Nitrogen source influences the interactions of comammox bacteria with aerobic nitrifiers.

While the co-existence of comammox Nitrospira with canonical nitrifiers is well documented in diverse ecosystems, there is still a dearth of knowledge about the mechanisms underpinning their interactions. Understanding these interaction mechanisms is important as they may play a critical role in governing nitrogen biotransformation in natural and engineered ecosystems. In this study, we tested the ability of two environmentally relevant factors (nitrogen source and availability) to shape interactions between strict ammonia and nitrite-oxidizing bacteria and comammox Nitrospira in continuous flow column reactors. The composition of inorganic nitrogen species in reactors fed either ammonia or urea was similar during the lowest input nitrogen concentration (1 mg-N/L), but higher concentrations (2 and 4 mg-N/L) promoted significant differences in nitrogen species composition and nitrifier abundances. The abundance and diversity of comammox Nitrospira were dependent on both nitrogen source and input concentrations as multiple comammox Nitrospira populations were preferentially enriched in the urea-fed system. In contrast, their abundance was reduced in response to higher nitrogen concentrations in the ammonia-fed system. The preferential enrichment of comammox Nitrospira in the urea-fed system could be associated with their ureolytic activity calibrated to their ammonia oxidation rates, thus minimizing ammonia accumulation, which may be partially inhibitory. However, an increased abundance of comammox Nitrospira was not associated with a reduced abundance of nitrite oxidizers in the urea-fed system while a negative correlation was found between them in the ammonia-fed system, the latter dynamic likely emerging from reduced availability of nitrite to strict nitrite oxidizers at low ammonia concentrations. IMPORTANCE: Nitrification is an essential biological process in drinking water and wastewater treatment systems for treating nitrogen pollution. The discovery of comammox Nitrospira and their detection alongside canonical nitrifiers in these engineered ecosystems have made it necessary to understand the environmental conditions that regulate their abundance and activity relative to other better-studied nitrifiers. This study aimed to evaluate two important factors that could potentially influence the behavior of nitrifying bacteria and, therefore, impact nitrification processes. Column reactors fed with either ammonia or urea were systematically monitored to capture changes in nitrogen biotransformation and the nitrifying community as a function of influent nitrogen concentration, nitrogen source, and reactor depth. Our findings show that with increased ammonia availability, comammox Nitrospira decreased in abundance while nitrite oxidizers abundance increased. Yet, in systems with increasing urea availability, comammox Nitrospira abundance and diversity increased without an associated reduction in the abundance of canonical nitrifiers.

Sunlight-Driven Photochemical Removal of Polypropylene Microplastics from Surface Waters Follows Linear Kinetics and Does Not Result in Fragmentation.

Floating microplastics are susceptible to sunlight-driven photodegradation, which can convert plastic carbon to dissolved organic carbon (DOC) and can facilitate microplastic fragmentation by mechanical forces. To understand the photochemical fate of sub-millimeter buoyant plastics, ∼0.6 mm polypropylene microplastics were photodegraded while tracking plastic mass, carbon, and particle size distributions. Plastic mass loss and carbon loss followed linear kinetics. At most time points DOC accumulation accounted for under 50% of the total plastic carbon lost. DOC accumulation followed sigmoidal kinetics, not the exponential kinetics previously reported for shorter irradiations. Thus, we suggest that estimates of plastic lifespan based on exponential DOC accumulation are inaccurate. Instead, linear plastic-C mass and plastic mass loss kinetics should be used, and these methods result in longer estimates of photochemical lifetimes for plastics in surface waters. Scanning electron microscopy revealed that photoirradiation produced two distinct patterns of cracking on the particles. However, size distribution analyses indicated that fragmentation was minimal. Instead, the initial population of microplastics shrank in size during irradiations, indicating photoirradiation in tranquil waters (i.e., without mechanical forcing) dissolved sub-millimeter plastics without fragmentation.

Molecular Signatures of Dissolved Organic Matter Generated from the Photodissolution of Microplastics in Sunlit Seawater.

