Samuel M. Webb

The fundamental mechanisms underlying kidney stone formation remain elusive despite extensive research, limiting prevention strategies and contributing to high recurrence rates. Traditionally understood to form through systemic urine supersaturation and often conceptualized as monolithic concretions, recent data indicate that kidney stones exhibit marked structural and compositional heterogeneity across distinct renal microenvironments. Investigating diverse anatomical niches will inform biochemical processes that govern renal biomineralization.Here, we integrate high-resolution micro–X-ray computed tomography with X-ray fluorescence microprobe and energy-dispersive X-ray spectroscopy to characterize physicochemical features and infer biochemical factors across three morphologically distinct renal biominerals from three anatomically distinct niches. We identify both overlapping and divergent compositional signatures, with strong similarity between papillary plaques and mineralized papillary plaques embedded within stones (termed stems), in contrast to predominantly inorganic calcium phosphate stones in the collecting system. These findings reveal spatial compositional gradients in zinc, calcium, and phosphorus from organic-rich papillary mineralization to inorganic-dominant stone maturation.The transition metal zinc (Zn), often regarded as a trace element, emerges here as a spatially organized, microenvironment-dependent component enriched in early papillary lesions, interstitial matrices, and cellular substructures. Zn-phosphate colocalization, discrete high-density domains, and conserved spherical micro- and nanoparticles across all mineral types suggest shared precursors and support a hierarchical mineralization model in which Zn-associated domains precede and potentially template calcium phosphate and calcium oxalate deposition. The coexistence of intratubular and interstitial mineral features further reconciles classical free- and fixed-particle theories, indicating that heterogeneous stone formation arises from combined mechanisms.Collectively, our findings demonstrate that kidney stones are anatomy-specific biominerals whose structure encodes the physicochemical conditions of their origin. We propose that Zn acts as a context-dependent modulator of renal biomineralization and highlight the importance of targeting localized microenvironments for improved diagnosis, prevention, and therapeutic intervention.

The marine dissolved organic sulfur (DOS) pool contains both labile metabolites that are rapidly cycled in the surface ocean and compounds that may persist for thousands of years in the marine environment. Here, we describe the sulfur speciation of marine solid‐phase extracted DOS (DOS _SPE ) from the North Atlantic surface ocean, revealing a diversity of oxidation states that include alkyl sulfides, disulfides, aromatics, sulfonates, and sulfate esters. As dissolved organic carbon concentrations decrease with depth in the water column, relative abundances of reduced sulfur species decrease while those of oxidized sulfur species increase, indicating preferential remineralization of reduced organic sulfur (OS) compounds. Although microorganisms are considered to be the origin of a vast majority of marine DOS _SPE , the DOS _SPE produced by cultures of phototrophs and heterotrophic bacteria is compositionally distinct and ³⁴ S‐enriched relative to environmental DOS _SPE . Ultimately, mechanisms spanning different timescales, including microbial reworking, uptake, and photochemical oxidation transform labile DOS in the surface ocean, and may generate recalcitrant compounds that contribute to the long‐lived dissolved organic matter pool. The oxidation states of OS function as powerful tools for tracking the sources, sinks, and transformations of organic matter in complex biogeochemical systems.

X-ray imaging is a powerful technique to scan samples in a variety of contexts including biological, environmental and materials science, but commonly requires a synchrotron light source to produce X-rays at sufficient intensity. As these facilities are expensive to operate, the available beam time is limited and always in high demand. Particularly if the illuminated samples are sparse, standard raster scanning methods can be time-consuming, with a majority of that time being spent on areas of the image that carry little information. To increase the efficiency and maximize the information gain for a given time budget, we split the scanning process into a series of steps where previous measurements are used to inform the decision making and adapt the exposure distribution at later stages of the sequence. We formulate this task as a reinforcement learning problem where the goal is to produce a sequence of exposure maps that maximize a predefined scalar metric. We demonstrate the potential of this approach in simulations where the adaptive illumination can accelerate the measurement process by up to an order of magnitude compared with standard raster scanning. Finally, we present the first results from deploying the trained agents on an X-ray fluorescence beamline at the Stanford Synchrotron Radiation Lightsource.

Blue carbon ecosystems such as seagrass meadows, mangrove forests, and salt marshes are important carbon sinks that can store carbon for millennia. Recently, organic matter sulfurization and pyritization have been proposed as mechanisms of net carbon storage in blue carbon ecosystems. At our study site, organic sulfur that is resistant to acid hydrolysis (protokerogen) is an order of magnitude less abundant than pyrite sulfur, suggesting a dominance of pyritization over sulfurization. The C/N ratios and carbon isotope compositions suggest that nearly half of total organic carbon and ≥ 80% of protokerogen is composed of marsh plant material. Sediment protokerogen appears to be sulfurized based on its low δ³⁴S values (− 10‰), abundance of disulfides, and higher S/C ratio (~ 1.0%) relative to potential biogenic sulfur sources. However, the interpretation of protokerogen δ³⁴S values is complicated by the wide range in sulfur isotope compositions of marsh plants. Evidence for sulfurization occurs within the shallowest sediments across different vegetation zones, yielding consistent products, while pyritization appears to be more sensitive to alterations in sediment redox conditions. Based on organic sulfur and pyrite content, sulfurization may be a more spatially consistent process than pyritization, with implications for carbon storage. The relative abundance of pyrite and protokerogen organic sulfur indicates that pyritization is favored at our study site, but this is likely to vary across the spectrum of blue carbon ecosystems.

