Pattern and sources of naturally produced organohalogens in the marine environment: biogenic formation of organohalogens

Concentrations and dietary exposure to persistent organic pollutants and naturally occurring halogenated contaminants in edible shrimp from Japanese coastal waters and the South China Sea

Shrimp are popular as food in Japan, but their contamination status is not well understood. In this study, 45 shrimp products (seven species) collected from eight locations in Japanese coastal waters and the South China Sea were analyzed for persistent organic pollutants (POPs) and naturally occurring halogenated contaminants (NHCs). The compounds with the highest mean concentration among shrimp species were endosulfans (4.0 ng g-1 dry weight, 41% of the total concentration), followed by polychlorinated biphenyls (PCBs, 26%), chlordanes (CHLs, 11%), methoxy-polybrominated diphenyl ethers (MeO-BDEs, 10%) and heptachlorinated methylbipyrrole (Cl7-MBP, 4%). Endosulfan concentrations were not correlated with the PCB and CHL concentrations, which suggested that these compounds had different sources and kinetics. Regional differences were observed in Sakura shrimp (Lucensosergia lucens), with higher concentrations of CHLs and Cl7-MBP from Suruga Bay in Japan, whereas MeO-BDEs were dominant in the south coast of Taiwan. The median estimated daily intake (EDI) of endosulfans through shrimp consumption was 60 pg kg-1 bw day-1. The EDIs of all analytes were well below reference doses set by the United States Environmental Protection Agency, indicating that health risks were unlikely, even in 95th percentile scenarios. The profiles and concentrations of these contaminants in shrimp in Japan suggest that shrimp is a potential dietary source of POPs (e.g., α-endosulfan) and NHCs (e.g., 2'- MeO-BDE68), and can serve as bioindicators of contamination status for dietary intake in Japan.

Synthesis and Investigation of Antibacterial Properties of Thymol, Carvacrol, Eugenol, and Perillyl Alcohol Based β-Halo Alcohol and β-Halo Thiol Compounds

A total of 12 new β-halo alcohols and 12 new β-halo thiol derivatives were synthesized. Natural alcohol compounds with known pharmacological properties were selected as starting substrates, aiming to synthesize compounds that have the potential to exhibit biological activity. The synthesis of β-halo alcohol derivatives involved a two-step process, while β-halo thiol derivatives were carried out in three steps. Effective and inexpensive methods were used for all transformations. Yields for β-halo alcohol derivatives ranged from 79% to 82%, and for β-halo thiol derivatives from 66% to 71%. Their antibacterial properties against some gram (+) (Staphylococcus aureus, Enterococcus faecalis) and gram (-) (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa) strains were investigated. The antibacterial effects of 24 newly synthesized compounds were compared to commercially available antibiotics Chloramphenicol and Streptomycin.

β-Dicarbonyls Facilitate Engineered Microbial Bromoform Biosynthesis

Ruminant livestock produce around 24% of global anthropogenic methane emissions. Methanogenesis in the animal rumen is significantly inhibited by bromoform, which is abundant in seaweeds of the genus Asparagopsis. This has prompted the development of livestock feed additives based on Asparagopsis to mitigate methane emissions, although this approach alone is unlikely to satisfy global demand. Here we engineer a non-native biosynthesis pathway to produce bromoform in vivo with yeast as an alternative biological source that may enable sustainable, scalable production of bromoform by fermentation. β-dicarbonyl compounds with low pKa values were identified as essential substrates for bromoform production and enabled bromoform synthesis in engineered Saccharomyces cerevisiae expressing a vanadate-dependent haloperoxidase gene. In addition to providing a potential route to the sustainable biological production of bromoform at scale, this work advances the development of novel microbial biosynthetic pathways for halogenation.

Photochemical demethylation of methylmercury (MeHg) in aquatic systems: A review of MeHg species, mechanisms, and influencing factors

Photodemethylation is the major pathway of methylmercury (MeHg) demethylation in surface water before uptake by the food chain, whose mechanisms and influence factors are still not completely understood. Here, we review the current knowledge on photodemethylation of MeHg and divide MeHg photolysis into three pathways: (1) direct photodemethylation, (2) free radical attack, and (3) intramolecular electron or energy transfer. In aquatic environments, dissolved organic matter is involved into all above pathways, and due to its complex compositions, properties and concentrations, DOM poses multiple functions during the PD of MeHg. DOM-MeHg complex (mainly by sulfur-containing molecules) might weaken the C-Hg bond and enhance PD through both direct and indirect pathways. In special, synergistic effects of both strong binding sites and chromophoric moieties in DOM might lead to intramolecular electron or energy transfer. Moreover, DOM might play a role of radical scavenger; while triplet state DOM, which is generated by chromophoric DOM under light, might become a source of free radicals. Apart from DOMs, transition metals, halides, NO3-, NO2-, and carbonates also act as radical initialaters or scavengers, and significantly pose effects on radical demethylation, which is generally mediated by hydroxyl radicals and singlet oxygen. Environmental factors such as pH, light wavelength, light intensity, dissolved oxygen, salinity, and suspended particles also affect the PD of MeHg. This study assessed previously published works on three major mechanisms, with the goal of providing general estimates for photodemethylation under various environment factors according to know effects, and highlighting the current uncertainties for future research directions.

