheses in young conifer plantations: H1: soil compaction and removal of surface organic matter produces sustained changes in microbial community size, activity, and structure in mineral soil; H2: microbial community characteristics in mineral soil are linked to the recovery of plant diversity...

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

PubMed

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L; de Bruijn, Ino; Andersson, Anders F; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-10-14

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

PubMed Central

Bagnoud, Alexandre; Chourey, Karuna; Hettich, Robert L.; de Bruijn, Ino; Andersson, Anders F.; Leupin, Olivier X.; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present. PMID:27739431

Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

PubMed

Zhang, Cui-Jing; Shen, Ju-Pei; Sun, Yi-Fei; Wang, Jun-Tao; Zhang, Li-Mei; Yang, Zhong-Ling; Han, Hong-Yan; Wan, Shi-Qiang; He, Ji-Zheng

2017-04-01

Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques, were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Life on the energetic edge: Iron oxidation by circumneutral lithotrophic bacteria in the wetland plant rhizosphere

NASA Astrophysics Data System (ADS)

Neubauer, S. C.; Emerson, D.; Megonigal, J. P.; Weiss, J. V.

2002-05-01

We have discovered a phylogenetically and genotypically coherent group of obligately lithotrophic Fe-oxidizing bacteria that grow at neutral pH and are globally distributed in a range of habitats, from the rhizosphere of freshwater wetlands to deep-sea hydrothermal vents. We have initiated bioreactor studies using pure cultures of these organisms to determine the significance of microbial Fe(II) oxidation at circumneutral pH and identify the biotic and abiotic variables that affect the partitioning between microbial and chemical oxidation. These studies have focused on strain BrT, which was isolated from an iron oxide precipitate in rhizosphere of a wetland plant. In one set of experiments, Fe(II) oxidation rates were measured before and after cultures of strain BrT were poisoned with sodium azide. These experiments indicated that 18 to 53 % of total iron oxidation was due to microbial metabolism. In a second set of experiments, Fe(II) was constantly added to bioreactors inoculated with live cells, killed cells, or no cells. A statistical model fit to the experimental data demonstrated that metabolic Fe(II) oxidation accounted for up to 62 % of total oxidation. Total Fe(II) oxidation rates in these experiments were strongly limited by the rate of Fe(II) delivery to the system, and were also influenced by O2 and total iron concentrations. Additionally, the model suggested that the microbes inhibited rates of abiotic Fe(II) oxidation, perhaps by binding Fe(II) to bacterial exopolymers. The net effect of strain BrT was to accelerate total oxidation rates by up to 18 % versus cell-free treatments. Using two independent techniques, we demonstrated that strain BrT actively metabolizes Fe(II) and can account for up to 50 to 60 % of total Fe(II) oxidation in laboratory cultures. These results suggest that neutrophilic Fe(II)-oxidizing bacteria may compete for limited O2 in the rhizosphere and influence the biogeochemistry of other elements including carbon, phosphorus, and sulfur.

Enriching acid rock drainage related microbial communities from surface-deposited oil sands tailings.

PubMed

Dean, Courtney; Xiao, Yeyuan; Roberts, Deborah J

2016-10-01

Little is known about the microbial communities native to surface-deposited pyritic oil sands tailings, an environment where acid rock drainage (ARD) could occur. The goal of this study was to enrich sulfur-oxidizing organisms from these tailings and determine whether different populations exist at pH levels 7, 4.5, and 2.5. Using growth-based methods provides model organisms for use in the future to predict potential activities and limitations of these organisms and to develop possible control methods. Thiosulfate-fed enrichment cultures were monitored for approximately 1 year. The results showed that the enrichments at pH 4.5 and 7 were established quicker than at pH 2.5. Different microbial community structures were found among the 3 pH environments. The sulfur-oxidizing microorganisms identified were most closely related to Halothiobacillus neapolitanus, Achromobacter spp., and Curtobacterium spp. While microorganisms related to Chitinophagaceae and Acidocella spp. were identified as the only possible iron-oxidizing and -reducing microbes. These results contribute to the general knowledge of the relatively understudied microbial communities that exist in pyritic oil sands tailings and indicate these communities may have a potential role in ARD generation, which may have implications for future tailings management.

Retardation of quality changes in camel meat sausages by phenolic compounds and phenolic extracts.

PubMed

Maqsood, Sajid; Manheem, Kusaimah; Abushelaibi, Aisha; Kadim, Isam Tawfik

2016-11-01

Impact of tannic acid (TA), date seed extract (DSE), catechin (CT) and green tea extract (GTE) on lipid oxidation, microbial load and textural properties of camel meat sausages during 12 days of refrigerated storage was investigated. TA and CT showed higher activities in all antioxidative assays compared to DSE and GTE. Lipid oxidation and microbial growth was higher for control sausages when compared to other samples. TA and CT at a level of 200 mg/kg were more effective in retarding lipid oxidation and lowering microbial count (P < 0.05). Sausages treated with TA and DSE were found to have higher hardness, gumminess and chewiness values compared to other treatments (P < 0.05). Addition of different phenolic compounds or extract did not influence the sensory color of sausages. Furthermore, sensory quality was also found to be superior in TA and CT treated sausages. Therefore, pure phenolic compounds (TA and CT) proved to be more effective in retaining microbial and sensorial qualities of camel meat sausages compared to phenolic extracts (GTE and DSE) over 12 days of storage at 4°C. © 2016 Japanese Society of Animal Science.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

PubMed Central

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

Microbial Iron(II) Oxidation in Littoral Freshwater Lake Sediment: The Potential for Competition between Phototrophic vs. Nitrate-Reducing Iron(II)-Oxidizers

PubMed Central

Melton, E. D.; Schmidt, C.; Kappler, A.

2012-01-01

The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediment, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e− donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic most probable number counted 3.4·105 cells·g−1 and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totaled 1.8·104 and 4.5·104 cells·g−1 dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e− donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle. PMID:22666221

Energetic Limitations on Microbial Respiration of Organic Compounds using Aqueous Fe(III) Complexes

NASA Astrophysics Data System (ADS)

Naughton, H.; Fendorf, S. E.

2015-12-01

Soil organic matter constitutes up to 75% of the terrestrial carbon stock. Microorganisms mediate the breakdown of organic compounds and the return of carbon to the atmosphere, predominantly through respiration. Microbial respiration requires an electron acceptor and an electron donor such as small fatty acids, organic acids, alcohols, sugars, and other molecules that differ in oxidation state of carbon. Carbon redox state affects how much energy is required to oxidize a molecule through respiration. Therefore, different organic compounds should offer a spectrum of energies to respiring microorganisms. However, microbial respiration has traditionally focused on the availability and reduction potential of electron acceptors, ignoring the organic electron donor. We found through incubation experiments that the organic compound serving as electron donor determined how rapidly Shewanella putrefaciens CN32 respires organic substrate and the extent of reduction of the electron acceptor. We simulated a range of energetically favorable to unfavorable electron acceptors using organic chelators bound to Fe(III) with equilibrium stability constants ranging from log(K) of 11.5 to 25.0 for the 1:1 complex, where more stable complexes are less favorable for microbial respiration. Organic substrates varied in nominal oxidation state of carbon from +2 to -2. The most energetically favorable substrate, lactate, promoted up to 30x more rapid increase in percent Fe(II) compared to less favorable substrates such as formate. This increased respiration on lactate was more substantial with less stable Fe(III)-chelate complexes. Intriguingly, this pattern contradicts respiration rate predicted by nominal oxidation state of carbon. Our results suggest that organic substrates will be consumed so long as the energetic toll corresponding to the electron donor half reaction is counterbalanced by the energy available from the electron accepting half reaction. We propose using the chemical structure of organic matter, elucidated with techniques such as FT-ICR MS, to improve microbial decomposition and carbon cycling models by incorporating energetic limitations due to carbon oxidation.

Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Green, K.; Murphy, M. A.; Shepard, C.; Chorover, J.; Rich, V. I.; Gallery, R. E.

2015-12-01

Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more reducing conditions typically occur in convergent zones and at depth. These results highlight the significance of fluctuating oxygen-depleted zones in aerobic soils on microbial community activity and structure, linking community response to larger scale ecosystem processes.

Biological Oxidation of Fe(II) in Reduced Nontronite Coupled with Nitrate Reduction by Pseudogulbenkiania sp. Strain 2002

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Linduo; Dong, Hailiang; Kukkadapu, Ravi K.

Nitrate contamination in soils, sediments, and water bodies is a significant issue. Although much is known about nitrate degradation in these environments, especially via microbial pathways, a complete understanding of all degradation processes, especially in clay mineral-rich soils, is still lacking. The objective of this study was to study the potential of removing nitrate contaminant using structural Fe(II) in clay mineral nontronite. Specifically, the coupled processes of microbial oxidation of Fe(II) in microbially reduced nontronite (NAu-2) and nitrate reduction by Pseudogulbenkiania species strain 2002 was investigated. Bio-oxidation experiments were conducted in bicarbonate-buffered medium under both growth and nongrowth conditions. Themore » extents of Fe(II) oxidation and nitrate reduction were measured by wet chemical methods. X-ray diffraction (XRD), scanning and transmission electron microscopy (SEM and TEM), and 57Fe-Mössbauer spectroscopy were used to observe mineralogical changes associated with Fe(III) reduction and Fe(II) oxidation in nontronite. The bio-oxidation extent under growth and nongrowth conditions reached 93% and 57%, respectively. Over the same time period, nitrate was completely reduced under both conditions to nitrogen gas (N2), via an intermediate product nitrite. Magnetite was a mineral product of nitrate-dependent Fe(II) oxidation, as evidenced by XRD data and TEM diffraction patterns. The results of this study highlight the importance of iron-bearing clay minerals in the global nitrogen cycle with potential applications in nitrate removal in soils.« less

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

PubMed

Daae, F L; Økland, I; Dahle, H; Jørgensen, S L; Thorseth, I H; Pedersen, R B

2013-07-01

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions. © 2013 John Wiley & Sons Ltd.

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.

PubMed

Detman, Anna; Mielecki, Damian; Pleśniak, Łukasz; Bucha, Michał; Janiga, Marek; Matyasik, Irena; Chojnacka, Aleksandra; Jędrysek, Mariusz-Orion; Błaszczyk, Mieczysław K; Sikora, Anna

2018-01-01

Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes , Firmicutes , Proteobacteria , Synergistetes , Actinobacteria , Spirochaetes , Tenericutes , Caldithrix , Verrucomicrobia , Thermotogae , Chloroflexi , Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate-oxidizing metabolic machinery homologous to those of Acetobacterium woodii and Desulfovibrio vulgaris . Furthermore, genes for enzymes of the reductive acetyl-CoA pathway were present in the microbial communities. The results indicate that lactate is oxidized mainly to acetate during the acetogenic step of AD and this comprises the acetotrophic pathway of methanogenesis. The genes for lactate utilization under anaerobic conditions are widespread in the domain Bacteria. Lactate oxidation to the substrates for methanogens is the most energetically attractive process in comparison to butyrate, propionate, or ethanol oxidation.

Carbon isotope fractionation during microbial methane oxidation

NASA Astrophysics Data System (ADS)

Barker, James F.; Fritz, Peter

1981-09-01

Methane, a common trace constituent of groundwaters, occasionally makes up more than 20% of the total carbon in groundwaters1,2. In aerobic environments CH4-rich waters can enable microbial food chain supporting a mixed culture of bacteria with methane oxidation as the primary energy source to develop3. Such processes may influence the isotopic composition of the residual methane and because 13C/12C analyses have been used to characterize the genesis of methanes found in different environments, an understanding of the magnitude of such effects is necessary. In addition, carbon dioxide produced by the methane-utilizing bacteria can be added to the inorganic carbon pool of affected groundwaters. We found carbon dioxide experimentally produced by methane-utilizing bacteria to be enriched in 12C by 5.0-29.6‰, relative to the residual methane. Where methane-bearing groundwaters discharged into aerobic environments microbial methane oxidation occurred, with the residual methane becoming progressively enriched in 13C. Various models have been proposed to explain the 13C/12C and 14C content of the dissolved inorganic carbon (DIC) of groundwaters in terms of additions or losses during flow in the subsurface4,5. The knowledge of both stable carbon isotope ratios in various pools and the magnitude of carbon isotope fractionation during various processes allows geochemists to use the 13C/12C ratio of the DIC along with water chemistry to estimate corrected 14C groundwater ages4,5. We show here that a knowledge of the carbon isotope fractionation between CH4 and CO2 during microbial methane-utilization could modify such models for application to groundwaters affected by microbial methane oxidation.

Microbial Fossils Detected in Desert Varnish

NASA Technical Reports Server (NTRS)

Flood, B. E.; Allen, C.; Longazo, T.

2003-01-01

Mars Global Surveyor Thermal Emission Spectrometer data indicate regions with significant levels of hematite (_Fe2O3). Fe-oxides, like hematite, can form as aqueous mineral precipitates and as such may preserve microscopic fossils or other biosignatures. Several potential terrestrial analogues to martian hematite like hydrothermal vents have preserved microfossils. Microbial fossilization in Fe-oxides is often a function of biomineralization. For example, goethite (FeO2H) encrustation of fungal mycelia from the mid-Tertiary preserved fungal morphologies such that their genera could be determined.

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA

PubMed Central

Lapakko, Kim A.; Wenz, Zachary J.; Olson, Michael C.; Roepke, Elizabeth W.; Novak, Paige J.; Bailey, Jake V.

2017-01-01

ABSTRACT The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria. Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste. IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits. PMID:28600313

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA.

PubMed

Jones, Daniel S; Lapakko, Kim A; Wenz, Zachary J; Olson, Michael C; Roepke, Elizabeth W; Sadowsky, Michael J; Novak, Paige J; Bailey, Jake V

2017-08-15

The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula , as well as from diverse clades of uncultivated Chloroflexi , Acidobacteria , and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste. IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits. Copyright © 2017 American Society for Microbiology.

High resolution and comprehensive techniques to analyze aerobic methane oxidation in mesocosm experiments

NASA Astrophysics Data System (ADS)

Chan, E. W.; Kessler, J. D.; Redmond, M. C.; Shiller, A. M.; Arrington, E. C.; Valentine, D. L.; Colombo, F.

2015-12-01

Many studies of microbially mediated aerobic methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on how quickly methane is oxidized once a microbial population is established and what factor(s) are limiting in these types of environments. These factors include the availability of CH4, O2, trace metals, nutrients, and the density of cell population. Limits to these factors can also control the temporal aspects of a methane oxidation event. In order to look at this process in its entirety and with higher temporal resolution, a mesocosm incubation system was developed with a Dissolved Gas Analyzer System (DGAS) coupled with a set of analytical tools to monitor aerobic methane oxidation in real time. With the addition of newer laser spectroscopy techniques (cavity ringdown spectroscopy), stable isotope fractionation caused by microbial processes can also be examined on a real time and automated basis. Cell counting, trace metal, nutrient, and DNA community analyses have also been carried out in conjunction with these mesocosm samples to provide a clear understanding of the biology in methane oxidation dynamics. This poster will detail the techniques involved to provide insights into the chemical and isotopic kinetics controlling aerobic methane oxidation. Proof of concept applications will be presented from seep sites in the Hudson Canyon and the Sleeping Dragon seep field, Mississippi Canyon 118 (MC 118). This system was used to conduct mesocosm experiments to examine methane consumption, O2 consumption, nutrient consumption, and biomass production.

Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

DOE PAGES

Sivan, Orit; Antler, Gilad; Turchyn, Alexandra V.; ...

2014-09-22

Seep sediments are dominated by intensive microbial sulfate reduction coupled to the anaerobic oxidation of methane (AOM). Through geochemical measurements of incubation experiments with methane seep sediments collected from Hydrate Ridge, we provide insight into the role of iron oxides in sulfate-driven AOM. Seep sediments incubated with 13C-labeled methane showed co-occurring sulfate reduction, AOM, and methanogenesis. The isotope fractionation factors for sulfur and oxygen isotopes in sulfate were about 40‰ and 22‰, respectively, reinforcing the difference between microbial sulfate reduction in methane seeps versus other sedimentary environments (for example, sulfur isotope fractionation above 60‰ in sulfate reduction coupled to organicmore » carbon oxidation or in diffusive sedimentary sulfate–methane transition zone). The addition of hematite to these microcosm experiments resulted in significant microbial iron reduction as well as enhancing sulfate-driven AOM. The magnitude of the isotope fractionation of sulfur and oxygen isotopes in sulfate from these incubations was lowered by about 50%, indicating the involvement of iron oxides during sulfate reduction in methane seeps. The similar relative change between the oxygen versus sulfur isotopes of sulfate in all experiments (with and without hematite addition) suggests that oxidized forms of iron, naturally present in the sediment incubations, were involved in sulfate reduction, with hematite addition increasing the sulfate recycling or the activity of sulfur-cycling microorganisms by about 40%. Furthermore, these results highlight a role for natural iron oxides during bacterial sulfate reduction in methane seeps not only as nutrient but also as stimulator of sulfur recycling.« less

Thermodynamically controlled preservation of organic carbon in floodplains

DOE PAGES

Boye, Kristin; Noel, Vincent; Tfaily, Malak M.; ...

