Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.

Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labeling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.

NanoSIMS sulfur isotopic analysis at 100 nm scale by imaging technique.

NanoSIMS has been widely used for in-situ sulfur isotopic analysis (32S and 34S) of micron-sized grains or complex zoning in sulfide in terrestrial and extraterrestrial samples. However, the conventional spot mode analysis is restricted by depth effects at the spatial resolution < 0.5-1 µm. Thus sufficient signal amount cannot be achieved due to limited analytical depths, resulting in low analytical precision (1.5‰). Here we report a new method that simultaneously improves spatial resolution and precision of sulfur isotopic analysis based on the NanoSIMS imaging mode. This method uses a long acquisition time (e.g., 3 h) for each analytical area to obtain sufficient signal amount, rastered with the Cs+ primary beam of ∼100 nm in diameter. Due to the high acquisition time, primary ion beam (FCP) intensity drifting and quasi-simultaneous arrival (QSA) significantly affects the sulfur isotopic measurement of secondary ion images. Therefore, the interpolation correction was used to eliminate the effect of FCP intensity variation, and the coefficients for the QSA correction were determined with sulfide isotopic standards. Then, the sulfur isotopic composition was acquired by the segmentation and calculation of the calibrated isotopic images. The optimal spatial resolution of ∼ 100 nm (Sampling volume of 5 nm × 1.5 µm2) for sulfur isotopic analysis can be implemented with an analytical precision of ∼1‰ (1SD). Our study demonstrates that imaging analysis is superior to spot-mode analysis in irregular analytical areas where relatively high spatial resolution and precision are required and may be widely applied to other isotopic analyses.

High abundance of solar wind-derived water in lunar soils from the middle latitude.

Remote sensing data revealed that the presence of water (OH/H2O) on the Moon is latitude-dependent and probably time-of-day variation, suggesting a solar wind (SW)-originated water with a high degassing loss rate on the lunar surface. However, it is unknown whether or not the SW-derived water in lunar soil grains can be preserved beneath the surface. We report ion microprobe analyses of hydrogen abundances, and deuterium/hydrogen ratios of the lunar soil grains returned by the Chang'e-5 mission from a higher latitude than previous missions. Most of the grain rims (topmost ~100 nm) show high abundances of hydrogen (1,116 to 2,516 ppm) with extremely low δD values (-908 to -992‰), implying nearly exclusively a SW origin. The hydrogen-content depth distribution in the grain rims is phase-dependent, either bell-shaped for glass or monotonic decrease for mineral grains. This reveals the dynamic equilibrium between implantation and outgassing of SW-hydrogen in soil grains on the lunar surface. Heating experiments on a subset of the grains further demonstrate that the SW-implanted hydrogen could be preserved after burial. By comparing with the Apollo data, both observations and simulations provide constraints on the governing role of temperature (latitude) on hydrogen implantation/migration in lunar soils. We predict an even higher abundance of hydrogen in the grain rims in the lunar polar regions (average ~9,500 ppm), which corresponds to an estimation of the bulk water content of ~560 ppm in the polar soils assuming the same grain size distribution as Apollo soils, consistent with the orbit remote sensing result.

Intracellular silicification by early-branching magnetotactic bacteria.

Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.

A dry lunar mantle reservoir for young mare basalts of Chang'e-5.

