Microbial iron oxide respiration coupled to sulfide oxidation.

Microorganisms have driven Earth's sulfur cycle since the emergence of life, yet the sulfur-cycling capacities of microorganisms and their integration with other element cycles remain incompletely understood. One such uncharacterized metabolism is the coupling of sulfide oxidation with iron(III) oxide reduction, a ubiquitous environmental process hitherto considered to be strictly abiotic. Here we present a comprehensive genomic analysis of sulfur metabolism across prokaryotes, and reveal bacteria that are capable of oxidizing sulfide using extracellular solid phase iron(III).

Anaerobic oxidation of short-chain volatile alkanes.

The short-chain volatile alkanes ethane, propane, and butane are major components of natural gas. Released from deep-seated subsurface reservoirs through natural seepage or gas extraction, they percolate through anoxic and oxic environments before reaching the atmosphere, where they contribute to tropospheric chemistry and act as greenhouse gases. While their aerobic biological oxidation is well established, their fate in anoxic environments has only recently come into focus.

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments.

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome.

Artificial light at night causes community instability of bacterial community in urban soils.

Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN.

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.

Taurine-respiring gut bacteria produce HS with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution.

High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.

Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes () including , , , , , , , and as well as energy-generating As respiratory oxidation () and reduction () genes. Somewhat unexpectedly, the relative DNA abundances and diversities of , , and genes were not significantly different between low and high (∼10 versus ∼100 mg kg) As soils.

The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling.

The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle of harmful metal(loids), including that of arsenic, which doubtlessly imposed substantial barriers to the physiology and diversification of life. Evaluating the adaptive biological responses to these environmental challenges is inherently difficult because of the paucity of fossil records.

Bioavailable arsenic and amorphous iron oxides provide reliable predictions for arsenic transfer in soil-wheat system.

The application of current soil quality standards based on total arsenic (As) fails to assess the ecological risks of soil arsenic or to ensure the safety of crops and foods. In this study, bioavailable arsenic instead of total arsenic was applied to improve predictive models for arsenic transfer from soil to wheat (Triticum turgidum L.).

Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.

Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps, and through ethane-dependent sulfate reduction in slurries. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown.

Organic Carbon Amendments Affect the Chemodiversity of Soil Dissolved Organic Matter and Its Associations with Soil Microbial Communities.

The "4 per mil" initiative recognizes the pivotal role of soil in carbon resequestration. The need for evidence to substantiate the influence of agricultural practices on chemical nature of soil carbon and microbial biodiversity has become a priority. However, owing to the molecular complexity of soil dissolved organic matter (DOM), specific linkages to microbial biodiversity have eluded researchers.

DNA stable-isotope probing identifies uncultivated members of Pseudonocardia associated with biodegradation of pyrene in agricultural soil.

Identifying functional microorganisms involved in the degradation of high-molecular-mass polycyclic aromatic hydrocarbons (HMM-PAHs) in agricultural soil environments could assist in developing bioremediation strategies for soil PAH contamination. Active populations of HMM-PAH degraders in agricultural soils are currently poorly understood. In this study, we identified aerobic pyrene-degrading bacteria in agricultural and industrial soils by [13C]pyrene incubations followed by DNA stable-isotope probing and high-throughput sequencing.

Molecular Chemodiversity of Dissolved Organic Matter in Paddy Soils.

Organic matter (OM), and dissolved organic matter (DOM), have a major influence upon biogeochemical processes; most significantly, the carbon cycle. To date, very few studies have examined the spatial heterogeneity of DOM in paddy soils. Thus, very little is known about the DOM molecular profiles and the key environmental factors that underpin DOM molecular chemodiversity in paddy soils.

Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic.

The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic.

Distribution of soil selenium in China is potentially controlled by deposition and volatilization?

Elucidating the environmental drivers of selenium (Se) spatial distribution in soils at a continental scale is essential to better understand it's biogeochemical cycling to improve Se transfer into diets. Through modelling Se biogeochemistry in China we found that deposition and volatilization are key factors controlling distribution in surface soil, rather than bedrock-derived Se (<0.1 mg/kg).

Draft Genome Sequence of Desulfitobacterium hafniense Strain DH, a Sulfate-Reducing Bacterium Isolated from Paddy Soils.

Desulfitobacterium hafniense strain DH is a sulfate-reducing species. Here, we report the draft genome sequence of strain DH, with a size of 5,368,588 bp, average G+C content of 47.48%, and 5,296 predicted protein-coding sequences.

Dynamic equilibrium of endogenous selenium nanoparticles in selenite-exposed cancer cells: a deep insight into the interaction between endogenous SeNPs and proteins.

Elemental selenium (Se) was recently found to exist as endogenous nanoparticles (i.e., SeNPs) in selenite-exposed cancer cells.

A novel kernelized fuzzy C-means algorithm with application in medical image segmentation.

Image segmentation plays a crucial role in many medical imaging applications. In this paper, we present a novel algorithm for fuzzy segmentation of magnetic resonance imaging (MRI) data. The algorithm is realized by modifying the objective function in the conventional fuzzy C-means (FCM) algorithm using a kernel-induced distance metric and a spatial penalty on the membership functions.