@article{french_chukwuma_linshitz_namba_duckworth_cubeta_baars_2024, title={Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont <i>Pyrenophora biseptata</i>}, volume={1}, ISSN={["1758-2229"]}, url={https://doi.org/10.1111/1758-2229.13234}, DOI={10.1111/1758-2229.13234}, abstractNote={The wheat root symbiont fungus Pyrenophora biseptata degrades iron‐chelating groups in extracellular siderophores, forming weaker and more labile iron complexes. As a result, iron is expected to become available to plants and microbes that do not possess specialized siderophore uptake mechanisms.}, journal={ENVIRONMENTAL MICROBIOLOGY REPORTS}, author={French, Katie S. and Chukwuma, Emmanuel and Linshitz, Ilan and Namba, Kosuke and Duckworth, Owen W. and Cubeta, Marc A. and Baars, Oliver}, year={2024}, month={Jan} }
 @article{doydora_baars_cubeta_duckworth_urbieta_castro_2024, title={Using Manganese Oxidizing Fungi to Recover Metals from Electronic Waste}, volume={14}, ISSN={["2075-163X"]}, url={https://doi.org/10.3390/min14010111}, DOI={10.3390/min14010111}, abstractNote={Discarded electronic materials (e-waste) contain economically valuable metals that can be hazardous to people and the environment. Current e-waste recycling approaches involve either energy-intensive smelting or bioleaching processes that capture metals in their dissolved forms. Our study aimed to use Mn oxidizing fungi for recovering metals from e-waste that could potentially transform recycled metals directly into solid forms. We hypothesized that Mn oxidizing fungi can extract metals through chelation by siderophores and subsequent metal (or metal-chelate) adsorption to Mn oxides produced by fungi. Pure cultures of the three fungal species examined were grown on solidified Leptothrix medium with or without ground lithium ion batteries and incubated under ambient room temperature. The results showed Mn and Co were recovered at the highest concentrations of 8.45% and 1.75%, respectively, when grown with Paraconiothyrium brasiliensis, whereas the greatest concentration of Cu was extracted by Paraphaeosphaeria sporulosa at 20.6% per weight of e-waste-derived metals. Although metal-siderophore complexes were detected in the fungal growth medium, metal speciation data suggested that these complexes only occurred with Fe. This observation suggests that reactions other than complexation with siderophores likely solubilized e-waste metals. Elemental mapping, particularly of P. brasiliensis structures, showed a close association between Mn and Co, suggesting potential adsorption or (co)precipitation of these two metals near fungal mycelium. These findings provide experimental evidence for the potential use of Mn oxidizing fungi in recycling and transforming e-waste metals into solid biominerals. However, optimizing fungal growth conditions with e-waste is needed to improve the efficiency of metal recovery.}, number={1}, journal={MINERALS}, author={Doydora, Sarah A. and Baars, Oliver and Cubeta, Marc A. and Duckworth, Owen W. and Urbieta, Maria Sofia and Castro, Laura}, year={2024}, month={Jan} }
 @article{srivastava_dong_baars_sheng_2023, title={Bioavailability of mineral-associated trace metals as cofactors for nitrogen fixation by Azotobacter vinelandii}, volume={2}, ISSN={["1472-4669"]}, DOI={10.1111/gbi.12552}, abstractNote={Life on Earth depends on N2‐fixing microbes to make ammonia from atmospheric N2 gas by the nitrogenase enzyme. Most nitrogenases use Mo as a cofactor; however, V and Fe are also possible. N2 fixation was once believed to have evolved during the Archean‐Proterozoic times using Fe as a cofactor. However, δ15N values of paleo‐ocean sediments suggest Mo and V cofactors despite their low concentrations in the paleo‐oceans. This apparent paradox is based on an untested assumption that only soluble metals are bioavailable. In this study, laboratory experiments were performed to test the bioavailability of mineral‐associated trace metals to a model N2‐fixing bacterium Azotobacter vinelandii. N2 fixation was observed when Mo in molybdenite, V in cavansite, and Fe in ferrihydrite were used as the sole sources of cofactors, but the rate of N2 fixation was greatly reduced. A physical separation between minerals and cells further reduced the rate of N2 fixation. Biochemical assays detected five siderophores, including aminochelin, azotochelin, azotobactin, protochelin, and vibrioferrin, as possible chelators to extract metals from minerals. The results of this study demonstrate that mineral‐associated trace metals are bioavailable as cofactors of nitrogenases to support N2 fixation in those environments that lack soluble trace metals and may offer a partial answer to the paradox.}, journal={GEOBIOLOGY}, author={Srivastava, Shreya and Dong, Hailiang and Baars, Oliver and Sheng, Yizhi}, year={2023}, month={Feb} }
 @article{patil_klobasa_espinoza‐rivera_baars_lorenzen_scott_2023, title={Development of transgenic corn planthopper <scp><i>Peregrinus maidis}, volume={32}, ISSN={0962-1075 1365-2583}, url={http://dx.doi.org/10.1111/imb.12836}, DOI={10.1111/imb.12836}, abstractNote={The corn planthopper, Peregrinus maidis, is a vector of several maize viruses and is consequently a significant agricultural pest in many tropical and subtropical regions. As P. maidis has developed resistance to insecticides, the aim of this study was to develop transgenic P. maidis strains that could be used for future genetic biocontrol programs. To facilitate the identification of transgenic P. maidis, we isolated and characterized the promoters for the P. maidis ubiquitin‐like and profilin genes. Transient expression assays with P. maidis embryos showed that both promoters were active. Transgenic lines were established using piggyBac vectors and fluorescent protein marker genes. The lines carried an auto‐regulated tetracycline transactivator (tTA) gene, which has been widely used to establish conditional lethal strains in other insect species. The transgenic lines showed low levels of tTA expression but were viable on diet with or without doxycycline, which inhibits the binding of tTA to DNA. We discuss possible modifications to the tTA overexpression system that could lead to the successful development of conditional lethal strains. To our knowledge, this is the first report of a transgenic Hemiptera. The approach we have taken could potentially be applied to other Hemiptera and, for P. maidis, the technology will facilitate future functional genomics studies.}, number={4}, journal={Insect Molecular Biology}, publisher={Wiley}, author={Patil, Anandrao A. and Klobasa, William and Espinoza‐Rivera, Dina and Baars, Oliver and Lorenzen, Marcé D. and Scott, Maxwell J.}, year={2023}, month={Mar}, pages={363–375} }
 @article{egan_wang_shen_baars_moxley_salmon_2023, title={Enzymatic textile fiber separation for sustainable waste processing}, volume={13}, ISSN={["2666-9161"]}, url={https://doi.org/10.1016/j.resenv.2023.100118}, DOI={10.1016/j.resenv.2023.100118}, journal={RESOURCES ENVIRONMENT AND SUSTAINABILITY}, author={Egan, Jeannie and Wang, Siyan and Shen, Jialong and Baars, Oliver and Moxley, Geoffrey and Salmon, Sonja}, year={2023}, month={Sep} }
