Arsenobetaine: an ecophysiologically important organoarsenical confers cytoprotection against osmotic stress and growth temperature extremes

Microbial arsenic methylation in soil-water systems and its environmental significance

In this review, we have summarized the current knowledge about the environmental importance, relevance, and consequences of microbial arsenic (As) methylation in various ecosystems. In this regard, we have presented As biomethylation in terrestrial and aquatic ecosystems particularly in rice paddy soils and wetlands. The functions of As biomethylation by microbial consortia in anaerobic and aerobic conditions are extensively discussed. In addition, we have tried to explain the interconnections between As transformation and carbon (C), such as microbial degradation of organic compounds and methane (CH4) emission. These processes can cause As release because of the reduction of arsenate (As(V)) to the more mobile arsenite (As(III)) as well as As methylation and the formation of toxic trivalent methylated As species in anaerobic conditions. Furthermore, the sulfur (S) transformation can form highly toxic thiolated As species owing to its interference with As biomethylation. Besides, we have focused on many other mutual interlinks that remain elusive between As and C, including As biomethylation, thiolation, and CH4 emission, in the soil-water systems. Recent developments have clarified the significant and complex interactions between the coupled microbial process in anoxic and submerged soils. These processes, performed by little-known/unknown microbial taxa or well-known members of microbial communities with unrecognized metabolic pathways, conducted several concurrent reactions that contributed to global warming on our planet and have unfavorable impacts on water quality and human food resources. Finally, some environmental implications in rice production and arsenic removal from soil-water systems are discussed. Generally, our understanding of the ecological and metabolic evidence for the coupling and synchronous processes of As, C, and S are involved in environmental contamination-caused toxicity in human food, including high As content in rice grain, water resources, and global warming through methanogenesis elucidate combating global rice safety, drinking water, and climate changes.

Recent developments in speciation and determination of arsenic in marine organisms using different analytical techniques. A review

Marine organisms play a vital role as the main providers of essential and functional food. Yet they also constitute the primary pathway through which humans are exposed to total arsenic (As) in their diets. Since it is well known that the toxicity of this metalloid ultimately depends on its chemical forms, speciation in As is an important issue. Most relevant articles about arsenic speciation have been investigated. This extended not only from general knowledge about As but also the toxicity and health related issues resulting from exposure to these As species from the food ecosystem. There can be enormous side effects originating from exposure to As species that must be measured quantitatively. Therefore, various convenient approaches have been developed to identify different species of As in marine samples. Different extraction strategies have been utilized based on the As species of interest including water, methanol and mixtures of both, and many other extraction agents have been explained in this article. Furthermore, details of hyphenated techniques which are available for detecting these As species have been documented, especially the most versatile and applied technique including inductively coupled plasma mass spectrometry.

Environmental pollution and human health risk due to tailings storage facilities in China

Tailings storage facilities (TSFs) represent an anthropogenic source of pollution, resulting in potential risks to both environmental integrity and human health. To date, the environmental and human health risks from TSFs in China have been under-researched. This study attempts to address this gap by developing, and geo-statistically analyzing two comprehensive databases. The first database (I) focuses on failed TSFs; we supply the statistics of environmental damages from 143 TSF failure incidents. Notably, approximately 75 % of the failure incidents involved tailings flows released into water bodies, resulting in a significant exacerbation of environmental pollution. To better inform ecological and human health risks, we present another database (II) for 147 non-failed TSFs to investigate the soil heavy metal contamination, considering 8 heavy metals. The findings reveal that (i) Cd, Pb, and Hg are the prominent pollutants across the non-failed TSF sites in China; (ii) lead‑zinc and tungsten mine tailings storage sites exhibit the most severe pollution; (iii) Pb, Cd, and Ni present noteworthy non-carcinogenic risks to human health; (iv) >85 % of TSF sites pose carcinogenic risks associated with arsenic; and (v) health risks resulting from dermal absorption surpass ingestion for the majority of heavy metals, with the exception of Pb, where ingestion presents a more pronounced route of exposure. Our study presents a comprehensive evaluation of environmental and human health risks due to TSFs, highlighting the necessity for risk assessment of >14,000 existing TSFs in China.

Characteristics of arsenic speciation in mainly cultured shellfish from Sanmen Bay, Zhejiang Province, China

Sanmen Bay plays a crucial role in economic shellfish aquaculture in China, yet few studies exist on the arsenic speciation of shellfish from this area. In this study, arsenic speciation of 11 cultured shellfish species from Sanmen Bay were analyzed by HPLC/ICP-MS. The results showed that organic arsenic particularly AsB, was the dominant arsenic species, constituting 21 %-71 % of the total arsenic. Conversely, the levels of inorganic arsenic were relatively low, ranging from 0.007 to 0.093 mg/kg, only accounted for 0.2 %-5.7 % of the total arsenic. There was no significant level correlation between inorganic arsenic and total arsenic in Sanmen Bay shellfish, so the concentration of inorganic arsenic did not increase with the total arsenic. Overall, the present study firstly revealed the arsenic speciation of shellfish from Sanmen Bay and also suggested that the proportion of inorganic arsenic should be considered in the revision of arsenic limit values.