Hidden dangers: High levels of organic pollutants in hadal trenches

The "V"-shaped structure of hadal trenches acts as a natural collector of organic pollutants, drawing attention to the need for extensive research in these areas. Our review identifies significant concentrations of organic pollutants, including persistent organic pollutants, black carbon, antibiotic-resistant genes, and plastics, which often match those in industrialized regions. They may trace back to both human activities and natural sources, underscoring the trenches' critical role in ocean biogeochemical cycles. We highlight the complex lateral and vertical transport mechanisms within these zones. Advanced methodologies, including stable isotope analysis, biomarker identification, and chiral analysis within isotope-based mixing models, are crucial for discerning the origins and pathways of these pollutants. In forthcoming studies, we aim to explore advanced methods for precise pollutant tracing, develop predictive models to forecast the future distribution and impacts of pollutants in hadal zones and on the Earth's larger ecological systems.

Occurrence of Volatile and Semi-Volatile Organic Pollutants in the Russian Arctic Atmosphere: The International Siberian Shelf Study Expedition (ISSS-2020)

Environmental issues in the Arctic region are of primary importance due to the fragility of the Arctic ecosystem. Mainly persistent organic compounds are monitored in the region by nine stationary laboratories. Information on the volatile (VOC) and semi volatile (SVOC) organic priority pollutants is very limited, especially for the Russian Arctic. Air samples from 16 sites along the Russian Arctic coast from the White Sea to the East Siberian Sea were collected on sorption tubes packed with Tenax, Carbograph, and Carboxen sorbents with different selectivity for a wide range of VOCs and SVOCs in 2020 within the framework of the International Siberian Shelf Study Expedition on the research vessel Akademik Keldysh. Thermal desorption gas chromatography–high-resolution mass spectrometry with Orbitrap was used for the analysis. Eighty-six VOCs and SVOCs were detected in the air samples at ng/m3 levels. The number of quantified compounds varied from 26 to 66 per sample. Benzoic acid was the major constituent, followed by BTEX, phenol, chloroform, bis(2-ethylhexyl) phthalate, and carbon tetrachloride. The study allowed for obtaining the first ever data on the presence of 138 priority pollutants in the air of Russian Arctic, whereas the thorough assessment of their possible sources will be the aim of a next investigation.

Marine volatile organic compounds and their impacts on marine aerosol-A review

Volatile organic compounds (VOCs) play a vital role in the global carbon budget and in the regional formation of ozone in the troposphere, and are emitted from both natural and anthropogenic activities. They can also serve as a source of secondary organic aerosol (SOA). Field and model studies showed evidences of a strong marine biogenic influence on marine aerosols. Although knowledge of terrestrial VOC emissions and SOA formation mechanisms has been advanced considerably over the last decades, processes constraining marine VOC emissions and marine SOA formation remain poorly understood. Seawater contains an extremely complex, diverse, and largely unidentified mixture of VOCs. Despite the fact that the ocean covers 70% of the Earth's surface, the role of the ocean in the global budget of VOCs is still unclear. The distribution and emission of sea surface VOCs exhibit considerable spatial-temporal variation, with higher concentrations often, but not always, correlated with biological activities. VOCs in surface seawater have been measured in various geographic regions, however, knowledge of the distribution of marine VOCs and the role of the oceans in the global atmospheric chemistry is still insufficient due to the paucity of measurements. This study reviews marine VOCs in terms of current analytical methods, global marine VOCs measurements, their effects on SOA, and future needs for understanding the role of marine VOCs in the chemistry of the atmosphere.

A Review: Halogenated Compounds from Marine Fungi

Marine fungi produce many halogenated metabolites with a variety of structures, from acyclic entities with a simple linear chain to multifaceted polycyclic molecules. Over the past few decades, their pharmaceutical and medical application have been explored and still the door is kept open due to the need of new drugs from relatively underexplored sources. Biological properties of halogenated compounds such as anticancer, antiviral, antibacterial, anti-inflammatory, antifungal, antifouling, and insecticidal activity have been investigated. This review describes the chemical structures and biological activities of 217 halogenated compounds derived mainly from Penicillium and Aspergillus marine fungal strains reported from 1994 to 2019.

The complexity and regulation of repair of alkylation damage to nucleic acids

DNA damaging agents have been a cornerstone of cancer therapy for nearly a century. The discovery of many of these chemicals, particularly the alkylating agents, are deeply entwined with the development of poisonous materials originally intended for use in warfare. Over the last decades, their anti-proliferative effects have focused on the specific mechanisms by which they damage DNA, and the factors involved in the repair of such damage. Due to the variety of aberrant adducts created even for the simplest alkylating agents, numerous pathways of repair are engaged as a defense against this damage. More recent work has underscored the role of RNA damage in the cellular response to these agents, although the understanding of their role in relation to established DNA repair pathways is still in its infancy. In this review, we discuss the chemistry of alkylating agents, the numerous ways in which they damage nucleic acids, as well as the specific DNA and RNA repair pathways which are engaged to counter their effects.

Characterizing changes of dissolved organic matter composition with the use of distinct feeds in recirculating aquaculture systems via high-resolution mass spectrometry

Recirculating aquaculture systems (RAS) are a new alternative to traditional aquaculture approaches, allowing full control over the fish production conditions, while reducing the water demand. The reduction of water exchange leads to an accumulation of dissolved organic matter (DOM) that can have potential effects on water quality, fish welfare and system performance. Despite the growing awareness of DOM in aquaculture, scarce scientific information exists for understanding the composition and transformation of DOM in RAS. In this study, a non-targeted approach using ultra-performance liquid chromatography coupled to a hybrid quadrupole-time of flight mass spectrometer (UPLC-QTOF-MS) was used to characterize compositional changes of low molecular weight (LMW) DOM in RAS, when operated under two different feed types. A total of 1823 chemicals were identified and the majority of those contained a CHON chemical group in their structure. Changes in the composition of LMW-DOM in RAS waters were observed when the standard feed was switched to RAS feed. The DOM with the use of standard feed, consisted mainly of lignin/CRAM-like, CHO and CHOS chemical groups, while the DOM that used RAS feed, was mainly composed by unsaturated hydrocarbon, CHNO and CHNOS chemical groups. The Bray-Curtis dissimilarity cluster demonstrated differences in the composition of DOM from RAS and was associated to the type of feed used. When the RAS feed was used, the Kendrick mass defect plots of -CH₂- homologous units in the pump-sump (after the water treatment) showed a high removal capacity for CHNO, CHNOS and halogenated chemicals with high Kendrick mass defect, KMD > 0.7. To our knowledge, this is the first report of LMW-DOM characterization of RAS by high-resolution mass spectrometry (HRMS).