The rise of atmospheric oxygen as a result of photosynthesis in cyanobacteria and chloroplasts has transformed most environmental iron into the ferric state. In contrast, cells within organisms maintain a reducing internal milieu and utilize predominantly ferrous iron. Ferric reductases are enzymes that transfer electrons to ferric ions, either extracellularly or within endocytic vesicles, enabling cellular ferrous iron uptake through Divalent Metal Transporter 1. In mammals, duodenal cytochrome b is a ferric reductase of the intestinal epithelium, but how insects reduce and absorb dietary iron remains unknown. Here we provide indirect evidence of extracellular ferric reductase activity in a small subset of Drosophila melanogaster intestinal epithelial cells, positioned at the neck of the midgut’s anterior region. Dietary-supplemented bathophenanthroline sulphate (BPS) captures locally generated ferrous iron and precipitates into pink granules, whose chemical identity was probed combining in situ X-ray absorption near edge structure and electron paramagnetic resonance spectroscopies. An increased presence of manganese ions upon BPS feeding was also found. Control animals were fed with ferric ammonium citrate, which is accumulated into ferritin iron in distinct intestinal subregions suggesting iron trafficking between different cells inside the animal. Spectroscopic signals from the biological samples were compared to purified Drosophila and horse spleen ferritin and to chemically synthesized BPS-iron and BPS-manganese complexes. The results corroborated the presence of BPS-iron in a newly identified ferric iron reductase region of the intestine, which we propose constitutes the major site of iron absorption in this organism. Graphical abstract

Organic sulfur plays a crucial role in the biogeochemistry of aquatic sediments, especially in low sulfate (< 500 μM) environments like freshwater lakes and the Earth's early oceans. To better understand organic sulfur cycling in these systems, we followed organic sulfur in the sulfate‐poor (< 40 μM) iron‐rich (30–80 μM) sediments of Lake Superior from source to sink. We identified microbial populations with shotgun metagenomic sequencing and characterized geochemical species in porewater and solid phases. In anoxic sediments, we found an active sulfur cycle fueled primarily by oxidized organic sulfur. Sediment incubations indicated a microbial capacity to hydrolyze sulfonates, sulfate esters, and sulfonic acids to sulfate. Gene abundances for dissimilatory sulfate reduction (dsrAB) increased with depth and coincided with sulfide maxima. Despite these indicators of sulfide formation, sulfide concentrations remain low (< 40 nM) due to both pyritization and organic matter sulfurization. Immediately below the oxycline, pyrite accounted for 13% of total sedimentary sulfur. Both free and intact lipids in this same interval accumulated disulfides, indicating rapid sulfurization even at low concentrations of sulfide. Our investigation revealed a new model of sulfur cycling in a low‐sulfate environment that likely extends to other modern lakes and possibly the ancient ocean, with organic sulfur both fueling sulfate reduction and consuming the resultant sulfide.

Nitrogen recovery from wastewater represents a sustainable route to recycle reactive nitrogen (Nr). It can reduce the demand of producing Nr from the energy‐extensive Haber‐Bosch process and lower the risk of causing eutrophication simultaneously. In this aspect, source‐separated fresh urine is an ideal source for nitrogen recovery given its ubiquity and high nitrogen contents. However, current techniques for nitrogen recovery from fresh urine require high energy input and are of low efficiencies because the recovery target, urea, is a challenge to separate. In this work, we developed a novel fresh urine nitrogen recovery treatment process based on modular functionalized metal–organic frameworks (MOFs). Specifically, we employed three distinct modification methods to MOF‐808 and developed robust functional materials for urea hydrolysis, ammonium adsorption, and ammonia monitoring. By integrating these functional materials into our newly developed nitrogen recovery treatment process, we achieved an average of 75 % total nitrogen reduction and 45 % nitrogen recovery with a 30‐minute treatment of synthetic fresh urine. The nitrogen recovery process developed in this work can serve as a sustainable and efficient nutrient management that is suitable for decentralized wastewater treatment. This work also provides a new perspective of implementing versatile advanced materials for water and wastewater treatment.

Nitrogen recovery from wastewater represents a sustainable route to recycle reactive nitrogen (Nr). It can reduce the demand of producing Nr from the energy‐extensive Haber‐Bosch process and lower the risk of causing eutrophication simultaneously. In this aspect, source‐separated fresh urine is an ideal source for nitrogen recovery given its ubiquity and high nitrogen contents. However, current techniques for nitrogen recovery from fresh urine require high energy input and are of low efficiencies because the recovery target, urea, is a challenge to separate. In this work, we developed a novel fresh urine nitrogen recovery treatment process based on modular functionalized metal–organic frameworks (MOFs). Specifically, we employed three distinct modification methods to MOF‐808 and developed robust functional materials for urea hydrolysis, ammonium adsorption, and ammonia monitoring. By integrating these functional materials into our newly developed nitrogen recovery treatment process, we achieved an average of 75 % total nitrogen reduction and 45 % nitrogen recovery with a 30‐minute treatment of synthetic fresh urine. The nitrogen recovery process developed in this work can serve as a sustainable and efficient nutrient management that is suitable for decentralized wastewater treatment. This work also provides a new perspective of implementing versatile advanced materials for water and wastewater treatment.