The distribution of water in the Moon's interior carries implications for the origin of the Moon1, the crystallization of the lunar magma ocean2 and the duration of lunar volcanism2. The Chang'e-5 mission returned some of the youngest mare basalt samples reported so far, dated at 2.0 billion years ago (Ga)3, from the northwestern Procellarum KREEP Terrane, providing a probe into the spatiotemporal evolution of lunar water. Here we report the water abundances and hydrogen isotope compositions of apatite and ilmenite-hosted melt inclusions from the Chang'e-5 basalts. We derive a maximum water abundance of 283 ± 22 µg g-1 and a deuterium/hydrogen ratio of (1.06 ± 0.25) × 10-4 for the parent magma. Accounting for low-degree partial melting of the depleted mantle followed by extensive magma fractional crystallization4, we estimate a maximum mantle water abundance of 1-5 µg g-1, suggesting that the Moon's youngest volcanism was not driven by abundant water in its mantle source. Such a modest water content for the Chang'e-5 basalt mantle source region is at the low end of the range estimated from mare basalts that erupted from around 4.0 Ga to 2.8 Ga (refs. 5,6), suggesting that the mantle source of the Chang'e-5 basalts had become dehydrated by 2.0 Ga through previous melt extraction from the Procellarum KREEP Terrane mantle during prolonged volcanic activity.

Intrinsic enzyme-like activity of magnetite particles is enhanced by cultivation with Trichoderma guizhouense.

Fungal-mineral interactions can produce large amounts of biogenic nano-size (~ 1-100 nm) minerals, yet their influence on fungal physiology and growth remains largely unexplored. Using Trichoderma guizhouense NJAU4742 and magnetite (Mt) as a model fungus and mineral system, we have shown for the first time that biogenic Mt nanoparticles formed during fungal-mineral cultivation exhibit intrinsic peroxidase-like activity. Specifically, the average peroxidase-like activity of Mt nanoparticles after 72 h cultivation was ~ 2.4 times higher than that of the original Mt. Evidence from high resolution X-ray photoelectron spectroscopy analyses indicated that the unique properties of magnetite nanoparticles largely stemmed from their high proportion of surface non-lattice oxygen, through occupying surface oxygen-vacant sites, rather than Fe redox chemistry, which challenges conventional Fenton reaction theories that assume iron to be the sole redox-active centre. Nanoscale secondary ion mass spectrometry with a resolution down to 50 nm demonstrated that a thin (< 1 µm) oxygen-film was present on the surface of fungal hyphae. Furthermore, synchrotron radiation-based micro-FTIR spectra revealed that surface oxygen groups corresponded mainly to organic OH, mineral OH and carbonyl groups. Together, these findings highlight an important, but unrecognized, catalytic activity of mineral nanoparticles produced by fungal-mineral interactions and contribute substantially to our understanding of mineral nanoparticles in natural ecosystems.

Extreme weather events recorded by daily to hourly resolution biogeochemical proxies of marine giant clam shells.

Paleoclimate research has built a framework for Earth's climate changes over the past 65 million years or even longer. However, our knowledge of weather-timescale extreme events (WEEs, also named paleoweather), which usually occur over several days or hours, under different climate regimes is almost blank because current paleoclimatic records rarely provide information with temporal resolution shorter than monthly scale. Here we show that giant clam shells (Tridacna spp.) from the tropical western Pacific have clear daily growth bands, and several 2-y-long (from January 29, 2012 to December 9, 2013) daily to hourly resolution biological and geochemical records, including daily growth rate, hourly elements/Ca ratios, and fluorescence intensity, were obtained. We found that the pulsed changes of these ultra-high-resolution proxy records clearly matched with the typical instrumental WEEs, for example, tropical cyclones during the summer-autumn and cold surges during the winter. When a tropical cyclone passes through or approaches the sampling site, the growth rate of Tridacna shell decreases abruptly due to the bad weather. Meanwhile, enhanced vertical mixing brings nutrient-enriched subsurface water to the surface, resulting in a high Fe/Ca ratio and strong fluorescence intensity (induced by phytoplankton bloom) in the shell. Our results demonstrate that Tridacna shell has the potential to be used as an ultra-high-resolution archive for paleoweather reconstructions. The fossil shells living in different geological times can be built as a Geological Weather Station network to lengthen the modern instrumental data and investigate the WEEs under various climate conditions.

Characterization of Cu distribution in clay-sized soil aggregates by NanoSIMS and micro-XRF.