 @article{luu_little_pierce_morin_ertekin_wolfe_baars_dutton_sanchez_2023, title={Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms}, volume={5}, ISSN={["1364-5528"]}, url={https://doi.org/10.1039/D3AN00408B}, DOI={10.1039/D3AN00408B}, abstractNote={Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.}, journal={ANALYST}, author={Luu, Gordon T. T. and Little, Jessica C. C. and Pierce, Emily C. C. and Morin, Manon and Ertekin, Celine A. A. and Wolfe, Benjamin E. E. and Baars, Oliver and Dutton, Rachel J. J. and Sanchez, Laura M. M.}, year={2023}, month={May} }
 @article{sheng_baars_guo_whitham_srivastava_dong_2023, title={Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation}, volume={4}, ISSN={["1520-5851"]}, url={https://doi.org/10.1021/acs.est.3c01371}, DOI={10.1021/acs.est.3c01371}, abstractNote={Nitrogenase is the only known biological enzyme capable of reducing N2 to bioavailable NH3. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={Sheng, Yizhi and Baars, Oliver and Guo, Dongyi and Whitham, Jason and Srivastava, Shreya and Dong, Hailiang}, year={2023}, month={Apr} }
 @article{molo_white_cornish_gell_baars_singh_carbone_isakeit_wise_woloshuk_et al._2022, title={Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control}, volume={17}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0276556}, DOI={10.1371/journal.pone.0276556}, abstractNote={Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B 1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A . flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A . flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A . flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A . flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.}, number={10}, journal={PLOS ONE}, author={Molo, Megan S. and White, James B. and Cornish, Vicki and Gell, Richard M. and Baars, Oliver and Singh, Rakhi and Carbone, Mary Anna and Isakeit, Thomas and Wise, Kiersten A. and Woloshuk, Charles P. and et al.}, editor={Nierman, William C.Editor}, year={2022}, month={Oct} }
 @article{molo_white_cornish_gell_baars_singh_carbone_isakeit_wise_woloshuk_et al._2022, title={Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: implications for biological control}, volume={3}, url={https://doi.org/10.1101/2022.03.12.484001}, DOI={10.1101/2022.03.12.484001}, abstractNote={Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins (AFs), of which B1 is the most potent carcinogen known. In the US, the management of AFs includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard® (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.}, publisher={Cold Spring Harbor Laboratory}, author={Molo, Megan S. and White, James B. and Cornish, Vicki and Gell, Richard M and Baars, Oliver and Singh, Rakhi and Carbone, Mary Anna and Isakeit, Thomas and Wise, Kiersten A. and Woloshuk, Charles P. and et al.}, year={2022}, month={Mar} }
 @article{jackson_baars_belcher_2022, title={Gestational Cd Exposure in the CD-1 Mouse Sex-Specifically Disrupts Essential Metal Ion Homeostasis}, volume={2}, ISSN={["1096-0929"]}, url={https://doi.org/10.1093/toxsci/kfac027}, DOI={10.1093/toxsci/kfac027}, abstractNote={Abstract In CD-1 mice, gestational-only exposure to cadmium (Cd) causes female-specific hepatic insulin resistance, metabolic disruption, and obesity. To evaluate whether sex differences in uptake and changes in essential metal concentrations contribute to metabolic outcomes, placental and liver Cd and essential metal concentrations were quantified in male and female offspring perinatally exposed to 500 ppb CdCl2. Exposure resulted in increased maternal liver Cd+2 concentrations (364 µg/kg) similar to concentrations found in non-occupationally exposed human liver. At gestational day (GD) 18, placental Cd and manganese concentrations were significantly increased in exposed males and females, and zinc was significantly decreased in females. Placental efficiency was significantly decreased in GD18-exposed males. Increases in hepatic Cd concentrations and a transient prenatal increase in zinc were observed in exposed female liver. Fetal and adult liver iron concentrations were decreased in both sexes, and decreases in hepatic zinc, iron, and manganese were observed in exposed females. Analysis of GD18 placental and liver metallothionein mRNA expression revealed significant Cd-induced upregulation of placental metallothionein in both sexes, and a significant decrease in fetal hepatic metallothionein in exposed females. In placenta, expression of metal ion transporters responsible for metal ion uptake was increased in exposed females. In liver of exposed adult female offspring, expression of the divalent cation importer (Slc39a14/Zip14) decreased, whereas expression of the primary exporter (Slc30a10/ZnT10) increased. These findings demonstrate that Cd can preferentially cross the female placenta, accumulate in the liver, and cause lifelong dysregulation of metal ion concentrations associated with metabolic disruption.}, journal={TOXICOLOGICAL SCIENCES}, publisher={Oxford University Press (OUP)}, author={Jackson, Thomas W. and Baars, Oliver and Belcher, Scott M.}, year={2022}, month={Feb} }
 @article{probst_garcia-santamarina_brooks_kloet_baars_ralle_thiele_alspaugh_2022, title={Interactions between copper homeostasis and the fungal cell wall affect copper stress resistance}, volume={18}, ISSN={["1553-7374"]}, DOI={10.1371/journal.ppat.1010195}, abstractNote={Copper homeostasis mechanisms are essential for microbial adaption to changing copper levels within the host during infection. In the opportunistic fungal pathogen Cryptococcus neoformans (Cn), the Cn Cbi1/Bim1 protein is a newly identified copper binding and release protein that is highly induced during copper limitation. Recent studies demonstrated that Cbi1 functions in copper uptake through the Ctr1 copper transporter during copper limitation. However, the mechanism of Cbi1 action is unknown. The fungal cell wall is a dynamic structure primarily composed of carbohydrate polymers, such as chitin and chitosan, polymers known to strongly bind copper ions. We demonstrated that Cbi1 depletion affects cell wall integrity and architecture, connecting copper homeostasis with adaptive changes within the fungal cell wall. The cbi1Δ mutant strain possesses an aberrant cell wall gene transcriptional signature as well as defects in chitin / chitosan deposition and exposure. Furthermore, using Cn strains defective in chitosan biosynthesis, we demonstrated that cell wall chitosan modulates the ability of the fungal cell to withstand copper stress. Given the previously described role for Cbi1 in copper uptake, we propose that this copper-binding protein could be involved in shuttling copper from the cell wall to the copper transporter Ctr1 for regulated microbial copper uptake.}, number={6}, journal={PLOS PATHOGENS}, author={Probst, Corinna and Garcia-Santamarina, Sarela and Brooks, Jacob T. and Kloet, Inge and Baars, Oliver and Ralle, Martina and Thiele, Dennis J. and Alspaugh, J. Andrew}, year={2022}, month={Jun} }