Gut Microbiota Control the Bioavailability and Metabolism of Organoarsenicals of Seaweeds in Mice after Oral Ingestion

Edible seaweed consumption is an essential route of human exposure to complex organoarsenicals, including arsenosugars and arsenosugar phospholipids. However, the effects of gut microbiota on the metabolism and bioavailability of arsenosugars in vivo are unknown. Herein, two nori and two kelp samples with phosphate arsenosugar and sulfonate arsenosugar, respectively, as the predominant arsenic species, were administered to normal mice and gut microbiota-disrupted mice treated with the broad-spectrum antibiotic cefoperazone for 4 weeks. Following exposure, the community structures of the gut microbiota, total arsenic concentrations, and arsenic species in excreta and tissues were analyzed. Total arsenic excreted in feces and urine did not differ significantly between normal and antibiotic-treated mice fed with kelp samples. However, the total urinary arsenic of normal mice fed with nori samples was significantly higher (p < 0.05) (urinary arsenic excretion factor, 34-38 vs 5-7%), and the fecal total arsenic was significantly lower than in antibiotic-treated mice. Arsenic speciation analysis revealed that most phosphate arsenosugars in nori were converted to arsenobetaine (53.5-74.5%) when passing through the gastrointestinal tract, whereas a large portion of sulfonate arsenosugar in kelp was resistant to speciation changes and was excreted in feces intact (64.1-64.5%). Normal mice exhibited greater oral bioavailability of phosphate arsenosugar from nori than sulfonate arsenosugar from kelp (34-38 vs 6-9%). Our work provides insights into organoarsenical metabolism and their bioavailability in the mammalian gut.

Bifunctional protein ArsRM contributes to arsenite methylation and resistance in Brevundimonas sp. M20

BACKGROUND

Arsenic (As) with various chemical forms, including inorganic arsenic and organic arsenic, is the most prevalent water and environmental toxin. This metalloid occurs worldwide and many of its forms, especially arsenite [As(III)], cause various diseases including cancer. Organification of arsenite is an effective way for organisms to cope with arsenic toxicity. Microbial communities are vital contributors to the global arsenic biocycle and represent a promising way to reduce arsenite toxicity.

METHODS

Brevundimonas sp. M20 with arsenite and roxarsone resistance was isolated from aquaculture sewage. The arsHRNBC cluster and the metRFHH operon of M20 were identified by sequencing. The gene encoding ArsR/methyltransferase fusion protein, arsRM, was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25-6 mM As(III), aresenate, or pentavalent roxarsone. The methylation activity and regulatory action of ArsRM were analyzed using Discovery Studio 2.0, and its functions were confirmed by methyltransferase activity analysis and electrophoretic mobility shift assays.

RESULTS

The minimum inhibitory concentration of the roxarsone resistant strain Brevundimonas sp. M20 to arsenite was 4.5 mM. A 3,011-bp arsenite resistance ars cluster arsHRNBC and a 5649-bp methionine biosynthesis met operon were found on the 3.315-Mb chromosome. Functional prediction analyses suggested that ArsRM is a difunctional protein with transcriptional regulation and methyltransferase activities. Expression of ArsRM in E. coli increased its arsenite resistance to 1.5 mM. The arsenite methylation activity of ArsRM and its ability to bind to its own gene promoter were confirmed. The As(III)-binding site (ABS) and S-adenosylmethionine-binding motif are responsible for the difunctional characteristic of ArsRM.

CONCLUSIONS

We conclude that ArsRM promotes arsenite methylation and is able to bind to its own promoter region to regulate transcription. This difunctional characteristic directly connects methionine and arsenic metabolism. Our findings contribute important new knowledge about microbial arsenic resistance and detoxification. Future work should further explore how ArsRM regulates the met operon and the ars cluster.

Biomarkers of seafood intake during pregnancy - Pollutants versus fatty acids and micronutrients

Intake of fish and seafood during pregnancy may have certain beneficial effects on fetal development, but measurement of intake using questionnaires is unreliable. Here, we assessed several candidate biomarkers of seafood intake, including long-chain omega 3 fatty acids (n-3 LCPUFA), selenium, iodine, methylmercury, and different arsenic compounds, in 549 pregnant women (gestational week 29) in the prospective birth cohort NICE (Nutritional impact on Immunological maturation during Childhood in relation to the Environment). Proportions of the fatty acids eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), and docosahexaenoic acid (DHA) in erythrocytes were measured using gas chromatography with flame ionization detector. Selenium was measured in blood plasma and erythrocytes, mercury and arsenic in erythrocytes, and iodine and several arsenic compounds in urine, using inductively coupled plasma mass spectrometry, arsenic compounds after first being separated by ion exchange high-performance liquid chromatography (HPLC). Each biomarker was related to intake of total seafood and to intake of fatty and lean fish, and shellfish in third trimester, estimated from a semi-quantitative food frequency questionnaire filled out in gestational week 34. The pregnant women reported a median total seafood intake of 184 g/week (5th-95th percentiles: 34-465 g/week). This intake correlated most strongly with erythrocyte mercury concentrations (rho = 0.49, p < 0.001), consisting essentially of methylmercury, followed by total arsenic in erythrocytes (rho = 0.34, p < 0.001), and arsenobetaine in urine (rho = 0.33, p < 0.001), the main form of urinary arsenic. These biomarkers correlated well with intake of both fatty fish, lean fish, and shellfish. Erythrocyte DHA and plasma selenium correlated, although weakly, mainly with fatty fish (rho = 0.25 and 0.22, respectively, both p < 0.001). In conclusion, elevated concentrations of erythrocyte mercury and urinary arsenobetaine can be useful indicators of seafood intake, more so than the n-3 LCPUFAs. However, the relative importance of the biomarkers may differ depending on the type and amount of seafood consumed.

