Environmental Biogeochemistry Research Articles

Appearance of Recalcitrant Dissolved Black Carbon and Dissolved Organic Sulfur in River Waters Following Wildfire Events.

Increasing wildfire frequency, a consequence of global climate change, releases incomplete combustion byproducts such as aquatic pyrogenic dissolved organic matter (DOM) and black carbon (DBC) into waters, posing a threat to water security. In August 2022, a series of severe wildfires occurred in Chongqing, China. Samples from seven locations along the Yangtze and Jialing Rivers revealed DBC, quantified by the benzene poly(carboxylic acid) (BPCA) method, comprising 9.5-19.2% of dissolved organic carbon (DOC). High concentrations of BPCA-DBC with significant polycondensation were detected near wildfire areas, likely due to atmospheric deposition driven by wind. Furthermore, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) revealed that wildfires were associated with an increase in condensed aromatics, proteins, and unsaturated hydrocarbons, along with a decrease in lignins. The condensed aromatics primarily consisted of dissolved black nitrogen (DBN), contributing to abundant high-nitrogen-containing compounds in locations highly affected by wildfires. Meanwhile, wildfires potentially induced the input of recalcitrant sulfur-containing protein-like compounds, characterized by high oxidation, aliphatic nature, saturation, and low aromaticity. Overall, this study revealed the appearance of recalcitrant DBC and dissolved organic sulfur in river waters following wildfire events, offering novel insights into the potential impacts of wildfires on water quality and environmental biogeochemistry.

Vivianite oxidation is not photocatalyzed

Vivianite is a hydrous Fe(II) phosphate mineral found in anoxic environments that plays an integral role in P cycling and environmental biogeochemistry. Imbued in the vivianite literature dating as far back as 1918 is the notion that vivianite is light-sensitive and susceptible to rapid photooxidation induced entirely by solar light. However, despite an exhaustive search, to our knowledge this conventionally accepted assumption has never been directly tested, nor has the band gap ever been measured. Resolving this question of photochemical control of vivianite redox chemistry is important for performing and interpreting experiments involving vivianite reactivity with contaminants, and potentially iron and phosphate cycling in the photic zone of aquatic systems. The present study was specifically designed to address this question. Pure synthetic vivianite samples were irradiated in aqueous suspensions with a Xe lamp at conditions mimicking the solar spectrum and compared to dark controls. Particles stirred in anoxic suspensions for up to 66 days showed no detectable oxidation irrespective of light exposure, according to colorimetric Fe(II)/Fe(III) assays, micro X-ray diffraction, and Raman spectroscopy. In contrast, the same experiment performed using air-equilibrated suspensions showed systematic oxidation of up to ∼80 mol% Fe(II) at 66 days, but again with no detectable light exposure effect. To test for UV reactivity, further experiments on vivianite powders under air versus N2 atmosphere were performed using a Hg lamp with a longpass filter. In contrast to oxidation in air where no effect of light was detected, after 24 h irradiation anoxically, an additional 0.8 % Fe was oxidized compared to dark controls, and after 13 days only an additional 0.3 % Fe was oxidized. The band gap of pure vivianite was measured by the Tauc method to be 3.5 eV. Contrary to previous reports, solar light has minimal impact on the oxidation of pure vivianite; any such effect would be insignificant when compared to its relatively fast oxidation by oxygen exposure. As such, light does not need to be excluded when running typical vivianite laboratory experiments. Long-term storage of natural vivianite in museums or private collections should continue protective measures given that a possible photocatalytic role of impurities cannot yet be ruled out.Nonetheless, at all depths in natural aquatic systems, including the photic zone, it appears that the primary abiotic control on the reactivity and half-life of vivianite particles would be the dissolved oxygen concentration, not light exposure.

Iodine in soils, pasture vegetation cuttings, and local food products of certain regions of Russia affected by the Chernobyl nuclear power plant accident

