scholarly journals Nitrate removal by a novel lithoautotrophic nitrate-reducing iron(II)-oxidizing culture enriched from a pyrite-rich limestone aquifer

2021 ◽  
Author(s):  
Natalia Jakus ◽  
Nia Blackwell ◽  
Karsten Osenbrück ◽  
Daniel Straub ◽  
James M. Byrne ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Carbon ◽  
Electron Donor ◽  
Nitrate Reduction ◽  
Nitrate Removal ◽  
Electron Donors ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Limestone Aquifer ◽  
Chemolithoautotrophic Bacteria

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer and as such there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic co-substrates for growth, within 7-11 days 0.3-0.5 mM of nitrate was reduced and 1.3-2 mM of iron(II) was oxidized leading to a stoichiometric NO 3 - /Fe(II) ratio of 0.2, with N 2 and N 2 O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, microaerophilic iron(II)-oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically impacted aquifers. Importance Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment and as such there are no model cultures available to study the rate-limiting factors of this potentially important process. Here we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II)-oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N 2 O and N 2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.

scholarly journals Groundwater cable bacteria conserve energy by sulfur disproportionation

2019 ◽  
Vol 14 (2) ◽  
pp. 623-634 ◽  
Author(s):  
Hubert Müller ◽  
Sviatlana Marozava ◽  
Alexander J. Probst ◽  
Rainer U. Meckenstock
Keyword(s):  
16S Rrna ◽  
Electron Donor ◽  
Nitrate Reduction ◽  
Elemental Sulfur ◽  
Single Cells ◽  
Sulfur Oxidation ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Long Distance ◽  
Sulfur Disproportionation

AbstractCable bacteria of the family Desulfobulbaceae couple spatially separated sulfur oxidation and oxygen or nitrate reduction by long-distance electron transfer, which can constitute the dominant sulfur oxidation process in shallow sediments. However, it remains unknown how cells in the anoxic part of the centimeter-long filaments conserve energy. We found 16S rRNA gene sequences similar to groundwater cable bacteria in a 1-methylnaphthalene-degrading culture (1MN). Cultivation with elemental sulfur and thiosulfate with ferrihydrite or nitrate as electron acceptors resulted in a first cable bacteria enrichment culture dominated >90% by 16S rRNA sequences belonging to the Desulfobulbaceae. Desulfobulbaceae-specific fluorescence in situ hybridization (FISH) unveiled single cells and filaments of up to several hundred micrometers length to belong to the same species. The Desulfobulbaceae filaments also showed the distinctive cable bacteria morphology with their continuous ridge pattern as revealed by atomic force microscopy. The cable bacteria grew with nitrate as electron acceptor and elemental sulfur and thiosulfate as electron donor, but also by sulfur disproportionation when Fe(Cl)2 or Fe(OH)3 were present as sulfide scavengers. Metabolic reconstruction based on the first nearly complete genome of groundwater cable bacteria revealed the potential for sulfur disproportionation and a chemo-litho-autotrophic metabolism. The presence of different types of hydrogenases in the genome suggests that they can utilize hydrogen as alternative electron donor. Our results imply that cable bacteria not only use sulfide oxidation coupled to oxygen or nitrate reduction by LDET for energy conservation, but sulfur disproportionation might constitute the energy metabolism for cells in large parts of the cable bacterial filaments.

scholarly journals pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion

2020 ◽  
Vol 8 (2) ◽  
pp. 286
Author(s):  
Nina Lackner ◽  
Andreas O. Wagner ◽  
Rudolf Markt ◽  
Paul Illmer
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Carbon Flow ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Ch4 Production ◽  
Ph Conditions ◽  
Ph Range ◽  
In The Beginning

pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0–8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.