Occurrence and fate studies (sunlight exposure and stable carbon isotope analysis) of the halogenated natural product MHC-1 and its producer Plocamium cartilagineum

MHC-1 is a halogenated natural product (HNP) produced by the red seaweed Plocamium cartilagineum. MHC-1 concentrations of 550-2700 μg/g dry weight were found in Plocamium collected by divers at Heligoland (Germany). Compared to that MHC-1 concentrations were much lower in samples collected on beaches in Ireland and Portugal. Exposure of leaves of Plocamium to sunlight showed that MHC-1 was readily transformed by hydrodebromination. At Heligoland in March, MHC-1 (δ¹³C value -45.2‰) was lighter in carbon by ~15‰ compared to the bulk δ¹³C value (‰) of Plocamium (-30.7‰). Collected at the same time and location at Heligoland, samples of Halichondria and Mastocarpus sp. were richer in carbon (by ~10‰) as Plocamium. However, the δ¹³C value of MHC-1 in Halichondria (-44.6‰) and Mastocarpus sp. (-42.1‰) was as negative as in Plocamium. This was indirect proof that MHC-1 was produced by Plocamium and then released into the water phase from where it then was bioconcentrated by Halichondria and Mastocarpus sp. In agreement with that, concentrations of MHC-1 in Halichondria and Mastocarpus sp. were much lower than in Plocamium. In addition, a potential isomer of MHC-1 (compound X) was detected in all samples from Heligoland at ~2% of the MHC-1 level.

Uptake, phytovolatilization, and interconversion of 2,4-dibromophenol and 2,4-dibromoanisole in rice plants

The structural analogs, 2,4-dibromophenol (2,4-DBP) and 2,4-dibromoanisole (2,4-DBA), have both natural and artificial sources and are frequently detected in environmental matrices. Their environmental fates, especially volatilization, including both direct volatilization from cultivation solution and phytovolatilization through rice plants were evaluated using hydroponic exposure experiments. Results showed that 2,4-DBA displayed stronger volatilization tendency and more bioaccumulation in aboveground rice tissues. Total volatilized 2,4-DBA accounted for 4.74% of its initial mass and was 3.43 times greater than 2,4-DBP. Phytovolatilization of 2,4-DBA and 2,4-DBP contributed to 6.78% and 41.7% of their total volatilization, enhancing the emission of these two contaminants from hydroponic solution into atmosphere. In this study, the interconversion processes between 2,4-DBP and 2,4-DBA were first characterized in rice plants. The demethylation ratio of 2,4-DBA was 12.0%, 32.0 times higher than methylation of 2,4-DBP. Formation of corresponding metabolites through methylation and demethylation processes also contributed to the volatilization of 2,4-DBP and 2,4-DBA from hydroponic solution into the air phase. Methylation and demethylation processes increased phytovolatilization by 12.1% and 36.9% for 2,4-DBP and 2,4-DBA. Results indicate that phytovolatilization and interconversion processes in rice plants serve as important pathways for the global cycles of bromophenols and bromoanisoles.

Will Climate Change Influence Production and Environmental Pathways of Halogenated Natural Products?

Thousands of halogenated natural products (HNPs) pervade the terrestrial and marine environment. HNPs are generated by biotic and abiotic processes and range in complexity from low molecular mass natural halocarbons (nHCs, mostly halomethanes and haloethanes) to compounds of higher molecular mass which often contain oxygen and/or nitrogen atoms in addition to halogens (hHNPs). nHCs have a key role in regulating tropospheric and stratospheric ozone, while some hHNPs bioaccumulate and have toxic properties similar those of anthropogenic-persistent organic pollutants (POPs). Both chemical classes have common sources: biosynthesis by marine bacteria, phytoplankton, macroalgae, and some invertebrate animals, and both may be similarly impacted by alteration of production and transport pathways in a changing climate. The nHCs scientific community is advanced in investigating sources, atmospheric and oceanic transport, and forecasting climate change impacts through modeling. By contrast, these activities are nascent or nonexistent for hHNPs. The goals of this paper are to (1) review production, sources, distribution, and transport pathways of nHCs and hHNPs through water and air, pointing out areas of commonality, (2) by analogy to nHCs, argue that climate change may alter these factors for hHNPs, and (3) suggest steps to improve linkage between nHCs and hHNPs science to better understand and predict climate change impacts.