Plastics are accumulating on Earth, including at sea. The photodegradation of microplastics floating in seawater produces dissolved organic matter (DOM), indicating that sunlight can photodissolve microplastics at the sea surface. To characterize the chemistry of DOM produced as microplastics photodissolve, three microplastics that occur in surface waters, polyethylene (PE), polypropylene (PP), and expanded polystyrene (EPS), were incubated floating on seawater in both the light and the dark. We present the molecular signatures of the DOM produced during these incubations, as determined via ultrahigh-resolution mass spectrometry. Zero to 12 products were identified in the dark, whereas 319-705 photoproducts were identified in the light. Photoproduced DOM included oxygen atoms, indicating that soluble, oxygen-containing organics were formed as plastics photodegrade. PP and PE plastics have hydrogen-to-carbon (H/C) ratios of 2 and generated DOM with average H/C values of 1.7 ± 0.1 to 1.8 ± 0.1, whereas EPS, which has an H/C of 1, generated DOM with an average H/C of 0.9 ± 0.2, indicating the stoichiometry of photoproduced DOM was related to the stoichiometry of the photodegrading polymer. The photodissolution of plastics produced hundreds of photoproducts with varying elemental stoichiometries, indicating that a single abiotic process (photochemistry) can generate hundreds of different chemicals from stoichiometrically monotonous polymers.

Shower thoughts: why scientists should spend more time in the rain.

Stormwater is a vital resource and dynamic driver of terrestrial ecosystem processes. However, processes controlling interactions during and shortly after storms are often poorly seen and poorly sensed when direct observations are substituted with technological ones. We discuss how human observations complement technological ones and the benefits of scientists spending more time in the storm. Human observation can reveal ephemeral storm-related phenomena such as biogeochemical hot moments, organismal responses, and sedimentary processes that can then be explored in greater resolution using sensors and virtual experiments. Storm-related phenomena trigger lasting, oversized impacts on hydrologic and biogeochemical processes, organismal traits or functions, and ecosystem services at all scales. We provide examples of phenomena in forests, across disciplines and scales, that have been overlooked in past research to inspire mindful, holistic observation of ecosystems during storms. We conclude that technological observations alone are insufficient to trace the process complexity and unpredictability of fleeting biogeochemical or ecological events without the shower thoughts produced by scientists' human sensory and cognitive systems during storms.

An optimized acidic digestion for the isolation of microplastics from biota-rich samples and cellulose acetate matrices.

Plastic pollution is a growing concern. To analyze plastics in environmental samples, plastics need to be isolated. We present an acidic/oxidative method optimized to preserve plastics while digesting synthetic cellulose acetate and a range of organics encountered in environmental samples. Cellulose acetate was chosen for optimization as it can be purchased as a reference material, can co-occur with plastics in environmental samples and, if it can be completely digested, is a potential filter material for the collection of nano- and micro-plastics from natural waters. Other forms of particulate organic matter (POM) were chosen to provide a range of chemistries that might alter digestion efficiency and due to the interest in the community of isolating plastics from samples where these organics occur. For instance, microalgal POM occurs in lake and ocean waters, riverine POM in rivers, and inclusion of tuna provides a test for the suitability of the method for isolating plastics from animal tissues. The method is a one-pot overnight (16-18 h) digestion in 5 M nitric acid with 0.3 M sodium persulfate heated to 80 °C. The method provides quantitative removal of cellulose acetate (exceeding detection limits), near quantitative removal of microalgal POM and Albacore tuna tissue (>99%), but only 86% of urban river POM, all while retaining >99% by mass of C-C bonded polymers polyethylene, polypropylene, and polystyrene and >96% by mass of polyethylene terephthalate. Fourier transform infrared spectroscopy (FT-IR) and %-C content analysis confirmed plastic polymer stability during digestion. However, some additives in appear susceptible to digestion with FT-IR results indicating the loss of N,N'-ethylenebis(stearamide) from polyethylene. This method provides a simpler and more effective method than many in the literature. We present recommendations for the application of this method, as well as limitations and areas for future improvement.

Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic.