2017-05-01

Organic matter decomposition in soils and terrestrial sediments has a prominent role in the global carbon cycle. Carbon stocks in anoxic environments, such as wetlands and the subsurface of floodplains, are large and presumed to decompose slowly. The degree of microbial respiration in anoxic environments is typically thought to depend on the energetics of available terminal electron acceptors such as nitrate or sulfate; microbes couple the reduction of these compounds to the oxidation of organic carbon. But, it is also possible that the energetics of the organic carbon itself can determine whether it is decomposed. We examined water-soluble organic carbonmore » by Fourier-transform ion-cyclotron-resonance mass spectrometry to compare the chemical composition and average nominal oxidation state of carbon—a metric reflecting whether microbial oxidation of organic matter is thermodynamically favourable—in anoxic (sulfidic) and oxic (non-sulfidic) floodplain sediments. We also observed distinct minima in the average nominal oxidation state of water-soluble carbon in sediments exhibiting anoxic, sulfate-reducing conditions, suggesting preservation of carbon compounds with nominal oxidation states below the threshold that makes microbial sulfate reduction thermodynamically favourable. Finally, we show that thermodynamic limitations constitute an important complement to other mechanisms of carbon preservation, such as enzymatic restrictions and mineral association, within anaerobic environments.« less

Thermodynamically controlled preservation of organic carbon in floodplains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boye, Kristin; Noel, Vincent; Tfaily, Malak M.

Organic matter decomposition in soils and terrestrial sediments has a prominent role in the global carbon cycle. Carbon stocks in anoxic environments, such as wetlands and the subsurface of floodplains, are large and presumed to decompose slowly. The degree of microbial respiration in anoxic environments is typically thought to depend on the energetics of available terminal electron acceptors such as nitrate or sulfate; microbes couple the reduction of these compounds to the oxidation of organic carbon. But, it is also possible that the energetics of the organic carbon itself can determine whether it is decomposed. We examined water-soluble organic carbonmore » by Fourier-transform ion-cyclotron-resonance mass spectrometry to compare the chemical composition and average nominal oxidation state of carbon—a metric reflecting whether microbial oxidation of organic matter is thermodynamically favourable—in anoxic (sulfidic) and oxic (non-sulfidic) floodplain sediments. We also observed distinct minima in the average nominal oxidation state of water-soluble carbon in sediments exhibiting anoxic, sulfate-reducing conditions, suggesting preservation of carbon compounds with nominal oxidation states below the threshold that makes microbial sulfate reduction thermodynamically favourable. Finally, we show that thermodynamic limitations constitute an important complement to other mechanisms of carbon preservation, such as enzymatic restrictions and mineral association, within anaerobic environments.« less

Thermodynamically controlled preservation of organic carbon in floodplains

NASA Astrophysics Data System (ADS)

Boye, Kristin; Noël, Vincent; Tfaily, Malak M.; Bone, Sharon E.; Williams, Kenneth H.; Bargar, John R.; Fendorf, Scott

2017-06-01

Organic matter decomposition in soils and terrestrial sediments has a prominent role in the global carbon cycle. Carbon stocks in anoxic environments, such as wetlands and the subsurface of floodplains, are large and presumed to decompose slowly. The degree of microbial respiration in anoxic environments is typically thought to depend on the energetics of available terminal electron acceptors such as nitrate or sulfate; microbes couple the reduction of these compounds to the oxidation of organic carbon. However, it is also possible that the energetics of the organic carbon itself can determine whether it is decomposed. Here we examined water-soluble organic carbon by Fourier-transform ion-cyclotron-resonance mass spectrometry to compare the chemical composition and average nominal oxidation state of carbon--a metric reflecting whether microbial oxidation of organic matter is thermodynamically favourable--in anoxic (sulfidic) and oxic (non-sulfidic) floodplain sediments. We observed distinct minima in the average nominal oxidation state of water-soluble carbon in sediments exhibiting anoxic, sulfate-reducing conditions, suggesting preservation of carbon compounds with nominal oxidation states below the threshold that makes microbial sulfate reduction thermodynamically favourable. We conclude that thermodynamic limitations constitute an important complement to other mechanisms of carbon preservation, such as enzymatic restrictions and mineral association, within anaerobic environments.

Anti-oxidative and Anti-microbial Activities of Purified MPN-1-1 from Persicaria nepalensis (Meisn.) Miyabe.

PubMed

Yang, Woong-Suk; Yang, Seung-Hoon; Lee, Jae-Yong; Jang, Seong-Ho; Kim, Cheorl-Ho; Hwnag, Cher-Won

2017-01-01

Persicaria is a genus of flowering plants generally used for traditional medicine and nutritional supplements in tropical and subtropical East Asian countries. Previous studies have shown that Persicaria extracts alleviate lipid peroxidation, hypertension, and inflammation. We investigated the anti-oxidative and anti-microbial effects of ethanol extracts of Persicaria nepalensis (Meisn.) Miyabe, and isolated and identified an active compound, MPN-1-1 from the ethanol extracts. Anti-oxidative values, as indicated by the Oxygen Radical Absorbance Capacity (ORAC) assay, were enhanced by treatment with Persicaria nepalensis (Meisn.) Miyabe ethanol extracts, and bacterial growth was inhibited. The active compound (MPN-1-1), which was further isolated and purified from a Persicaria nepalensis (Meisn.) Miyabe ethanol extract by medium pressure liquid chromatography (MPLC), also had strong anti-oxidative and anti-microbial activity. 1H-NMR spectroscopy identified MPN-1-1 as a 1-ethenyl-4,8-dimethoxy-9H-pyrido(3,4-β) indole compound, which is an alkaloid. Our results provide evidence that Persicaria nepalensis (Meisn.) Miyabe extract has strong physiological activity without any toxic effects, and furthermore, MPN-1-1 can be potentially utilized as a natural dietary supplement as well as an anti-oxidant. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Liquefaction/solubilization of low-rank Turkish coals by white-rot fungus (Phanerochaete chrysosporium)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elbeyli, I.Y.; Palantoken, A.; Piskin, S.

2006-08-15

Microbial coal liquefaction/solubilization of three low-rank Turkish coals (Bursa-Kestelek, Kutahya-Seyitomer and Mugla-Yatagan lignite) was attempted by using a white-rot fungus (Phanerochaete chrysosporium DSM No. 6909); chemical compositions of the products were investigated. The lignite samples were oxidized by nitric acid under moderate conditions and then oxidized samples were placed on the agar medium of Phanerochaete chrysosporium. FTIR spectra of raw lignites, oxidized lignites and liquid products were recorded, and the acetone-soluble fractions of these samples were identified by GC-MS technique. Results show that the fungus affects the nitro and carboxyl/carbonyl groups in oxidized lignite sample, the liquid products obtained bymore » microbial effects are the mixture of water-soluble compounds, and show limited organic solubility.« less

ISCO'S LONG-TERM IMPACT ON AQUIFER CONDITIONS AND MICROBIAL ACTIVITY

EPA Science Inventory

Potential for lasting negative environmental effects has clouded remediation programs using permanganate and other oxidants. A major concern about using In-Situ Chemical Oxidation (ISCO) for remediation of CVOCs is that application of strong oxidants to subsurface systems may pe...

Microbial heterotrophy coupled to Fe-S-As cycling in a shallow-sea hydrothermal system

NASA Astrophysics Data System (ADS)

Lu, G.; Amend, J.

2013-12-01

To date, there are only a few known heterotrophic arsenite oxidizers and arsenate reducers. They utilize organic compounds as their carbon source and/or as important electron donors in the transfer arsenic in high temperature environments. Arsenic in hydrothermal vent systems can be immobilized at low temperatures through (ad)sorption on iron oxide and other iron-bearing minerals. Interactions with sulfur species can also affect the redox state of arsenic species. A better understanding of microbially-catalyzed reactions involving carbon, arsenic, iron and sulfur would provide constraints on the mobility of arsenic in a wide variety of natural and engineered systems. The aim of this study is to establish links between microbial distribution and in situ Fe-S-As cycling processes in a shallow-sea hydrothermal vent system. We investigated three shallow-sea hydrothermal vents, Champagne Hot Spring (CHS), Soufriere Spring (SOU) and Portsmouth Spring (PM), located off the western coast of Dominica, Lesser Antilles. CHS and SOU are characterized by moderate temperatures (46oC and 55oC, respectively), and PM is substantially hotter (~90-111 oC). Two sediment cores (one close to and one far from the thermal source) were collected from CHS and from SOU. Porewaters in both background cores had low concentrations of arsenic (mostly As3+, to a lesser extent As5+, DMA, MMA) and ferrous iron. The arsenic concentrations (predominantly As3+) in the CHS high temperature core were 30-90 nM, tracking with dissolved iron. Similar to CHS, the arsenic concentration in the SOU high temperature core was dominated by As3+ and controlled by ferrous iron. However, the arsenic concentration at SOU is comparatively higher, up to 1.9 mM. At the hotter and deeper PM site, highly elevated arsenic levels (1-2.5 mM) were measured, values that are among the highest arsenic concentrations ever reported in a marine hydrothermal system. Several autotrophic and heterotrophic media at two pHs (5.5 and 8.0) were designed to target microbial reductive and oxidative metabolisms of arsenic, iron and sulfur. Incubations were carried out at four temperatures (30, 50, 70, 90 oC), covering the mesophilic to hyperthermophilic range. Sediment and biofilm samples from all three sites were used as inocula in enrichments targeting heterotrophic arsenite oxidation and arsenate reduction. From these enrichments, multiple pure strains were isolated at 30, 50 and 70 oC. From the 50oC enrichments on oxic, heterotrophic media inoculated with both SOU sediment and biofilm, we isolated aerobic thermophilic sulfate reducers producing high concentration of sulfide. The produced sulfide transforms ferrihydrite to an amorphous arsenic-metal-sulfide mineral. The current culturing results not only expand the diversity of arsenic oxidizing, arsenate reducing, and aerobic sulfate reducing organisms, but also show that the microbes influence in situ Fe-S-As transformation. More molecular and physiological tests are underway to better characterize the microbe-mineral interactions in laboratory enrichments and natural environments to determine the biological effects on the cycling of As-Fe-S in shallow-sea hydrothermal systems.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOEpatents

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

Microbial oxidation of lithospheric organic carbon in rapidly eroding tropical mountain soils

NASA Astrophysics Data System (ADS)

Hemingway, Jordon D.; Hilton, Robert G.; Hovius, Niels; Eglinton, Timothy I.; Haghipour, Negar; Wacker, Lukas; Chen, Meng-Chiang; Galy, Valier V.

2018-04-01

Lithospheric organic carbon (“petrogenic”; OCpetro) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO2) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OCpetro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OCpetro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO2 emission fluxes that increase with erosion rate, thereby counteracting CO2 drawdown by silicate weathering and biospheric OC burial.

Geomicrobiological Features of Ferruginous Sediments from Lake Towuti, Indonesia

PubMed Central

Vuillemin, Aurèle; Friese, André; Alawi, Mashal; Henny, Cynthia; Nomosatryo, Sulung; Wagner, Dirk; Crowe, Sean A.; Kallmeyer, Jens

2016-01-01

Lake Towuti is a tectonic basin, surrounded by ultramafic rocks. Lateritic soils form through weathering and deliver abundant iron (oxy)hydroxides but very little sulfate to the lake and its sediment. To characterize the sediment biogeochemistry, we collected cores at three sites with increasing water depth and decreasing bottom water oxygen concentrations. Microbial cell densities were highest at the shallow site—a feature we attribute to the availability of labile organic matter (OM) and the higher abundance of electron acceptors due to oxic bottom water conditions. At the two other sites, OM degradation and reduction processes below the oxycline led to partial electron acceptor depletion. Genetic information preserved in the sediment as extracellular DNA (eDNA) provided information on aerobic and anaerobic heterotrophs related to Nitrospirae, Chloroflexi, and Thermoplasmatales. These taxa apparently played a significant role in the degradation of sinking OM. However, eDNA concentrations rapidly decreased with core depth. Despite very low sulfate concentrations, sulfate-reducing bacteria were present and viable in sediments at all three sites, as confirmed by measurement of potential sulfate reduction rates. Microbial community fingerprinting supported the presence of taxa related to Deltaproteobacteria and Firmicutes with demonstrated capacity for iron and sulfate reduction. Concomitantly, sequences of Ruminococcaceae, Clostridiales, and Methanomicrobiales indicated potential for fermentative hydrogen and methane production. Such first insights into ferruginous sediments showed that microbial populations perform successive metabolisms related to sulfur, iron, and methane. In theory, iron reduction could reoxidize reduced sulfur compounds and desorb OM from iron minerals to allow remineralization to methane. Overall, we found that biogeochemical processes in the sediments can be linked to redox differences in the bottom waters of the three sites, like oxidant concentrations and the supply of labile OM. At the scale of the lacustrine record, our geomicrobiological study should provide a means to link the extant subsurface biosphere to past environments. PMID:27446046

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

PubMed Central

Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Glazer, Brian T.; Krepski, Sean T.; Emerson, David

2016-01-01

Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history. PMID:27313567

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone.

PubMed

Fuchsman, Clara A; Devol, Allan H; Saunders, Jaclyn K; McKay, Cedar; Rocap, Gabrielle

2017-01-01

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N 2 O and N 2 . This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N 2 O reductases ( nosZ ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK . A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N 2 O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N 2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N 2 O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N 2 O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N 2 O production rates from ammonia oxidation were insufficient to support the observed oxycline N 2 O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N 2 O and N 2 . Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.

Stimulating soil microorganisms for mineralizing the herbicide isoproturon by means of microbial electroremediating cells.

PubMed

Rodrigo Quejigo, Jose; Dörfler, Ulrike; Schroll, Reiner; Esteve-Núñez, Abraham

2016-05-01

The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Microbial electroremediating cells (MERCs) consist in a variety of bioelectrochemical devices that aim to overcome electron acceptor limitation and maximize metabolic oxidation with the purpose of enhancing the biodegradation of a pollutant in the environment. The objective of this work was to use MERCs principles for stimulating soil bacteria to achieve the complete biodegradation of the herbicide (14) C-isoproturon (IPU) to (14) CO(2) in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] enhanced the mineralization by 20-fold respect the electrode-free control. We also report an overall profile of the (14) C-IPU metabolites and a (14) C mass balance in response to the different treatments. The remarkable impact of electrodes on the microbial activity of natural communities suggests a promising future for this emerging environmental technology that we propose to name bioelectroventing. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Assessing the impact of nano- and micro-scale zerovalent iron particles on soil microbial activities: particle reactivity interferes with assay conditions and interpretation of genuine microbial effects.

PubMed

Cullen, Laurence G; Tilston, Emma L; Mitchell, Geoff R; Collins, Chris D; Shaw, Liz J

2011-03-01

The effects of nano-scale and micro-scale zerovalent iron (nZVI and mZVI) particles on general (dehydrogenase and hydrolase) and specific (ammonia oxidation potential, AOP) activities mediated by the microbial community in an uncontaminated soil were examined. nZVI (diameter 12.5 nm; 10 mg g⁻¹ soil) apparently inhibited AOP and nZVI and mZVI apparently stimulated dehydrogenase activity but had minimal influence on hydrolase activity. Sterile experiments revealed that the apparent inhibition of AOP could not be interpreted as such due to the confounding action of the particles, whereas, the nZVI-enhanced dehydrogenase activity could represent the genuine response of a stimulated microbial population or an artifact of ZVI reactivity. Overall, there was no evidence for negative effects of nZVI or mZVI on the processes studied. When examining the impact of redox active particles such as ZVI on microbial oxidation-reduction reactions, potential confounding effects of the test particles on assay conditions should be considered. Copyright © 2010 Elsevier Ltd. All rights reserved.

21 CFR 186.1839 - Sorbose.

Code of Federal Regulations, 2010 CFR

2010-04-01

... microbial oxidation of sorbitol. It also occurs naturally in other plants. Sorbose can be synthesized by the catalytic hydrogenation of glucose to D-sorbitol. The resulting sorbitol can be oxidized by Acetobacter...

Similar microbial communities found on two distant seafloor basalts

NASA Astrophysics Data System (ADS)

Singer, E.; Chong, L. S.; Heidelberg, J. F.; Edwards, K. J.

2016-12-01

The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present a comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR) (9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy.

Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process.

PubMed

Zhu, Weihuang; Shi, Mengran; Yu, Dan; Liu, Chongxuan; Huang, Tinglin; Wu, Fengchang

2016-03-29

The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into "redox mediator-iron oxide" interaction in the presence of DIRB. Two pre-incubation reaction systems of the "strain S12- goethite" and the "strain S12-AQS" were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for "Quinone-Iron" interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among "quinone-DIRB- goethite" under biotic/abiotic driven.

Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record

NASA Astrophysics Data System (ADS)

Bailey, Jake V.; Orphan, Victoria J.; Joye, Samantha B.; Corsetti, Frank A.

2009-11-01

Putative microbialites are commonly regarded to have formed in association with photosynthetic microorganisms, such as cyanobacteria. However, many modern microbial mat ecosystems are dominated by chemotrophic bacteria and archaea. Like phototrophs, filamentous sulfur-oxidizing bacteria form large mats at the sediment/water interface that can act to stabilize sediments, and their metabolic activities may mediate the formation of marine phosphorites. Similarly, bacteria and archaea associated with the anaerobic oxidation of methane (AOM) catalyze the precipitation of seafloor authigenic carbonates. When preserved, lipid biomarkers, isotopic signatures, body fossils, and lithological indicators of the local depositional environment may be used to identify chemotrophic mats in the rock record. The recognition of chemotrophic communities in the rock record has the potential to transform our understanding of ancient microbial ecologies, evolution, and geochemical conditions. Chemotrophic microbes on Earth occupy naturally occurring interfaces between oxidized and reduced chemical species and thus may provide a new set of search criteria to target life-detection efforts on other planets.