Novel approach for the detection of alkylated bases using the enzyme-modified comet assay

The enzyme-modified comet assay is widely used for the detection of oxidized DNA lesions. Here we describe for the first time the use of the human alkyladenine DNA glycosylase (hAAG) for the detection of alkylated bases. hAAG was titrated using untreated and methyl methanesulfonate (MMS)-treated TK-6 cells. The hAAG-modified comet assay was compared to the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay, widely used to detect oxidized lesions but that also detects ring-opened purines derived from some alkylated lesions, using cells treated with potassium bromate (oxidizing agent) or MMS. Moreover, neutral and alkaline lysis conditions were used to determine the nature of detected lesions. When alkaline lysis was employed (condition normally used), the level of hAAG-sensitive sites was higher than the Fpg-sensitive sites in MMS-treated cells and hAAG, unlike Fpg, did not detect oxidized bases. After neutral lysis, Fpg did not detect MMS-induced lesions; however, results obtained with hAAG remained unchanged. As expected, Fpg detected oxidized purines and imidazole ring-opened purines, derived from N7-methylguanines under alkaline conditions. It seems that hAAG detected N7-methylguanines, the ring-opened purines derived at high pH, and 3-methlyladenines. Specificity of hAAG towards different DNA lesions was evaluated using a multiplex oligonucleotide-cleavage assay, confirming the ability of hAAG to detect ethenoadenines and hypoxanthine. The hAAG-modified comet assay is a new tool for the detection of alkylated bases.

Mutation signatures specific to DNA alkylating agents in yeast and cancers

Alkylation is one of the most ubiquitous forms of DNA lesions. However, the motif preferences and substrates for the activity of the major types of alkylating agents defined by their nucleophilic substitution reactions (SN1 and SN2) are still unclear. Utilizing yeast strains engineered for large-scale production of single-stranded DNA (ssDNA), we probed the substrate specificity, mutation spectra and signatures associated with DNA alkylating agents. We determined that SN1-type agents preferably mutagenize double-stranded DNA (dsDNA), and the mutation signature characteristic of the activity of SN1-type agents was conserved across yeast, mice and human cancers. Conversely, SN2-type agents preferably mutagenize ssDNA in yeast. Moreover, the spectra and signatures derived from yeast were detectable in lung cancers, head and neck cancers and tumors from patients exposed to SN2-type alkylating chemicals. The estimates of mutation loads associated with the SN2-type alkylation signature were higher in lung tumors from smokers than never-smokers, pointing toward the mutagenic activity of the SN2-type alkylating carcinogens in cigarettes. In summary, our analysis of mutations in yeast strains treated with alkylating agents, as well as in whole-exome and whole-genome-sequenced tumors identified signatures highly specific to alkylation mutagenesis and indicate the pervasive nature of alkylation-induced mutagenesis in cancers.

Halogenated natural products and anthropogenic persistent organic pollutants in chokka squid (Loligo reynaudii) from three sites along the South Atlantic and Indian Ocean coasts of South Africa

Chokka squid (Loligo reynaudii) from three sites along the South African coast were analyzed for halogenated natural products (HNPs) and anthropogenic persistent organic pollutants (POPs). HNPs were generally more than one order of magnitude more abundant than POPs. The most prevalent pollutant, i.e. the HNP 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (Q1), was detected in all chokka squid samples with mean concentrations of 105, 98 and 45 ng/g lipid mass, respectively, at the Indian Ocean (site A), between both oceans (site B) and the South Atlantic Ocean (site C). In addition, bromine containing polyhalogenated 1'-methyl-1,2'-bipyrroles (PMBPs), 2,4,6-tribromophenol (2,4,6-TBP, up to 28 ng/g lipid mass), polybrominated methoxy diphenyl ethers, MHC-1, TBMP and other HNPs were also detected. Polychlorinated biphenyls (PCBs) were the predominant class of anthropogenic POPs. PCB 153 was the most abundant PCB congener in chokka squid from the Indian Ocean, and PCB 138 in samples from the South Atlantic Ocean and between both oceans.

How do cells cope with RNA damage and its consequences?

Similar to many other biological molecules, RNA is vulnerable to chemical insults from endogenous and exogenous sources. Noxious agents such as reactive oxygen species or alkylating chemicals have the potential to profoundly affect the chemical properties and hence the function of RNA molecules in the cell. Given the central role of RNA in many fundamental biological processes, including translation and splicing, changes to its chemical composition can have a detrimental impact on cellular fitness, with some evidence suggesting that RNA damage has roles in diseases such as neurodegenerative disorders. We are only just beginning to learn about how cells cope with RNA damage, with recent studies revealing the existence of quality-control processes that are capable of recognizing and degrading or repairing damaged RNA. Here, we begin by reviewing the most abundant types of chemical damage to RNA, including oxidation and alkylation. Focusing on mRNA damage, we then discuss how alterations to this species of RNA affect its function and how cells respond to these challenges to maintain proteostasis. Finally, we briefly discuss how chemical damage to noncoding RNAs such as rRNA, tRNA, small nuclear RNA, and small nucleolar RNA is likely to affect their function.

Ballast water management system: Assessment of chemical quality status of several ports in Adriatic Sea

Oxidant treatment of ballast water (BW) is commonly used in BW systems in order to minimize the transport of alien species. The release of disinfection by-products (DBPs) associated to the treatment of BW and cross-contamination of butyltin (BT) compounds through BW discharge is a topic of environmental concern. A chemical port baseline survey has been conducted in seven ports of the Adriatic Sea. Analysis have been performed on transplanted mussels, surface sediment, seawater, BW. Results showed an evidence of BT contamination, particularly in sediments, probably related to their illegal usage or to intensive shipping activities. Therefore, BW may act as a vector and contribute to re-buildup of BT contamination in the coastal regions. A baseline set of data concerning DBPs is provided, showing the preferential distribution of these compounds in the marine environment that will be useful for future considerations on monitoring and assessment of chemical contamination associated with BW.

RNA Modifications: Reversal Mechanisms and Cancer

An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.