COVID-19 pandemic-related building restrictions heightened drinking water microbiological safety concerns post-reopening due to the unprecedented nature of commercial building closures. Starting with phased reopening (i.e., June 2020), we sampled drinking water for 6 months from three commercial buildings with reduced water usage and four occupied residential households. Samples were analyzed using flow cytometry and full-length 16S rRNA gene sequencing along with comprehensive water chemistry characterization. Prolonged building closures resulted in 10-fold higher microbial cell counts in the commercial buildings [(2.95 ± 3.67) × 105 cells mL-1] than in residential households [(1.11 ± 0.58) × 104 cells mL-1] with majority intact cells. While flushing reduced cell counts and increased disinfection residuals, microbial communities in commercial buildings remained distinct from those in residential households on the basis of flow cytometric fingerprinting [Bray-Curtis dissimilarity (dBC) = 0.33 ± 0.07] and 16S rRNA gene sequencing (dBC = 0.72 ± 0.20). An increase in water demand post-reopening resulted in gradual convergence in microbial communities in water samples collected from commercial buildings and residential households. Overall, we find that the gradual recovery of water demand played a key role in the recovery of building plumbing-associated microbial communities as compared to short-term flushing after extended periods of reduced water demand.

Assessing inputs of aquaculture-derived nutrients to streams using dissolved organic matter fluorescence.

Salmon aquaculture is an important economic activity globally where local freshwater supplies permit land-based salmon aquaculture facilities to cultivate early life stage salmon. Nitrogen, phosphorus and organic matter in aquaculture effluents contribute to the eutrophication of adjacent and downstream rivers and lakes. This study quantifies the enrichment of nutrients in land-based salmon aquaculture facility effluents compared to receiving waters. We measured nutrient concentrations and dissolved organic matter (DOM) quantity and quality via fluorescence spectroscopy in streams and effluent waters associated with 27 facilities in Chile. We found that facilities added on average 0.9 (s.d. = 2.0) mg-C L-1, 542 (s.d. = 637) µg-total N L-1, and 104 (s.d. = 104) µg-total P L-1 to effluents compared to stream waters. DOM in stream water was enriched in humic-like fluorescence, while aquaculture effluents were enriched in protein-like DOM fluorophores. Principal component and correlation analysis revealed that tryptophan-like fluorescence was a good predictor of total N and P in effluents, but the strength of significant linear relationships varied among individual facilities (r2: 0.2 to 0.9). Agreement between laboratory fluorescence and a portable fluorometer indicates the utility of in-situ sensors for monitoring of both tryptophan-like fluorescence and covarying nutrients in effluents. Thus, continuous in-situ sensors are likely to improve industry management and allow more robust estimates of aquaculture-derived nutrients delivered to receiving waters.

Plastics in the Earth system.

Plastic contamination of the environment is a global problem whose magnitude justifies the consideration of plastics as emergent geomaterials with chemistries not previously seen in Earth's history. At the elemental level, plastics are predominantly carbon. The comparison of plastic stocks and fluxes to those of carbon reveals that the quantities of plastics present in some ecosystems rival the quantity of natural organic carbon and suggests that geochemists should now consider plastics in their analyses. Acknowledging plastics as geomaterials and adopting geochemical insights and methods can expedite our understanding of plastics in the Earth system. Plastics also can be used as global-scale tracers to advance Earth system science.

Carbonaceous matter in the atmosphere and glaciers of the Himalayas and the Tibetan plateau: An investigative review.

Carbonaceous matter, including organic carbon (OC) and black carbon (BC), is an important climate forcing agent and contributes to glacier retreat in the Himalayas and the Tibetan Plateau (HTP). The HTP - the so-called "Third Pole" - contains the most extensive glacial area outside of the polar regions. Considerable research on carbonaceous matter in the HTP has been conducted, although this research has been challenging due to the complex terrain and strong spatiotemporal heterogeneity of carbonaceous matter in the HTP. A comprehensive investigation of published atmospheric and snow data for HTP carbonaceous matter concentration, deposition and light absorption is presented, including how these factors vary with time and other parameters. Carbonaceous matter concentrations in the atmosphere and glaciers of the HTP are found to be low. Analysis of water-insoluable organic carbon and BC from snowpits reveals that concentrations of OC and BC in the atmosphere and glacier samples in arid regions of the HTP may be overestimated due to contributions from inorganic carbon in mineral dust. Due to the remote nature of the HTP, carbonaceous matter found in the HTP has generally been transported from outside the HTP (e.g., South Asia), although local HTP emissions may also be important at some sites. This review provides essential data and a synthesis of current thinking for studies on atmospheric transport modeling and radiative forcing of carbonaceous matter in the HTP.