Heavy metals and metalloid in aquatic invertebrates: A review of single/mixed forms, combination with other pollutants, and environmental factors

Heavy metals (HMs) and metalloid occur naturally and are found throughout the Earth's crust but they are discharged into aquatic environments at high concentrations by human activities, increasing heavy metal pollution. HMs can bioaccumulate in higher organisms through the food web and consequently affect humans. In an aquatic environment, various HMs mixtures can be present. Furthermore, HMs adsorb on other environmental pollutants, such as microplastics and persistent organic pollutants, causing a synergistic or antagonistic effect on aquatic organisms. Therefore, to understand the biological and physiological effects of HMs on aquatic organisms, it is important to evaluate the effects of exposure to combinations of complex HM mixtures and/or pollutants and other environmental factors. Aquatic invertebrates occupy an important niche in the aquatic food chain as the main energy link between higher and lower organisms. The distribution of heavy metals and the resulting toxic effects in aquatic invertebrates have been extensively studied, but few reports have dealt with the relationship between HMs, pollutants, and environmental factors in biological systems with regard to biological availability and toxicity. This review describes the overall properties of individual HM and their effects on aquatic invertebrates and comprehensively reviews physiological and biochemical endpoints in aquatic invertebrates depending on interactions among HMs, other pollutants, and environmental factors.

Accumulation and speciation of arsenic in Eisenia fetida in sodium arsenite spiked soils - A dynamic interaction between soil and earthworms

Arsenic (As) is a toxic metalloid that is a significant global pollutant of the environment and a persistent bioaccumulation carcinogen. Earthworms are frequently employed as sentinel organisms to investigate the bioavailability of As in contaminated soils. However, the process of As accumulation in earthworms and the mechanism of transformation of As species in their bodies are not well understood. The accumulation of As and variation of As species in the earthworms (Eisenia fetida) exposed to sodium arsenite (0, 20, and 80 mg kg^-1 As) were investigated in this study. The total As concentration of earthworms in the three treatments at various sample times was dose-dependent on soil As content. After 56 days of exposure, the high concentration treatment had the highest total As content (772 ± 21 mg kg^-1) in earthworms, followed by the low concentration treatment (579 ± 42 mg kg^-1) and control (31 ± 1 mg kg^-1). During 56 days, the proportion of trivalent As in earthworms increased from 70% to more than 90%, while pentavalent As decreased by 11-18%. On day 28, the sum of the four organic As species reached a maximum (<1%). Changes in soil As species and an increase in bioavailable As cause earthworms to accumulate more As. The total As in soil after 56 days of exposure was 9.51 ± 0.50, 25.6 ± 0.60, and 82.8 ± 0.28 mg kg^-1, which was not significantly different from the total As in soil before the experiment. These findings are useful in assessing the risk of earthworm exposure to sodium arsenite in the soil.

Comparison of prokaryotes between Mount Everest and the Mariana Trench

BACKGROUND

Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS

Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO₂ fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION

Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.

Key genes for arsenobetaine synthesis in marine medaka (Oryzias melastigma) by transcriptomics

Marine fish undergo detoxification to overcome As stress, forming non-toxic metabolites arsenobetaine (AsB). Genes associated with AsB synthesis remain unknown. Therefore, in this study, we explored the key genes involved in the synthesis of AsB by transcriptomic analysis in marine medaka (Oryzias melastigma), and then screened candidate genes related to AsB synthesis. In the liver, 40 genes were up-regulated and 23 genes were down-regulated, whereas in muscle, 83 genes were up-regulated and 331 genes were down-regulated. We revealed that bhmt, mat2aa, and gstt1a can play a significant role in the glutathione and methionine metabolic pathway. These three genes can affect the conversion of arsenocholine (AsC) to AsB by the vitro gene transformation experiments of E. coli BL21(DE3). E. coli BL21-bhmt overexpressing bhmt resulted in more oxidation of precursor AsC to AsB. Furthermore, the AsB concentration was decreased after E. coli BL21 overexpressing mat2aa and gstt1a, which were down-regulated in marine medaka. Therefore, we concluded that bhmt, mat2aa, and gstt1a are involved in AsB synthesis. Overall, this is the first report on transcriptome screening and identification of key genes for AsB synthesis in marine medaka. We provided important insights to reveal the mystery of AsB synthesis in marine fish.

ProX from marine Synechococcus spp. show a sole preference for glycine-betaine with differential affinity between ecotypes

Osmotic stress, caused by high or fluctuating salt concentrations, is a crucial abiotic factor affecting microbial growth in aquatic habitats. Many organisms utilize common responses to osmotic stress, generally requiring active extrusion of toxic inorganic ions and accumulation of compatible solutes to protect cellular machinery. We heterologously expressed and purified predicted osmoprotectant, proline/glycine betaine-binding proteins (ProX) from two phylogenetically distinct Synechococcus spp. MITS9220 and WH8102. Homologues of this protein are conserved only among Prochlorococcus LLIV and Synechococcus clade I, III and CRD1 strains. Our biophysical characterization show Synechococcus ProX exists as a dimer, with specificity solely for glycine betaine but not to other osmoprotectants tested. We discovered that MITS9220_ProX has a 10-fold higher affinity to glycine betaine than WH8102_ProX, which is further elevated (24-fold) in high salt conditions. The stronger affinity and effect of ionic strength on MITS9220_ProX glycine betaine binding but not on WH8102_ProX alludes to a novel regulatory mechanism, providing critical functional insights into the phylogenetic divergence of picocyanobacterial ProX proteins that may be necessary for their ecological success.