Analysis of Nitrification Efficiency and Microbial Community in a Membrane Bioreactor Fed with Low COD/N-Ratio Wastewater

PubMed Central

Ma, Jinxing; Wang, Zhiwei; Zhu, Chaowei; Liu, Shumeng; Wang, Qiaoying; Wu, Zhichao

2013-01-01

In this study, an approach using influent COD/N ratio reduction was employed to improve process performance and nitrification efficiency in a membrane bioreactor (MBR). Besides sludge reduction, membrane fouling alleviation was observed during 330 d operation, which was attributed to the decreased production of soluble microbial products (SMP) and efficient carbon metabolism in the autotrophic nitrifying community. 454 high-throughput 16S rRNA gene pyrosequencing revealed that the diversity of microbial sequences was mainly determined by the feed characteristics, and that microbes could derive energy by switching to a more autotrophic metabolism to resist the environmental stress. The enrichment of nitrifiers in an MBR with a low COD/N-ratio demonstrated that this condition stimulated nitrification, and that the community distribution of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) resulted in faster nitrite uptake rates. Further, ammonia oxidation was the rate-limiting step during the full nitrification. PMID:23667573

Linking Specific Heterotrophic Bacterial Populations to Bioreduction of Uranium and Nitrate in Contaminated Subsurface Sediments by Using Stable Isotope Probing▿†

PubMed Central

Akob, Denise M.; Kerkhof, Lee; Küsel, Kirsten; Watson, David B.; Palumbo, Anthony V.; Kostka, Joel E.

2011-01-01

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [13C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions. PMID:21948831

MICROBIAL METABOLISM OF AROMATIC COMPOUNDS I.

PubMed Central

Tabak, Henry H.; Chambers, Cecil W.; Kabler, Paul W.

1964-01-01

Tabak, Henry H. (Robert A. Taft Sanitary Engineering Center, Cincinnati, Ohio), Cecil W. Chambers, and Paul W. Kabler. Microbial metabolism of aromatic carbon compounds. I. Decomposition of phenolic compounds and aromatic hydrocarbons by phenol-adapted bacteria. J. Bacteriol. 87:910–919. 1964.—Bacteria from soil and related environments were selected or adapted to metabolize phenol, hydroxy phenols, nitrophenols, chlorophenols, methylphenols, alkylphenols, and arylphenols when cultured in mineral salts media with the specific substrate as the sole source of carbon. A phenol-adapted culture (substrate-induced enzyme synthesis proven) was challenged in respirometric tests with 104 related compounds; probable significant oxidative activity occurred with 65. Dihydric phenols were generally oxidized; trihydric phenols were not. Cresols and dimethylphenols were oxidized; adding a chloro group increased resistance. Benzoic and hydroxybenzoic acids were oxidized; sulfonated, methoxylated, nitro, and chlorobenzoic acids were not; m-toluic acid was utilized but not the o- and p-isomers. Benzaldehyde and p-hydroxybenzaldehyde were oxidized. In general, nitro- and chloro-substituted compounds and the benzenes were difficult to oxidize. PMID:14137630

Spatial distributions of sulphur species and sulphate-reducing bacteria provide insights into sulphur redox cycling and biodegradation hot-spots in a hydrocarbon-contaminated aquifer

NASA Astrophysics Data System (ADS)

Einsiedl, Florian; Pilloni, Giovanni; Ruth-Anneser, Bettina; Lueders, Tillman; Griebler, Christian

2015-05-01

Dissimilatory sulphate reduction (DSR) has been proven to be one of the most relevant redox reactions in the biodegradation of contaminants in groundwater. However, the possible role of sulphur species of intermediate oxidation state, as well as the role of potential re-oxidative sulphur cycling in biodegradation particularly at the groundwater table are still poorly understood. Here we used a combination of stable isotope measurements of SO42-, H2S, and S0 as well as geochemical profiling of sulphur intermediates with special emphasis on SO32-, S2O32-, and S0 to unravel possible sulphur cycling in the biodegradation of aromatics in a hydrocarbon-contaminated porous aquifer. By linking these results to the quantification of total bacterial rRNA genes and respiratory genes of sulphate reducers, as well as pyrotag sequencing of bacterial communities over depth, light is shed on possible key-organisms involved. Our results substantiate the role of DSR in biodegradation of hydrocarbons (mainly toluene) in the highly active plume fringes above and beneath the plume core. In both zones the concentration of sulphur intermediates (S0, SO32- and S2O32-) was almost twice that of other sampling-depths, indicating intense sulphur redox cycling. The dual isotopic fingerprint of oxygen and sulphur in dissolved sulphate suggested a re-oxidation of reduced sulphur compounds to sulphate especially at the upper fringe zone. An isotopic shift in δ34S of S0 of nearly +4‰ compared to the δ34S values of H2S from the same depth linked to a high abundance (∼10%) of sequence reads related to Sulphuricurvum spp. (Epsilonproteobacteria) in the same depth were indicative of intensive oxidation of S0 to sulphate in this zone. At the lower plume fringe S0 constituted the main inorganic sulphur species, possibly formed by abiotic re-oxidation of H2S with Fe(III)oxides subsequent to sulphate reduction. These results provide first insights into intense sulphur redox cycling in a hydrocarbon contaminant plume, which widens the perspective of redox processes and microbial interactions ongoing in contaminated aquifers.

Fe(III) oxides accelerate microbial nitrate reduction and electricity generation by Klebsiella pneumoniae L17.

PubMed

Liu, Tongxu; Li, Xiaomin; Zhang, Wei; Hu, Min; Li, Fangbai

2014-06-01

Klebsiella pneumoniae L17 is a fermentative bacterium that can reduce iron oxide and generate electricity under anoxic conditions, as previously reported. This study reveals that K. pneumoniae L17 is also capable of dissimilatory nitrate reduction, producing NO2(-), NH4(+), NO and N2O under anoxic conditions. The presence of Fe(III) oxides (i.e., α-FeOOH, γ-FeOOH, α-Fe2O3 and γ-Fe2O3) significantly accelerates the reduction of nitrate and generation of electricity by K. pneumoniae L17, which is similar to a previous report regarding another fermentative bacterium, Bacillus. No significant nitrate reduction was observed upon treatment with Fe(2+) or α-FeOOH+Fe(2+), but a slight facilitation of nitrate reduction and electricity generation was observed upon treatment with L17+Fe(2+). This result suggests that aqueous Fe(II) or mineral-adsorbed Fe(II) cannot reduce nitrate abiotically but that L17 can catalyze the reduction of nitrate and generation of electricity in the presence of Fe(II) (which might exist as cell surface-bound Fe(II)). To rule out the potential effect of Fe(II) produced by L17 during microbial iron reduction, treatments with the addition of TiO2 or Al2O3 instead of Fe(III) oxides also exhibited accelerated microbial nitrate reduction and electricity generation, indicating that cell-mineral sorption did account for the acceleration effect. However, the acceleration caused by Fe(III) oxides is only partially attributed to the cell surface-bound Fe(II) and cell-mineral sorption but may be driven by the iron oxide conduction band-mediated electron transfer from L17 to nitrate or an electrode, as proposed previously. The current study extends the diversity of bacteria of which nitrate reduction and electricity generation can be facilitated by the presence of iron oxides and confirms the positive role of Fe(III) oxides on microbial nitrate reduction and electricity generation by particular fermentative bacteria in anoxic environments. Copyright © 2014 Elsevier Inc. All rights reserved.

Microbial Nitrogen Cycle Hotspots in the Plant-Bed/Ditch System of a Constructed Wetland with N2O Mitigation.

PubMed

Wang, Shanyun; Wang, Weidong; Liu, Lu; Zhuang, Linjie; Zhao, Siyan; Su, Yu; Li, Yixiao; Wang, Mengzi; Wang, Cheng; Xu, Liya; Zhu, Guibing

2018-05-24

Artificial microbial nitrogen (N) cycle hotspots in the plant-bed/ditch system were developed and investigated based on intact core and slurry assays measurement using isotopic tracing technology, quantitative PCR and high-throughput sequencing. By increasing hydraulic retention time and periodically fluctuating water level in heterogeneous riparian zones, hotspots of anammox, nitrification, denitrification, ammonium (NH 4 + ) oxidation, nitrite (NO 2 - ) oxidation, nitrate (NO 3 - ) reduction and DNRA were all stimulated at the interface sediments, with the abundance and activity being about 1-3 orders of magnitude higher than those in nonhotspots. Isotopic pairing experiments revealed that in microbial hotspots, nitrite sources were higher than the sinks, and both NH 4 + oxidation (55.8%) and NO 3 - reduction (44.2%) provided nitrite for anammox, which accounted for 43.0% of N-loss and 44.4% of NH 4 + removal in riparian zones but did not involve nitrous oxide (N 2 O) emission risks. High-throughput analysis identified that bacterial quorum sensing mediated this anammox hotspot with B.fulgida dominating the anammox community, but it was B. anammoxidans and Jettenia sp. that contributed more to anammox activity. In the nonhotspot zones, the NO 2 - source (NO 3 - reduction dominated) was lower than the sink, limiting the effects on anammox. The in situ N 2 O flux measurement showed that the microbial hotspot had a 27.1% reduced N 2 O emission flux compared with the nonhotspot zones.

Mechanism of microbial flotation using Thiobacillus ferrooxidans for pyrite suppression.

PubMed

Ohmura, N; Kitamura, K; Saiki, H

1993-03-15

Microbial desulfurization might be developed as a new process for the removal of pyrite sulfur from coal sluries such as coal-water mixture (CWM). An application of iron-oxidizing bacterium Thiobacillus ferrooxidans to flotation would shorten the periods of the microbial removal of pyrite from some weeks by leaching methods to a few minutes. The floatability of pyrite in flotation was mainly reduced by T. ferrooxidans itself rather than by other microbial substances in bacterial culture as additive of flotation liquor. Floatability was suppressed within a few seconds by bacterial contact. The suppression was proportional to increasing the number of cells observed between bacterial adhesion and the suppression of floatability. If 25% of the total pyrite surface area covered with the bacteria, pyrite floatability would be completely depressed. Bacteria that lost their iron-oxidizing activities by sodium cyanide treatment were also able to adhere to pyrite and reduced pyrite floatability as much as normal bacteria did. Thiobacillus ferrooxidans ATCC 23270, T-1, 9, and 11, which had different iron-oxidizing abilities, suppressed floatability to similar-levels. The oxidizing ability of bacteria did not influence the suppressing effect. These results showed the mechanism of the suppression of pyrite floatability by bacteria. Quick bacterial adhesion to pyrite induced floatability suppression by changing the surface property from hydrophobic. The quick adhesion of the bacterium was the novel function which worked to change the surface property of pyrite to remove it from coal. (c) 1993 John Wiley & Sons, Inc.

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

PubMed Central

Wilbanks, Elizabeth G; Jaekel, Ulrike; Salman, Verena; Humphrey, Parris T; Eisen, Jonathan A; Facciotti, Marc T; Buckley, Daniel H; Zinder, Stephen H; Druschel, Gregory K; Fike, David A; Orphan, Victoria J

2014-01-01

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria. PMID:24428801

Microbial communities in carbonate rocks-from soil via groundwater to rocks.

PubMed

Meier, Aileen; Singh, Manu K; Kastner, Anne; Merten, Dirk; Büchel, Georg; Kothe, Erika

2017-09-01

Microbial communities in soil, groundwater, and rock of two sites in limestone were investigated to determine community parameters differentiating habitats in two lithostratigraphic untis. Lower Muschelkalk and Middle Muschelkalk associated soils, groundwater, and rock samples showed different, but overlapping microbial communities linked to carbon fluxes. The microbial diversities in soil were highest, groundwater revealed overlapping taxa but lower diversity, and rock samples were predominantly characterized by endospore forming bacteria and few archaea. Physiological profiles could establish a differentiation between habitats (soil, groundwater, rock). From community analyses and physiological profiles, different element cycles in limestone could be identified for the three habitats. While in soil, nitrogen cycling was identified as specific determinant, in rock methanogenesis linked carbonate rock to atmospheric methane cycles. These patterns specifically allowed for delineation of lithostratigraphic connections to physiological parameters. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Resistant Starch and β-Glucan Combination on Oxidative Stability, Frying Performance, Microbial Count and Shelf Life of Prebiotic Sausage During
Refrigerated Storage

PubMed Central

2017-01-01

Summary This study aims to evaluate the performance of two types of prebiotic sausages formulated with resistant starch (RS) and β-glucan (BG) extract (in ratios of 2.22:1.33 and 2.75:1.88) during frying and chilled storage. The oxidative stability indices and microbial counts were determined. The incorporation of two types of prebiotic dietary fibre increased frying loss and oil absorption. However, the moisture content of prebiotic sausages after production was higher than of conventional sausages and it decreased significantly during storage. The use of sausage sample containing 2.22% RS and 1.33% BG as a recommended formulation can decrease fat oxidation of sausages during storage due to antioxidant properties of BG extract, but higher levels of RS and BG could not be used due to further increase in fat oxidation. Total viable count increased up to day 45 and decreased afterwards. The addition of BG extract improved the antioxidant properties of sausages. Additionally, the antimicrobial properties of BG and moisture reduction could inhibit microbial growth. Moreover, the addition of RS caused an increase in thiobarbituric acid and peroxide values. PMID:29540982

Characteristics of environmental correlations between iron (oxyhydr)oxide nanoparticles and microbial activity

NASA Astrophysics Data System (ADS)

Tamura, T.; Kyono, A.; Muratani, M.

2014-12-01

Nanoparticulate iron oxides and oxyhydroxides with large surface area and high chemical reactivity cause the immobilization of heavy metals and the provision of essential nutrients to organisms. Environmental correlations between microbial activity and nanomorphology of iron (oxyhydr)oxides are significantly important for earth surface processes. In this study, we characterize iron (oxyhydr)oxide nanoparticles and microorganisms in natural lake sediments and describe their association observed between particle nanostructures and microbial species. About 40 cm depth of boring core sample was collected from Lake Kasumigaura, Lake Ushiku, Kokai River and Lake Tega, Japan. To distinguish both iron nanoparticles and growing bacterial colonies with depths, boring core samples were divided into three to five pieces. Particle morphologies, size, aggregation states, mineral species, and microorganisms were observed by transmission electron microscopy (TEM), X-ray diffraction (XRD), and rRNA gene sequences. Redox potential and pH of the lake sediments were also measured. The core sample from top is mainly composed of quartz of coarse-grained materials, while that from bottom is of ferrihydrite of fine grained materials. The authors will show the results of experiments and discuss the interrelation between iron nanoparticles and microorganisms.

Microbial mats in the Black Sea that anaerobically oxidise methane

NASA Astrophysics Data System (ADS)

Nauhaus, K.; Knittel, K.; Krüger, M.; Boetius, A.; Michaelis, W.; Widdel, F.

2003-04-01

Reef-forming microbial mats were recovered from methane seeps in anoxic waters of the northwestern Black Sea (BS) shelf. The microbial mats consist mainly of archaea (ANME-1 cluster) and sulfate-reducing bacteria (Desulfosarcina/Desulfococcus group). Laboratory incubations with homogenized subsamples of the mats revealed their ability for the anaerobic oxidation of methane (AOM). The phylogentic relationship of the sulfate reducing partner is the same as in the AOM consortia studied in sediment samples from a methane hydrate area (Hydrate Ridge (HR), Oregon, USA (1,2)). The archaeal partner however belongs to a different cluster than in the HR samples (ANME-2). Methane oxidation is coupled to sulfate reduction in a 1:1 stoichiometry. Elevated methane partial pressures (0.1 to 1.1 MPa) increased the sulfate reduction rates in the Black Sea samples only two-fold in contrast to 5-fold in HR samples. The optimal temperature for the BS samples is between 10 and 25^oC. In both samples AOM was not taking place if typical inhibitors for sulfate-reduction or methanogenesis were added, thus indicating a syntrophic relationship between the partner organisms. The intermediate that is exchanged between the methane oxidizing archaea and the sulfate-reducing bacterium is still unknown. Additions of the possible intermediates (Acetate, Formate, Hydrogen) did not result in higher sulfate reduction rates in the absence of methane. (1) Boetius, A. et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature. 407: 623--626 (2) Nauhaus, K., Boetius, A., Krüger, M., Widdel, F. (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ. Microbiol. 4 (5): 296--305

Enterosalivary nitrate metabolism and the microbiome: Intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health.

PubMed

Koch, Carl D; Gladwin, Mark T; Freeman, Bruce A; Lundberg, Jon O; Weitzberg, Eddie; Morris, Alison

2017-04-01

Recent insights into the bioactivation and signaling actions of inorganic, dietary nitrate and nitrite now suggest a critical role for the microbiome in the development of cardiac and pulmonary vascular diseases. Once thought to be the inert, end-products of endothelial-derived nitric oxide (NO) heme-oxidation, nitrate and nitrite are now considered major sources of exogenous NO that exhibit enhanced vasoactive signaling activity under conditions of hypoxia and stress. The bioavailability of nitrate and nitrite depend on the enzymatic reduction of nitrate to nitrite by a unique set of bacterial nitrate reductase enzymes possessed by specific bacterial populations in the mammalian mouth and gut. The pathogenesis of pulmonary hypertension (PH), obesity, hypertension and CVD are linked to defects in NO signaling, suggesting a role for commensal oral bacteria to shape the development of PH through the formation of nitrite, NO and other bioactive nitrogen oxides. Oral supplementation with inorganic nitrate or nitrate-containing foods exert pleiotropic, beneficial vascular effects in the setting of inflammation, endothelial dysfunction, ischemia-reperfusion injury and in pre-clinical models of PH, while traditional high-nitrate dietary patterns are associated with beneficial outcomes in hypertension, obesity and CVD. These observations highlight the potential of the microbiome in the development of novel nitrate- and nitrite-based therapeutics for PH, CVD and their risk factors. Copyright © 2017 Elsevier Inc. All rights reserved.