Transient isomers in the photodissociation of bromoiodomethane

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH₂IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH₂I-Br and CH₂Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH₂Br-I to CH₂I-Br in cyclohexane by extending the time window up to 3 μs. We track the photoproduct kinetics of CH₂Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

Atmospheric Transport and Deposition of Bromoanisoles Along a Temperate to Arctic Gradient

Bromoanisoles (BAs) arise from O-methylation of bromophenols, produced by marine algae and invertebrates. BAs undergo sea-air exchange and are transported over the oceans. Here we report 2,4-DiBA and 2,4,6-TriBA in air and deposition on the Swedish west coast (Råö) and the interior of arctic Finland (Pallas). Results are discussed in perspective with previous measurements in the northern Baltic region in 2011-2013. BAs in air decreased from south to north in the order Råö > northern Baltic > Pallas. Geometric mean concentrations at Pallas increased significantly (p < 0.05) between 2002 and 2015 for 2,4-DiBA but not for 2,4,6-TriBA. The logarithm of BA partial pressures correlated significantly to reciprocal air temperature at the coastal station Råö and over the Baltic, but only weakly (2,4-DiBA) or not significantly (2,4,6-TriBA) at inland Pallas. Deposition fluxes of BAs were similar at both sites despite lower air concentrations at Pallas, due to greater precipitation scavenging at lower temperatures. Proportions of the two BAs in air and deposition were related to Henry's law partitioning and source regions. Precipitation concentrations were 10-40% of those in surface water of Bothnian Bay, northern Baltic Sea. BAs deposited in the bay catchment likely enter rivers and provide an unexpected source to northern estuaries. BAs may be precursors to higher molecular weight compounds identified by others in Swedish inland lakes.

The trans-continental distributions of pentachlorophenol and pentachloroanisole in pine needles indicate separate origins

The production and use of pentachlorophenol (PCP) was recently prohibited/restricted by the Stockholm Convention on persistent organic pollutants (POPs), but environmental data are few and of varying quality. We here present the first extensive dataset of the continent-wide (Eurasia and Canada) occurrence of PCP and its methylation product pentachloroanisole (PCA) in the environment, specifically in pine needles. The highest concentrations of PCP were found close to expected point sources, while PCA chiefly shows a northern and/or coastal distribution not correlating with PCP distribution. Although long-range transport and environmental methylation of PCP or formation from other precursors cannot be excluded, the distribution patterns suggest that such processes may not be the only source of PCA to remote regions and unknown sources should be sought. We suggest that natural sources, e.g., chlorination of organic matter in Boreal forest soils enhanced by chloride deposition from marine sources, should be investigated as a possible partial explanation of the observed distributions. The results show that neither PCA nor total PCP (ΣPCP = PCP + PCA) should be used to approximate the concentrations of PCP; PCP and PCA must be determined and quantified separately to understand their occurrence and fate in the environment. The background work shows that the accumulation of airborne POPs in plants is a complex process. The variations in life cycles and physiological adaptations have to be taken into account when using plants to evaluate the concentrations of POPs in remote areas.

Metagenome-derived haloalkane dehalogenases with novel catalytic properties

Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8-13 closely related putative HLD-encoding genes. A phylogenetic analysis of the translated genes revealed that three HLDs are members of the HLD-I subfamily, whereas one gene encodes an enzyme from the subfamily HLD-II. Two metagenome-derived HLDs, eHLD-B and eHLD-C, each from a different subfamily, were heterologously produced in active form, purified and characterized in terms of their thermostability, pH and temperature optimum, quaternary structure, substrate specificity towards 30 halogenated compounds, and enantioselectivity. eHLD-B and eHLD-C showed striking differences in their activities, substrate preferences, and tolerance to temperature. Profound differences were also determined in the enantiopreference and enantioselectivity of these enzymes towards selected substrates. Comparing our data with those of known HLDs revealed that eHLD-C exhibits a unique combination of high thermostability, high activity, and an unusually broad pH optimum, which covers the entire range of pH 5.5-8.9. Moreover, a so far unreported high thermostability for HLDs was determined for this enzyme at pH values lower than 6.0. Thus, eHLD-C represents an attractive and novel biocatalyst for biotechnological applications.

Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι

N1-methyl-deoxyadenosine (1-MeA) is formed by methylation of deoxyadenosine at the N1 atom. 1-MeA presents a block to replicative DNA polymerases due to its inability to participate in Watson-Crick (W-C) base pairing. Here we determine how human DNA polymerase-ι (Polι) promotes error-free replication across 1-MeA. Steady state kinetic analyses indicate that Polι is ~100 fold more efficient in incorporating the correct nucleotide T versus the incorrect nucleotide C opposite 1-MeA. To understand the basis of this selectivity, we determined ternary structures of Polι bound to template 1-MeA and incoming dTTP or dCTP. In both structures, template 1-MeA rotates to the syn conformation but pairs differently with dTTP versus dCTP. Thus, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold" and is largely disordered. Together, our kinetic and structural studies show how Polι maintains discrimination between correct and incorrect incoming nucleotide opposite 1-MeA in preserving genome integrity.

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil

In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas. We detected a so far unknown diversity of genes encoding for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases as well as metabolic and cometabolic dehalogenases. Genes for non-heme, no-metal chloroperoxidases and haloalkane dehalogenases were the most abundant halogenase and dehalogenase genes, respectively. The high diversity and abundance of (de)halogenating enzymes suggests a strong microbial contribution to natural halogen cycling. This was also confirmed in microcosm experiments in which we quantified the biotic formation of chloroform and bromoform. Knowledge on microorganisms and genes that catalyze (de)halogenation reactions is critical because they are highly relevant to industrial biotechnologies and bioremediation applications.