Aggregates are the basic structural units of soils. Fine soil aggregates are crucial pools for the retention of heavy metals. In this study, we evaluated the accumulation characteristics of exogenous Cu in the <2 µm aggregate fractions from a Histosol for an aging of 28 months by nano-scale secondary ion mass spectrometry (NanoSIMS) and synchrotron micro-X-ray fluorescence (micro-XRF). Results showed that the correlations between Cu and Fe/Al/Mn increased from 0.10-0.17 to 0.55-0.63, while those between Cu and C decreased sharply from 0.61 to 0.10 and then increased to 0.36, indicating that exogenous Cu tended to accumulate on inorganic mineral components. The carbon NEXAFS data suggested that the relative content of aromatic and carboxyl carbon decreased from 8.1% and 30.8% to 3.6% and 17.8% at month 12, and increased to 5.9% and 26.0% at month 28, respectively. However, an opposite trend was found for alkyl and carbonyl carbon which showed an increase at month 12 followed by a decrease afterwards. The consistency for the correlations between Cu and C with the changes of aromatic and carboxyl carbon indicated their key roles in the binding of Cu on the organic components in the <2 µm aggregates of Histosol. These direct observations offer a better understanding on the interactions of heavy metals with various soil components which is critical for the risk assessment and fate evaluation of exogenous Cu in soil ecosystems.

Enrichment of Lignin-Derived Carbon in Mineral-Associated Soil Organic Matter.

A modern paradigm of soil organic matter proposes that persistent carbon (C) derives primarily from microbial residues interacting with minerals, challenging older ideas that lignin moieties contribute to soil C because of inherent recalcitrance. We proposed that aspects of these old and new paradigms can be partially reconciled by considering interactions between lignin decomposition products and redox-sensitive iron (Fe) minerals. An Fe-rich tropical soil (with C4 litter and either 13C-labeled or unlabeled lignin) was pretreated with different durations of anaerobiosis (0-12 days) and incubated aerobically for 317 days. Only 5.7 ± 0.2% of lignin 13C was mineralized to CO2 versus 51.2 ± 0.4% of litter C. More added lignin-derived C (48.2 ± 0.9%) than bulk litter-derived C (30.6 ± 0.7%) was retained in mineral-associated organic matter (MAOM; density >1.8 g cm-3), and 12.2 ± 0.3% of lignin-derived C vs 6.4 ± 0.1% of litter C accrued in clay-sized (<2 µm) MAOM. Longer anaerobic pretreatments increased added lignin-derived C associated with Fe, according to extractions and nanoscale secondary ion mass spectrometry (NanoSIMS). Microbial residues are important, but lignin-derived C may also contribute disproportionately to MAOM relative to bulk litter-derived C, especially following redox-sensitive biogeochemical interactions.

Influencing mechanisms of hematite on benzo(a)pyrene degradation by the PAH-degrading bacterium Paracoccus sp. Strain HPD-2: insight from benzo(a)pyrene bioaccessibility and bacteria activity.

Iron oxides are reactive inorganic soil components that play an important role in the fate and transport of organic pollutants. Here, hematite was selected to investigate its effect on the biodegradation of benzo[a]pyrene (BaP) by Paracoccus sp. strain HPD-2. Approximately 60% of the total BaP was degraded in the absence of hematite after 7 days but only 30.8 and 20.8% of that was degraded after the addition of 10 and 20 mg  mL-1 hematite, respectively, indicating that the addition of hematite could significantly inhibit the biodegradation of BaP (P < 0.05). The hematite also lowered bacterium activity by coating the cells and by generating reactive oxygen species that destroyed the cells. Two-photon confocal laser scanning microscope images showed that the addition of hematite substantially decreased the amount of BaP combined with the bacterium, and this also enabled us to observe directly the migration and regression of BaP in the interaction between HPD-2 and hematite. Higher death ratio of HPD-2 might lower the BaP access to live cells because dead cells have a higher adsorption affinity for BaP than live cells. These observations enhance our understanding of the mechanisms by which metal oxides, organic pollutants and degrading-bacteria interact during the biodegradation process.