Data-Driven Microbial Modeling for Soil Carbon Decomposition and Stabilization

NASA Astrophysics Data System (ADS)

Luo, Yiqi; Chen, Ji; Chen, Yizhao; Feng, Wenting

2017-04-01

Microorganisms have long been known to catalyze almost all the soil organic carbon (SOC) transformation processes (e.g., decomposition, stabilization, and mineralization). Representing microbial processes in Earth system models (ESMs) has the potential to improve projections of SOC dynamics. We have recently examined (1) relationships of microbial functions with environmental factors and (2) microbial regulations of decomposition and other key soil processes. According to three lines of evidence, we have developed a data-driven enzyme (DENZY) model to simulate soil microbial decomposition and stabilization. First, our meta-analysis of 64 published field studies showed that field experimental warming significantly increased soil microbial communities abundance, which is negatively correlated with the mean annual temperature. The negative correlation indicates that warming had stronger effects in colder than warmer regions. Second, we found that the SOC decomposition, especially the transfer between labile SOC and protected SOC, is nonlinearly regulated by soil texture parameters, such as sand and silt contents. Third, we conducted a global analysis of the C-degrading enzyme activities, soil respiration, and SOC content under N addition. Our results show that N addition has contrasting effects on cellulase (hydrolytic C-degrading enzymes) and ligninase (oxidative C-degrading enzymes) activities. N-enhanced cellulase activity contributes to the minor stimulation of soil respiration whereas N-induced repression on ligninase activity drives soil C sequestration. Our analysis links the microbial extracellular C-degrading enzymes to the SOC dynamics at ecosystem scales across scores of experimental sites around the world. It offers direct evidence that N-induced changes in microbial community and physiology play fundamental roles in controlling the soil C cycle. Built upon those three lines of empirical evidence, the DENZY model includes two enzyme pools and explicitly characterizes two classes of extracellular enzyme activities: one that degrades organic molecules containing both C and N (e.g., chitin or protein) and another that degrades only C (e.g., cellulose). The DENZY model assumes that the microbes allocate resources to different enzyme pools so as to exactly satisfy microbial CN ratio stoichiometry in response to changes in climate conditions and soil attributes. The DENZY model can simulate differential effects of nitrogen fertilization on the two groups of enzymes and thus soil respiration and SOC dynamics. We will select field experimental sites to test the DENZY model. With increasing amounts of available observations and data synthesis, this DENZY model will be better parameterized and have a potential to reveal how responses of microbial enzymes to environmental changes regulate soil carbon decomposition and stabilization.

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

PubMed Central

Pasulka, Alexis L.; Marlow, Jeffrey J.; Grupe, Benjamin M.; Levin, Lisa A.

2015-01-01

ABSTRACT Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages. PMID:26695630

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester.

PubMed

Hagen, Live H; Frank, Jeremy A; Zamanzadeh, Mirzaman; Eijsink, Vincent G H; Pope, Phillip B; Horn, Svein J; Arntzen, Magnus Ø

2017-01-15

In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg/liter NH 3 -N). The microbial community was strongly dominated (76% of all 16S rRNA amplicon sequences) by populations closely related to the proteolytic bacterium Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies. Genome reconstructions provided metabolic insight into the microbes that performed biomass deconstruction and fermentation, including the deeply branching phyla Dictyoglomi and Planctomycetes and the candidate phylum "Atribacteria" These biomass degraders were complemented by a synergistic network of microorganisms that convert key fermentation intermediates (fatty acids) via syntrophic interactions with hydrogenotrophic methanogens to ultimately produce methane. Interpretation of the proteomics data also suggested activity of a Methanosaeta phylotype acclimatized to high ammonia levels. In particular, we report multiple novel phylotypes proposed as syntrophic acetate oxidizers, which also exert expression of enzymes needed for both the Wood-Ljungdahl pathway and β-oxidation of fatty acids to acetyl coenzyme A. Such an arrangement differs from known syntrophic oxidizing bacteria and presents an interesting hypothesis for future studies. Collectively, these findings provide increased insight into active metabolic roles of uncultured phylotypes and presents new synergistic relationships, both of which may contribute to the stability of the biogas reactor. Biogas production through anaerobic digestion of organic waste provides an attractive source of renewable energy and a sustainable waste management strategy. A comprehensive understanding of the microbial community that drives anaerobic digesters is essential to ensure stable and efficient energy production. Here, we characterize the intricate microbial networks and metabolic pathways in a thermophilic biogas reactor. We discuss the impact of frequently encountered microbial populations as well as the metabolism of newly discovered novel phylotypes that seem to play distinct roles within key microbial stages of anaerobic digestion in this stable high-temperature system. In particular, we draft a metabolic scenario whereby multiple uncultured syntrophic acetate-oxidizing bacteria are capable of syntrophically oxidizing acetate as well as longer-chain fatty acids (via the β-oxidation and Wood-Ljundahl pathways) to hydrogen and carbon dioxide, which methanogens subsequently convert to methane. Copyright © 2016 American Society for Microbiology.

Environmental context affects microbial ecophysiological mechanisms underpinning soil carbon storage under different land use

NASA Astrophysics Data System (ADS)

Malik, A. A.; Puissant, J.; Buckeridge, K. M.; Goodall, T.; Jehmlich, N.; Chowdhury, S.; Gleixner, G.; Griffiths, R.

2017-12-01

Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of organic matter in soil. Increasing evidence now exists to suggest that microbial biomass contributes significantly to soil organic carbon formation. However, we do not fully understand the microbial mechanisms of organic matter processing and this hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically link key microbial ecophysiological traits to soil carbon storage in temperate grassland habitats ranging in land use from pristine species-rich grasslands to intensive croplands in 56 different soils across Britain. Physiological mechanisms of soil microorganisms were assessed using stable carbon isotope tracing and soil proteomics. Through spatial patterns and path analysis of structural equation modeling we discern two distinct pH-related mechanisms of soil carbon storage and highlight that the response of these mechanistic indicators is shaped by the environmental context. Land use intensification in low pH soils that increases soil pH above a threshold value ( 6.2) leads to loss of carbon due to increased microbial degradation as a result of lower acid retardation of organic matter decomposition. On the contrary, the loss of carbon through intensification in high pH (> 6.2) soils was linked to decreased microbial biomass and reduced carbon use efficiency that was linked to tradeoffs with stress alleviation and resource acquisition. We conclude that land use intensification-induced changes in soil pH can be used as a proxy to determine the effect of land management strategies on microbial soil carbon cycling processes and emphasize that more extensive land management practices at higher soil pH have greater potential for soil carbon storage through increased microbial metabolic efficiency, whereas in acidic soils abiotic factors exert a greater influence on the fate of soil carbon.

New insight into stratification of anaerobic methanotrophs in cold seep sediments.

PubMed

Roalkvam, Irene; Jørgensen, Steffen Leth; Chen, Yifeng; Stokke, Runar; Dahle, Håkon; Hocking, William Peter; Lanzén, Anders; Haflidason, Haflidi; Steen, Ida Helene

2011-11-01

Methane seepages typically harbor communities of anaerobic methane oxidizers (ANME); however, knowledge about fine-scale vertical variation of ANME in response to geochemical gradients is limited. We investigated microbial communities in sediments below a white microbial mat in the G11 pockmark at Nyegga by 16S rRNA gene tag pyrosequencing and real-time quantitative PCR. A vertical stratification of dominating ANME communities was observed at 4 cmbsf (cm below seafloor) and below in the following order: ANME-2a/b, ANME-1 and ANME-2c. The ANME-1 community was most numerous and comprised single or chains of cells with typical rectangular morphology, accounting up to 89.2% of the retrieved 16S rRNA gene sequences. Detection rates for sulfate-reducing Deltaproteobacteria possibly involved in anaerobic oxidation of methane were low throughout the core. However, a correlation in the abundance of Candidate division JS-1 with ANME-2 was observed, indicating involvement in metabolisms occurring in ANME-2-dominated horizons. The white microbial mat and shallow sediments were dominated by organisms affiliated with Sulfurovum (Epsilonproteobacteria) and Methylococcales (Gammaproteobacteria), suggesting that aerobic oxidation of sulfur and methane is taking place. In intermediate horizons, typical microbial groups associated with methane seeps were recovered. The data are discussed with respect to co-occurring microbial assemblages and interspecies interactions. FEMS Microbiology Ecology © 2011 Federation of Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original Norwegian works.

Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

2017-04-01

Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial community responds different to environmental change dependent on the soil moisture regime. These results are important to include in future modeling efforts to predict changes in soil-atmosphere exchange of CH4 under global change.

Biomineralization associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals

USGS Publications Warehouse

Zhang, G.; Dong, H.; Jiang, H.; Kukkadapu, R.K.; Kim, J.; Eberl, D.; Xu, Z.

2009-01-01

Iron-reducing and oxidizing microorganisms gain energy through reduction or oxidation of iron, and by doing so play an important role in the geochemical cycling of iron. This study was undertaken to investigate mineral transformations associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals. A fluid sample from the 2450 m depth of the Chinese Continental Scientific Drilling project was collected, and Fe3+-reducing and Fe2+-oxidizing microorganisms were enriched. The enrichment cultures displayed reduction of Fe3+ in nontronite and ferric citrate, and oxidation of Fe2+ in vivianite, siderite, and monosulfide (FeS). Additional experiments verified that the iron reduction and oxidation was biological. Oxidation of FeS resulted in the formation of goethite, lepidocrocite, and ferrihydrite as products. Although our molecular microbiological analyses detected Thermoan-aerobacter ethanolicus as a predominant organism in the enrichment culture, Fe3+ reduction and Fe2+ oxidation may be accomplished by a consortia of organisms. Our results have important environmental and ecological implications for iron redox cycling in solid minerals in natural environments, where iron mineral transformations may be related to the mobility and solubility of inorganic and organic contaminants.

Metabolic activity of subterranean microbial communities in deep granitic groundwater supplemented with methane and H2

PubMed Central

Pedersen, Karsten

2013-01-01

It was previously concluded that opposing gradients of sulphate and methane, observations of 16S ribosomal DNA sequences displaying great similarity to those of anaerobic methane-oxidizing Archaea and a peak in sulphide concentration in groundwater from a depth of 250–350 m in Olkiluoto, Finland, indicated proper conditions for methane oxidation with sulphate. In the present research, pressure-resistant, gas-tight circulating systems were constructed to enable the investigation of attached and unattached anaerobic microbial populations from a depth of 327 m in Olkiluoto under in situ pressure (2.4 MPa), diversity, dissolved gas and chemistry conditions. Three parallel flow cell cabinets were configured to allow observation of the influence on microbial metabolic activity of 11 mℳ methane, 11 mℳ methane plus 10 mℳ H2 or 2.1 mℳ O2 plus 7.9 mℳ N2 (that is, air). The concentrations of these gases and of organic acids and carbon, sulphur chemistry, pH and Eh, ATP, numbers of cultivable micro-organisms, and total numbers of cells and bacteriophages were subsequently recorded under batch conditions for 105 days. The system containing H2 and methane displayed microbial reduction of 0.7 mℳ sulphate to sulphide, whereas the system containing only methane resulted in 0.2 mℳ reduced sulphate. The system containing added air became inhibited and displayed no signs of microbial activity. Added H2 and methane induced increasing numbers of lysogenic bacteriophages per cell. It appears likely that a microbial anaerobic methane-oxidizing process coupled to acetate formation and sulphate reduction may be ongoing in aquifers at a depth of 250–350 m in Olkiluoto. PMID:23235288

Geomicrobiology and hopanoid content of sulfidic subsurface vent biofilms, Little Salt Spring, Florida

NASA Astrophysics Data System (ADS)

Yang, E.; Schaperdoth, I.; Albrecht, H.; Freeman, K. H.; Macalady, J. L.

2008-12-01

Sulfide-rich, oxygen-poor environments are widespread in the subsurface and were prevalent at the earth's surface during critical intervals in the geologic past. Modern microbial communities in sulfidic niches have the potential to shed light on the biogeochemistry and biosignatures of anoxia and euxinia in earth history. Caves and sinkholes provide rare windows into microbially-dominated, sulfidic subsurface environments that are otherwise difficult and expensive to access. Little Salt Spring (Sarasota County, Florida) is a cover-collapse sinkhole lake with oxic surface water and anoxic, sulfidic bottom water (Alvarez Zarikian 2005). The site is famous for excellent preservation of human and animal archaeological remains (Clausen 1979), and its microbiology has never been investigated. Abundant white biofilms develop seasonally at a warm vent that feeds into the anoxic bottom water at 73 m depth below the water surface. The biofilms are of interest both as potential sources of biomarker compounds and because of their likely role in sulfuric acid production and limestone dissolution (speleogenesis). Biofilm samples were collected by expert science divers and investigated using microscopy, nucleic acid, and lipid analytical methods. Microscopy of the live biofilm revealed clusters of microbial filaments with holdfasts and dendritic, sulfur-rich colonial structures similar to those described in the 1960s for Thiobacterium, a sulfur-oxidizing genus with undetermined phylogeny. A 16S rDNA library constructed from the biofilm was split into three main phylotypes, with multiple clones representing (1) a Betaproteobacterial clade with no cultivated representatives, (2) filamentous Epsilonproteobacteria, and (3) a major bacterial lineage without named isolates (OP11/OD2). A full cycle rRNA approach is currently underway to link 16S rDNA phylotypes with specific populations in the biofilm. We confirmed using fluorescence in situ hybridization (FISH) that abundant filamentous cells with holdfasts are Epsilonproteobacteria. Additional FISH experiments will target the Betaproteobacterial and OP11/OD2 phylotypes retrieved by cloning. Based on HPLC-MS analyses, the biofilm contains at least 5 membrane hopanoid structures distinct from the suite of hopanoids present in sinking organic particles from the photic zone of the sinkhole. Future efforts will be aimed at linking hopanoid structures to specific sulfur-oxidizing populations and to geochemical parameters such as sulfide and oxygen concentrations. References Alvarez Zarikian,C. A., P. K. Swart, J. A. Gifford, P. L. Blackwelder, Palaeogeography, Palaeoclimatology, Palaeoecology 225, 134 (2005). Clausen, C. J., A. D. Cohen, C. Emiliani, J. A. Holman, J. J. Stipp, Science 203, 609 (1979).

Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

PubMed Central

Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

2015-01-01

Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

Geochemistry and microbial community composition across a range of acid mine drainage impact and implications for the Neoarchean-Paleoproterozoic transition

NASA Astrophysics Data System (ADS)

Havig, Jeff R.; Grettenberger, Christen; Hamilton, Trinity L.

2017-06-01

Streams impacted by acid mine drainage (AMD, also known as acid rock drainage) represent local environmental and ecological disasters; however, they may also present an opportunity to study microbial communities in environments analogous to past conditions. Neoarchean continents had streams and rivers replete with detrital pyrites. Following the emergence of oxygenic photosynthesis, Cyanobacteria colonized streams and rivers on continental surfaces. The combination of labile detrital pyrite grains and locally produced O2 generated by Cyanobacteria produced ideal conditions for pyrite oxidation similar to that found at modern AMD-impacted sites. To explore the connection of modern sites to ancient conditions, we sampled sites that exhibited a range of AMD-impact (e.g., pH from 2.1 to 7.9 [Fe2+] up to 5.2 mmol/L [SO42-] from 0.3 to 52.4 mmol/L) and found (i) nearly all analytes correlated to sulfate concentration; (ii) all sites exhibited the predominance of a single taxon most closely related to Ferrovum myxofaciens, an Fe-oxidixing betaproteoabacterium capable of carbon and nitrogen fixation, and (iii) signs of potential inorganic carbon limitation and nitrogen cycling. From these findings and building on the work of others, we present a conceptual model of continental surfaces during the Neoarchean and Paleoproterozoic linking local O2 production to pyrite oxidation on continental surfaces to sulfate production and delivery to nearshore environments. The delivery of sulfate drives sulfate reduction and euxinia—favoring anoxygenic photosynthesis over cyanobacterial O2 generation in near-continent/shelf marine environments.

Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities.

PubMed

Eduok, Samuel; Ferguson, Robert; Jefferson, Bruce; Villa, Raffaella; Coulon, Frédéric

2017-12-31

To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800mgkg -1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p=0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Temperature dependence and coupling of iron and arsenic reduction and release during flooding of a contaminated soil.

PubMed

Weber, Frank-Andreas; Hofacker, Anke F; Voegelin, Andreas; Kretzschmar, Ruben

2010-01-01

Arsenic (As) in soils and sediments is commonly mobilized when anoxic conditions promote microbial iron (Fe) and As reduction. Recent laboratory studies and field observations have suggested a decoupling between Fe and As reduction and release, but the links between these processes are still not well understood. In microcosm experiments, we monitored the formation of Fe(II) and As(III) in the porewater and in the soil solid-phase during flooding of a contaminated floodplain soil at temperatures of 23, 14, and 5 degrees C. At all temperatures, flooding induced the development of anoxic conditions and caused increasing concentrations of dissolved Fe(II) and As(III). Decreasing the temperature from 23 to 14 and 5 degrees C strongly slowed down soil reduction and Fe and As release. Speciation of As in the soil solid-phase by X-ray absorption spectroscopy (XAS) and extraction of the Fe(II) that has formed by reductive Fe(III) (hydr)oxide dissolution revealed that less than 3.9% of all As(III) and less than 3.2% of all Fe(II) formed during 52 days of flooding at 23 degrees C were released into the porewater, although 91% of the initially ascorbate-extractable Fe and 66% of the total As were reduced. The amount of total As(III) formed during soil reduction was linearly correlated to the amount of total Fe(II) formed, indicating that the rate of As(V) reduction was controlled by the rate of microbial Fe(III) (hydr)oxide reduction.