 @article{jackson_baars_belcher_2021, title={Gestational Cd Exposure in the CD-1 Mouse Sex-Specifically Disrupts Essential Metal Ion Homeostasis}, volume={11}, url={https://doi.org/10.1101/2021.11.06.467551}, DOI={10.1101/2021.11.06.467551}, abstractNote={In CD-1 mice, gestational-only exposure to cadmium (Cd) causes female-specific hepatic insulin resistance, metabolic disruption, and obesity. To evaluate whether sex differences in cadmium uptake and changes in essential metal concentrations contribute to metabolic outcomes, placental and liver cadmium and essential metal concentrations were quantified in male and female offspring perinatally exposed to 500 ppb CdCl2. Exposure resulted in increased maternal liver Cd+2 concentrations (364 μg/kg) similar to concentrations found in non-occupationally exposed human liver. At gestational day (GD) 18, placental cadmium and manganese concentrations were significantly increased in exposed males and females, and zinc was significantly decreased in females. Placental efficiency was significantly decreased in GD18 exposed males. Increases in hepatic Cd concentrations and a transient prenatal increase in zinc were observed in exposed female liver. Fetal and adult liver iron concentrations were decreased in both sexes, and decreases in hepatic zinc, iron, and manganese were observed in exposed females. Analysis of GD18 placental and liver metallothionein mRNA expression revealed significant Cd-induced upregulation of placental metallothionein in both sexes, and a significant decrease in fetal hepatic metallothionein in exposed females. In placenta, expression of metal ion transporters responsible for metal ion uptake was increased in exposed females. In liver of exposed adult female offspring, expression of the divalent cation importer (Slc39a14/Zip14) decreased, whereas expression of the primary exporter (Slc30a10) increased. These findings demonstrate that Cd can preferentially cross the female placenta, accumulate in the liver, and cause lifelong dysregulation of metal ion concentrations associated with metabolic disruption.}, publisher={Cold Spring Harbor Laboratory}, author={Jackson, Thomas W. and Baars, Oliver and Belcher, Scott M.}, year={2021}, month={Nov} }
 @article{doydora_baars_harrington_duckworth_2021, title={Salicylate coordination in metal-protochelin complexes}, volume={11}, ISSN={["1572-8773"]}, DOI={10.1007/s10534-021-00352-7}, abstractNote={["Molybdenum (Mo) is an essential trace element for bacteria that is utilized in myriad metalloenzymes that directly couple to the biogeochemical cycling of nitrogen, sulfur, and carbon. In particular, Mo is found in the most common nitrogenase enzyme, and the scarcity and low bioavailability of Mo in soil may be a critical factor that contributes to the limitation of nitrogen fixation in forests and agroenvironments. To overcome this scarcity, microbes produce exudates that specifically chelate scarce metals, promoting their solubilization and uptake. Here, we have determined the structure and stability constants of Mo bound by protochelin, a siderophore produced by bacteria under Mo-depleted conditions. Spectrophotometric titration spectra indicated a coordination shift from a catecholate to salicylate binding mode for Mo", {:sup=>"VI"}, "-protochelin (Mo-Proto) complexes at pH < 5. pKa values obtained from analysis of titrations were 4.8 ± 0.3 for Mo", {:sup=>"VI"}, "O", {:sub=>"2"}, "H", {:sub=>"3"}, "Proto", {:sup=>"-"}, " and 3.3 ± 0.1 for Mo", {:sup=>"VI"}, "O", {:sub=>"2"}, "H", {:sub=>"4"}, "Proto. The occurrence of negatively charged Mo-Proto complexes at pH 6 was also confirmed by mass spectrometry. K-edge Extended X-ray absorption fine structure spectroscopy confirmed the change in Mo coordination at low pH, and structural fitting provides insights into the physical architecture of complexes at neutral and acidic pH. These findings suggest that Mo can be chelated by protochelin across a wide environmental pH range, with a coordination shift occurring at pH < 5. This chelation and associated coordination shift may impact biological availability and mineral surface retention of Mo under acidic conditions."]}, journal={BIOMETALS}, author={Doydora, Sarah A. and Baars, Oliver and Harrington, James M. and Duckworth, Owen W.}, year={2021}, month={Nov} }
 @article{reyes_hodgskiss_baars_kerou_bayer_schleper_kraemer_2020, title={Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis}, volume={171}, ISSN={["1769-7123"]}, DOI={10.1016/j.resmic.2020.01.003}, abstractNote={Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N′, N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10−15 mol L−1 free Cu2+ compared to standard conditions (10−12 mol L−1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10−16 mol L−1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10−12.7 mol L−1), which also possesses a high amount of Cu-dependent enzymes.}, number={3-4}, journal={RESEARCH IN MICROBIOLOGY}, author={Reyes, Carolina and Hodgskiss, Logan H. and Baars, Oliver and Kerou, Melina and Bayer, Barbara and Schleper, Christa and Kraemer, Stephan M.}, year={2020}, pages={134–142} }
 @article{rai_fisher_duckworth_baars_2020, title={Extraction and Detection of Structurally Diverse Siderophores in Soil}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.581508}, abstractNote={Although the biochemistry of bacterial and fungal siderophores has been intensively studied in laboratory cultures, their distribution and impacts on nutrient cycling and microbial communities in soils remain poorly understood. The detection of siderophores in soil is an analytical challenge because of the complexity of the soil matrix and their structural diversity. Liquid chromatography-mass spectrometry (LC-MS) is a suitable method for the sensitive analysis of siderophores in complex samples; however, siderophore extraction into liquid phases for analysis by LC-MS is problematic because of their adsorption to soil particles and organic matter. To determine extraction efficiencies of structurally diverse siderophores, spike-recovery experiments were set up with standards representing the three main siderophore classes: the hydroxamate desferrioxamine B (DFOB), the α-hydroxycarboxylate rhizoferrin, and the catecholate protochelin. Previously used solvent extractions with water or methanol recovered only a small fraction (< 35%) of siderophores, including < 5% for rhizoferrin and protochelin. We designed combinatorial chemical extractions (22 total solutions) to target siderophores associated with different soil components. A combination of calcium chloride and ascorbate achieved high and, for some soils, quantitative extraction of DFOB and rhizoferrin. Protochelin analysis was complicated by potential fast oxidation and interactions with colloidal soil components. Using the optimized extraction method, we detected α-hydroxycarboxylate type siderophores (viz. rhizoferrin, vibrioferrin, and aerobactin) in soil for the first time. Concentrations reached 461 pmol g–1, exceeding previously reported concentrations of siderophores in soil and suggesting a yet unrecognized importance of α-hydroxycarboxylate siderophores for biological interactions and biogeochemical processes in soil.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Rai, Vineeta and Fisher, Nathaniel and Duckworth, Owen W. and Baars, Oliver}, year={2020}, month={Sep} }