Hydrocarbons to carboxyl-rich alicyclic molecules: A continuum model to describe biodegradation of petroleum-derived dissolved organic matter in contaminated groundwater plumes.

Relationships between dissolved organic matter (DOM) reactivity and chemical composition in a groundwater plume containing petroleum-derived DOM (DOMHC) were examined by quantitative and qualitative measurements to determine the source and chemical composition of the compounds that persist downgradient. Samples were collected from a transect down the core of the plume in the direction of groundwater flow. An exponential decrease in dissolved organic carbon concentration resulting from biodegradation along the transect correlated with a continuous shift in fluorescent DOMHC from shorter to longer wavelengths. Moreover, ultrahigh resolution mass spectrometry showed a shift from low molecular weight (MW) aliphatic, reduced compounds to high MW, unsaturated (alicyclic/aromatic), high oxygen compounds that are consistent with carboxyl-rich alicyclic molecules. The degree of condensed aromaticity increased downgradient, indicating that compounds with larger, conjugated aromatic core structures were less susceptible to biodegradation. Nuclear magnetic resonance spectroscopy showed a decrease in alkyl (particularly methyl) and an increase in aromatic/olefinic structural motifs. Collectively, data obtained from the combination of these complementary analytical techniques indicated that changes in the DOMHC composition of a groundwater plume are gradual, as relatively low molecular weight (MW), reduced, aliphatic compounds from the oil source were selectively degraded and high MW, alicyclic/aromatic, oxidized compounds persisted.

ICBM-OCEAN: Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures.

Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg-complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.

Photochemical dissolution of buoyant microplastics to dissolved organic carbon: Rates and microbial impacts.

Trillions of plastic fragments are afloat at sea, yet they represent only 1-2% of the plastics entering the ocean annually. The fate of the missing plastic and its impact on marine life remains largely unknown. To address these unknowns, we irradiated post-consumer microplastics (polyethylene, PE; polypropylene, PP; and expanded polystyrene, EPS), standard PE, and plastic-fragments collected from the surface waters of the North Pacific Gyre under a solar simulator. We report that simulated sunlight can remove plastics from the sea surface. Simulated sunlight also fragmented, oxidized, and altered the color of the irradiated polymers. Dissolved organic carbon (DOC) is identified as a major byproduct of sunlight-driven plastic photodegradation. Rates of removal depended upon polymer chemistry with EPS degrading more rapidly than PP, and PE being the most photo-resistant polymer studied. The DOC released as most plastics photodegraded was readily utilized by marine bacteria. However, one sample of PE microplastics released organics or co-leachates that inhibited microbial growth. Thus, although sunlight may remove plastics from the ocean's surface, leachates formed during plastic photodegradation may have mixed impacts on ocean microbes and the food webs they support.

Isotopic composition of oceanic dissolved black carbon reveals non-riverine source.

A portion of the charcoal and soot produced during combustion processes on land (e.g., wildfire, burning of fossil fuels) enters aquatic systems as dissolved black carbon (DBC). In terms of mass flux, rivers are the main identified source of DBC to the oceans. Since DBC is believed to be representative of the refractory carbon pool, constraining sources of marine DBC is key to understanding the long-term persistence of carbon in our global oceans. Here, we use compound-specific stable carbon isotopes (δ13C) to reveal that DBC in the oceans is ~6‰ enriched in 13C compared to DBC exported by major rivers. This isotopic discrepancy indicates most riverine DBC is sequestered and/or rapidly degraded before it reaches the open ocean. Thus, we suggest that oceanic DBC does not predominantly originate from rivers and instead may be derived from another source with an isotopic signature similar to that of marine phytoplankton.

Photochemical Alteration of Dissolved Organic Sulfur from Sulfidic Porewater.