Nitrous oxide emissions from soils: how well do we understand the processes and their controls?

PubMed Central

Butterbach-Bahl, Klaus; Baggs, Elizabeth M.; Dannenmann, Michael; Kiese, Ralf; Zechmeister-Boltenstern, Sophie

2013-01-01

Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N2O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N2O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N2O to dinitrogen (N2) have increased our understanding of N2O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N2O emissions to changes in environmental conditions, land management and land use. PMID:23713120

Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

USGS Publications Warehouse

Haack, S.K.; Garchow, H.; Klug, M.J.; Forney, L.J.

1995-01-01

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

Could Methane Oxidation in Lakes Be Enhanced by Eutrophication?

NASA Astrophysics Data System (ADS)

Van Grinsven, S.; Villanueva, L.; Harrison, J.; S Sinninghe Damsté, J.

2017-12-01

Climate change and eutrophication both affect aquatic ecosystems. Eutrophication is caused by high nutrient inputs, leading to algal blooms, oxygen depletion and disturbances of the natural balances in aquatic systems. Methane, a potent greenhouse gas produced biologically by anaerobic degradation of organic matter, is often released from the sediments of lakes and marine systems to overlying water and the atmosphere. Methane oxidation, a microbial methane consumption process, can limit methane emission from lakes and reservoirs by 50-80%. Here, we studied methane oxidation in a seasonally stratified reservoir: Lacamas Lake in Washington, USA. We found this lake has a large summer storage capacity of methane in its deep water layer, with a very active microbial community capable of oxidizing exceptionally high amounts of methane. The natural presence of terminal electron acceptors is, however, too low to support these high potential rates. Addition of eutrophication-related nutrients such as nitrate and sulfate increased the methane removal rates by 4 to 7-fold. The microbial community was studied using 16S rRNA gene amplicon sequencing and preliminary results indicate the presence of a relatively unknown facultative anaerobic methane oxidizer of the genus Methylomonas, capable of using nitrate as an electron donor. Experiments in which anoxic and oxic conditions were rapidly interchanged showed this facultative anaerobic methane oxidizer has an impressive flexibility towards large, rapid changes in environmental conditions and this feature might be key to the unexpectedly high methane removal rates in eutrophied and anoxic watersheds.

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep

NASA Astrophysics Data System (ADS)

Mendes, Stephanie D.; Redmond, Molly C.; Voigritter, Karl; Perez, Christian; Scarlett, Rachel; Valentine, David L.

2015-03-01

Simple hydrocarbon gases containing two to four carbons (ethane, propane, and butane) are among the most abundant compounds present in petroleum reservoirs, and are introduced into the ocean through natural seepage and industrial discharge. Yet little is known about the bacterial consumption of these compounds in ocean waters. To assess the timing by which microbes metabolize these gases, we conducted a three-phase study that tested and applied a radiotracer-based method to quantify the oxidation rates of ethane, propane, and butane in fresh seawater samples. Phase 1 involved the synthesis of tritiated ethane, propane, and butane using Grignard reagents and tritiated water. Phase 2 was a systematic assessment of experimental conditions, wherein the indigenous microbial community was found to rapidly oxidize ethane, propane, and butane. Phase 3 was the application of this tritium method near the Coal Oil Point seeps, offshore California. Spatial and temporal patterns of ethane, propane, and butane oxidation down current from the hydrocarbon seeps demonstrated that >99% of these gases are metabolized within 1.3 days following initial exposure. The oxidation of ethane outpaced oxidation of propane and butane with patterns indicating the microbial community responded to these gases by rapid adaptation or growth. Methane oxidation responded the slowest in plume waters. Estimates based on the observed metabolic rates and carbon mass balance suggest that ethane, propane, and butane-consuming microorganisms may transiently account for a majority of the total microbial community in these impacted waters.

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco).

PubMed

Bruneel, Odile; Mghazli, N; Hakkou, R; Dahmani, I; Filali Maltouf, A; Sbabou, L

2017-07-01

In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland

NASA Astrophysics Data System (ADS)

Bomberg, Malin; Lamminmäki, Tiina; Itävaara, Merja

2016-11-01

The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is high, but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. Between 1.7 × 104 and 1.2 × 106 bacterial or archaeal sequence reads per sample were obtained. These sequences revealed that up to 95 and 99 % of the bacterial and archaeal sequences obtained from the 12 samples, respectively, belonged to only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3- and 6-fold more bacterial and archaeal taxa. The metabolic properties of the microbial communities were predicted using PICRUSt. The approximate estimation showed that the metabolic pathways commonly included fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation, and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle, and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier environmental conditions, but could also be induced again if changes in their living conditions occur.

Metagenomic and Biochemical Characterizations of Sulfur Oxidation Metabolism in Uncultured Large Sausage-Shaped Bacterium in Hot Spring Microbial Mats

PubMed Central

Tamaki, Hideyuki; Kamagata, Yoichi; Hanada, Satoshi

2012-01-01

So-called “sulfur-turf” microbial mats in sulfide containing hot springs (55–70°C, pH 7.3–8.3) in Japan were dominated by a large sausage-shaped bacterium (LSSB) that is closely related to the genus Sulfurihydrogenibium. Several previous reports proposed that the LSSB would be involved in sulfide oxidation in hot spring. However, the LSSB has not been isolated yet, thus there has been no clear evidence showing whether it possesses any genes and enzymes responsible for sulfide oxidation. To verify this, we investigated sulfide oxidation potential in the LSSB using a metagenomic approach and subsequent biochemical analysis. Genome fragments of the LSSB (a total of 3.7 Mb sequence including overlapping fragments) were obtained from the metagenomic fosmid library constructed from genomic DNA of the sulfur-turf mats. The sequence annotation clearly revealed that the LSSB possesses sulfur oxidation-related genes coding sulfide dehydrogenase (SD), sulfide-quinone reductase and sulfite dehydrogenase. The gene encoding SD, the key enzyme for sulfide oxidation, was successfully cloned and heterologously expressed in Escherichia coli. The purified recombinant enzyme clearly showed SD activity with optimum temperature and pH of 60°C and 8.0, respectively, which were consistent with the environmental conditions in the hot spring where the sulfur-turf thrives. Furthermore, the affinity of SD to sulfide was relatively high, which also reflected the environment where the sulfide could be continuously supplied. This is the first report showing that the LSSB harbors sulfide oxidizing metabolism adapted to the hot spring environment and can be involved in sulfide oxidation in the sulfur-turf microbial mats. PMID:23185438

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils.

PubMed

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability.

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

PubMed Central

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability. PMID:27486444

The role of biology in planetary evolution: cyanobacterial primary production in low‐oxygen Proterozoic oceans

PubMed Central

Bryant, Donald A.; Macalady, Jennifer L.

2016-01-01

Summary Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well‐preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and membrane‐derived hydrocarbon molecules that are still challenging to interpret. However, it is clear from the sulfur isotope record and other geochemical proxies that the production of oxygen or oxidizing power radically changed Earth's surface and atmosphere during the Proterozoic Eon, pushing it away from the more reducing conditions prevalent during the Archean. In addition to ancient rocks, our reconstruction of Earth's redox evolution is informed by our knowledge of biogeochemical cycles catalysed by extant biota. The emergence of oxygenic photosynthesis in ancient cyanobacteria represents one of the most impressive microbial innovations in Earth's history, and oxygenic photosynthesis is the largest source of O 2 in the atmosphere today. Thus the study of microbial metabolisms and evolution provides an important link between extant biota and the clues from the geologic record. Here, we consider the physiology of cyanobacteria (the only microorganisms capable of oxygenic photosynthesis), their co‐occurrence with anoxygenic phototrophs in a variety of environments and their persistence in low‐oxygen environments, including in water columns as well as mats, throughout much of Earth's history. We examine insights gained from both the rock record and cyanobacteria presently living in early Earth analogue ecosystems and synthesize current knowledge of these ancient microbial mediators in planetary redox evolution. Our analysis supports the hypothesis that anoxygenic photosynthesis, including the activity of metabolically versatile cyanobacteria, played an important role in delaying the oxygenation of Earth's surface ocean during the Proterozoic Eon. PMID:26549614

Modelling geochemical and microbial consumption of dissolved oxygen after backfilling a high level radiactive waste repository.

PubMed

Yang, Changbing; Samper, Javier; Molinero, Jorge; Bonilla, Mercedes

2007-08-15

Dissolved oxygen (DO) left in the voids of buffer and backfill materials of a deep geological high level radioactive waste (HLW) repository could cause canister corrosion. Available data from laboratory and in situ experiments indicate that microbes play a substantial role in controlling redox conditions near a HLW repository. This paper presents the application of a coupled hydro-bio-geochemical model to evaluate geochemical and microbial consumption of DO in bentonite porewater after backfilling of a HLW repository designed according to the Swedish reference concept. In addition to geochemical reactions, the model accounts for dissolved organic carbon (DOC) respiration and methane oxidation. Parameters for microbial processes were derived from calibration of the REX in situ experiment carried out at the Aspö underground laboratory. The role of geochemical and microbial processes in consuming DO is evaluated for several scenarios. Numerical results show that both geochemical and microbial processes are relevant for DO consumption. However, the time needed to consume the DO trapped in the bentonite buffer decreases dramatically from several hundreds of years when only geochemical processes are considered to a few weeks when both geochemical reactions and microbially-mediated DOC respiration and methane oxidation are taken into account simultaneously.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2.

PubMed

Jin, Qusheng; Kirk, Matthew F

2016-01-01

Geological carbon sequestration captures CO 2 from industrial sources and stores the CO 2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO 2 concentration. This study uses biogeochemical modeling to explore the influence of CO 2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO 2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO 2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO 2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO 2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.

Thermodynamic and Kinetic Response of Microbial Reactions to High CO2

PubMed Central

Jin, Qusheng; Kirk, Matthew F.

2016-01-01

Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses. PMID:27909425

Microbial iron oxidation in the Arctic tundra and its implications for biogeochemical cycling.

PubMed

Emerson, David; Scott, Jarrod J; Benes, Joshua; Bowden, William B

2015-12-01

The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long -149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Arsenophilic Bacterial Processes in Searles Lake: A Salt-saturated, Arsenic-rich, Alkaline Soda Lake.

NASA Astrophysics Data System (ADS)

Oremland, R. S.; Kulp, T. R.; Hoeft, S. E.; Miller, L. G.; Swizer Blum, J.; Stolz, J. F.

2005-12-01

Searles Lake, located in the Mojave Desert of California, is essentially a chemically-similar, concentrated version of Mono Lake, but having a much higher salinity (e.g., 340 vs. 90 g/L) and a greater dissolved inorganic arsenic content in its brine (e.g., 3.9 vs. 0.2 mM). The source of all this arsenic ultimately comes from hydrothermal spring inputs, thereby underscoring the importance of volcanic and fluvial processes in transporting this toxic element into these closed basin lakes. Nonetheless, the presence of microbial activities with regard to respiration of arsenate oxyanions under anaerobic conditions and the oxidation of arsenite oxyanions under aerobic conditions can be inferred from porewater profiles taken from handcores retrieved beneath Searles Lake's salt crust. Sediment slurry incubations confirmed biological arsenate respiration and arsenite oxidation, with the former processes notably enhanced by provision of the inorganic electron donor sulfide or H2. Hence, arsenic-linked chemo-autotrophy appears to be an important means of carbon fixation in this system. Subsequent efforts using 73As-arsenate as radiotracer detected dissimilatory arsenate reduction activity down the length of the core, but we were unable to detect any evidence for sulfate-reduction using 35S-sulfate. An extremely halophilic anaerobic bacterium of the order Haloanaerobiales [strain SLAS-1] was isolated from the sediments that grew via arsenate respiration using lactate or sulfide as its electron donors. These results show that, unlike sulfate-reduction, arsenic metabolism (i.e., both oxidation of arsenite and dissimilatory reduction of arsenate) is operative and even vigorous under the extreme conditions of salt-saturation and high pH. The occurrence of arsenophilic microbial processes in Searles Lake is relevant to the search for extant or extinct microbial life on Mars. It is evident from surface imagery that Mars had past episodes of volcanism, fluvial transport, and most likely brine concentration reactions (e.g., evapo- and cryo-concentration) occurring in its early Noachian/Hesperian epochs. We speculate that these processes may have created arsenic-rich, dense brines on the Martian surface or even within its underlying regolith. Whether such brines persisted long enough for prokaryotic life to evolve in them, and if so, was such life capable of adapting to and exploiting arsenic redox reactions for the purpose of generating metabolic energy remain tantalizing, but still hypothetical questions.

LIPID ANALYSIS TO DETERMINE THE EFFECT OF A SOURCE REMEDIAL TECHNOLOGY IN MICROBIAL ECOLOGY

EPA Science Inventory

Microbial community structures and related changes in the subsurface environment were investigated following in situ chemical oxidation (ISCO) treatment at Launch Complex 34, Cape Canaveral Air Station, Florida. The site has dense non-aqueous phase (DNAPL) concentrations of TCE ...

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium.

PubMed

Vardanyan, Narine; Sevoyan, Garegin; Navasardyan, Taron; Vardanyan, Arevik

2018-05-28

Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.

Total RNA concentration as an index of microbial activity and oxygen supply in an oxidation ditch.

PubMed

Kanazawa, Nobuhiro; Urushigawa, Yoshikuni; Yato, Yumio

2005-06-01

Total RNA and chromosomal DNA concentrations at a municipal wastewater treatment plant with an oxidation ditch (OD) were monitored for 1.5 years using commercial extraction kits for DNA and RNA. No parameters correlated with the chromosomal DNA concentration. The total RNA concentration exhibited better correlation than the solids retention time and the mixed liquor suspended solids with the removal rate of total organic carbon, and can be regarded as an index of microbial activity. The total RNA concentration varied with a cycle of one year and increased at lower water temperatures in this OD. When diffusion theory was taken into account, it was found that the oxygen dissolution rate increased at lower temperature, and a small change in the oxygen dissolution rate caused a large variation in microbial activity and also affected nitrification and denitrification. The information was insufficient to clarify the various reaction relationships, but total RNA concentration will likely be useful as an index of microbial activity in actual wastewater treatment reactors.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, Paul M.

2000-01-01

 The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Microbial degradation of chloroethenes in groundwater systems

USGS Publications Warehouse

Bradley, P.M.

2000-01-01

The chloroethenes, tetrachloroethene (PCE) and trichloroethene (TCE) are among the most common contaminants detected in groundwater systems. As recently as 1980, the consensus was that chloroethene compounds were not significantly biodegradable in groundwater. Consequently, efforts to remediate chloroethene-contaminated groundwater were limited to largely unsuccessful pump-and-treat attempts. Subsequent investigation revealed that under reducing conditions, aquifer microorganisms can reductively dechlorinate PCE and TCE to the less chlorinated daughter products dichloroethene (DCE) and vinyl chloride (VC). Although recent laboratory studies conducted with halorespiring microorganisms suggest that complete reduction to ethene is possible, in the majority of groundwater systems reductive dechlorination apparently stops at DCE or VC. However, recent investigations conducted with aquifer and stream-bed sediments have demonstrated that microbial oxidation of these reduced daughter products can be significant under anaerobic redox conditions. The combination of reductive dechlorination of PCE and TCE under anaerobic conditions followed by anaerobic microbial oxidation of DCE and VC provides a possible microbial pathway for complete degradation of chloroethene contaminants in groundwater systems.

Microbial Photoelectrosynthesis for Self-Sustaining Hydrogen Generation.

PubMed

Lu, Lu; Williams, Nicholas B; Turner, John A; Maness, Pin-Ching; Gu, Jing; Ren, Zhiyong Jason

2017-11-21

Current artificial photosynthesis (APS) systems are promising for the storage of solar energy via transportable and storable fuels, but the anodic half-reaction of water oxidation is an energy intensive process which in many cases poorly couples with the cathodic half-reaction. Here we demonstrate a self-sustaining microbial photoelectrosynthesis (MPES) system that pairs microbial electrochemical oxidation with photoelectrochemical water reduction for energy efficient H 2 generation. MPES reduces the overall energy requirements thereby greatly expanding the range of semiconductors that can be utilized in APS. Due to the recovery of chemical energy from waste organics by the mild microbial process and utilization of cost-effective and stable catalyst/electrode materials, our MPES system produced a stable current of 0.4 mA/cm 2 for 24 h without any external bias and ∼10 mA/cm 2 with a modest bias under one sun illumination. This system also showed other merits, such as creating benefits of wastewater treatment and facile preparation and scalability.

In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.

2009-09-23

An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to thosemore » of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.« less

Analysis of key microbial community during the start-up of anaerobic ammonium oxidation process with paddy soil as inoculated sludge.