 @article{liang_lau_baars_robb_onstott_2019, title={Aspartic acid racemization constrains long-term viability and longevity of endospores}, volume={95}, ISSN={0168-6496 1574-6941}, url={http://dx.doi.org/10.1093/femsec/fiz132}, DOI={10.1093/femsec/fiz132}, abstractNote={Certain microorganisms survive long periods of time as endospores to cope with adverse conditions. Since endospores are metabolically inactive the extent of aspartic acid (Asp) racemization will increase over time and might kill the spores by preventing their germination. Therefore, understanding the relationship between endospore survivability and Asp racemization is important for constraining the long-term survivability and global dispersion of spore-forming bacteria in nature. Geobacillus stearothermophilus was selected as a model organism to investigate racemization kinetics and survivability of its endospores at 65°C, 75°C and 98°C. This study found that the Asp racemization rates of spores and autoclaved spores were similar at all temperatures. The Asp racemization rate of spores was not significantly different from that of vegetative cells at 65°C. The Asp racemization rate of G. stearothermophilus spores was not significantly different from that of Bacillus subtilis spores at 98°C. The viability of spores and vegetative cells decreased dramatically over time, and the mortality of spores correlated exponentially with the degree of racemization (R2 = 0.9). This latter correlation predicts spore half-lives on the order of hundreds of years for temperatures typical of shallow marine sediments, a result consistent with studies about the survivability of thermophilic spores found in these environments.}, number={10}, journal={FEMS Microbiology Ecology}, publisher={Oxford University Press (OUP)}, author={Liang, Renxing and Lau, Maggie C Y and Baars, Oliver and Robb, Frank T and Onstott, Tullis C}, year={2019}, month={Aug} }
 @article{mcrose_lee_kopf_baars_kraepiel_sigman_morel_zhang_2019, title={Effect of iron limitation on the isotopic composition of cellular and released fixed nitrogen in Azotobacter vinelandii}, volume={244}, ISSN={["1872-9533"]}, DOI={10.1016/j.gca.2018.09.023}, abstractNote={Abstract Most biological nitrogen transformations have characteristic kinetic isotope effects used to track these processes in modern and past environments. The isotopic fractionation associated with nitrogen fixation, the only biological source of fixed nitrogen (N), provides a particularly important constraint for studies of nitrogen cycling. Nitrogen fixation using the ‘canonical’ Mo-nitrogenase produces biomass with a δ15N value of ca. −1‰ (vs. atmospheric N2). If the ‘alternative’ V- and Fe-only nitrogenases are used, biomass δ15N can be between −6‰ and −7‰. These biomass values are assumed to be relatively invariant and to reflect the cellular level expressed isotope effect of nitrogen fixation. However, field and laboratory studies report wide ranges of diazotrophic biomass δ15N (from −3.6‰ to +0.5‰ for Mo-based nitrogen fixation). This variation could be partly explained by the release of dissolved organic N (DON) that is isotopically distinct from biomass. The model nitrogen fixer Azotobacter vinelandii secretes siderophores, small molecules that aid in Fe uptake and can comprise >30% of fixed nitrogen. To test whether siderophores (and other released N) can decouple biomass δ15N from the isotope effect of nitrogen fixation we measured the isotopic composition of biomass and released N in Fe-limited A. vinelandii cultures fixing nitrogen with Mo- and V-nitrogenases. We report that biomass δ15N was elevated under Fe limitation with a maximum value of +1.2‰ for Mo-based nitrogen fixation. Regardless of the nitrogenase isozyme used, released nitrogen δ15N was also 2–3‰ lower than biomass δ15N. Siderophore nitrogen was found to have a slightly higher δ15N than the rest of the DON pool but was still produced in large enough concentrations to account for increases in biomass δ15N. The low δ15N of siderophores (relative to biomass) is consistent with what is known from compound specific isotope studies of the amino acids used in siderophore biosynthesis, and indicates that other amino-acid derived siderophores should also have a low δ15N. The implications for studies of nitrogen fixation are discussed.}, journal={GEOCHIMICA ET COSMOCHIMICA ACTA}, author={McRose, D. L. and Lee, A. and Kopf, S. H. and Baars, O. and Kraepiel, A. M. L. and Sigman, D. M. and Morel, F. M. M. and Zhang, X.}, year={2019}, month={Jan}, pages={12–23} }
 @article{zhang_baars_morel_2019, title={Genetic, structural, and functional diversity of low and high-affinity siderophores in strains of nitrogen fixing Azotobacter chroococcum}, volume={11}, ISSN={1756-5901 1756-591X}, url={http://dx.doi.org/10.1039/c8mt00236c}, DOI={10.1039/c8mt00236c}, abstractNote={To increase iron (Fe) bioavailability in surface soils, microbes secrete siderophores, chelators with widely varying Fe affinities. Strains of the soil bacterium Azotobacter chroococcum (AC), plant-growth promoting rhizobacteria used as agricultural inoculants, require high Fe concentrations for aerobic respiration and nitrogen fixation. Recently, A. chroococcum str. NCIMB 8003 was shown to synthesize three siderophore classes: (1) vibrioferrin, a low-affinity α-hydroxy carboxylate (pFe = 18.4), (2) amphibactins, high-affinity tris-hydroxamates, and (3) crochelin A, a high-affinity siderophore with mixed Fe-chelating groups (pFe = 23.9). The relevance and specific functions of these siderophores in AC strains remain unclear. We analyzed the genome and siderophores of a second AC strain, A. chroococcum str. B3, and found that it also produces vibrioferrin and amphibactins, but not crochelin A. Genome comparisons indicate that vibrioferrin production is a vertically inherited, conserved strategy for Fe uptake in A. chroococcum and other species of Azotobacter. Amphibactin and crochelin biosynthesis reflects a more complex evolutionary history, shaped by vertical gene transfer, gene gain and loss through recombination at a genomic hotspot. We found conserved patterns of low vs. high-affinity siderophore production across strains: the low-affinity vibrioferrin was produced by mildly Fe limited cultures. As cells became more severely Fe starved, vibrioferrin production decreased in favor of high-affinity amphibactins (str. B3, NCIMB 8003) and crochelin A (str. NCIMB 8003). Our results show the evolution of low and high-affinity siderophore families and conserved patterns for their production in response to Fe bioavailability in a common soil diazotroph.}, number={1}, journal={Metallomics}, publisher={Royal Society of Chemistry (RSC)}, author={Zhang, Xinning and Baars, Oliver and Morel, François M. M.}, year={2019}, pages={201–212} }