Natural iodine deficiency, which in some regions of Russia provokes thyroid diseases, increases the consequences of the entry of short-lived radioactive isotopes of this element into the food chain as a result of the Chernobyl accident (1986). The aim of the work is to assess the risk of morbidity of the population of the Kaluga, Bryansk and Oryol regions with thyroid cancer at the level of individual settlements based on experimental data. The iodine content in soils and vegetation cuttings of pastures in geochemically contrasting landscapes, as well as in cows' milk and potatoes of private household farms in the regions affected by the Chernobyl accident in 1986: Bryansk (2021), Oryol (2022) and Kaluga (2023) regions was studied. Joint expeditions of the Laboratory of Environmental Biogeochemistry of GEOKHI RAS and the Department of Human Ecology and Bioelementology of the Institute of Ecology of RUDN, carried out on the initiative and with the participation of the authors, revealed a significant variation of iodine concentration in soils and food products, which may be crucial for assessing the risk of thyroid diseases, including thyroid cancer, among the local rural population. The iodine content was found to be highly variable in both topsoil (0.31-3.04 mg/kg) and grass cuttings (0.14-0.29 mg/kg) of the study area. The maximum natural and technogenic risk of thyroid cancer morbidity in the rural population as a result of the consequences of the Chernobyl accident of 1986 is specific for the studied settlements of Zhizdrinsky district of Kaluga region, Bolkhovsky, Dmitrovsky and Sverdlovsky districts of Oryol region, Rognedinsky district of Bryansk region.

The overlooked role of denitrifying bacteria in mediating vanadate reduction

Microbial vanadate [V(V)] reduction is the key process of vanadium geochemical cycling, while the identified functional microbes are rather limited. Considering the structural similarity of metavanadate and nitrate, widespread denitrifying bacteria are expected to be able to mediate V(V) reduction, but this process has not been fully understood. This study confirmed the effectiveness of two denitrifying bacteria, i.e., Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002, in reducing V(V). During 120-h incubation, the V(V) removal efficiency was 89.0 ± 1.83% and 96.0 ± 1.43% by strain BoFeN1 and strain 2002, respectively. V(V) was reduced to tetravalent vanadium [V(IV)] both intracellularly and extracellularly. Use of inhibitors and metabolomic analysis revealed enzyme catalysis and electron transfer pathways for V(V) reduction. Enzyme catalysis was identified by analyses of gene abundance, transcript abundance, and enzymatic activity. Electron transfer was verified through quantifying electron transporters, monitoring electron transport system activity, and performing cyclic voltammetry analysis. For strain BoFeN1, nitrite and nitrous oxide reductases played vital roles in V(V) reduction, together with cytochrome c (Cyt c) and nicotinamide adenine dinucleotide (NADH) mediated electron transfer. Differentially expressed riboflavin produced by strain BoFeN1 also promoted electron transfer. Strain 2002 mainly utilized periplasmic nitrate reductase to reduce V(V). Aquifer sediment bioaugmented with these strains enhanced V(V) reduction by 10.5%−51.1%. They well colonized and collaborated with indigenous microorganisms to reduce V(V) to V(IV). This study advances understanding of environmental biogeochemistry of vanadium and provides molecular insights into V(V) bio-reduction as a sustainable bioremediation strategy.

From biomolecules to biogeochemistry: Exploring the interaction of an indigenous bacterium with gold

Specialised microbial communities colonise the surface of gold particles in soils/sediments, and catalyse gold dissolution and re-precipitation, thereby contributing to the environmental mobility and toxicity of this ‘inert’ precious metal. We assessed the proteomic and physiological response of Serratia proteamaculans, the first metabolically active bacterium enriched and isolated directly from natural gold particles, when exposed to toxic levels of soluble Au3+ (10 μM). The results were compared to a metal-free blank, and to cultures exposed to similarly toxic levels of soluble Cu2+ (0.1 mM); Cu was chosen for comparison because it is closely associated with Au in nature due to similar geochemical properties. A total of 273 proteins were detected from the cells that experienced the oxidative effects of soluble Au, of which 139 (51%) were upregulated with either sole expression (31%) or had synthesis levels greater than the Au-free control (20%). The majority (54%) of upregulated proteins were functionally different from up-regulated proteins in the bacteria-copper treatment. These proteins were related to broad functions involving metabolism and biogenesis, followed by cellular process and signalling, indicating significant specificity for Au. This proteomic study revealed that the bacterium upregulates the synthesis of various proteins related to oxidative stress response (e.g., Monothiol-Glutaredoxin, Thiol Peroxidase, etc.) and cellular damage repair, which leads to the formation of metallic gold nanoparticles less toxic than ionic gold. Therefore, indigenous bacteria may mediate the toxicity of Au through two different yet simultaneous processes: i) repairing cellular components by replenishing damaged proteins and ii) neutralising reactive oxygen species (ROS) by up-regulating the synthesis of antioxidants. By connecting the fields of molecular bacteriology and environmental biogeochemistry, this study is the first step towards the development of biotechnologies based on indigenous bacteria applied to gold bio-recovery and bioremediation of contaminated environments.