PubMed

Xu, Xianglong; Liu, Guohua; Wang, Yuanyuan; Zhang, Yuankai; Wang, Hao; Qi, Lu; Wang, Hongchen

2018-02-01

A sequencing batch reactor (SBR)-anaerobic ammonium oxidation (anammox) system was started up with the paddy soil as inoculated sludge. The key microbial community structure in the system along with the enrichment time was investigated by using molecular biology methods (e.g., high-throughput 16S rRNA gene sequencing and quantitative PCR). Meanwhile, the influent and effluent water quality was continuously monitored during the whole start-up stage. The results showed that the microbial diversity decreased as the operation time initially and increased afterwards, and the microbial niches in the system were redistributed. The anammox bacterial community structure in the SBR-anammox system shifted during the enrichment, the most dominant anammox bacteria were CandidatusJettenia. The maximum biomass of anammox bacteria achieved 1.68×10 9 copies/g dry sludge during the enrichment period, and the highest removal rate of TN achieved around 75%. Copyright © 2017. Published by Elsevier B.V.

Segregation and Alteration of Phenolic and Aliphatic Components of Root and Leaf Litter by Detritivores and Microbes

NASA Astrophysics Data System (ADS)

Filley, T. R.; Altmann, J.; Szlavecz, K. A.; Kalbitz, K.; Gamblin, D.; Nierop, K.

2012-12-01

The physical and microbial transformation of plant detritus in the litter layer and soil is accompanied by chemical separation of progressively soluble fractions and their movement into the rhizosphere driving subsequent soil processes. We investigated the combined action of specific detritivores, microbial decay, and leaching on the chemical separation of plant aromatic and aliphatic components from root, wood, and leaf tissue using 13C-TMAH thermochemolysis. This method enabled the simultaneous analysis of hydrolyzable tannin and lignin fragments, substituted fatty acids, and condensed tannin composition and revealed process-specific chemical transformations to plant secondary compounds. Long-term incubation and field sampling demonstrated how plant residues are progressively leached of the water soluble, oxidized fragments generated through decay. The residues appeared only slightly altered, in the case of brown rot wood, or enriched in aliphatic fragments, in the case of leaf and root tissue. Water extractable fractions were always selectively dominated by polyphenolics, either as demethylated lignin or tannins, and nearly devoid of aliphatic materials, despite high concentrations in the starting materials. Additionally, for plant materials with high tannin contents, such as pine needles, consumption and passage through some arthropod guts revealed what appeared to be microbially-mediated methylation of phenols, and a loss of tannins in leachates. These findings are indications for an in-situ phenol detoxification mechanism. This research provides important information regarding the links between biochemical decay and the chemical nature of organic matter removed and remaining in the soil profile.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Redox Transformations of Arsenic Oxyanions in Periphyton Communities

PubMed Central

Kulp, Thomas R.; Hoeft, Shelley E.; Oremland, Ronald S.

2004-01-01

Periphyton (Cladophora sp.) samples from a suburban stream lacking detectable dissolved As were able to reduce added As(V) to As(III) when incubated under anoxic conditions and, conversely, oxidized added As(III) to As(V) with aerobic incubation. Both types of activity were abolished in autoclaved controls, thereby demonstrating its biological nature. The reduction of As(V) was inhibited by chloramphenicol, indicating that it required the synthesis of new protein. Nitrate also inhibited As(V) reduction, primarily because it served as a preferred electron acceptor to which the periphyton community was already adapted. However, part of the inhibition was also caused by microbial reoxidation of As(III) linked to nitrate. Addition of [14C]glucose to anoxic samples resulted in the production of 14CO2, suggesting that the observed As(V) reduction was a respiratory process coupled to the oxidation of organic matter. The population density of As(V)-reducing bacteria within the periphyton increased with time and with the amount of As(V) added, reaching values as high as ∼106 cells ml−1 at the end of the incubation. This indicated that dissimilatory As(V) reduction in these populations was linked to growth. However, As(V)-respiring bacteria were found to be present, albeit at lower numbers (∼102 ml−1), in freshly sampled periphyton. These results demonstrate the presence of a bacterial population within the periphyton communities that is capable of two key arsenic redox transformations that were previously studied in As-contaminated environments, which suggests that these processes are widely distributed in nature. This assumption was reinforced by experiments with estuarine samples of Cladophora sericea in which we detected a similar capacity for anaerobic As(V) reduction and aerobic As(III) oxidation. PMID:15528502

Redox transformations of arsenic oxyanions in periphyton communities

USGS Publications Warehouse

Kulp, T.R.; Hoeft, S.E.; Oremland, R.S.

2004-01-01

Periphyton (Cladophora sp.) samples from a suburban stream lacking detectable dissolved As were able to reduce added As(V) to As(III) when incubated under anoxic conditions and, conversely, oxidized added As(III) to As(V) with aerobic incubation. Both types of activity were abolished in autoclaved controls, thereby demonstrating its biological nature. The reduction of As(V) was inhibited by chloramphenicol, indicating that it required the synthesis of new protein. Nitrate also inhibited As(V) reduction, primarily because it served as a preferred electron acceptor to which the periphyton community was already adapted. However, part of the inhibition was also caused by microbial reoxidation of As(III) linked to nitrate. Addition of [ 14C]glucose to anoxic samples resulted in the production of 14CO2, suggesting that the observed As(V) reduction was a respiratory process coupled to the oxidation of organic matter. The population density of As(V)-reducing bacteria within the periphyton increased with time and with the amount of As(V) added, reaching values as high as ???106 cells ml-1 at the end of the incubation. This indicated that dissimilatory As(V) reduction in these populations was linked to growth. However, As(V)-respiring bacteria were found to be present, albeit at lower numbers (???102 ml-1), in freshly sampled periphyton. These results demonstrate the presence of a bacterial population within the periphyton communities that is capable of two key arsenic redox transformations that were previously studied in As-contaminated environments, which suggests that these processes are widely distributed in nature. This assumption was reinforced by experiments with estuarine samples of Cladophora sericea in which we detected a similar capacity for anaerobic As(V) reduction and aerobic As(III) oxidation.

Interactions between microbial iron reduction and metal geochemistry: effect of redox cycling on transition metal speciation in iron bearing sediments.

PubMed

Cooper, D Craig; Picardal, Flynn F; Coby, Aaron J

2006-03-15

Microbial iron reduction is an important biogeochemical process that can affect metal geochemistry in sediments through direct and indirect mechanisms. With respectto Fe(III) (hydr)oxides bearing sorbed divalent metals, recent reports have indicated that (1) microbial reduction of goethite/ferrihydrite mixtures preferentially removes ferrihydrite, (2) this process can incorporate previously sorbed Zn(II) into an authigenic crystalline phase that is insoluble in 0.5 M HCl, (3) this new phase is probably goethite, and (4) the presence of nonreducible minerals can inhibit this transformation. This study demonstrates that a range of sorbed transition metals can be selectively sequestered into a 0.5 M HCl insoluble phase and that the process can be stimulated through sequential steps of microbial iron reduction and air oxidation. Microbial reduction experiments with divalent Cd, Co, Mn, Ni, Pb, and Zn indicate that all metals save Mn experienced some sequestration, with the degree of metal incorporation into the 0.5 M HCl insoluble phase correlating positively with crystalline ionic radius at coordination number = 6. Redox cycling experiments with Zn adsorbed to synthetic goethite/ferrihydrite or iron-bearing natural sediments indicate that redox cycling from iron reducing to iron oxidizing conditions sequesters more Zn within authigenic minerals than microbial iron reduction alone. In addition, the process is more effective in goethite/ferrihydrite mixtures than in iron-bearing natural sediments. Microbial reduction alone resulted in a -3x increase in 0.5 M HCl insoluble Zn and increased aqueous Zn (Zn-aq) in goethite/ferrihydrite, but did not significantly affect Zn speciation in natural sediments. Redox cycling enhanced the Zn sequestration by approximately 12% in both goethite/ferrihydrite and natural sediments and reduced Zn-aq to levels equal to the uninoculated control in goethite/ferrihydrite and less than the uninoculated control in natural sediments. These data suggest that in situ redox cycling may serve as an effective method for

Microbial As(III) Oxidation in Water Treatment Plant Filters

EPA Science Inventory

Arsenic exists in two oxidation states in water - arsenite [As(III)] and arsenate [As(V)]. As(III) is relatively mobile in water and difficult to remove by arsenic-removal treatment processes. Source waters that contain As(III) must add a strong oxidant such as free chlorine or p...

A meta-analysis of soil exoenzyme responses to simulated climate change

NASA Astrophysics Data System (ADS)

Gebhardt, M.; Espinosa, N. J.; Blankinship, J. C.; Gallery, R. E.

2017-12-01

Microorganisms produce extracellular enzymes to decompose plant matter and drive biogeochemical transformations in soils. Climate change factors, such as warming and altered precipitation patterns, can impact enzyme activity through both direct and indirect mechanisms. Although many individual studies have examined how soil exoenzyme activities respond to climate change manipulations, there is disagreement surrounding the direction of these responses. We performed a synthesis of published studies to examine the influence of warming and altered precipitation on microbial exoenzyme activity. We found that warming increased enzyme activity with a more pronounced effect for oxidative relative to hydrolytic enzymes. Reduced precipitation consistently decreased exoenzyme activity. These responses, however, varied by season, biome, and enzyme type. The majority of studies fitting our criteria (e.g., experiments lasting a minimum of one growing season, paired treatments and controls) were located in North America and Europe. Inferences from this analysis therefore exclude many important ecosystems such as hyper-arid, wetlands, and artic systems. Carbon degrading enzyme activities were less sensitive to climate change manipulations when compared to phosphorus and nitrogen degrading enzyme activities. Linking enzyme activity to biogeochemical processes requires concomitant measurements of organic and inorganic carbon pools, mineralogy, nutrients, microbial biomass and community structure, and heterotrophic respiration within individual studies. Furthermore, linking these parameters to climate and environmental factors will require a comprehensive and consistent inclusion of biotic and abiotic variables among researchers and experiments. Globally, soils contain the largest carbon pools. Understanding the impacts of large-scale perturbations on soil enzyme activity will help to constrain predictions on the fate of biogeochemical transformations and improve model projections.

The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale.

PubMed

Włodarczyk, Agnieszka; Lirski, Maciej; Fogtman, Anna; Koblowska, Marta; Bidziński, Grzegorz; Matlakowska, Renata

2018-01-01

Black shales are one of the largest reservoirs of fossil organic carbon and inorganic reduced sulfur on Earth. It is assumed that microorganisms play an important role in the transformations of these sedimentary rocks and contribute to the return of organic carbon and inorganic sulfur to the global geochemical cycles. An outcrop of deep subterrestrial ~256-million-year-old Kupferschiefer black shale was studied to define the metabolic processes of the deep biosphere important in transformations of organic carbon and inorganic reduced sulfur compounds. This outcrop was created during mining activity 12 years ago and since then it has been exposed to the activity of oxygen and microorganisms. The microbial processes were described based on metagenome and metaproteome studies as well as on the geochemistry of the rock. The microorganisms inhabiting the subterrestrial black shale were dominated by bacterial genera such as Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhizobium , and Sulfuricaulis . This study on black shale was the first to detect archaea and fungi, represented by Nitrososphaera and Aspergillus genera, respectively. The enzymatic oxidation of fossil aliphatic and aromatic hydrocarbons was mediated mostly by chemoorganotrophic bacteria, but also by archaea and fungi. The dissimilative enzymatic oxidation of primary reduced sulfur compounds was performed by chemolithotrophic bacteria. The geochemical consequences of microbial activity were the oxidation and dehydrogenation of kerogen, as well as oxidation of sulfide minerals.

Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

PubMed

Florio, Alessandro; Felici, Barbara; Migliore, Melania; Dell'Abate, Maria Teresa; Benedetti, Anna

2016-05-01

A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

The results of a field and laboratory investigation of unconsolidated sediments contaminated by petroleum hydrocarbons and undergoing natural biodegradation are presented. Fundamental to geophysical investigations of hydrocarbon impacted sediments is the assessment of how microbi...

Impact of the gut microbiota on inflammation, obesity, and metabolic disease.

PubMed

Boulangé, Claire L; Neves, Ana Luisa; Chilloux, Julien; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

2016-04-20

The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have been associated with increased metabolic and immune disorders in animals and humans. Molecular interactions linking the gut microbiota with host energy metabolism, lipid accumulation, and immunity have also been identified. However, the exact mechanisms that link specific variations in the composition of the gut microbiota with the development of obesity and metabolic diseases in humans remain obscure owing to the complex etiology of these pathologies. In this review, we discuss current knowledge about the mechanistic interactions between the gut microbiota, host energy metabolism, and the host immune system in the context of obesity and metabolic disease, with a focus on the importance of the axis that links gut microbes and host metabolic inflammation. Finally, we discuss therapeutic approaches aimed at reshaping the gut microbial ecosystem to regulate obesity and related pathologies, as well as the challenges that remain in this area.

Different Intestinal Microbial Profile in Over-Weight and Obese Subjects Consuming a Diet with Low Content of Fiber and Antioxidants

PubMed Central

Fernández-Navarro, Tania; Salazar, Nuria; Gutiérrez-Díaz, Isabel; de los Reyes-Gavilán, Clara G.; Gueimonde, Miguel; González, Sonia

2017-01-01

Obesity has been related to an increased risk of multiple diseases in which oxidative stress and inflammation play a role. Gut microbiota has emerged as a mediator in this interaction, providing new mechanistic insights at the interface between fat metabolism dysregulation and obesity development. Our aim was to analyze the interrelationship among obesity, diet, oxidative stress, inflammation and the intestinal microbiota in 68 healthy adults (29.4% normal-weight). Diet was assessed through a food frequency questionnaire and converted into nutrients and dietary compounds using food composition tables. The intestinal microbiota was assessed by quantitative PCR, fecal short chain fatty acids by gas chromatography and serum biomarkers by standard protocols. Higher levels of malondialdehyde (MDA), C reactive protein (CRP), serum leptin, glucose, fat percentage and the intestinal Lactobacillus group were found in the obese people. Cluster analysis of body mass index, fat mass, glucose, LDL/HDL ratio, leptin, MDA and CRP classified the subjects into two groups. The levels of the intestinal Bacteroides-Prevotella-Porphyromonas group were lower in the cluster and linked to a higher pro-oxidant and pro-inflammatory status, whose individuals also had lower intake of fruits, dried fruits, and fish. These results could be useful for designing strategies targeted to obesity prevention. PMID:28555008

Preparation of ordered mesoporous and macroporous thermoplastic polyurethane surfaces for potential medical applications.

PubMed

Chennell, Philip; Feschet-Chassot, Emmanuelle; Sautou, Valérie; Mailhot-Jensen, Bénédicte

2018-05-01

Thermoplastic polyurethanes are widely used in medical devices. In order to limit some of their shortfalls, like microbial attachment, surfaces modifications can be required. In this work, a two-step replication method was used to create ordered macroporous and mesoporous thermoplastic polyurethane surfaces using anodic aluminum oxide as master template. The intermediate mould materials that were tested were polystyrene and a polyacrylate resin with inorganic filler. All obtained surfaces were characterized by scanning electron microscopy. The initial anodic aluminum oxide surfaces possessed macro or mesopores, function of anodization conditions. The intermediate mould structure correctly replicated the pattern, but the polystyrene surface structures (pillars) were less resistant than the polyacrylate resin ones. The thermoplastic polyurethane pattern possessed macropores or mesopores of about 130 nm or 46 nm diameter and of about 300 nm or 99 nm interpore distances, respectively, in accordance with the initial pattern. Thermoplastic polyurethanes pore depth was however less than initial anodic aluminum oxide pore depth, linked to an incomplete replication during intermediate mould preparation (60 to 90% depth replication). The correct replication of the original pattern confirms that this novel fabrication method is a promising route for surface patterning of thermoplastic polyurethanes that could be used for medical applications.

Microbial degradation of lignin: how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this

PubMed Central

Ruiz‐Dueñas, Francisco J.; Martínez, Ángel T.

2009-01-01

Summary Lignin is the second most abundant constituent of the cell wall of vascular plants, where it protects cellulose towards hydrolytic attack by saprophytic and pathogenic microbes. Its removal represents a key step for carbon recycling in land ecosystems, as well as a central issue for industrial utilization of plant biomass. The lignin polymer is highly recalcitrant towards chemical and biological degradation due to its molecular architecture, where different non‐phenolic phenylpropanoid units form a complex three‐dimensional network linked by a variety of ether and carbon–carbon bonds. Ligninolytic microbes have developed a unique strategy to handle lignin degradation based on unspecific one‐electron oxidation of the benzenic rings in the different lignin substructures by extracellular haemperoxidases acting synergistically with peroxide‐generating oxidases. These peroxidases posses two outstanding characteristics: (i) they have unusually high redox potential due to haem pocket architecture that enables oxidation of non‐phenolic aromatic rings, and (ii) they are able to generate a protein oxidizer by electron transfer to the haem cofactor forming a catalytic tryptophanyl‐free radical at the protein surface, where it can interact with the bulky lignin polymer. The structure–function information currently available is being used to build tailor‐made peroxidases and other oxidoreductases as industrial biocatalysts. PMID:21261911

Advanced Oxidation Process sanitation of hatching eggs reduces Salmonella in broiler chicks

USDA-ARS?s Scientific Manuscript database

Reduction of Salmonella contamination of eggs is important in improving the microbial food safety of poultry and poultry products. Developing interventions to reduce Salmonella contamination of eggs is important to improving the microbial quality of eggs entering the hatchery. Previously, the hydr...

Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

NASA Astrophysics Data System (ADS)

Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

2014-12-01

Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a detailed understanding of the vertical and longitudinal distribution of microbial taxa throughout CP. These studies will provide insight into the operation of the microbial Fe redox cycle, demonstrating how genomic properties relate to and control geochemical conditions with depth and distance in a Fe-rich, neutral pH geothermal environment.