 @article{mcrose_baars_seyedsayamdost_morel_2018, title={Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi}, volume={115}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1805791115}, DOI={10.1073/pnas.1805791115}, abstractNote={Significance Siderophores are small molecules used by microbes to acquire the essential metal Fe in environments ranging from infections to the open ocean. Although many bacteria use quorum sensing (QS) to regulate siderophore production, the resulting siderophore concentrations and their utility for Fe uptake have been underexplored. We report that Vibrio harveyi uses a “two-for-one,” QS- and Fe-repressed gene cluster to produce cell-associated siderophores at low cell density and accumulate soluble siderophores at high cell density. Fe-uptake experiments show that these soluble siderophores are used in Fe acquisition. We also find that QS repression helps prevent the accumulation of siderophore concentrations in excess of cellular uptake capacities, an explanation that may be generalizable to other bacteria. The secretion of small Fe-binding molecules called siderophores is an important microbial strategy for survival in Fe-limited environments. Siderophore production is often regulated by quorum sensing (QS), a microbial counting technique that allows organisms to alter gene expression based on cell density. However, the identity and quantities of siderophores produced under QS regulation are rarely studied in the context of their roles in Fe uptake. We investigated the link between QS, siderophores, and Fe uptake in the model marine organism Vibrio harveyi where QS is thought to repress siderophore production. We find that V. harveyi uses a single QS- and Fe-repressed gene cluster to produce both cell-associated siderophores (amphiphilic enterobactins) as well as several related soluble siderophores, which we identify and quantify using liquid chromatography-coupled (LC)-MS as well as tandem high-resolution MS (LC-HR-MS/MS). Measurements of siderophore production show that soluble siderophores are present at ∼100× higher concentrations than amphi-enterobactin and that over the course of growth V. harveyi decreases amphi-enterobactin concentrations but accumulates soluble siderophores. 55Fe radio-tracer uptake experiments demonstrate that these soluble siderophores play a significant role in Fe uptake and that the QS-dictated concentrations of soluble siderophores in stationary phase are near the limit of cellular uptake capacities. We propose that cell-associated and soluble siderophores are beneficial to V. harveyi in different environmental and growth contexts and that QS allows V. harveyi to exploit “knowledge” of its population size to avoid unnecessary siderophore production.}, number={29}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={McRose, Darcy L. and Baars, Oliver and Seyedsayamdost, Mohammad R. and Morel, François M. M.}, year={2018}, month={Jun}, pages={7581–7586} }
 @article{schlitzer_anderson_dodas_lohan_geibere_tagliabue_bowie_jeandel_maldonado_landing_et al._2018, title={The GEOTRACES Intermediate Data Product 2017}, volume={493}, ISSN={["1872-6836"]}, DOI={10.1016/j.chemgeo.2018.05.040}, abstractNote={The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: "Cycles of trace elements and isotopes in the ocean – GEOTRACES and beyond" - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González.}, journal={CHEMICAL GEOLOGY}, author={Schlitzer, Reiner and Anderson, Robert F. and Dodas, Elena Masferrer and Lohan, Maeve and Geibere, Walter and Tagliabue, Alessandro and Bowie, Andrew and Jeandel, Catherine and Maldonado, Maria T. and Landing, William M. and et al.}, year={2018}, month={Aug}, pages={210–223} }
 @article{baars_morel_zhang_2018, title={The purple non-sulfur bacterium Rhodopseudomonas palustris produces novel petrobactin-related siderophores under aerobic and anaerobic conditions}, volume={20}, ISSN={["1462-2920"]}, url={https://doi.org/10.1111/1462-2920.14078}, DOI={10.1111/1462-2920.14078}, abstractNote={Many bacteria produce siderophores to bind and take up Fe(III), an essential trace metal with extremely low solubility in oxygenated environments at circumneutral pH. The purple non-sulfur bacterium Rhodopseudomonas palustris str. CGA009 is a metabolically versatile model organism with high iron requirements that is able to grow under aerobic and anaerobic conditions. Siderophore biosynthesis has been predicted by genomic analysis, however, siderophore structures were not identified. Here, we elucidate the structure of two novel siderophores from R. palustris: rhodopetrobactin A and B. Rhodopetrobactins are structural analogues of the known siderophore petrobactin in which the Fe chelating moieties are conserved, including two 3,4-dihydroxybenzoate and a citrate substructure. In the place of two spermidine linker groups in petrobactin, rhodopetrobactins contain two 4,4'-diaminodibutylamine groups of which one or both are acetylated at the central amine. We analyse siderophore production under different growth modes and show that rhodopetrobactins are produced in response to Fe limitation under aerobic as well as under anaerobic conditions. Evaluation of the chemical characteristics of rhodopetrobactins indicates that they are well suited to support Fe acquisition under variable oxygen and light conditions.}, number={5}, journal={ENVIRONMENTAL MICROBIOLOGY}, publisher={Wiley}, author={Baars, Oliver and Morel, Francois M. M. and Zhang, Xinning}, year={2018}, month={May}, pages={1667–1676} }
 @article{baars_zhang_gibson_stone_morel_seyedsayamdost_2017, title={Crochelins, siderophores with a novel iron-chelating moiety from the nitrogen-fixing bacterium Azotobacter chroococcum}, volume={11}, DOI={10.1002/ange.201709720}, abstractNote={Abstract Microbes use siderophores to access essential iron resources in the environment. Over 500 siderophores are known, but they utilize a small set of common moieties to bind iron. Azotobacter chroococcum expresses iron‐rich nitrogenases, with which it reduces N 2 . Though an important agricultural inoculant, the structures of its iron‐binding molecules remain unknown. Here, the “chelome” of A. chroococcum is examined using small molecule discovery and bioinformatics. The bacterium produces vibrioferrin and amphibactins as well as a novel family of siderophores, the crochelins. Detailed characterization shows that the most abundant member, crochelin A, binds iron in a hexadentate fashion using a new iron‐chelating γ‐amino acid. Insights into the biosynthesis of crochelins and the mechanism by which iron may be removed upon import of the holo‐siderophore are presented. This work expands the repertoire of iron‐chelating moieties in microbial siderophores.}, journal={Angewandte Chemie}, publisher={Wiley-Blackwell}, author={Baars, Oliver and Zhang, Xinning and Gibson, Marcus I. and Stone, Alan T. and Morel, Francois M. M. and Seyedsayamdost, Mohammad R.}, year={2017}, month={Nov} }