Seasonal Flooding Impact on Land Surface Temperature(LST) in Response to Vegetation Index Using Spectral Radiance Model in Kirkuk, Iraq

Change detection of land use is essential in management and planning decisions. Land Surface Temperature (LST) has a significant importance in many geoscience aspects, such as heat transportation between land and atmosphere, state of corps, heat flux, greenhouse effect both locally and regionally, surface moisture and surface energy budget estimation, the monitoring of urban heat island, evapotranspiration and environmental biogeochemistry process simulation. A geographic information system was efficiently utilized to observe the changes in land use different categories and to map annual and seasonal LST variations. In this study, Land sat 5 and 8 images for the years 2010, 2017 and 2019 were used to study the flooding imact on the LST. The Mono-Window algorithm and sepectral rediance model on Landsat-5 TM and OLI were used to estimate LST. Taking 2010 as a reference, an empirical study shows that the No-vegetation category percentage was 9.28 % and 11.03% in the 2017 and 2019 summer seasons, respectively, while it was -1.48% and -0.46% in winter. Vegetation change was -60.9% and -50.04% in the 2017 and 2019 summer seasons, respectively, while it was 28.28% and -6.11% in winter. Water area change was -65.8% and 84.1% in the 2017 and 2019 summer seasons, respectively, while it was -38.5% and 59.89% in winter. The results indicate that the water area had greatly decreased during 2017 which led to increase the LST and the floods in 2019 led to decrease the LST by 5-8 degrees. The temperature trend analysis reveals a definite negative association between LST and flooded area, representing this study’s significant finding.

Considerations for environmental biogeochemistry and food security for aquaculture around Lake Victoria, Kenya

The impact of population expansion through economic growth and development has been identified as one of the key drivers of both water and sediment contamination from potentially harmful elements (PHEs). This presents a major hazard not only to aquatic ecosystems but local riparian communities and beyond who rely heavily on this natural resource for drinking water and fish—a valuable source of dietary micronutrients and protein. The present study measured biogeochemical concentration of PHEs in water, sediment and fish from locations pooled into four zones within Winam Gulf and Lake Victoria area of Kenya. Captured fish were used as a sentinel receptor of lake health to evaluate potential risks to fisheries and aquaculture food security. In water, concentrations of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu) and lead (Pb) were observed above the United States Environmental Protection Agency (US EPA) maximum contamination level drinking water guidelines (MCL), with aluminium (Al) observed above the Aquatic Life Criteria in all four zones. Similarly, sediment concentrations in all four zones exceeded the US EPA Effects range low (ERL) threshold guidelines for Cu, nickel (Ni), zinc (Zn) and Pb, with Cu, Zn and Pb classed at moderate contamination levels using the contamination factor. Fish tissue concentrations from the four zones were calculated using recommended daily intakes (RDI) and for PHEs as provisional maximum tolerable intakes (PMTIs) and indicated most macro- and micronutrients were at or below 10% RDI from aquaculture and wild fish, with Se indicating a greater RDI (16–29%) in all the zones. Contributions of PHEs to PMTIs were below threshold guidelines for both aquaculture and wild fish with only Cd, Cr and Pb levels being above the PMTI thresholds. There is a need to assess the long-term effects of persistent anthropogenic PHE input into Winam Gulf and the wider Lake Victoria basin. Continued monitoring of PHEs using both historical and more recent data will enable future management policies to be implemented through improved mitigation strategies to reduce their impact on water quality, fish health and subsequent human health.

Cooperative Evolution of China’s Excellent Innovative Research Groups from the Perspective of Innovation Ecosystem: Taking an “Environmental Biogeochemistry” Research Innovation Group as a Case Study