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

PubMed

Hubalek, Valerie; Wu, Xiaofen; Eiler, Alexander; Buck, Moritz; Heim, Christine; Dopson, Mark; Bertilsson, Stefan; Ionescu, Danny

2016-10-01

Little research has been conducted on microbial diversity deep under the Earth's surface. In this study, the microbial communities of three deep terrestrial subsurface aquifers were investigated. Temporal community data over 6 years revealed that the phylogenetic structure and community dynamics were highly dependent on the degree of isolation from the earth surface biomes. The microbial community at the shallow site was the most dynamic and was dominated by the sulfur-oxidizing genera Sulfurovum or Sulfurimonas at all-time points. The microbial community in the meteoric water filled intermediate aquifer (water turnover approximately every 5 years) was less variable and was dominated by candidate phylum OD1. Metagenomic analysis of this water demonstrated the occurrence of key genes for nitrogen and carbon fixation, sulfate reduction, sulfide oxidation and fermentation. The deepest water mass (5000 year old waters) had the lowest taxon richness and surprisingly contained Cyanobacteria. The high relative abundance of phylogenetic groups associated with nitrogen and sulfur cycling, as well as fermentation implied that these processes were important in these systems. We conclude that the microbial community patterns appear to be shaped by the availability of energy and nutrient sources via connectivity to the surface or from deep geological processes.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Microbial community response reveals underlying mechanism of industrial-scale manganese sand biofilters used for the simultaneous removal of iron, manganese and ammonia from groundwater.

PubMed

Zhang, Yu; Sun, Rui; Zhou, Aijuan; Zhang, Jiaguang; Luan, Yunbo; Jia, Jianna; Yue, Xiuping; Zhang, Jie

2018-01-08

Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied. The effluent were all far below the permitted concentration level in the current drinking water standard. Pyrosequencing illustrated that shifts in microbial community structure were observed in the microbial samples from different depths of filter. Microbial networks showed that the microbial community structure in the middle- and deep-layer samples was similar, in which a wide range of manganese-oxidizing bacteria was identified. By contrast, canonical correlation analysis showed that the bacteria capable of ammonia-oxidizing and nitrification was enriched in the upper-layer, i.e., Propionibacterium, Nitrosomonas, Nitrosomonas and Candidatus Nitrotoga. The stable biofilm on the biofilter media, created by certain microorganisms from the groundwater microflora, played a crucial role in the simultaneous removal of the three pollutants.

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

NASA Astrophysics Data System (ADS)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

Effect of magnesium oxide nanoparticles on microbial diversity and removal performance of sequencing batch reactor.

PubMed

Ma, Bingrui; Yu, Naling; Han, Yuetong; Gao, Mengchun; Wang, Sen; Li, Shanshan; Guo, Liang; She, Zonglian; Zhao, Yangguo; Jin, Chunji; Gao, Feng

2018-06-13

The performance, microbial enzymatic activity and microbial community of a sequencing batch reactor (SBR) have been explored under magnesium oxide nanoparticles (MgO NPs) stress. The NH 4 + -N removal efficiency kept relatively stable during the whole operational process. The MgO NPs at 30-60 mg/L slightly restrained the removal of chemical oxygen demand (COD), and the presence of MgO NPs also affected the denitrification and phosphorus removal. The specific oxygen uptake rate, nitrifying and denitrifying rates, phosphorus removal rate, and microbial enzymatic activities distinctly varied with the increase of MgO NPs concentration. The appearance of MgO NPs promoted more reactive oxygen species generation and lactate dehydrogenase leakage from activated sludge, suggesting that MgO NPs had obvious toxicity to activated sludge in the SBR. The protein and polysaccharide contents of extracellular polymeric substances from activated sludge increased with the increase of MgO NPs concentration. The microbial richness and diversity at different MgO NPs concentrations obviously varied at the phylum, class and genus levels due to the biological toxicity of MgO NPs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial utilization of low molecular weight organic substrates in soil depends on their carbon oxidation state

NASA Astrophysics Data System (ADS)

Gunina, Anna; Smith, Andrew; Jones, Davey; Kuzyakov, Yakov

2017-04-01

Removal of low molecular weight organic substances (LMWOS), originating from plants and microorganisms, from soil solution is regulated by microbial uptake. In addition to the concentration of LMWOS in soil solution, the chemical properties of each substance (e.g. C oxidation state, number of C atoms, number of -COOH groups) can affect their uptake and subsequent partitioning of C within the soil microbial community. The aim of this study was to trace the initial fate of three dominant classes of LMWOS in soil (sugars, carboxylic and amino acids), including their removal from solution and utilization by microorganisms, and to reveal the effect of substance chemical properties on these processes. Soil solution, spiked at natural abundance levels with 14C-labelled glucose, fructose, malate, succinate, formate, alanine or glycine, was added to the soil and 14C was traced in the dissolved organic carbon (DOC), CO2, cytosol and soil organic carbon (SOC) over 24 hours. The half-life time of all LMWOS in the DOC (T1 /2-solution) varied between 0.6-5.0 min showing extremely fast initial uptake of LMWOS. The T1 /2-solution of substances was dependent on C oxidation state, indicating that less oxidized organic substances (with C oxidation state "0") were retained longer in soil solution than oxidized substances. The LMWOS-C T1 /2-fast, characterizing the half-life time of 14C in the fast mineralization pool, ranged between 30 and 80 min, with the T1 /2-fast of carboxylic acids (malic acid) being the fastest and the T1 /2-fast of amino acids (glycine) being the slowest. An absence of correlation between T1 /2-fast and either C oxidation state, number of C atoms, or number of -COOH groups suggests that intercellular metabolic pathways are more important for LMWOS transformation in soil than their basic chemical properties. The CO2 release during LMWOS mineralization accounted for 20-90% of 14C applied. Mineralization of LMWOS was the least for sugars and the greatest for carboxylic (formic) acids, whereas the 14C incorporations into cytosol and SOC were opposite. The portion of LMWOS mineralized to CO2 increased with their C oxidation state corresponding to the decrease of C incorporated into the cytosol and SOC pools. The ratio of 14C incorporated into cytosol to 14C incorporated into CO2 pool ranged between 0.03 and 1.19, being the lowest for carboxylic acids and highest for sugars, and decreased with substances C oxidation state. Thus, the C oxidation state is one of the crucial parameter of LMWOS determining their partitioning between two main C fluxes: mineralization and microbial stabilization/immobilization. Our data suggests that the uptake of common LMWOS from soil solution by microorganisms and final LMWOS-C partitioning within microbial biomass may be possible to predict from the physicochemical properties of the substance.

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens.

PubMed

Peltoniemi, Krista; Laiho, Raija; Juottonen, Heli; Kiikkilä, Oili; Mäkiranta, Päivi; Minkkinen, Kari; Pennanen, Taina; Penttilä, Timo; Sarjala, Tytti; Tuittila, Eeva-Stiina; Tuomivirta, Tero; Fritze, Hannu

2015-07-01

Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer

PubMed Central

Avrahamov, N; Antler, G; Yechieli, Y; Gavrieli, I; Joye, S B; Saxton, M; Turchyn, A V; Sivan, O

2014-01-01

Geochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ13CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed (34ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate-driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment. PMID:25039851

Anaerobic oxidation of methane by sulfate in hypersaline groundwater of the Dead Sea aquifer.

PubMed

Avrahamov, N; Antler, G; Yechieli, Y; Gavrieli, I; Joye, S B; Saxton, M; Turchyn, A V; Sivan, O

2014-11-01

Geochemical and microbial evidence points to anaerobic oxidation of methane (AOM) likely coupled with bacterial sulfate reduction in the hypersaline groundwater of the Dead Sea (DS) alluvial aquifer. Groundwater was sampled from nine boreholes drilled along the Arugot alluvial fan next to the DS. The groundwater samples were highly saline (up to 6300 mm chlorine), anoxic, and contained methane. A mass balance calculation demonstrates that the very low δ(13) CDIC in this groundwater is due to anaerobic methane oxidation. Sulfate depletion coincident with isotope enrichment of sulfur and oxygen isotopes in the sulfate suggests that sulfate reduction is associated with this AOM. DNA extraction and 16S amplicon sequencing were used to explore the microbial community present and were found to be microbial composition indicative of bacterial sulfate reducers associated with anaerobic methanotrophic archaea (ANME) driving AOM. The net sulfate reduction seems to be primarily controlled by the salinity and the available methane and is substantially lower as salinity increases (2.5 mm sulfate removal at 3000 mm chlorine but only 0.5 mm sulfate removal at 6300 mm chlorine). Low overall sulfur isotope fractionation observed ((34) ε = 17 ± 3.5‰) hints at high rates of sulfate reduction, as has been previously suggested for sulfate reduction coupled with methane oxidation. The new results demonstrate the presence of sulfate-driven AOM in terrestrial hypersaline systems and expand our understanding of how microbial life is sustained under the challenging conditions of an extremely hypersaline environment. © 2014 The Authors. Geobiology Published by John Wiley & Sons Ltd.

Effect of advanced oxidation on N-nitrosodimethylamine (NDMA) formation and microbial ecology during pilot-scale biological activated carbon filtration.

PubMed

Li, Dong; Stanford, Ben; Dickenson, Eric; Khunjar, Wendell O; Homme, Carissa L; Rosenfeldt, Erik J; Sharp, Jonathan O

2017-04-15

Water treatment combining advanced oxidative processes with subsequent exposure to biological activated carbon (BAC) holds promise for the attenuation of recalcitrant pollutants. Here we contrast oxidation and subsequent biofiltration of treated wastewater effluent employing either ozone or UV/H 2 O 2 followed by BAC during pilot-scale implementation. Both treatment trains largely met target water quality goals by facilitating the removal of a suite of trace organics and bulk water parameters. N-nitrosodimethylamine (NDMA) formation was observed in ozone fed BAC columns during biofiltration and to a lesser extent in UV/H 2 O 2 fed columns and was most pronounced at 20 min of empty bed contact time (EBCT) when compared to shorter EBCTs evaluated. While microbial populations were highly similar in the upper reaches, deeper samples revealed a divergence within and between BAC filtration systems where EBCT was identified to be a significant environmental predictor for shifts in microbial populations. The abundance of Nitrospira in the top samples of both columns provides an explanation for the oxidation of nitrite and corresponding increases in nitrate concentrations during BAC transit and support interplay between nitrogen cycling with nitrosamine formation. The results of this study demonstrate that pretreatments using ozone versus UV/H 2 O 2 impart modest differences to the overall BAC microbial population structural and functional attributes, and further highlight the need to evaluate NDMA formation prior to full-scale implementation of BAC in potable reuse applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Environmental implications of herbicide resistance: soil biology and ecology

USDA-ARS?s Scientific Manuscript database

Soil microbial community structure and activity are clearly linked to plant communities established in natural and agricultural ecosystems. A limited number of studies confirm that weeds alter their soil environment and select for specific microbial communities in the rhizosphere. Such rhizosphere m...

Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

USDA-ARS?s Scientific Manuscript database

Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji-Won

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component comprising at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes duringmore » consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.« less

Microbial oxidation of lithospheric organic carbon in rapidly eroding tropical mountain soils.

PubMed

Hemingway, Jordon D; Hilton, Robert G; Hovius, Niels; Eglinton, Timothy I; Haghipour, Negar; Wacker, Lukas; Chen, Meng-Chiang; Galy, Valier V

2018-04-13

Lithospheric organic carbon ("petrogenic"; OC petro ) is oxidized during exhumation and subsequent erosion of mountain ranges. This process is a considerable source of carbon dioxide (CO 2 ) to the atmosphere over geologic time scales, but the mechanisms that govern oxidation rates in mountain landscapes are poorly constrained. We demonstrate that, on average, 67 ± 11% of the OC petro initially present in bedrock exhumed from the tropical, rapidly eroding Central Range of Taiwan is oxidized in soils, leading to CO 2 emissions of 6.1 to 18.6 metric tons of carbon per square kilometer per year. The molecular and isotopic evolution of bulk OC and lipid biomarkers during soil formation reveals that OC petro remineralization is microbially mediated. Rapid oxidation in mountain soils drives CO 2 emission fluxes that increase with erosion rate, thereby counteracting CO 2 drawdown by silicate weathering and biospheric OC burial. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

An Experiment in Autotrophic Fermentation: Microbial Oxidation of Hydrogen Sulfide.

ERIC Educational Resources Information Center

Sublette, Kerry L.

1989-01-01

Described is an experiment which uses an autotrophic bacterium to anaerobically oxidize hydrogen sulfide to sulfate in a batch-stirred tank reactor. Discusses background information, experimental procedure, and sample results of this activity. (CW)

Effects of inorganic carbon on the nitrous oxide emissions and microbial diversity of an anaerobic ammonia oxidation reactor.

PubMed

Zhang, Wenjie; Wang, Dunqiu; Jin, Yue

2018-02-01

Inorganic carbon (IC) is important for anaerobic ammonium oxidation (anammox). In this study, the effects of the IC concentration on N 2 O emissions and microbial diversity in an anammox reactor were investigated. N 2 O emissions were positively correlated with IC concentrations, and IC concentrations in the range of 55-130 mg/L were optimal, considering the nitrogen removal rate and N 2 O emissions. High IC concentrations resulted in the formation of CaCO 3 on the surface of anammox granules, which impacted the diffusion conditions of the substrate. Microbial community analysis indicated that high IC concentrations decreased the populations of specific bacteria, such as Achromobacter spanius strain YJART-7, Achromobacter xylosoxidans strain IHB B 6801, and Denitratisoma oestradiolicum clone 20b_15. D. oestradiolicum clone 20b_15 appeared to be the key contributor to N 2 O emissions. High N 2 O emissions may result from changes in organic carbon sources, which lead to denitrification by D. oestradiolicum clone 20b_15. Copyright © 2017 Elsevier Ltd. All rights reserved.

Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

PubMed

Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

2017-07-01

Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

Sensitivity of Geoelectrical Measurements to the Presence of Bacteria in Porous Media

EPA Science Inventory

We investigated the sensitivity of low frequency electrical measurements (0.1-1000 Hz) to (i) microbial cell density, (ii) live and dead cells, and (iii) microbial attachment onto mineral surfaces of clean quartz sands and iron oxide coated sands. Three strains of Pseudomonas aer...

Soil nitrogen dynamics as an indicator for longleaf pine restoration

Treesearch

George L. McCaskill; Shibu Jose; Ashvini Chauhan; Andrew V. Ogram

2017-01-01

Assessing the status of soil nutrients with their corresponding microbial communities provides important information about degraded soils during the restoration of coastal wet pine forests. Net nitrogen mineralization, nitrogen-oxidizing bacteria (NOB), and soil microbial biomass were compared with patch-derived volume along a 110-year longleaf pine (Pinus...

Year-round metagenomes reveal remarkably stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

USDA-ARS?s Scientific Manuscript database

Insight to what underlies the seasonal dynamics of indigenous soil microbial communities in agricultural soils, especially after major activities such as nitrogen fertilization, remain elusive. More detailed understanding of population dynamics will have important implications for modeling efforts a...

Analysis of microbial populations, denitrification, and nitrous oxide production in riparian buffers

USDA-ARS?s Scientific Manuscript database

Riparian buffers are used extensively to protect water bodies from nonpoint source nitrogen pollution. However there is relatively little information on the impact of these buffers on production of nitrous oxide (N2O). In this study, we assessed nitrous oxide production in riparian buffers of the so...

Microbial Oxidation of Fe2+ and Pyrite Exposed to Flux of Micromolar H2O2 in Acidic Media

PubMed Central

Ma, Yingqun; Lin, Chuxia

2013-01-01

At an initial pH of 2, while abiotic oxidation of aqueous Fe2+ was enhanced by a flux of H2O2 at micromolar concentrations, bio-oxidation of aqueous Fe2+ could be impeded due to oxidative stress/damage in Acidithiobacillus ferrooxidans caused by Fenton reaction-derived hydroxyl radical, particularly when the molar ratio of Fe2+ to H2O2 was low. When pyrite cubes were intermittently exposed to fluxes of micromolar H2O2, the reduced Fe2+-Fe3+ conversion rate in the solution (due to reduced microbial activity) weakened the Fe3+-catalyzed oxidation of cubic pyrite and added to relative importance of H2O2-driven oxidation in the corrosion of mineral surfaces for the treatments with high H2O2 doses. This had effects on reducing the build-up of a passivating coating layer on the mineral surfaces. Cell attachment to the mineral surfaces was only observed at the later stage of the experiment after the solutions became less favorable for the growth of planktonic bacteria. PMID:23760258

Microbial Oxidation of Fe2+ and Pyrite Exposed to Flux of Micromolar H2O2 in Acidic Media

NASA Astrophysics Data System (ADS)

Ma, Yingqun; Lin, Chuxia

2013-06-01

At an initial pH of 2, while abiotic oxidation of aqueous Fe2+ was enhanced by a flux of H2O2 at micromolar concentrations, bio-oxidation of aqueous Fe2+ could be impeded due to oxidative stress/damage in Acidithiobacillus ferrooxidans caused by Fenton reaction-derived hydroxyl radical, particularly when the molar ratio of Fe2+ to H2O2 was low. When pyrite cubes were intermittently exposed to fluxes of micromolar H2O2, the reduced Fe2+-Fe3+ conversion rate in the solution (due to reduced microbial activity) weakened the Fe3+-catalyzed oxidation of cubic pyrite and added to relative importance of H2O2-driven oxidation in the corrosion of mineral surfaces for the treatments with high H2O2 doses. This had effects on reducing the build-up of a passivating coating layer on the mineral surfaces. Cell attachment to the mineral surfaces was only observed at the later stage of the experiment after the solutions became less favorable for the growth of planktonic bacteria.