 @article{baars_zhang_gibson_stone_morel_seyedsayamdost_2017, title={Crochelins: Siderophores with an Unprecedented Iron-Chelating Moiety from the Nitrogen-Fixing Bacterium Azotobacter chroococcum}, volume={57}, ISSN={1433-7851}, url={http://dx.doi.org/10.1002/anie.201709720}, DOI={10.1002/anie.201709720}, abstractNote={Microbes use siderophores to access essential iron resources in the environment. Over 500 siderophores are known, but they utilize a small set of common moieties to bind iron. Azotobacter chroococcum expresses iron-rich nitrogenases, with which it reduces N2 . Though an important agricultural inoculant, the structures of its iron-binding molecules remain unknown. Here, the "chelome" of A. chroococcum is examined using small molecule discovery and bioinformatics. The bacterium produces vibrioferrin and amphibactins as well as a novel family of siderophores, the crochelins. Detailed characterization shows that the most abundant member, crochelin A, binds iron in a hexadentate fashion using a new iron-chelating γ-amino acid. Insights into the biosynthesis of crochelins and the mechanism by which iron may be removed upon import of the holo-siderophore are presented. This work expands the repertoire of iron-chelating moieties in microbial siderophores.}, number={2}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Baars, Oliver and Zhang, Xinning and Gibson, Marcus I. and Stone, Alan T. and Morel, François M. M. and Seyedsayamdost, Mohammad R.}, year={2017}, month={Dec}, pages={536–541} }
 @article{mcrose_baars_morel_kraepiel_2017, title={Siderophore production in Azotobacter vinelandii in response to Fe-, Mo- and V-limitation}, volume={19}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85029385186&partnerID=MN8TOARS}, DOI={10.1111/1462-2920.13857}, abstractNote={Azotobacter vinelandii is a terrestrial diazotroph well studied for its siderophore production capacity and its role as a model nitrogen fixer. In addition to Fe, A. vinelandii siderophores are used for the acquisition of the nitrogenase co-factors Mo and V. However, regulation of siderophore production by Mo- and V-limitation has been difficult to confirm and knowledge of the full suite of siderophores synthesized by this organism has only recently become available. Using this new information, we conducted an extensive study of siderophore production in N2 -fixing A. vinelandii under a variety of trace metal conditions. Our results show that under Fe-limitation the production of all siderophores increases, while under Mo-limitation only catechol siderophore production is increased, with the strongest response seen in protochelin. We also find that the newly discovered A. vinelandii siderophore vibrioferrin is almost completely repressed under Mo- and V-limitation. An examination of the potential nitrogen 'cost' of siderophore production reveals that investments in siderophore N can represent as much as 35% of fixed N, with substantial differences between cultures using the Mo- as opposed to the less efficient V-nitrogenase.}, number={9}, journal={Environmental Microbiology}, author={McRose, D.L. and Baars, O. and Morel, F.M.M. and Kraepiel, A.M.L.}, year={2017}, pages={3595–3605} }
 @article{hellmer_rhein_heinemann_abalichin_abouchami_baars_cubasch_dethloff_ebner_fahrbach_et al._2016, title={Meteorology and oceanography of the Atlantic sector of the Southern Ocean—a review of German achievements from the last decade}, url={http://dx.doi.org/10.1007/s10236-016-0988-1}, DOI={10.1007/s10236-016-0988-1}, abstractNote={In the early 1980s, Germany started a new era of modern Antarctic research. The Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI) was founded and important research platforms such as the German permanent station in Antarctica, today called Neumayer III, and the research icebreaker Polarstern were installed. The research primarily focused on the Atlantic sector of the Southern Ocean. In parallel, the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) started a priority program ‘Antarctic Research’ (since 2003 called SPP-1158) to foster and intensify the cooperation between scientists from different German universities and the AWI as well as other institutes involved in polar research. Here, we review the main findings in meteorology and oceanography of the last decade, funded by the priority program. The paper presents field observations and modelling efforts, extending from the stratosphere to the deep ocean. The research spans a large range of temporal and spatial scales, including the interaction of both climate components. In particular, radiative processes, the interaction of the changing ozone layer with large-scale atmospheric circulations, and changes in the sea ice cover are discussed. Climate and weather forecast models provide an insight into the water cycle and the climate change signals associated with synoptic cyclones. Investigations of the atmospheric boundary layer focus on the interaction between atmosphere, sea ice and ocean in the vicinity of polynyas and leads. The chapters dedicated to polar oceanography review the interaction between the ocean and ice shelves with regard to the freshwater input and discuss the changes in water mass characteristics, ventilation and formation rates, crucial for the deepest limb of the global, climate-relevant meridional overturning circulation. They also highlight the associated storage of anthropogenic carbon as well as the cycling of carbon, nutrients and trace metals in the ocean with special emphasis on the Weddell Sea.}, author={Hellmer, Hartmut H. and Rhein, Monika and Heinemann, Günther and Abalichin, Janna and Abouchami, Wafa and Baars, Oliver and Cubasch, Ulrich and Dethloff, Klaus and Ebner, Lars and Fahrbach, Eberhard and et al.}, year={2016} }
 @article{baars_perlman_2016, title={Small Molecule LC-MS/MS Fragmentation Data Analysis and Application to Siderophore Identification}, DOI={10.5772/63018}, abstractNote={Rapid developments in tandem liquid chromatography-mass spectrometry (LC- MS/MS) have created wide interest in applications for the analysis of small molecule mixtures. MS/MS spectra can contain rich structural information, but because of the structural diversity of small molecules and different data acquisition methods, analysis algorithms and workflows frequently need to be tailored to individual research questions. This chapter shows how MATLAB can be used for LC-MS/MS-based structural characterization of small molecules. Starting with the import of raw data, ways for visualization and the creation of graphical user interfaces (GUIs) for individ‐ ual applications are demonstrated. A selection of frequently used algorithms for pre- processing and data analysis is reviewed in context of their MATLAB implementation. The approaches are then tailored and applied to the analysis of iron-binding peptides (peptidic siderophores) by high-resolution LC-MS/MS. The method uses a database with siderophore structures to exploit prior knowledge about siderophore structural diversity for the interpretation of MS/MS spectra from known and new siderophores.}, journal={Applications from Engineering with MATLAB Concepts}, publisher={InTech}, author={Baars, Oliver and Perlman, David H.}, year={2016}, month={Jul} }