The strategy of arsenic metabolism in an arsenic-resistant bacterium Stenotrophomonas maltophilia SCSIOOM isolated from fish gut

Bacteria are candidates for the biotransformation of environmental arsenic (As), while As metabolism in bacteria is not yet fully understood. In this study, we sequenced the genome of an As-resistant bacterium strain Stenotrophomonas maltophilia SCSIOOM isolated from the fish gut. After arsenate (As(V)) exposure, S. maltophilia transformed As(V) to organoarsenicals, along with the significant change of the expression of 40 genes, including the upregulation of arsH, arsRBC and betIBA. The heterogeneous expression of arsH and arsRBC increased As resistance of E. coli AW3110 by increasing As efflux and transformation. E. coli AW3110 (pET-betIBA) could transform inorganic As into dimethylarsinate (DMA) and nontoxic arsenobetaine (AsB), which suggested that AsB could be synthesized through the synthetic pathway of its analog-glycine betaine. In addition, the existence of arsRBC, betIBA and arsH reduced the reactive oxygen species (ROS) induced by As exposure. In total, these results demonstrated that S. maltophilia adopted an As metabolism strategy by reducing As accumulation and synthesizing less toxic As species. We first reported the production and potential synthetic pathway of AsB in bacteria, which improved our knowledge of As toxicology in microorganisms.

Arsenic Metabolism, Toxicity and Accumulation in the White Button Mushroom Agaricus bisporus

Mushrooms have unique properties in arsenic metabolism. In many commercial and wild-grown mushrooms, arsenobetaine (AsB), a non-toxic arsenical, was found as the dominant arsenic species. The AsB biosynthesis remains unknown, so we designed experiments to study conditions for AsB formation in the white button mushroom, Agaricus bisporus. The mushrooms were treated with various arsenic species including arsenite (As(III)), arsenate (As(V)), methylarsenate (MAs(V)), dimethylarsenate (DMAs(V)) and trimethylarsine oxide (TMAsO), and their accumulation and metabolism were determined using inductively coupled mass spectrometer (ICP-MS) and high-pressure liquid chromatography coupled with ICP-MS (HPLC-ICP-MS), respectively. Our results showed that mycelia have a higher accumulation for inorganic arsenicals while fruiting bodies showed higher accumulation for methylated arsenic species. Two major arsenic metabolites were produced in fruiting bodies: DMAs(V) and AsB. Among tested arsenicals, only MAs(V) was methylated to DMAs(V). Surprisingly, AsB was only detected as the major arsenic product when TMAsO was supplied. Additionally, AsB was only detected in the fruiting body, but not mycelium, suggesting that methylated products were transported to the fruiting body for arsenobetaine formation. Overall, our results support that methylation and AsB formation are two connected pathways where trimethylated arsenic is the optimal precursor for AsB formation.

Arsenic bioaccumulation and biotransformation in aquatic organisms

Arsenic exists universally in freshwater and marine environments, threatening the survival of aquatic organisms and human health. To elucidate arsenic bioaccumulation and biotransformation processes in aquatic organisms, this review evaluates the dissolved uptake, dietary assimilation, biotransformation, and elimination of arsenic in aquatic organisms and discusses the major factors influencing these processes. Environmental factors such as phosphorus concentration, pH, salinity, and dissolved organic matter influence arsenic absorption from aquatic systems, whereas ingestion rate, gut passage time, and gut environment affect the assimilation of arsenic from foodstuffs. Arsenic bioaccumulation and biotransformation mechanisms differ depending on specific arsenic species and the involved aquatic organism. Although some enzymes engaged in arsenic biotransformation are known, deciphering the complicated synthesis and degradation pathway of arsenobetaine remains a challenge. The elimination of arsenic involves many processes, such as fecal excretion, renal elimination, molting, and reproductive processes. This review facilitates our understanding of the environmental behavior and biological fate of arsenic and contributes to regulation of the environmental risk posed by arsenic pollution.

Microbiomes in the Challenger Deep slope and bottom-axis sediments

Hadal trenches are the deepest and most remote regions of the ocean. The 11-kilometer deep Challenger Deep is the least explored due to the technical challenges of sampling hadal depths. It receives organic matter and heavy metals from the overlying water column that accumulate differently across its V-shaped topography. Here, we collected sediments across the slope and bottom-axis of the Challenger Deep that enable insights into its in situ microbial communities. Analyses of 586 metagenome-assembled genomes retrieved from 37 metagenomes show distinct diversity and metabolic capacities between bottom-axis and slope sites. 26% of prokaryotic 16S rDNA reads in metagenomes were novel, with novelty increasing with water and sediment depths. These predominantly heterotrophic microbes can recycle macromolecules and utilize simple and complex hydrocarbons as carbon sources. Metagenome and metatranscriptome data support reduction and biotransformation of arsenate for energy gain in sediments that present a two-fold greater accumulation of arsenic compared to non-hadal sites. Complete pathways for anaerobic ammonia oxidation are predominantly identified in genomes recovered from bottom-axis sediments compared to slope sites. Our results expand knowledge of microbially-mediated elemental cycling in hadal sediments, and reveal differences in distribution of processes involved in nitrogen loss across the trench.

The V-shaped Challenger Deep in the Mariana Trench is the deepest part of the world’s oceans. Using 586 prokaryotic metagenome-assembled genomes and metatranscriptomic data, this study explores metabolic capabilities and activities of microorganisms involved in elemental cycling in hadal sediments, and reveals the different distribution of processes between its bottom-axis and slope.

Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification

Phosphocholine molecules decorating bacterial cell wall teichoic acids and outer-membrane lipopolysaccharide have fundamental roles in adhesion to host cells, immune evasion, and persistence. Bacteria carrying the operon that performs phosphocholine decoration synthesize phosphocholine after uptake of the choline precursor by LicB, a conserved transporter among divergent species. Streptococcus pneumoniae is a prominent pathogen where phosphocholine decoration plays a fundamental role in virulence. Here, we present cryo-electron microscopy and crystal structures of S. pneumoniae LicB, revealing distinct conformational states and describing architectural and mechanistic elements essential to choline import. Together with in vitro and in vivo functional characterization, we found that LicB displays proton-coupled import activity and promiscuous selectivity involved in adaptation to choline deprivation conditions, and describe LicB inhibition by synthetic nanobodies (sybodies). Our results provide previously unknown insights into the molecular mechanism of a key transporter involved in bacterial pathogenesis and establish a basis for inhibition of the phosphocholine modification pathway across bacterial phyla.

Xanthomonas transcriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptations at early infection stages

Xanthomonas campestris pv. campestris (Xcc) is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wild Brassicaceae. Xcc enters the plant tissues preferentially via hydathodes, which are organs localized at leaf margins. To decipher both physiological and virulence strategies deployed by Xcc during early stages of infection, the transcriptomic profile of Xcc was analysed 3 days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and despite a biotrophic lifestyle, 18% of Xcc genes were differentially expressed, including a striking repression of chemotaxis and motility functions. The Xcc full repertoire of virulence factors had not yet been activated but the expression of the HrpG regulon composed of 95 genes, including genes coding for the type III secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulphur and phosphate metabolism was upregulated while limited stress responses were observed 3 days postinfection. We confirmed experimentally that high-affinity phosphate transport is needed for bacterial fitness inside hydathodes. This analysis provides information about the nutritional and stress status of bacteria during the early biotrophic infection stages and helps to decipher the adaptive strategy of Xcc to the hydathode environment.

The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus

The nucleotide messenger (p)ppGpp allows bacteria to adapt to fluctuating environments by reprogramming the transcriptome. Despite its well-recognized role in gene regulation, (p)ppGpp is only known to directly affect transcription in Proteobacteria by binding to the RNA polymerase. Here, we reveal a different mechanism of gene regulation by (p)ppGpp in Firmicutes: (p)ppGpp directly binds to the transcription factor PurR to downregulate purine biosynthesis gene expression upon amino acid starvation. We first identified PurR as a receptor of (p)ppGpp in Bacillus anthracis. A co-structure with Bacillus subtilis PurR reveals that (p)ppGpp binds to a PurR pocket reminiscent of the active site of phosphoribosyltransferase enzymes that has been repurposed to serve a purely regulatory role, where the effectors (p)ppGpp and PRPP compete to allosterically control transcription. PRPP inhibits PurR DNA binding to induce transcription of purine synthesis genes, whereas (p)ppGpp antagonizes PRPP to enhance PurR DNA binding and repress transcription. A (p)ppGpp-refractory purR mutant in B. subtilis fails to downregulate purine synthesis genes upon amino acid starvation. Our work establishes the precedent of (p)ppGpp as an effector of a classical transcription repressor and reveals the key function of (p)ppGpp in regulating nucleotide synthesis through gene regulation, from soil bacteria to pathogens.

Interactions with Arsenic: Mechanisms of Toxicity and Cellular Resistance in Eukaryotic Microorganisms

Arsenic (As) is quite an abundant metalloid, with ancient origin and ubiquitous distribution, which represents a severe environmental risk and a global problem for public health. Microbial exposure to As compounds in the environment has happened since the beginning of time. Selective pressure has induced the evolution of various genetic systems conferring useful capacities in many microorganisms to detoxify and even use arsenic, as an energy source. This review summarizes the microbial impact of the As biogeochemical cycle. Moreover, the poorly known adverse effects of this element on eukaryotic microbes, as well as the As uptake and detoxification mechanisms developed by yeast and protists, are discussed. Finally, an outlook of As microbial remediation makes evident the knowledge gaps and the necessity of new approaches to mitigate this environmental challenge.

Functions of elements in soil microorganisms

The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.

Arsenocholine-O-sulfate: A novel compound as major arsenic species in the parasitic mushroom Tolypocladium ophioglossoides

The As concentrations, along with 34 other elements, and the As speciation were investigated in wild-grown samples of the parasitic mushroom Tolypocladium ophioglossoides with inductively coupled plasma mass spectrometry (ICPMS) and high performance liquid chromatography coupled to ICPMS. The As concentrations were 0.070-3.44 mg kg^-1 dry mass. More remarkable was the As speciation, where up to 56% of the extracted As were found to be an unknown As species, which was marginally retained under anion- and also cation-exchange conditions. After testing several different chromatographic settings, the compound was finally isolated and identified as 2-(sulfoxyethyl) trimethylarsonium ion (in short: arsenocholine-O-sulfate) with high resolution mass spectrometry. The compound was synthesized and further quantified in all investigated samples via ion-pair chromatography coupled to ICPMS. In addition to the high abundance of arsenocholine-O-sulfate in T. ophioglossoides, small amounts of this As species were also detected in one sample of the host mushroom, Elaphomyces asperulus. In a sample of another parasitic mushroom, Ophiocordyceps sinensis, arsenocholine-O-sulfate could not be detected, but the main species was another unknown compound that was oxidized to inorganic As(V) with hydrogen peroxide. This is the first discovery of arsenocholine-O-sulfate in nature. It is possible that it is present in many other organisms, at least in low concentrations, and just has not been detected there yet because of its unusual chromatographic behavior. The existence of arsenocholine-O-sulfate brings up questions again about the biotransformation pathways of As in the environment and the specific behavior of fungi.