Reactivity of pyrite and organic carbon as electron donors for biogeochemical processes in the fractured Jurassic Lincolnshire limestone aquifer, UK

2012 ◽  
Vol 332-333 ◽  
pp. 26-31 ◽  
Author(s):  
Kieran M. Baker ◽  
Simon H. Bottrell ◽  
David Hatfield ◽  
Robert J.G. Mortimer ◽  
Robert J. Newton ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Electron Donors ◽  
Biogeochemical Processes ◽  
Limestone Aquifer

scholarly journals Impact of Different In Vitro Electron Donor/Acceptor Conditions on Potential Chemolithoautotrophic Communities from Marine Pelagic Redoxclines

2005 ◽  
Vol 71 (11) ◽  
pp. 6664-6672 ◽  
Author(s):  
Matthias Labrenz ◽  
Günter Jost ◽  
Christa Pohl ◽  
Sabrina Beckmann ◽  
Willm Martens-Habbena ◽  
...  
Keyword(s):  
Electron Donor ◽  
Nitrate Reduction ◽  
Single Strand Conformation Polymorphism ◽  
General Importance ◽  
Donor Acceptor ◽  
Dark Fixation ◽  
Enrichment Experiments ◽  
Chemolithoautotrophic Bacteria ◽  
The Impact

ABSTRACT Anaerobic or microaerophilic chemolithoautotrophic bacteria have been considered to be responsible for CO2 dark fixation in different pelagic redoxclines worldwide, but their involvement in redox processes is still not fully resolved. We investigated the impact of 17 different electron donor/acceptor combinations in water of pelagic redoxclines from the central Baltic Sea on the stimulation of bacterial CO2 dark fixation as well as on the development of chemolithoautotrophic populations. In situ, the highest CO2 dark fixation rates, ranging from 0.7 to 1.4 μmol liter−1 day−1, were measured directly below the redoxcline. In enrichment experiments, chemolithoautotrophic CO2 dark fixation was maximally stimulated by the addition of thiosulfate, reaching values of up to 9.7 μmol liter−1 CO2 day−1. Chemolithoautotrophic nitrate reduction proved to be an important process, with rates of up to 33.5 μmol liter−1 NO3 − day−1. Reduction of Fe(III) or Mn(IV) was not detected; nevertheless, the presence of these potential electron acceptors influenced the development of stimulated microbial assemblages. Potential chemolithoautotrophic bacteria in the enrichment experiments were displayed on 16S ribosomal complementary DNA single-strand-conformation polymorphism fingerprints and identified by sequencing of excised bands. Sequences were closely related to chemolithoautotrophic Thiomicrospira psychrophila and Maorithyas hadalis gill symbiont (both Gammaproteobacteria) and to an uncultured nitrate-reducing Helicobacteraceae bacterium (Epsilonproteobacteria). Our data indicate that this Helicobacteraceae bacterium could be of general importance or even a key organism for autotrophic nitrate reduction in pelagic redoxclines.

scholarly journals Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

PLoS ONE ◽  
2016 ◽  
Vol 11 (1) ◽  
pp. e0146689 ◽  
Author(s):  
Man Jae Kwon ◽  
Edward J. O’Loughlin ◽  
Maxim I. Boyanov ◽  
Jennifer M. Brulc ◽  
Eric R. Johnston ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Carbon ◽  
Community Development ◽  
Electron Donors ◽  
Sulfate Reducing ◽  
Reducing Conditions

Effect of high electron donor supply on dissimilatory nitrate reduction pathways in a bioreactor for nitrate removal

2014 ◽  
Vol 171 ◽  
pp. 291-297 ◽  
Author(s):  
Anna Behrendt ◽  
Sheldon Tarre ◽  
Michael Beliavski ◽  
Michal Green ◽  
Judith Klatt ◽  
...  
Keyword(s):  
Electron Donor ◽  
Nitrate Reduction ◽  
Nitrate Removal ◽  
High Electron ◽  
Dissimilatory Nitrate Reduction

scholarly journals Soil Microbial Community Responses to Additions of Organic Carbon Substrates and Heavy Metals (Pb and Cr)

2005 ◽  
Vol 71 (12) ◽  
pp. 7679-7689 ◽  
Author(s):  
Cindy H. Nakatsu ◽  
Nadia Carmosini ◽  
Brett Baldwin ◽  
Federico Beasley ◽  
Peter Kourtev ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Microbial Community ◽  
Organic Carbon ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Carbon Sources ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Copy ◽  
Organic Substrates ◽  
Gradient Gel Electrophoresis

