Impact of pH and salinity fluctuations on oxidation of Fe(II) by nitrate-reducing microorganisms enriched from the reduced tidal sediment of an extreme acidic river (Río Tinto, Spain).

Nitrate reduction coupled to Fe(II) oxidation (NRFeOx) contributes to Fe cycling in the estuarian sediments of the Río Tinto river (Huelva, Spain). However, it is not yet known (i) whether and which NRFeOx microorganisms can be enriched from the reduced sediment layer and (ii) how in-situ pH and salinity fluctuations affect NRFeOx. Therefore, we (i) used two different approaches such as microcosm experiments (sediment amended with either NO3-/Fe2+aq or acetate/NO3-/Fe2+aq) and enrichment cultures (medium amended with acetate/NO3-/Fe2+aq) to enrich NRFeOx microorganisms to (ii) test their salinity and pH tolerance under simulated high tide and low tide conditions.

Electron acceptors modulate methane oxidation and active methanotrophic communities in anoxic urban wetland sediments.

Unlabelled: Urban wetlands, although often overlooked, are hotspots for CH cycling. However, the understanding of anaerobic CH oxidation and microbial responses to different electron acceptors in urban wetlands remains limited. Here, we employed DNA-stable isotope probing (SIP) and metagenomic techniques to identify the core CH-oxidizing microbial groups in the presence of NO, SO, or ferrihydrite (Fe(III)) in anoxic urban-lake sediments.

In Situ Metabolic Rates of Alkane-Degrading Sulphate-Reducing Bacteria in Hydrocarbon Seep Sediments Revealed by Combining CARD-FISH, NanoSIMS, and Mathematical Modelling.

Marine hydrocarbon seeps are hotspots for sulphate reduction coupled to hydrocarbon oxidation. In situ metabolic rates of sulphate-reducing bacteria (SRB) degrading hydrocarbons other than methane, however, remain poorly understood. Here, we assessed the environmental role of Desulfosarcinaceae clades SCA1, SCA2 for degradation of n-butane and clade LCA2 for n-dodecane.

Unravelling the Activity and Presence of NO Reducers on Urban Greening Tree Leaves.

Nitrous oxide (NO) is a potent greenhouse gas and can be biotically emitted from soils, water, and the less recognised plant leaves. Leaves can produce NO and may host NO-reducing microbes that use it as a respiratory substrate, potentially mitigating climate warming. This study examines the ecophysiology of NO reducers in the plant phyllosphere.

Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant.

Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g.

Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations.

Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g.

Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding.

Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding.

Substrate-independent expression of key functional genes in strain PS-1 limits their use as markers for PAH biodegradation.

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including , , and .

Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures.

A major source of anthropogenic polycyclic aromatic hydrocarbon (PAH) inputs into marine environments are diffuse emissions which result in low PAH concentrations in the ocean water, posing a potential threat for the affected ecosystems. However, the remediation of low-dosage PAH contaminations through microbial processes remains largely unknown. Here, we developed a process-based numerical model to simulate batch cultures receiving repeated low-dosage naphthalene pulses compared to the conventionally used one-time high-dosage.

Mechanistic modeling indicates rapid glyphosate dissipation and sorption-driven persistence of its metabolite AMPA in soil.

Residual concentrations of glyphosate and its main transformation product aminomethylphosphonic acid (AMPA) are often observed in soils. The factors controlling their biodegradation are currently not well understood. We analyzed sorption-limited biodegradation of glyphosate and AMPA in soil with a set of microcosm experiments.

Microbial communities contribute to the elimination of As, Fe, Mn, and NH from groundwater in household sand filters.

Household sand filters (SFs) are widely applied to remove iron (Fe), manganese (Mn), arsenic (As), and ammonium (NH) from groundwater in the Red River delta, Vietnam. Processes in the filters probably include a combination of biotic and abiotic reactions. However, there is limited information on the microbial communities treating varied groundwater compositions and on whether biological oxidation of Fe(II), Mn(II), As(III), and NH contributes to the overall performance of SFs.

Seasonal Fluctuations in Iron Cycling in Thawing Permafrost Peatlands.

In permafrost peatlands, up to 20% of total organic carbon (OC) is bound to reactive iron (Fe) minerals in the active layer overlying intact permafrost, potentially protecting OC from microbial degradation and transformation into greenhouse gases (GHG) such as CO and CH. During the summer, shifts in runoff and soil moisture influence redox conditions and therefore the balance of Fe oxidation and reduction. Whether reactive iron minerals could act as a stable sink for carbon or whether they are continuously dissolved and reprecipitated during redox shifts remains unknown.

'Candidatus ferrigenium straubiae' sp. nov., 'Candidatus ferrigenium bremense' sp. nov., 'Candidatus ferrigenium altingense' sp. nov., are autotrophic Fe(II)-oxidizing bacteria of the family Gallionellaceae.

Iron(II) [Fe(II)] oxidation coupled to denitrification is recognized as an environmentally important process in many ecosystems. However, the Fe(II)-oxidizing bacteria (FeOB) dominating autotrophic nitrate-reducing Fe(II)-oxidizing enrichment cultures, affiliated with the family Gallionellaceae, remain poorly taxonomically defined due to lack of representative isolates. We describe the taxonomic classification of three novel FeOB based on metagenome-assembled genomes (MAGs) acquired from the autotrophic nitrate-reducing enrichment cultures KS, BP and AG.

Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain.

In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl on Fe-cycling microorganisms.

Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp.

Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer.

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants.

Background: Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.

Results: Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment.

A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction.

Fe(II) oxidation coupled to nitrate reduction (NRFO) has been described for many environments. Yet very few autotrophic microorganisms catalysing NRFO have been cultivated and their diversity, as well as their mechanisms for NRFO in situ remain unclear. A novel autotrophic NRFO enrichment culture, named culture BP, was obtained from freshwater sediment.

Nitrate Removal by a Novel Lithoautotrophic Nitrate-Reducing, Iron(II)-Oxidizing Culture Enriched from a Pyrite-Rich Limestone Aquifer.

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.

Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam.

High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them.

Meta-omics Reveal and Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS.

Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.

Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer.

Fe(III) minerals play a crucial role for arsenic (As) mobility in aquifers as they usually represent the main As-bearing phases. Microbial reductive dissolution of As-bearing Fe(III) minerals is responsible for the release of As and the resulting groundwater contamination in many sites worldwide. So far, in most studies mainly abiogenic iron minerals have been considered.

Comparative Proteomics of sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation.

The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates.

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.

The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam.

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.