Sulfidic sediments are a source of dissolved organic sulfur (DOS) to the ocean but the fate of sedimentary DOS in the oxic, sunlit water column is unknown. We hypothesized that photodegradation after discharge from the dark sedimentary environment results in DOS molecular transformation and decomposition. To test this hypothesis, sulfidic porewater from a saltmarsh was exposed to potential abiotic transformations of dissolved organic matter (DOM) in the water column. We quantitatively investigated DOM transformations via elemental analysis and molecularly via ultrahigh-resolution mass spectrometry. Our study indicated that photoreactivity is dependent on DOM elemental composition as DOS molecular formulas were more photolabile than those without sulfur. Prior to solar irradiation, of the 6451 identified molecular formulas in sulfidic porewater, 39% contained sulfur. After 29 days of irradiation, the DOS concentration was depleted from 13 to 1 µM, together with a 9% decrease in the number of DOS molecular formulas. Comparing porewater and oceanic DOS molecular formulas, solar irradiation increased the similarity due to the removal of photolabile DOS formulas not present in the ocean. In conclusion, DOS from sulfidic sediments is preferentially photolabile and solar irradiation can be a potential mechanism controlling the stability and fate of porewater DOS.

Correction: Aged dissolved organic carbon exported from rivers of the Tibetan Plateau.

[This corrects the article DOI: 10.1371/journal.pone.0178166.].

Aged dissolved organic carbon exported from rivers of the Tibetan Plateau.

The role played by river networks in regional and global carbon cycle is receiving increasing attention. Despite the potential of radiocarbon measurements (14C) to elucidate sources and cycling of different riverine carbon pools, there remain large regions such as the climate-sensitive Tibetan Plateau for which no data are available. Here we provide new 14C data on dissolved organic carbon (DOC) from three large Asian rivers (the Yellow, Yangtze and Yarlung Tsangpo Rivers) running on the Tibetan Plateau and present the carbon transportation pattern in rivers of the plateau versus other river system in the world. Despite higher discharge rates during the high flow season, the DOC yield of Tibetan Plateau rivers (0.41 gC m-2 yr-1) was lower than most other rivers due to lower concentrations. Radiocarbon ages of the DOC were older/more depleted (511±294 years before present, yr BP) in the Tibetan rivers than those in Arctic and tropical rivers. A positive correlation between radiocarbon age and permafrost watershed coverage was observed, indicating that 14C-deplted/old carbon is exported from permafrost regions of the Tibetan Plateau during periods of high flow. This is in sharp contrast to permafrost regions of the Arctic which export 14C-enriched carbon during high discharge periods.

Comment on "Dissolved organic sulfur in the ocean: Biogeochemistry of a petagram inventory".

Ksionzek et al (Reports, 28 October 2016, p. 456) provide important data describing the distribution of dissolved organic sulfur (DOS) in the Atlantic Ocean. Here, we show that mixing between water masses is sufficient to explain the observed distribution of DOS, concluding that the turnover time of refractory DOS that Ksionzek et al present cannot be deduced from their data.

Spatial Dependence of Reduced Sulfur in Everglades Dissolved Organic Matter Controlled by Sulfate Enrichment.

Sulfate inputs to the Florida Everglades stimulate sulfidic conditions in freshwater wetland sediments that affect ecological and biogeochemical processes. An unexplored implication of sulfate enrichment is alteration of the content and speciation of sulfur in dissolved organic matter (DOM), which influences the reactivity of DOM with trace metals. Here, we describe the vertical and lateral spatial dependence of sulfur chemistry in the hydrophobic organic acid fraction of DOM from unimpacted and sulfate-impacted Everglades wetlands using X-ray absorption spectroscopy and ultrahigh-resolution mass spectrometry. Spatial variation in DOM sulfur content and speciation reflects the degree of sulfate enrichment and resulting sulfide concentrations in sediment pore waters. Sulfur is incorporated into DOM predominantly as highly reduced species in sulfidic pore waters. Sulfur-enriched DOM in sediment pore waters exchanges with overlying surface waters and the sulfur likely undergoes oxidative transformations in the water column. Across all wetland sites and depths, the total sulfur content of DOM correlated with the relative abundance of highly reduced sulfur functionality. The results identify sulfate input as a primary determinant on DOM sulfur chemistry to be considered in the context of wetland restoration and sulfur and trace metal cycling.