Toward a List of Molecules as Potential Biosignature Gases for the Search for Life on Exoplanets and Applications to Terrestrial Biochemistry

Thousands of exoplanets are known to orbit nearby stars. Plans for the next generation of space-based and ground-based telescopes are fueling the anticipation that a precious few habitable planets can be identified in the coming decade. Even more highly anticipated is the chance to find signs of life on these habitable planets by way of biosignature gases. But which gases should we search for? Although a few biosignature gases are prominent in Earth's atmospheric spectrum (O2, CH4, N2O), others have been considered as being produced at or able to accumulate to higher levels on exo-Earths (e.g., dimethyl sulfide and CH3Cl). Life on Earth produces thousands of different gases (although most in very small quantities). Some might be produced and/or accumulate in an exo-Earth atmosphere to high levels, depending on the exo-Earth ecology and surface and atmospheric chemistry. To maximize our chances of recognizing biosignature gases, we promote the concept that all stable and potentially volatile molecules should initially be considered as viable biosignature gases. We present a new approach to the subject of biosignature gases by systematically constructing lists of volatile molecules in different categories. An exhaustive list up to six non-H atoms is presented, totaling about 14,000 molecules. About 2500 of these are CNOPSH compounds. An approach for extending the list to larger molecules is described. We further show that about one-fourth of CNOPSH molecules (again, up to N = 6 non-H atoms) are known to be produced by life on Earth. The list can be used to study classes of chemicals that might be potential biosignature gases, considering their accumulation and possible false positives on exoplanets with atmospheres and surface environments different from Earth's. The list can also be used for terrestrial biochemistry applications, some examples of which are provided. We provide an online community usage database to serve as a registry for volatile molecules including biogenic compounds.

KEY WORDS

Astrobiology-Atmospheric gases-Biosignatures-Exoplanets. Astrobiology 16, 465-485.

Contributions of DNA repair and damage response pathways to the non-linear genotoxic responses of alkylating agents

From a risk assessment perspective, DNA-reactive agents are conventionally assumed to have genotoxic risks at all exposure levels, thus applying a linear extrapolation for low-dose responses. New approaches discussed here, including more diverse and sensitive methods for assessing DNA damage and DNA repair, strongly support the existence of measurable regions where genotoxic responses with increasing doses are insignificant relative to control. Model monofunctional alkylating agents have in vitro and in vivo datasets amenable to determination of points of departure (PoDs) for genotoxic effects. A session at the 2013 Society of Toxicology meeting provided an opportunity to survey the progress in understanding the biological basis of empirically-observed PoDs for DNA alkylating agents. Together with the literature published since, this review discusses cellular pathways activated by endogenous and exogenous alkylation DNA damage. Cells have evolved conserved processes that monitor and counteract a spontaneous steady-state level of DNA damage. The ubiquitous network of DNA repair pathways serves as the first line of defense for clearing of the DNA damage and preventing mutation. Other biological pathways discussed here that are activated by genotoxic stress include post-translational activation of cell cycle networks and transcriptional networks for apoptosis/cell death. The interactions of various DNA repair and DNA damage response pathways provide biological bases for the observed PoD behaviors seen with genotoxic compounds. Thus, after formation of DNA adducts, the activation of cellular pathways can lead to the avoidance of a mutagenic outcome. The understanding of the cellular mechanisms acting within the low-dose region will serve to better characterize risks from exposures to DNA-reactive agents at environmentally-relevant concentrations.

Cytotoxic and mutagenic properties of O4-alkylthymidine lesions in Escherichia coli cells

Due to the abundant presence of alkylating agents in living cells and the environment, DNA alkylation is generally unavoidable. Among the alkylated DNA lesions, O⁴-alkylthymidine (O⁴-alkyldT) are known to be highly mutagenic and persistent in mammalian tissues. Not much is known about how the structures of the alkyl group affect the repair and replicative bypass of the O⁴-alkyldT lesions, or how the latter process is modulated by translesion synthesis polymerases. Herein, we synthesized oligodeoxyribonucleotides harboring eight site-specifically inserted O⁴-alkyldT lesions and examined their impact on DNA replication in Escherichia coli cells. We showed that the replication past all the O⁴-alkyldT lesions except (S)- and (R)-sBudT was highly efficient, and these lesions directed very high frequencies of dGMP misincorporation in E. coli cells. While SOS-induced DNA polymerases play redundant roles in bypassing most of the O⁴-alkyldT lesions, the bypass of (S)- and (R)-sBudT necessitated Pol V. Moreover, Ada was not involved in the repair of any O⁴-alkyldT lesions, Ogt was able to repair O⁴-MedT and, to a lesser extent, O⁴-EtdT and O⁴-nPrdT, but not other O⁴-alkyldT lesions. Together, our study provided important new knowledge about the repair of the O⁴-alkyldT lesions and their recognition by the E. coli replication machinery.

Distributions and sources of volatile chlorocarbons and bromocarbons in the Yellow Sea and East China Sea

Six volatile halogenated organic compounds (VHOC), namely, chloroform, carbon tetrachloride, trichloroethylene, bromodichloromethane, dibromochloromethane, and bromoform, were studied in the Yellow Sea and East China Sea from April to May, 2009. The spatial variability of these VHOC was influenced by various factors, including anthropogenic inputs, biogenic production and complicated hydrographic features such as Changjiang Diluted Water, Yellow Sea Cold Water Mass, and Kuroshio Current. Diurnal study results showed that factors such as solar irradiation, biological activity, and tide affected the abundance of these VHOC. Correlation analyses revealed that bromodichloromethane was positively correlated with chlorophyll a in surface seawater. Principal component analysis suggested that chlorinated compounds like carbon tetrachloride originated from anthropogenic sources whereas brominated compounds such as bromodichloromethane originated from biogenic sources. Sources of other chlorinated and brominated compounds may not be governed by biological processes in the marine environment.