The response of Pyropia haitanensis to inorganic arsenic under laboratory culture

Up to now, complicated organoarsenicals were mainly identified in marine organisms, suggesting that these organisms play a critical role in arsenic biogeochemical cycling because of low phosphate and relatively high arsenic concentration in the marine environment. However, the response of marine macroalgae to inorganic arsenic remains unknown. In this study, Pyropia haitanensis were exposed to arsenate [As(V)] (0.1, 1, 10, 100 μM) or arsenite [As(III)] (0.1, 1, 10 μM) under laboratory conditions for 3 d. The species of water-soluble arsenic, the total concentration of lipid-soluble and cell residue arsenic of the algae cells was analyzed. As(V) was mainly transformed into oxo-arsenosugar-phosphate, with other arsenic compounds such as monomethylated, As(III), demethylated arsenic and oxo-arsenosugar-glycerol being likely the intermediates of arsenosugar synthesis. When high concentration of As(III) was toxic to P. haitanensis, As(III) entered into the cells and was transformed into less toxic organoarsenicals and As(V). Transcriptome results showed genes involved in DNA replication, mismatch repair, base excision repair, and nucleotide excision repair were up-regulated in the algae cells exposed to 10 μM As(V), and multiple genes involved in glutathione metabolism and photosynthetic were up-regulated by 1 μM As(III). A large number of ABC transporters were down-regulated by As(V) while ten genes related to ABC transporters were up-regulated by As(III), indicating that ABC transporters were involved in transporting As(III) to vacuoles in algae cells. These results indicated that P. haitanensis detoxifies inorganic arsenic via transforming them into organoarsenicals and enhancing the isolation of highly toxic As(III) in vacuoles.

TiO2 Nanoparticles in the Marine Environment: Enhancing Bioconcentration, While Limiting Biotransformation of Arsenic in the Mussel Perna viridis

The increasing use of nanoscale TiO₂ particles (nTiO₂) and their subsequent leakage into aquatic environments poses a threat to the ecosystem. One major concern is that nTiO₂ may alter the environmental behaviors of arsenic (As) and disrupt the equilibrium of As accumulation and speciation in organisms. In this study, we investigated the effects of nTiO₂ on the bioaccumulation and biotransformation of As(V) in the mussel Perna viridis. Exposure to nTiO₂ significantly increased As accumulation in mussels. Our As speciation analysis demonstrated that nTiO₂ treatment increased the proportion of inorganic As and reduced that of organic As, displaying inhibitory effects on the methylation and detoxification of inorganic As in mussels. Analysis of enzyme systems related to As metabolism in mussels demonstrated that nTiO₂ might limit the methylation of inorganic As by suppressing the GST activity and GSH content. The strong adsorption capacity and weak desorption rate of As by nTiO₂, which could result in the disruption of As distribution and decrease of the amount of As involved in biotransformation, might serve as another mechanism to the limition on As methylation in mussels. Moreover, exposure to nTiO₂ disturbed the osmotic adjustment system in mussels by reducing arsenobetaine and Na⁺-K⁺-ATPase activity, resulting in enhanced toxicity of As after coexposure. The findings indicate, for the first time, that nTiO₂ can block the transformation and detoxification of As in mussels, which would increase the risk of As to marine animals and even humans via the food chain, and may disrupt the biogeochemical cycle of As in natural environments.

Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress

Bacillus subtilis adjusts to high osmolarity surroundings through the amassing of compatible solutes. It synthesizes the compatible solute glycine betaine from prior imported choline and scavenges many pre-formed osmostress protectants, including glycine betaine, from environmental sources. Choline is imported through the substrate-restricted ABC transporter OpuB and the closely related, but promiscuous, OpuC system, followed by its GbsAB-mediated oxidation to glycine betaine. We have investigated the impact of two MarR-type regulators, GbsR and OpcR, on gbsAB, opuB, and opuC expression. Judging by the position of the previously identified OpcR operator in the regulatory regions of opuB and opuC [Lee et al. (2013) Microbiology 159, 2087−2096], and that of the GbsR operator identified in the current study, we found that the closely related GbsR and OpcR repressors use different molecular mechanisms to control transcription. OpcR functions by sterically hindering access of RNA-polymerase to the opuB and opuC promoters, while GbsR operates through a roadblock mechanism to control gbsAB and opuB transcription. Loss of GbsR or OpcR de-represses opuB and opuC transcription, respectively. With respect to the osmotic control of opuB and opuC expression, we found that this environmental cue operates independently of the OpcR and GbsR regulators. When assessed over a wide range of salinities, opuB and opuC exhibit a surprisingly different transcriptional profile. Expression of opuB increases monotonously in response to incrementally increase in salinity, while opuC transcription levels decrease after an initial up-regulation at moderate salinities. Transcription of the gbsR and opcR regulatory genes is up-regulated in response to salt stress, and is also affected through auto-regulatory processes. The opuB and opuC operons have evolved through a gene duplication event. However, evolution has shaped their mode of genetic regulation, their osmotic-stress dependent transcriptional profile, and the substrate specificity of the OpuB and OpuC ABC transporters in a distinctive fashion.

Everybody loves cheese: crosslink between persistence and virulence of Shiga-toxin Escherichia coli

General cheese manufacturing involves high temperatures, fermentation and ripening steps that function as hurdles to microbial growth. On the other hand, the application of several different formulations and manufacturing techniques may create a bacterial protective environment. In cheese, the persistent behavior of Shiga toxin-producing Escherichia coli (STEC) relies on complex mechanisms that enable bacteria to respond to stressful conditions found in cheese matrix. In this review, we discuss how STEC manages to survive to high and low temperatures, hyperosmotic conditions, exposure to weak organic acids, and pH decreasing related to cheese manufacturing, the cheese matrix itself and storage. Moreover, we discuss how these stress responses interact with each other by enhancing adaptation and consequently, the persistence of STEC in cheese. Further, we show how virulence genes eae and tir are affected by stress response mechanisms, increasing either cell adherence or virulence factors production, which leads to a selection of more resistant and virulent pathogens in the cheese industry, leading to a public health issue.