 @article{kim_baars_morel_2016, title={The effect of acidifcation on the bioavailability and electrochemical lability of zinc in seawater}, volume={374}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84992346110&partnerID=MN8TOARS}, DOI={10.1098/rsta.2015.0296}, abstractNote={A poorly studied but potentially important consequence of the CO2-induced acidification of the surface ocean is a possible change in the bioavailability of trace metals, which play a critical role in the productivity and population dynamics of marine ecosystems. We report laboratory and field experiments designed to compare quantitatively the effects of acidification on the bioavailability of Zn, a metal essential to the growth of phytoplankton and on the extent of its complexation by model and natural ligands. We observed a good correspondence between the effects of pH on the rate of Zn uptake by a model diatom and the chemical lability of Zn measured by anodic stripping voltammetry (ASV). In model laboratory systems, the chemical lability and the bioavailability of Zn could either increase or decrease at low pH depending on the mix of complexing ligands. In a sample of coastal surface water, we observed similar increases in the ASV-labile and bioavailable Zn concentrations upon acidification, a result contrary to previous observations. These results, which can likely be generalized to other bioactive trace metals, mutatis mutandis, demonstrate the intricacy of the effects of ocean acidification on the chemistry and the ecology of surface seawater. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’.}, number={2081}, journal={Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, author={Kim, J.-M. and Baars, O. and Morel, F.M.M.}, year={2016} }
 @article{kim_baars_morel_2015, title={Bioavailability and Electroreactivity of Zinc Complexed to Strong and Weak Organic Ligands}, volume={49}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84941710645&partnerID=MN8TOARS}, DOI={10.1021/acs.est.5b02098}, abstractNote={Laboratory experiments have established the importance of complexation by organic ligands in determining the bioavailability of trace metals to marine phytoplankton, while electrochemical measurements with field samples have demonstrated that a large fraction of bioactive trace metals are complexed to strong organic ligands in seawater. Using the model organic ligands, EDTA and histidine, we show a quantitative correspondence between the bioavailability of Zn to the diatom Thalassiosira weissflogii, and its reduction at -1.2 V (vs Ag/AgCl) on a hanging mercury drop electrode. Equilibrium calculations and polarographic data indicate that Zn bound in inorganic complexes and the 1:1 Zn-histidine complex, but not in the 1:2 Zn-histidine complex or the Zn-EDTA complexes, is taken up by the organism and reduced at the electrode surface, confirming a previous report of the bioavailability of weak Zn complexes. Electrochemical measurements of Zn speciation in seawater do not generally reveal the presence of weak (and potentially bioavailable) complexes; but such measurements (particularly by Anodic Stripping Voltammetry) should nonetheless often provide good estimates of the bioavailable Zn concentrations. These results can likely be generalized to other bioactive divalent trace metals.}, number={18}, journal={Environmental Science and Technology}, author={Kim, J.-M. and Baars, O. and Morel, F.M.M.}, year={2015}, pages={10894–10902} }
 @article{baars_croot_2015, title={Dissolved cobalt speciation and reactivity in the eastern tropical North Atlantic}, volume={173}, DOI={10.1016/j.marchem.2014.10.006}, abstractNote={Recent studies highlight the role of cobalt (Co) as an important micro-nutrient with a complex scavenged type oceanic distribution. To better understand the biogeochemical cycle of Co we investigate the distribution, speciation and reactivity of dissolved Co in the eastern tropical North Atlantic in the upper 800 m of the water column. For this purpose, we complement classical Co ligand titrations that require a thermodynamic equilibrium with evaluations of ligand-exchange kinetics and reducibility of potential Co(III) species. The experiments include additions of the artificial Co binding ligands dimethylglyoxime or Nioxime and detection by cathodic stripping voltammetry. We find two pools of Co compounds: a labile fraction that exchanges Co within minutes and a strong/inert fraction that does not react within a 24-h period. No intermediate, slowly exchanging fraction is observed. Detection window experiments to determine complex stability constants show that the labile Co fraction is weak and likely consists of Co(II) complexes with no detectable free Co(II) ligands. The fraction of inert Co is always highest at the depth of the chlorophyll-a maximum. Addition of the reductant ascorbate increases the fraction of Co with rapid ligand-exchange kinetics and indicates the presence of dissolved reducible Co(III). The apparent Co(III) reducibility is highest at the chlorophyll-a maximum and decreases in deeper waters. Our results are in agreement with phytoplankton and associated bacteria being a source of Co(III) species, such as vitamin B12. The presented results have important implications for our understanding of the biological availability and the marine cycle of Co.}, journal={Marine Chemistry}, publisher={Elsevier BV}, author={Baars, Oliver and Croot, Peter L.}, year={2015}, month={Jul}, pages={310–319} }
 @article{pizeta_sander_hudson_omanovic_baars_barbeau_buck_bundy_carrasco_croot_et al._2015, title={Interpretation of complexometric titration data: An intercomparison of methods for estimating models of trace metal complexation by natural organic ligands}, url={http://oceanrep.geomar.de/28528/}, DOI={10.1016/j.marchem.2015.03.006}, abstractNote={With the common goal of more accurately and consistently quantifying ambient concentrations of free metal ions and natural organic ligands in aquatic ecosystems, researchers from 15 laboratories that routinely analyze trace metal speciation participated in an intercomparison of statistical methods used to model their most common type of experimental dataset, the complexometric titration. All were asked to apply statistical techniques that they were familiar with to model synthetic titration data that are typical of those obtained by applying state-of-the-art electrochemical methods – anodic stripping voltammetry (ASV) and competitive ligand equilibration-adsorptive cathodic stripping voltammetry (CLE-ACSV) – to the analysis of natural waters. Herein, we compare their estimates for parameters describing the natural ligands, examine the accuracy of inferred ambient free metal ion concentrations ([Mf]), and evaluate the influence of the various methods and assumptions used on these results. The ASV-type titrations were designed to test each participant's ability to correctly describe the natural ligands present in a sample when provided with data free of measurement error, i.e., random noise. For the three virtual samples containing just one natural ligand, all participants were able to correctly identify the number of ligand classes present and accurately estimate their parameters. For the four samples containing two or three ligand classes, a few participants detected too few or too many classes and consequently reported inaccurate ‘measurements’ of ambient [Mf]. Since the problematic results arose from human error rather than any specific method of analyzing the data, we recommend that analysts should make a practice of using one's parameter estimates to generate