Predominance of biotic over abiotic formation of halogenated hydrocarbons in hypersaline sediments in Western Australia

Volatile halogenated organic compounds (VOX) contribute to ozone depletion and global warming. There is evidence of natural VOX formation in many environments ranging from forest soils to salt lakes. Laboratory studies have suggested that VOX formation can be chemically stimulated by reactive Fe species while field studies have provided evidence for direct biological (enzymatic) VOX formation. However, the relative contribution of abiotic and biotic processes to global VOX budgets is still unclear. The goals of this study were to quantify VOX release from sediments from a hypersaline lake in Western Australia (Lake Strawbridge) and to distinguish between the relative contributions of biotic and abiotic VOX formation in microbially active and sterilized microcosms. Our experiments demonstrated that the release of organochlorines from Lake Strawbridge sediments was mainly biotic. Among the organochlorines detected were monochlorinated, e.g., chloromethane (CH3Cl), and higher chlorinated VOX compounds such as trichloromethane (CHCl3). Amendment of sediments with either Fe(III) oxyhydroxide (ferrihydrite) or a mixture of lactate/acetate or both ferrihydrite and lactate/acetate did not stimulate VOX formation. This suggests that although microbial Fe(III) reduction took place, there was no stimulation of VOX formation via Fe redox transformations or the formation of reactive Fe species under our experimental conditions.

Air-water exchange of brominated anisoles in the northern Baltic Sea

Bromophenols produced by marine algae undergo O-methylation to form bromoanisoles (BAs), which are exchanged between water and air. BAs were determined in surface water of the northern Baltic Sea (Gulf of Bothnia, consisting of Bothnian Bay and Bothnian Sea) during 2011-2013 and on a transect of the entire Baltic in September 2013. The abundance decreased in the following order: 2,4,6-tribromoanisole (2,4,6-TBA)>2,4-dibromoanisole (2,4-DBA)≫2,6-dibromoanisole (2,6-DBA). Concentrations of 2,4-DBA and 2,4,6-TBA in September were higher in the southern than in the northern Baltic and correlated well with the higher salinity in the south. This suggests south-to-north advection and dilution with fresh riverine water enroute, and/or lower production in the north. The abundance in air over the northern Baltic also decreased in the following order: 2,4,6-TBA>2,4-DBA. However, 2,6-DBA was estimated as a lower limit due to breakthrough from polyurethane foam traps used for sampling. Water/air fugacity ratios ranged from 3.4 to 7.6 for 2,4-DBA and from 18 to 94 for 2,4,6-TBA, indicating net volatilization. Flux estimates using the two-film model suggested that volatilization removes 980-1360 kg of total BAs from Bothnian Bay (38000 km2) between May and September. The release of bromine from outgassing of BAs could be up to 4-6% of bromine fluxes from previously reported volatilization of bromomethanes and bromochloromethanes.

Methylation damage to RNA induced in vivo in Escherichia coli is repaired by endogenous AlkB as part of the adaptive response

Cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions induced in DNA and RNA in vitro and in pre-damaged DNA and RNA bacteriophages in vivo are repaired by the Escherichia coli (E. coli) protein AlkB and a human homolog, ALKBH3. However, it is not known whether endogenous RNA is repaired in vivo by repair proteins present at physiological concentrations. The concept of RNA repair as a biologically relevant process has therefore remained elusive. Here, we demonstrate AlkB-mediated repair of endogenous RNA in vivo by measuring differences in lesion-accumulation in two independent AlkB-proficient and deficient E. coli strains during exposure to methyl methanesulfonate (MMS). Repair was observed both in AlkB-overproducing strains and in the wild-type strains after AlkB induction. RNA repair appeared to be highest in RNA species below 200 nucleotides in size, mainly comprising tRNAs. Strikingly, at least 10-fold more lesions were repaired in RNA than in DNA. This may be a consequence of some 30-fold higher levels of aberrant methylation in RNA than in DNA after exposure to MMS. A high primary kinetic isotope effect (>10) was measured using a deuterated methylated RNA substrate, D3-1me(rA), demonstrating that it is the catalytic step, and not the search step that is rate-limiting. Our results demonstrate that RNA repair by AlkB takes place in endogenous RNA as part of an adaptive response in wild-type E. coli cells.

Abiotic degradation of chlorinated ethanes and ethenes in water

INTRODUCTION

Chlorinated ethanes and ethenes are among the most frequently detected organic pollutants of water. Their physicochemical properties are such that they can contaminate aquifers for decades. In favourable conditions, they can undergo degradation. In anaerobic conditions, chlorinated solvents can undergo reductive dechlorination.

DEGRADATION PATHWAYS

Abiotic dechlorination is usually slower than microbial but abiotic dechlorination is usually complete. In favourable conditions, abiotic reactions bring significant contribution to natural attenuation processes. Abiotic agents that may enhance the reductive dechlorination of chlorinated ethanes and ethenes are zero-valent metals, sulphide minerals or green rusts.

OXIDATION

At some sites, permanganate and Fenton's reagent can be used as remediation tool for oxidation of chlorinated ethanes and ethenes.

SUMMARY

Nanoscale iron or bimetallic particles, due to high efficiency in degradation of chlorinated ethanes and ethenes, have gained much interest. They allow for rapid degradation of chlorinated ethanes and ethenes in water phase, but they also give benefit of treating dense non-aqueous phase liquid.

Acetogenesis in the energy-starved deep biosphere - a paradox?