Research, understanding, and prediction of complex systems is an important starting point for human beings to tackle major problems and emergencies such as global warming and COVID-19. Research on innovation ecosystem is an important part of research on complex systems. With the rapid development of sophisticated industries, the rise of innovative countries, and the newly developed innovation theory, innovation ecosystem has become a new explanation and new paradigm for adapting to today’s global innovation cooperation network and the scientific development of complex systems, which is also in line with China’s concept of building an innovative country and promoting comprehensive innovation and international cooperation with scientific and technological innovation as the core. The Innovative Research Group at Peking University is the most representative scientific and technological innovation team in the frontier field of basic research in China. The characteristics of its organization mechanism and dynamic evolution connotation are consistent with the characteristics and evolution of innovation ecosystem. An excellent innovative research group is regarded as a small innovation ecosystem. We selected the “Environmental Biogeochemistry” Innovation Research Group at Peking University as a typical case in order to understand and analyze the evolution of cooperation among scientific and technological innovation teams, improve the healthy development as well as internal and external governance of this special small innovation ecosystem, promote the expansion of an innovation team cooperation network and the improvement of cooperation quality, promote the linkage supports of funding and management departments, and improve their scientific and technological governance abilities. Through scientometrics, visual analysis of knowledge maps, and an exploratory case study, we study the evolution process and development law of team cooperation. It is found that the main node authors of the cooperation network maintain strong cooperation frequency and centrality, and gradually strengthen with the expansion of the cooperation network and the evolution of time. Driven by the internal cooperative governance of the team and the external governance of the funding and management departments, this group has gradually formed a healthy, orderly, open, and cooperative special innovation ecosystem, which is conducive to the stability and sustainable development of the national innovation ecosystem and the global innovation ecosystem.

NanoSIP: NanoSIMS Applications for Microbial Biology.

High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using 15N and 13C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

AbstractIn studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

Reflections about three influential Ambio articles impacting environmental biogeochemistry research and knowledge : This article belongs to Ambio's 50th Anniversary Collection. Theme: Environmental contaminants.

Reflections about three influential environmental contaminants papers published in Ambio are presented. The PCB Story by Jensen in (1972) had a very important influence on environmental chemistry. This is captured by way of comments and personal anecdotes. Wania's and MacKay's (1993) paper highlights the physical chemistry underlying transport of PCBs and organochlorine pesticides from temperate zone ecosystems to Polar Regions. Their paper exemplifies how principles of chemistry and environmental processes informed understanding the biogeochemical cycles of chemicals of environmental concern (CEC). Mergler et al.'s (2007) paper reviews knowledge of methyl mercury exposure and impacts in humans and served as an example of how to approach exposure and human health concerns for all CECs. All great progress. Then, the question: "How we missed for two decades the importance of plastics in the environment identified in a paper published the same year as The PCB Story? Are we missing yet another important environmental contaminant now?

METAL-ORGANIC COMPLEXES IN ENVIRONMENTAL SOLID SAMPLES: ON THE SELECTIVITY OF PYROPHOSPHATE EXTRACTION

Sequential extraction procedures (SEP) have been widely used for the fractionation of trace elements in soils according to their physicochemical mobility and bioaccessibility. Potassium/sodium pyrophosphate in alkaline medium may be considered as the most appropriate extracting reagent for the recovery of amorphous metal-organic complexes, which play a very important role in biological, physical, and chemical processes in soil. However, the selectivity of pyrophosphate has been poorly studied. In the present work the ability of pyrophosphate to attack mineral inorganic phases of environmental solids was assessed using dynamic extraction, which allows one to minimize artifacts and mimic natural conditions. Samples of gabbro and granite containing nearly no organic compounds were taken as example. The eluents applied addressed exchangeable, specifically sorbed, bound to Mn oxides, and bound to metal-organic complexes fractions extractable by 0.05 M Ca(NO3)2, 0.43 M CH3COOH, 0.1 M NH2OH · HCl, and 0.1 M K4P2O7 at pH 11, respectively. As expected, pyrophosphate extraction leads to a partial dissolution of elements bound to inorganic compounds. The recovery of aluminum, iron, manganese, and rare earth elements by pyrophosphate is up to 4% of their total concentrations in samples. The results were discussed on the basis of coordination chemistry of pyrophosphate complexes. In general, pyrophosphate extraction could be further regarded to be sufficiently selective for the dissolution of metal-organic complexes while using SEP in environmental analysis, soil science, and biogeochemistry. Nevertheless, in the interpretation of the fractionation results, a partial dissolution of mineral inorganic phases should be taken into consideration, especially for soils with low content of organic compounds.

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea.