Aging shapes the distribution of copper in soil aggregate size fractions.

Soil aggregates are often considered the basic structural elements of soils. Aggregates of different size vary in their ability to retain or transfer heavy metals in the environment. Here, after incubation of a sieved (<2 mm) topsoil with copper, bulk soil was separated into four aggregate-size fractions and their adsorption characteristics for Cu were determined. By combining nano-scale secondary ion mass spectrometry and C-1s Near Edge X-ray Absorption Fine Structure Spectroscopy, we found that copper tends to bind onto organic matter in the <2 µm and 20-63 µm aggregates. Surprisingly, Cu correlated with carboxyl-C in the <2 µm aggregates but with alkyl-C in the 20-63 µm aggregates. This is the first attempt to visualize the spatial distribution of copper in aggregate size fractions. These direct observations can help improve the understanding of interactions between heavy metals and various soil components.

K(+) accumulation in the cytoplasm and nucleus of the salt gland cells of Limonium bicolor accompanies increased rates of salt secretion under NaCl treatment using NanoSIMS.

Recretohalophytes with specialized salt-secreting structures (salt glands) can secrete excess salts from plant, while discriminating between Na(+) and K(+). K(+)/Na(+) ratio plays an important role in plant salt tolerance, but the distribution and role of K(+) in the salt gland cells is poorly understood. In this article, the in situ subcellular localization of K and Na in the salt gland of the recretohalophyte Limonium bicolor Kuntze is described. Samples were prepared by high-pressure freezing (HPF), freeze substitution (FS) and analyzed using NanoSIMS. The salt gland of L. bicolor consists of sixteen cells. Higher signal strength of Na(+) was located in the apoplast of salt gland cells. Compared with control, 200 mM NaCl treatment led to higher signal strength of K(+) and Na(+) in both cytoplasm and nucleus of salt gland cells although K(+)/Na(+) ratio in both cytoplasm and nucleus were slightly reduced by NaCl. Moreover, the rate of Na(+) secretion per salt gland of L. bicolor treated with 200 mM NaCl was five times that of controls. These results suggest that K(+) accumulation both in the cytoplasm and nucleus of salt gland cells under salinity may play an important role in salt secretion, although the exact mechanism is unknown.

In situ visualisation and characterisation of the capacity of highly reactive minerals to preserve soil organic matter (SOM) in colloids at submicron scale.

Mineral-organo associations (MOAs) are a mixture of identifiable biopolymers associated with highly reactive minerals and microorganisms. However, the in situ characterization and correlation between soil organic matter (SOM) and highly reactive Al and Fe minerals are still unclear for the lack of technologies, particularly in the long-term agricultural soil colloids at submicron scale. We combined several novel techniques, including nano-scale secondary ion mass spectrometry (NanoSIMS), X-ray absorption near edge structure (XANES) and confocal laser scanning microscopy (CLSM) to characterise the capacity of highly reactive Al and Fe minerals to preserve SOM in Ferralic Cambisol in south China. Our results demonstrated that: (1) highly reactive minerals were strongly related to SOM preservation, while SOM had a more significant line correlation with the highly reactive Al minerals than the highly reactive Fe minerals, according to the regions of interest correlation analyses using NanoSIMS; (2) allophane and ferrihydrite were the potential mineral species to determine the SOM preservation capability, which was evaluated by the X-ray photoelectron spectroscopy (XPS) and Fe K-edge XANES spectroscopy techniques; and (3) soil organic biopolymers with dominant compounds, such as proteins, polysaccharides and lipids, were distributed at the rough and clustered surface of MOAs with high chemical and spatial heterogeneity according to the CLSM observation. Our results also promoted the understanding of the roles played by the highly reactive Al and Fe minerals in the spatial distribution of soil organic biopolymers and SOM sequestration.