Under anoxic conditions in sediments, acetogens are often thought to be outcompeted by microorganisms performing energetically more favorable metabolic pathways, such as sulfate reduction or methanogenesis. Recent evidence from deep subseafloor sediments suggesting acetogenesis in the presence of sulfate reduction and methanogenesis has called this notion into question, however. Here I argue that acetogens can successfully coexist with sulfate reducers and methanogens for multiple reasons. These include (1) substantial energy yields from most acetogenesis reactions across the wide range of conditions encountered in the subseafloor, (2) wide substrate spectra that enable niche differentiation by use of different substrates and/or pooling of energy from a broad range of energy substrates, (3) reduced energetic cost of biosynthesis among acetogens due to use of the reductive acetyl CoA pathway for both energy production and biosynthesis coupled with the ability to use many organic precursors to produce the key intermediate acetyl CoA. This leads to the general conclusion that, beside Gibbs free energy yields, variables such as metabolic strategy and energetic cost of biosynthesis need to be taken into account to understand microbial survival in the energy-depleted deep biosphere.

Balancing repair and tolerance of DNA damage caused by alkylating agents

Alkylating agents constitute a major class of frontline chemotherapeutic drugs that inflict cytotoxic DNA damage as their main mode of action, in addition to collateral mutagenic damage. Numerous cellular pathways, including direct DNA damage reversal, base excision repair (BER) and mismatch repair (MMR), respond to alkylation damage to defend against alkylation-induced cell death or mutation. However, maintaining a proper balance of activity both within and between these pathways is crucial for a favourable response of an organism to alkylating agents. Furthermore, the response of an individual to alkylating agents can vary considerably from tissue to tissue and from person to person, pointing to genetic and epigenetic mechanisms that modulate alkylating agent toxicity.

1-Bromo-2-chloro-4,5-dimethoxy-benzene

The two meth­oxy groups of the title compound, C₈H₈BrClO₂, are approximately coplanar with the benzene ring, the dihedral angles in all four mol­ecules in the asymmetric unit ranging from of 0.9 (3) to 12.3 (3)°. All four independent mol­ecules are disordered by different amounts about non-crystallographic twofold axes which nearly superimpose the Cl and Br sites.

Anthropogenic and naturally-produced organobrominated compounds in bluefin tuna from the Mediterranean Sea

Anthropogenic compounds, such as polybrominated diphenyl ethers (PBDEs), together with naturally-produced organobromines, such as methoxylated PBDEs (MeO-PBDEs), polybrominated hexahydroxanthene derivatives (PBHDs), 2,4,6-tribromoanisole (TBA) and a mixed halogenated monoterpene (MHC-1), were measured in muscle from 26 farmed and wild bluefin tuna (Thunnus thynnus) caught in the Mediterranean Sea. This species is ecological attractive because of the changes of geographic habitat throughout its long lifespan which affect its feeding. PBDE concentrations were similar between tuna samples of different groups (17-149 ng g(-1) lipid weight - lw in farmed tuna, 25-219 ng g(-1)lw in longline fished tuna and 26-126 ng g(-1)lw in net-fished tuna). However, higher concentrations of naturally-produced MeO-PBDEs and PBHDs were observed in the two types of wild tuna (longline fished and net-fished) compared to farmed tuna suggesting that wild tunas come easily in contact with sources of these compounds. In all cases PBHDs presented the highest contribution to the sum of organobromines (50% in farmed tuna and >90% in wild tuna). TBA was detected at low concentrations (<6 ng g(-1)lw), while MHC-1 was found at higher concentrations (up to 42 ng g(-1)lw) in farmed tuna. The estimated daily ingestion of PBDEs from tuna was 830 ng PBDEs day(-1), regardless of the origin of the tuna. While this value is approximately 600 times lower than the minimum risk level set by the US Department of Health and Human Services, it is approximately eight times higher than the total intake of PBDEs via diet, suggesting that consumption of tuna can add considerably to the total daily intake of PBDEs.

Natural abiotic formation of trihalomethanes in soil: results from laboratory studies and field samples

Trihalomethanes (THM), especially trichloromethane, play an important role in photochemical processes of the lower atmosphere, but the current knowledge of the known sources and sinks of trichloromethane is still incomplete. The trichloromethane flux through the environment is estimated at approximately 660 kt year(-1) and 90% of the emissions are of natural origin. Next to offshore seawater contributing approximately 360 kt year(-1) unknown soil processes are the most prominent source (approximately 220 kt year(-1)). This paper describes a new abiotic source of trichloromethane from the terrestrial environment induced by the oxidation of organic matter by iron(III) and hydrogen peroxide in the presence of chloride. Different organic-rich soils and a series of organic substances regarded as monomeric constituents of humus were investigated for their release of trichloromethene. The influence of iron(III), hydrogen peroxide, halide, and pH on its formation was assayed. The optimal reaction turn over for the representative compound catechol was 58.4 ng of CHCl3 from 1.8 mg of carbon applying chloride and 1.55 microg of CHBr3 from 1.8 mg of carbon applying bromide; resorcin and hydroquinone displayed similar numbers. Results presented in this paper pinpoint 1,2,4,5-tetrahydroxybenzene as playing a key role as intermediate in the formation pathway of the trihalomethanes. The highest THM yields were obtained when applying the oxidized form of 1,2,4,5-tetrahydroxybenzene as THM precursor. These findings are consistent with the well-known degradation pathway starting from resorcin-like dihydroxylated compounds proceeding via further hydroxylation and after halogenation finally ending up in trihalomethanes. In conclusion, Fenton-like reaction conditions (iron(III) and hydrogen peroxide), elevated halide content and an extended reaction time can be seen as the most important parameters required for an optimal THM formation.