Microbial oxidation of Fe²⁺ and pyrite exposed to flux of micromolar H₂O₂ in acidic media.

PubMed

Ma, Yingqun; Lin, Chuxia

2013-01-01

At an initial pH of 2, while abiotic oxidation of aqueous Fe(2+) was enhanced by a flux of H2O2 at micromolar concentrations, bio-oxidation of aqueous Fe(2+) could be impeded due to oxidative stress/damage in Acidithiobacillus ferrooxidans caused by Fenton reaction-derived hydroxyl radical, particularly when the molar ratio of Fe(2+) to H2O2 was low. When pyrite cubes were intermittently exposed to fluxes of micromolar H2O2, the reduced Fe(2+)-Fe(3+) conversion rate in the solution (due to reduced microbial activity) weakened the Fe(3+)-catalyzed oxidation of cubic pyrite and added to relative importance of H2O2-driven oxidation in the corrosion of mineral surfaces for the treatments with high H2O2 doses. This had effects on reducing the build-up of a passivating coating layer on the mineral surfaces. Cell attachment to the mineral surfaces was only observed at the later stage of the experiment after the solutions became less favorable for the growth of planktonic bacteria.

Power generation using spinel manganese-cobalt oxide as a cathode catalyst for microbial fuel cell applications.

PubMed

Mahmoud, Mohamed; Gad-Allah, Tarek A; El-Khatib, K M; El-Gohary, Fatma

2011-11-01

This study focused on the use of spinel manganese-cobalt (Mn-Co) oxide, prepared by a solid state reaction, as a cathode catalyst to replace platinum in microbial fuel cells (MFCs) applications. Spinel Mn-Co oxides, with an Mn/Co atomic ratios of 0.5, 1, and 2, were prepared and examined in an air cathode MFCs which was fed with a molasses-laden synthetic wastewater and operated in batch mode. Among the three Mn-Co oxide cathodes and after 300 h of operation, the Mn-Co oxide catalyst with Mn/Co atomic ratio of 2 (MnCo-2) exhibited the highest power generation 113 mW/m2 at cell potential of 279 mV, which were lower than those for the Pt catalyst (148 mW/m2 and 325 mV, respectively). This study indicated that using spinel Mn-Co oxide to replace platinum as a cathodic catalyst enhances power generation, increases contaminant removal, and substantially reduces the cost of MFCs. Copyright © 2011 Elsevier Ltd. All rights reserved.

Changes of microbial spoilage, lipid-protein oxidation and physicochemical properties during post mortem refrigerated storage of goat meat.

PubMed

Sabow, Azad Behnan; Sazili, Awis Qurni; Aghwan, Zeiad Amjad; Zulkifli, Idrus; Goh, Yong Meng; Ab Kadir, Mohd Zainal Abidin; Nakyinsige, Khadijah; Kaka, Ubedullah; Adeyemi, Kazeem Dauda

2016-06-01

Examined was the effect of post mortem refrigerated storage on microbial spoilage, lipid-protein oxidation and physicochemical traits of goat meat. Seven Boer bucks were slaughtered, eviscerated and aged for 24 h. The Longissimus lumborum (LL) and Semitendinosus (ST) muscles were excised and subjected to 13 days post mortem refrigerated storage. The pH, lipid and protein oxidation, tenderness, color and drip loss were determined in LL while microbiological analysis was performed on ST. Bacterial counts generally increased with increasing aging time and the limit for fresh meat was reached at day 14 post mortem. Significant differences were observed in malondialdehyde (MDA) content at day 7 of storage. The thiol concentration significantly reduced as aging time increased. The band intensities of myosin heavy chain (MHC) and troponin-T significantly decreased as storage progressed, while actin remained relatively stable. After 14 days of aging, tenderness showed significant improvement while muscle pH and drip loss reduced with increase in storage time. Samples aged for 14 days had higher lightness (P < 0.05) and lower (P < 0.05) yellowness and redness. Post mortem refrigerated storage influenced oxidative and microbial stability and physico-chemical properties of goat meat. © 2016 Japanese Society of Animal Science.

Effect of Phospholipid on Pyrite Oxidation and Microbial Communities under Simulated Acid Mine Drainage (AMD) Conditions.

PubMed

Pierre Louis, Andro-Marc; Yu, Hui; Shumlas, Samantha L; Van Aken, Benoit; Schoonen, Martin A A; Strongin, Daniel R

2015-07-07

The effect of phospholipid on the biogeochemistry of pyrite oxidation, which leads to acid mine drainage (AMD) chemistry in the environment, was investigated. Metagenomic analyses were carried out to understand how the microbial community structure, which developed during the oxidation of pyrite-containing coal mining overburden/waste rock (OWR), was affected by the presence of adsorbed phospholipid. Using columns packed with OWR (with and without lipid adsorption), the release of sulfate (SO4(2-)) and soluble iron (FeTot) was investigated. Exposure of lipid-free OWR to flowing pH-neutral water resulted in an acidic effluent with a pH range of 2-4.5 over a 3-year period. The average concentration of FeTot and SO4(2-) in the effluent was ≥20 and ≥30 mg/L, respectively. In contrast, in packed-column experiments where OWR was first treated with phospholipid, the effluent pH remained at ∼6.5 and the average concentrations of FeTot and SO4(2-) were ≤2 and l.6 mg/L, respectively. 16S rDNA metagenomic pyrosequencing analysis of the microbial communities associated with OWR samples revealed the development of AMD-like communities dominated by acidophilic sulfide-oxidizing bacteria on untreated OWR samples, but not on refuse pretreated with phospholipid.

Conductive iron oxides accelerate thermophilic methanogenesis from acetate and propionate.

PubMed

Yamada, Chihaya; Kato, Souichiro; Ueno, Yoshiyuki; Ishii, Masaharu; Igarashi, Yasuo

2015-06-01

Anaerobic digester is one of the attractive technologies for treatment of organic wastes and wastewater, while continuous development and improvements on their stable operation with efficient organic removal are required. Particles of conductive iron oxides (e.g., magnetite) are known to facilitate microbial interspecies electron transfer (termed as electric syntrophy). Electric syntrophy has been reported to enhance methanogenic degradation of organic acids by mesophilic communities in soil and anaerobic digester. Here we investigated the effects of supplementation of conductive iron oxides (magnetite) on thermophilic methanogenic microbial communities derived from a thermophilic anaerobic digester. Supplementation of magnetite accelerated methanogenesis from acetate and propionate under thermophilic conditions, while supplementation of ferrihydrite also accelerated methanogenesis from propionate. Microbial community analysis revealed that supplementation of magnetite drastically changed bacterial populations in the methanogenic acetate-degrading cultures, in which Tepidoanaerobacter sp. and Coprothermobacter sp. dominated. These results suggest that supplementation of magnetite induce electric syntrophy between organic acid-oxidizing bacteria and methanogenic archaea and accelerate methanogenesis even under thermophilic conditions. Findings from this study would provide a possibility for the achievement of stably operating thermophilic anaerobic digestion systems with high efficiency for removal of organics and generation of CH4. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Geochemical control of microbial Fe(III) reduction potential in wetlands: Comparison of the rhizosphere to non-rhizosphere soil

USGS Publications Warehouse

Weiss, J.V.; Emerson, D.; Megonigal, J.P.

2004-01-01

We compared the reactivity and microbial reduction potential of Fe(III) minerals in the rhizosphere and non-rhizosphere soil to test the hypothesis that rapid Fe(III) reduction rates in wetland soils are explained by rhizosphere processes. The rhizosphere was defined as the area immediately adjacent to a root encrusted with Fe(III)-oxides or Fe plaque, and non-rhizosphere soil was 0.5 cm from the root surface. The rhizosphere had a significantly higher percentage of poorly crystalline Fe (66??7%) than non-rhizosphere soil (23??7%); conversely, non-rhizosphere soil had a significantly higher proportion of crystalline Fe (50??7%) than the rhizosphere (18??7%, P<0.05 in all cases). The percentage of poorly crystalline Fe(III) was significantly correlated with the percentage of FeRB (r=0.76), reflecting the fact that poorly crystalline Fe(III) minerals are labile with respect to microbial reduction. Abiotic reductive dissolution consumed about 75% of the rhizosphere Fe(III)-oxide pool in 4 h compared to 23% of the soil Fe(III)-oxide pool. Similarly, microbial reduction consumed 75-80% of the rhizosphere pool in 10 days compared to 30-40% of the non-rhizosphere soil pool. Differences between the two pools persisted when samples were amended with an electron-shuttling compound (AQDS), an Fe(III)-reducing bacterium (Geobacter metallireducens), and organic carbon. Thus, Fe(III)-oxide mineralogy contributed strongly to differences in the Fe(III) reduction potential of the two pools. Higher amounts of poorly crystalline Fe(III) and possibly humic substances, and a higher Fe(III) reduction potential in the rhizosphere compared to the non-rhizosphere soil, suggested the rhizosphere is a site of unusually active microbial Fe cycling. The results were consistent with previous speculation that rapid Fe cycling in wetlands is due to the activity of wetland plant roots. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Pure and Oxidized Copper Materials as Potential Antimicrobial Surfaces for Spaceflight Activities.

PubMed

Hahn, C; Hans, M; Hein, C; Mancinelli, R L; Mücklich, F; Wirth, R; Rettberg, P; Hellweg, C E; Moeller, R

2017-12-01

Microbial biofilms can lead to persistent infections and degrade a variety of materials, and they are notorious for their persistence and resistance to eradication. During long-duration space missions, microbial biofilms present a danger to crew health and spacecraft integrity. The use of antimicrobial surfaces provides an alternative strategy for inhibiting microbial growth and biofilm formation to conventional cleaning procedures and the use of disinfectants. Antimicrobial surfaces contain organic or inorganic compounds, such as antimicrobial peptides or copper and silver, that inhibit microbial growth. The efficacy of wetted oxidized copper layers and pure copper surfaces as antimicrobial agents was tested by applying cultures of Escherichia coli and Staphylococcus cohnii to these metallic surfaces. Stainless steel surfaces were used as non-inhibitory control surfaces. The production of reactive oxygen species and membrane damage increased rapidly within 1 h of exposure on pure copper surfaces, but the effect on cell survival was negligible even after 2 h of exposure. However, longer exposure times of up to 4 h led to a rapid decrease in cell survival, whereby the survival of cells was additionally dependent on the exposed cell density. Finally, the release of metal ions was determined to identify a possible correlation between copper ions in suspension and cell survival. These measurements indicated a steady increase of free copper ions, which were released indirectly by cells presumably through excreted complexing agents. These data indicate that the application of antimicrobial surfaces in spaceflight facilities could improve crew health and mitigate material damage caused by microbial contamination and biofilm formation. Furthermore, the results of this study indicate that cuprous oxide layers were superior to pure copper surfaces related to the antimicrobial effect and that cell density is a significant factor that influences the time dependence of antimicrobial activity. Key Words: Contact killing-E. coli-S. cohnii-Antimicrobial copper surfaces-Copper oxide layers-Human health-Planetary protection. Astrobiology 17, 1183-1191.

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

PubMed

Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

2011-03-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Biomineralization of metal-containing ores and concentrates.

PubMed

Rawlings, Douglas E; Dew, David; du Plessis, Chris

2003-01-01

Biomining is the use of microorganisms to extract metals from sulfide and/or iron-containing ores and mineral concentrates. The iron and sulfide is microbially oxidized to produce ferric iron and sulfuric acid, and these chemicals convert the insoluble sulfides of metals such as copper, nickel and zinc to soluble metal sulfates that can be readily recovered from solution. Although gold is inert to microbial action, microbes can be used to recover gold from certain types of minerals because as they oxidize the ore, they open its structure, thereby allowing gold-solubilizing chemicals such as cyanide to penetrate the mineral. Here, we review a strongly growing microbially-based metal extraction industry, which uses either rapid stirred-tank or slower irrigation technology to recover metals from an increasing range of minerals using a diversity of microbes that grow at a variety of temperatures.

Arsenic transformation and mobilization from minerals by the arsenite oxidizing strain WAO

USGS Publications Warehouse

Rhine, E.D.; Onesios, K.M.; Serfes, M.E.; Reinfelder, J.R.; Young, L.Y.

2008-01-01

Analysis of arsenic concentrations in New Jersey well water from the Newark Basin showed up to 15% of the wells exceed 10 ??g L-1, with a maximum of 215 ??g L-1. In some geologic settings in the basin, this mobile arsenic could be from the weathering of pyrite (FeS2) found in black shale that contains up to 4% arsenic by weight. We hypothesized that under oxic conditions at circumneutral pH, the microbially mediated oxidation of sulfide in the pyrite lattice would lead to the release of pyrite-bound arsenic. Moreover, the oxidation of aqueous As(III) to As(V) by aerobic microorganisms could further enhance arsenic mobilization from the solid phase. Enrichment cultures under aerobic, As(III)-oxidizing conditions were established under circumneutral pH with weathered black shale from the Newark Basin as the inoculum source. Strain WAO, an autotrophic inorganic-sulfur and As(III)-oxidizer, was isolated and phylogenetically and physiologically characterized. Arsenic mobilization studies from arsenopyrite (FeAsS) mineral, conducted with strain WAO at circumneutral pH, showed microbially enhanced mobilization of arsenic and complete oxidation of released arsenic and sulfur to stoichiometric amounts of arsenate and sulfate. In addition, WAO preferentially colonized pyrite on the surface of arsenic-bearing, black shale thick sections. These findings support the hypothesis that microorganisms can directly mobilize and transform arsenic bound in mineral form at circumneutral pH and suggest that the microbial mobilization of arsenic into groundwater may be important in other arsenic-impacted aquifers. ?? 2008 American Chemical Society.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments.

PubMed

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-11-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration--a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder.

Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments

PubMed Central

Hansel, Colleen M; Lentini, Chris J; Tang, Yuanzhi; Johnston, David T; Wankel, Scott D; Jardine, Philip M

2015-01-01

A central tenant in microbial biogeochemistry is that microbial metabolisms follow a predictable sequence of terminal electron acceptors based on the energetic yield for the reaction. It is thereby oftentimes assumed that microbial respiration of ferric iron outcompetes sulfate in all but high-sulfate systems, and thus sulfide has little influence on freshwater or terrestrial iron cycling. Observations of sulfate reduction in low-sulfate environments have been attributed to the presumed presence of highly crystalline iron oxides allowing sulfate reduction to be more energetically favored. Here we identified the iron-reducing processes under low-sulfate conditions within columns containing freshwater sediments amended with structurally diverse iron oxides and fermentation products that fuel anaerobic respiration. We show that despite low sulfate concentrations and regardless of iron oxide substrate (ferrihydrite, Al-ferrihydrite, goethite, hematite), sulfidization was a dominant pathway in iron reduction. This process was mediated by (re)cycling of sulfur upon reaction of sulfide and iron oxides to support continued sulfur-based respiration—a cryptic sulfur cycle involving generation and consumption of sulfur intermediates. Although canonical iron respiration was not observed in the sediments amended with the more crystalline iron oxides, iron respiration did become dominant in the presence of ferrihydrite once sulfate was consumed. Thus, despite more favorable energetics, ferrihydrite reduction did not precede sulfate reduction and instead an inverse redox zonation was observed. These findings indicate that sulfur (re)cycling is a dominant force in iron cycling even in low-sulfate systems and in a manner difficult to predict using the classical thermodynamic ladder. PMID:25871933

Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage

PubMed Central

Brantner, Justin S.; Haake, Zachary J.; Burwick, John E.; Menge, Christopher M.; Hotchkiss, Shane T.; Senko, John M.

2014-01-01

We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O2 at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O2. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O2 and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O2. PMID:24860562

Humic substances as a mediator for microbially catalyzed metal reduction

USGS Publications Warehouse

Lovley, D.R.; Fraga, J.L.; Blunt-Harris, E. L.; Hayes, L.A.; Phillips, E.J.P.; Coates, J.D.

1998-01-01

The potential for humic substances to serve as a terminal electron acceptor in microbial respiration and to function as an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides was investigated. The Fe(III)-reducing microorganism Geobacter metallireducens conserved energy to support growth from electron transport to humics as evidenced by continued oxidation of acetate to carbon dioxide after as many as nine transfers in a medium with acetate as the electron donor and soil humic acids as the electron acceptor. Growth of G. metallireducens with poorly crystalline Fe(III) oxide as the electron acceptor was greatly stimulated by the addition of as little as 100 ??M of the humics analog, anthraquinone-2,6-disulfonate. Other quinones investigated, including lawsone, menadione, and anthraquinone-2-sulfonate, also stimulated Fe(III) oxide reduction. A wide phylogenetic diversity of microorganisms capable of Fe(III) reduction were also able to transfer electrons to humics. Microorganisms which can not reduce Fe(III) could not reduce humics. Humics stimulated the reduction of structural Fe(III) in clay and the crystalline Fe(III) forms, goethite and hematite. These results demonstrate that electron shuttling between Fe(III)-reducing microorganisms and Fe(III) via humics not only accelerates the microbial reduction of poorly crystalline Fe(III) oxide, but also can facilitate the reduction of Fe(III) forms that are not typically reduced by microorganisms in the absence of humics. Addition of humic substances to enhance electron shuttling between Fe(III)-reducing microorganisms and Fe(III) oxides may be a useful strategy to stimulate the remediation of soils and sediments contaminated with organic or metal pollutants.