Management of Osmoprotectant Uptake Hierarchy in Bacillus subtilis via a SigB-Dependent Antisense RNA

Under hyperosmotic conditions, bacteria accumulate compatible solutes through synthesis or import. Bacillus subtilis imports a large set of osmostress protectants via five osmotically controlled transport systems (OpuA to OpuE). Biosynthesis of the particularly effective osmoprotectant glycine betaine requires the exogenous supply of choline. While OpuB is rather specific for choline, OpuC imports a broad spectrum of compatible solutes, including choline and glycine betaine. One previously mapped antisense RNA of B. subtilis, S1290, exhibits strong and transient expression in response to a suddenly imposed salt stress. It covers the coding region of the opuB operon and is expressed from a strictly SigB-dependent promoter. By inactivation of this promoter and analysis of opuB and opuC transcript levels, we discovered a time-delayed osmotic induction of opuB that crucially depends on the S1290 antisense RNA and on the degree of the imposed osmotic stress. Time-delayed osmotic induction of opuB is apparently caused by transcriptional interference of RNA-polymerase complexes driving synthesis of the converging opuB and S1290 mRNAs. When our data are viewed in an ecophysiological framework, it appears that during the early adjustment phase of B. subtilis to acute osmotic stress, the cell prefers to initially rely on the transport activity of the promiscuous OpuC system and only subsequently fully induces opuB. Our data also reveal an integration of osmostress-specific adjustment systems with the SigB-controlled general stress response at a deeper level than previously appreciated.

Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1

Transcription is of the most crucial steps of gene expression in bacteria, whose regulation guarantees the bacteria's ability to adapt to varying environmental conditions. Discovering the molecular basis and genomic principles of the transcriptional regulation is thus one of the most important tasks in cellular and molecular biology. Here, a comprehensive phylogenetic footprinting framework was implemented to predict maximal regulons of Lactococcus lactis subsp. lactis IO-1, a lactic acid bacterium known for its high potentials in nisin Z production as well as efficient xylose consumption which have made it a promising biotechnological strain. A total set of 321 regulons covering more than 90% of all the bacterium's operons have been elucidated and validated according to available data. Multiple novel biologically-relevant members were introduced amongst which arsC, mtlA and mtl operon for BusR, MtlR and XylR regulons can be named, respectively. Moreover, the effect of riboflavin on nisin biosynthesis was assessed in vitro and a negative correlation was observed. It is believed that understandings from such networks not only can be useful for studying transcriptional regulatory potentials of the target organism but also can be implemented in biotechnology to rationally design favorable production conditions.

Identification of Steps in the Pathway of Arsenosugar Biosynthesis

Arsenosugars are arsenic-containing ribosides that play a substantial role in arsenic biogeochemical cycles. Arsenosugars were identified more than 30 years ago, and yet their mechanism of biosynthesis remains unknown. In this study we report identification of the arsS gene from the cyanobacterium Synechocystis sp. PCC 6803 and show that it is involved in arsenosugar biosynthesis. In the Synechocystis sp. PCC 6803 ars operon, arsS is adjacent to the arsM gene that encodes an As(III) S-adenosylmethionine (SAM) methyltransferase. The gene product, ArsS, contains a characteristic CX3CX2C motif which is typical for the radical SAM superfamily. The function of ArsS was identified from a combination of arsS disruption in Synechocystis sp. PCC 6803 and heterologous expression of arsM and arsS in Escherichia coli. Both genes are necessary, indicating a multistep pathway of arsenosugar biosynthesis. In addition, we demonstrate that ArsS orthologs from three other freshwater cyanobacteria and one picocyanobacterium are involved in arsenosugar biosynthesis in those microbes. This study represents the identification of the first two steps in the pathway of arsenosugar biosynthesis. Our discovery expands the catalytic repertoire of the diverse radical SAM enzyme superfamily and provides a basis for studying the biogeochemistry of complex organoarsenicals.

The GbsR Family of Transcriptional Regulators: Functional Characterization of the OpuAR Repressor

Accumulation of compatible solutes is a common stress response of microorganisms challenged by high osmolarity; it can be achieved either through synthesis or import. These processes have been intensively studied in Bacillus subtilis, where systems for the production of the compatible solutes proline and glycine betaine have been identified, and in which five transporters for osmostress protectants (Opu) have been characterized. Glycine betaine synthesis relies on the import of choline via the substrate-restricted OpuB system and the promiscuous OpuC transporter and its subsequent oxidation by the GbsAB enzymes. Transcription of the opuB and gbsAB operons is under control of the MarR-type regulator GbsR, which acts as an intracellular choline-responsive repressor. Modeling studies using the X-ray structure of the Mj223 protein from Methanocaldococcus jannaschii as the template suggest that GbsR is a homo-dimer with an N-terminal DNA-reading head and C-terminal dimerization domain; a flexible linker connects these two domains. In the vicinity of the linker region, an aromatic cage is predicted as the inducer-binding site, whose envisioned architecture resembles that present in choline and glycine betaine substrate-binding proteins of ABC transporters. We used bioinformatics to assess the phylogenomics of GbsR-type proteins and found that they are widely distributed among Bacteria and Archaea. Alignments of GbsR proteins and analysis of the genetic context of the corresponding structural genes allowed their assignment into four sub-groups. In one of these sub-groups of GbsR-type proteins, gbsR-type genes are associated either with OpuA-, OpuB-, or OpuC-type osmostress protectants uptake systems. We focus here on GbsR-type proteins, named OpuAR by us, that control the expression of opuA-type gene clusters. Using such a system from the marine bacterium Bacillus infantis, we show that OpuAR acts as a repressor of opuA transcription, where several compatible solutes (e.g., choline, glycine betaine, proline betaine) serve as its inducers. Site-directed mutagenesis studies allowed a rational improvement of the putative inducer-binding site in OpuAR with respect to the affinity of choline and glycine betaine binding. Collectively, our data characterize GbsR-/OpuAR-type proteins as an extended sub-group within the MarR-superfamily of transcriptional regulators and identify a novel type of substrate-inducible import system for osmostress protectants.