Despite the explosion of metagenomic sequencing data, using -omics data to predict environmental biogeochemistry remains a challenge. One or a few genes (referred to as marker genes) in a metabolic pathway of interest in meta-omic data are typically used to represent the prevalence of a biogeochemical reaction. This approach often fails to demonstrate a consistent relationship between gene abundance and an ecosystem process rate. One reason this may occur is if a marker gene is not a good representative of a complete pathway. Here, we map the presence of 11 nitrogen (N)-cycling pathways in over 6000 complete bacterial and archaeal genomes using the Integrated Microbial Genomes database. Incomplete N-cycling pathways occurred in 39% of surveyed archaeal and bacterial species revealing a weakness in current marker-gene analyses. Furthermore, we found that most organisms have limited ability to utilize inorganic N in multiple oxidation states. This suggests that inter-organism exchange of inorganic N compounds is common, highlighting the importance of both community composition and spatial structure in determining the extent of recycling versus loss in an ecosystem.

Environmental Biogeochemistry of Elements and Emerging Contaminants

Environmental Biogeochemistry of Elements and Emerging Contaminants

“MALDI-FLIP-on-a-chip” and “MALDI-FRAP-on-a-flap”: Novel Techniques for Soil Microbiology and Environmental Biogeochemistry. II – Polymer Chip Prototyping (Invited Paper)

“MALDI-FLIP-on-a-chip” and “MALDI-FRAP-on-a-flap”: Novel Techniques for Soil Microbiology and Environmental Biogeochemistry. II – Polymer Chip Prototyping (Invited Paper)

DETERMINING TAPHONOMIC CONTROLS AND RATES OF DECAY IN CAVE ENVIRONMENTS USING MICROCOSMS

Abstract Caves are important sites of fossil preservation, especially for Quaternary vertebrates. Taphonomic processes operating in caves are not well understood and have never been experimentally examined. This study focuses on the potential role of bat guano, which impacts environmental biogeochemistry and serves as the base of the food chain in cave ecosystems. The presence or absence of guano is expected to be a major control of preservation potential in caves. Bats first appear in the fossil record in the early Eocene so bat guano likely influenced cave preservation only during the Cenozoic. This is a probable megabias of the cave fossil record. Microcosm experiments were used to determine the impact of guano presence and composition, moisture, temperature, and time on preservation potential of small mammal bones, leaves, and crickets. Guano came from insectivorous and frugivorous bats. The guano of insectivorous bats has an acidic pH, while the guano of frugivorous bats is close to neutral. Lab stud...

Развитие исследований по применению новых информационных технологий в экологическом мониторинге и биогеохимии

Развитие исследований по применению новых информационных технологий в экологическом мониторинге и биогеохимии

“MALDI-FLIP-on-a-chip” and “MALDI-FRAP-on-a-flap”: Novel Techniques for Soil Microbiology and Environmental Biogeochemistry. I – MALDI Chip Fingerprinting (Invited Paper)

“MALDI-FLIP-on-a-chip” and “MALDI-FRAP-on-a-flap”: Novel Techniques for Soil Microbiology and Environmental Biogeochemistry. I – MALDI Chip Fingerprinting (Invited Paper)

Synchrotron Radiation‐Based Methods for Environmental Biogeochemistry

Synchrotron Radiation‐Based Methods for Environmental Biogeochemistry

Application of Synchrotron Radiation-based Methods for Environmental Biogeochemistry: Introduction to the Special Section.

To understand the biogeochemistry of nutrients and contaminants in environmental media, their speciation and behavior under different conditions and at multiple scales must be determined. Synchrotron radiation-based X-ray techniques allow scientists to elucidate the underlying mechanisms responsible for nutrient and contaminant mobility, bioavailability, and behavior. The continuous improvement of synchrotron light sources and X-ray beamlines around the world has led to a profound transformation in the field of environmental biogeochemistry and, subsequently, to significant scientific breakthroughs. Following this introductory paper, this special collection includes 10 papers that either present targeted reviews of recent advancements in spectroscopic methods that are applicable to environmental biogeochemistry or describe original research studies conducted on complex environmental samples that have been significantly enhanced by incorporating synchrotron radiation-based X-ray technique(s). We believe that the current focus on improving the speciation of ultra-dilute elements in environmental media through the ongoing optimization of synchrotron technologies (e.g., brighter light sources, improved monochromators, more efficient detectors) will help to significantly push back the frontiers of environmental biogeochemistry research. As many of the relevant techniques produce extremely large datasets, we also identify ongoing improvements in data processing and analysis (e.g., software improvements and harmonization of analytical methods) as a significant requirement for environmental biogeochemists to maximize the information that can be gained using these powerful tools.