ABSTRACT Microcosm experiments were conducted with soils contaminated with heavy metals (Pb and Cr) and aromatic hydrocarbons to determine the effects of each upon microbial community structure and function. Organic substrates were added as a driving force for change in the microbial community. Glucose represented an energy source used by a broad variety of bacteria, whereas fewer soil species were expected to use xylene. The metal amendments were chosen to inhibit the acute rate of organic mineralization by either 50% or 90%, and lower mineralization rates persisted over the entire 31-day incubation period. Significant biomass increases were abolished when metals were added in addition to organic carbon. The addition of organic carbon alone had the most significant impact on community composition and led to the proliferation of a few dominant phylotypes, as detected by PCR-denaturing gradient gel electrophoresis of bacterial 16S rRNA genes. However, the community-wide effects of heavy metal addition differed between the two carbon sources. For glucose, either Pb or Cr produced large changes and replacement with new phylotypes. In contrast, many phylotypes selected by xylene treatment were retained when either metal was added. Members of the Actinomycetales were very prevalent in microcosms with xylene and Cr(VI); gene copy numbers of biphenyl dioxygenase and phenol hydroxylase (but not other oxygenases) were elevated in these microcosms, as determined by real-time PCR. Much lower metal concentrations were needed to inhibit the catabolism of xylene than of glucose. Cr(VI) appeared to be reduced during the 31-day incubations, but in the case of glucose there was substantial microbial activity when much of the Cr(VI) remained. In the case of xylene, this was less clear.

scholarly journals Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community – Enabling Continuous Production of Microalgal Biomass

2021 ◽  
Vol 12 ◽  
Author(s):  
Eva Sörenson ◽  
Eric Capo ◽  
Hanna Farnelid ◽  
Elin Lindehoff ◽  
Catherine Legrand
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Environmental Change ◽  
Term Structure ◽  
Continuous Production ◽  
Rrna Gene ◽  
Community Interactions ◽  
Microalgal Biomass ◽  
Diverse Community

To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 ± 2 and 11 ± 1°C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).

scholarly journals Microbial Community Analysis Provides Insights into the Effects of Tetrahydrofuran on 1,4-Dioxane Biodegradation

2019 ◽  
Vol 85 (11) ◽  
Author(s):  
Yi Xiong ◽  
Olivia U. Mason ◽  
Ashlee Lowe ◽  
Chao Zhou ◽  
Gang Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Electron Donor ◽  
Landfill Leachate ◽  
Synthetic Medium ◽  
High Energy ◽  
Community Context ◽  
Rrna Gene ◽  
Content Type ◽  
Donor Substrate ◽  
Degrading Bacteria

ABSTRACTTetrahydrofuran (THF) is known to induce the biodegradation of 1,4-dioxane (dioxane), an emerging contaminant, but the mechanisms by which THF affects dioxane biodegradation in microbial communities are not well understood. To fill this knowledge gap, changes in the microbial community structure in microcosm experiments with synthetic medium and landfill leachate were examined over time using 16S rRNA gene amplicon sequencing and functional gene quantitative PCR assays. The overarching hypothesis being tested was that THF promoted dioxane biodegradation by increasing the abundance of dioxane-degrading bacteria in the consortium. The data revealed that in experiments with synthetic medium, the addition of THF significantly increased the abundance ofPseudonocardia, a genus with several representatives that can grow on both dioxane and THF, and ofRhodococcus ruber, a species that can use THF as the primary growth substrate while cometabolizing dioxane. However, in similar experiments with landfill leachate, onlyR. ruberwas significantly enriched. When the THF concentration was higher than the dioxane concentration, THF competitively inhibited dioxane degradation since dioxane degradation was negligible, while the dioxane-degrading bacteria and the corresponding THF/dioxane monooxygenase gene copies increased by a few orders of magnitude.IMPORTANCEWidespread in groundwater and carcinogenic to humans, 1,4-dioxane (dioxane) is attracting significant attention in recent years. Advanced oxidation processes can effectively remove dioxane but require high energy consumption and operation costs. Biological removal of dioxane is of particular interest due to the ability of some bacteria to mineralize dioxane at a low energy cost. Although dioxane is generally considered recalcitrant to biodegradation, more than 20 types of bacteria can degrade dioxane as the sole electron donor substrate or the secondary electron donor substrate. In the latter case, tetrahydrofuran (THF) is commonly studied as the primary electron donor substrate. Previous work has shown that THF promotes dioxane degradation at a low THF concentration but inhibits dioxane degradation at a high THF concentration. Our work expanded on the previous work by mechanically examining the effects of THF on dioxane degradation in a microbial community context.

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