OpuF, a New Bacillus Compatible Solute ABC Transporter with a Substrate-Binding Protein Fused to the Transmembrane Domain

The accumulation of compatible solutes is a common defense of bacteria against the detrimental effects of high osmolarity. Uptake systems for these compounds are cornerstones in cellular osmostress responses because they allow the energy-preserving scavenging of osmostress protectants from environmental sources. Bacillus subtilis is well studied with respect to the import of compatible solutes and its five transport systems (OpuA, OpuB, OpuC, OpuD, and OpuE), for these stress protectants have previously been comprehensively studied. Building on this knowledge and taking advantage of the unabated appearance of new genome sequences of members of the genus Bacillus, we report here the discovery, physiological characterization, and phylogenomics of a new member of the Opu family of transporters, OpuF (OpuFA-OpuFB). OpuF is not present in B. subtilis but it is widely distributed in members of the large genus Bacillus OpuF is a representative of a subgroup of ATP-binding cassette (ABC) transporters in which the substrate-binding protein (SBP) is fused to the transmembrane domain (TMD). We studied the salient features of the OpuF transporters from Bacillus infantis and Bacillus panaciterrae by functional reconstitution in a B. subtilis chassis strain lacking known Opu transporters. A common property of the examined OpuF systems is their substrate profile; OpuF mediates the import of glycine betaine, proline betaine, homobetaine, and the marine osmolyte dimethylsulfoniopropionate (DMSP). An in silico model of the SBP domain of the TMD-SBP hybrid protein OpuFB was established. It revealed the presence of an aromatic cage, a structural feature commonly present in ligand-binding sites of compatible solute importers.IMPORTANCE The high-affinity import of compatible solutes from environmental sources is an important aspect of the cellular defense of many bacteria and archaea against the harmful effects of high external osmolarity. The accumulation of these osmostress protectants counteracts high-osmolarity-instigated water efflux, a drop in turgor to nonphysiological values, and an undue increase in molecular crowding of the cytoplasm; they thereby foster microbial growth under osmotically unfavorable conditions. Importers for compatible solutes allow the energy-preserving scavenging of osmoprotective and physiologically compliant organic solutes from environmental sources. We report here the discovery, exemplary physiological characterization, and phylogenomics of a new compatible solute importer, OpuF, widely found in members of the Bacillus genus. The OpuF system is a representative of a growing subgroup of ABC transporters in which the substrate-scavenging function of the substrate-binding protein (SBP) and the membrane-embedded substrate translocating subunit (TMD) are fused into a single polypeptide chain.

Homoarsenocholine - A novel arsenic compound detected for the first time in nature

The arsenic speciation was determined in macrofungi of the Ramaria genus with HPLC coupled to inductively coupled plasma mass spectrometry. Besides arsenic species that are already known for macrofungi, like arsenobetaine or arsenocholine, two compounds that were only known from marine samples so far (trimethylarsoniopropanate and dimethylarsinoylacetate) were found for the first time in a terrestrial sample. An unknown arsenical was isolated and identified as homoarsenocholine. This could be a key intermediate for further elucidation of the biotransformation mechanisms of arsenic.

Arsenic and high affinity phosphate uptake gene distribution in shallow submarine hydrothermal sediments

The toxicity of arsenic (As) towards life on Earth is apparent in the dense distribution of genes associated with As detoxification across the tree of life. The ability to defend against As is particularly vital for survival in As-rich shallow submarine hydrothermal ecosystems along the Hellenic Volcanic Arc (HVA), where life is exposed to hydrothermal fluids containing up to 3000 times more As than present in seawater. We propose that the removal of dissolved As and phosphorus (P) by sulfide and Fe(III)(oxyhydr)oxide minerals during sediment-seawater interaction, produces nutrient-deficient porewaters containing < 2.0 ppb P. The porewater arsenite-As(III) to arsenate-As(V) ratios, combined with sulfide concentration in the sediment and/or porewater, suggest a hydrothermally-induced seafloor redox gradient. This gradient overlaps with changing high affinity phosphate uptake gene abundance. High affinity phosphate uptake and As cycling genes are depleted in the sulfide-rich settings, relative to the more oxidizing habitats where mainly Fe(III)(oxyhydr)oxides are precipitated. In addition, a habitat-wide low As-respiring and As-oxidizing gene content relative to As resistance gene richness, suggests that As detoxification is prioritized over metabolic As cycling in the sediments. Collectively, the data point to redox control on Fe and S mineralization as a decisive factor in the regulation of high affinity phosphate uptake and As cycling gene content in shallow submarine hydrothermal ecosystems along the HVA.

Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics

Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.