simulated (back-calculated) titration curves for comparison to the original data. The root–mean–squared relative error between the fitted observations and the simulated curves should be comparable to the expected precision of the analytical method and upon visual inspection the distribution of residuals should not be skewed. Modeling the synthetic, CLE-ACSV-type titration dataset, which comprises 5 titration curves generated at different analytical windows or levels of competing ligand added to the virtual sample, proved to be more challenging due to the random measurement error that was incorporated. Comparison of the submitted results was complicated by the participants' differing interpretations of their task. Most adopted the provided ‘true’ instrumental sensitivity in modeling the CLE-ACSV curves, but several estimated sensitivities using internal calibration, exactly as is required for actual samples. Since most fitted sensitivities were biased low, systematic error in inferred ambient [Mf] and in estimated weak ligand (L2) concentrations resulted. The main distinction between the mathematical approaches taken by participants lies in the functional form of the speciation model equations, with their implicit definition of independent and dependent or manipulated variables. In ‘direct modeling’, the dependent variable is the measured [Mf] (or Ip) and the total metal concentration ([M]T) is considered independent. In other, much more widely used methods of analyzing titration data – classical linearization, best known as van den Berg/Ružić, and isotherm fitting by nonlinear regression, best known as the Langmuir or Gerringa methods – [Mf] is defined as independent and the dependent variable calculated from both [M]T and [Mf]. Close inspection of the biases and variability in the estimates of ligand parameters and in predictions of ambient [Mf] revealed that the best results were obtained by the direct approach. Linear regression of transformed data yielded the largest bias and greatest variability, while non-linear isotherm fitting generated results with mean bias comparable to direct modeling, but also with greater variability. Participants that performed a unified analysis of ACSV titration curves at multiple detection windows for a sample improved their results regardless of the basic mathematical approach taken. Overall, the three most accurate sets of results were obtained using direct modeling of the unified multiwindow dataset, while the single most accurate set of results also included simultaneous calibration. We therefore recommend that where sample volume and time permit, titration experiments for all natural water samples be designed to include two or more detection windows, especially for coastal and estuarine waters. It is vital that more practical experimental designs for multi-window titrations be developed. Finally, while all mathematical approaches proved to be adequate for some datasets, matrix-based equilibrium models proved to be most naturally suited for the most challenging cases encountered in this work, i.e., experiments where the added ligand in ACSV became titrated. The ProMCC program (Omanović et al., this issue) as well as the Excel Add-in based KINETEQL Multiwindow Solver spreadsheet (Hudson, 2014) have this capability and have been made available for public use as a result of this intercomparison exercise.}, author={Pizeta, I. and Sander, S. G. and Hudson, R. J. M. and Omanovic, D. and Baars, O. and Barbeau, K. A. and Buck, K. N. and Bundy, R. M. and Carrasco, G. and Croot, Peter and et al.}, year={2015} }
 @article{the geotraces group: mawji_schlitzer_masferrer dodas_abadie_abouchami_anderson_baars_bakker_2015, title={The GEOTRACES Intermediate Data Product 2014}, url={http://www.sciencedirect.com/science/article/pii/S0304420315000997}, DOI={10.1016/j.marchem.2015.04.005}, abstractNote={The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes.}, author={The GEOTRACES Group: Mawji, E. and Schlitzer, R. and Masferrer Dodas, E. and Abadie, C. and Abouchami, W. and Anderson, R.F. and Baars, O. and Bakker, K.; Baskaran}, year={2015} }
 @article{baars_zhang_morel_seyedsayamdost_2015, title={The Siderophore Metabolome of Azotobacter vinelandii}, volume={82}, DOI={10.1128/aem.03160-15}, abstractNote={ABSTRACT In this study, we performed a detailed characterization of the siderophore metabolome, or “chelome,” of the agriculturally important and widely studied model organism Azotobacter vinelandii. Using a new high-resolution liquid chromatography-mass spectrometry (LC-MS) approach, we found over 35 metal-binding secondary metabolites, indicative of a vast chelome in A. vinelandii. These include vibrioferrin, a siderophore previously observed only in marine bacteria. Quantitative analyses of siderophore production during diazotrophic growth with different sources and availabilities of Fe showed that, under all tested conditions, vibrioferrin was present at the highest concentration of all siderophores and suggested new roles for vibrioferrin in the soil environment. Bioinformatic searches confirmed the capacity for vibrioferrin production in Azotobacter spp. and other bacteria spanning multiple phyla, habitats, and lifestyles. Moreover, our studies revealed a large number of previously unreported derivatives of all known A. vinelandii siderophores and rationalized their origins based on genomic analyses, with implications for siderophore diversity and evolution. Together, these insights provide clues as to why A. vinelandii harbors multiple siderophore biosynthesis gene clusters. Coupled with the growing evidence for alternative functions of siderophores, the vast chelome in A. vinelandii may be explained by multiple, disparate evolutionary pressures that act on siderophore production.}, number={1}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Baars, Oliver and Zhang, Xinning and Morel, François M. M. and Seyedsayamdost, Mohammad R.}, editor={Kivisaar, M.Editor}, year={2015}, month={Oct}, pages={27–39} }
 @article{baars_morel_perlman_2014, title={ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS}, volume={86}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84922551455&partnerID=MN8TOARS}, DOI={10.1021/ac503000e}, abstractNote={Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).}, number={22}, journal={Analytical Chemistry}, author={Baars, O. and Morel, F.M.M. and Perlman, D.H.}, year={2014}, pages={11298–11305} }
 @article{baars_abouchami_galer_boye_croot_2014, title={Dissolved cadmium in the Southern Ocean: Distribution, speciation, and relation to phosphate}, volume={59}, DOI={10.4319/lo.2014.59.2.0385}, abstractNote={We report isotope dilution analyses of dissolved cadmium (Cd) and electrochemical Cd speciation measurements in the Atlantic sector of the Southern Ocean. Bioavailable inorganic Cd is > 100 times higher in near‐surface waters south of the Polar Front compared to the Subantarctic Zone because of upwelling and reduced complexation by organic Cd ligands. To trace local changes in the relation between Cd and P, we examine the deviations from a linear deep‐water Cd vs. P relation (Cd*), and find that changes in Cd* coincide with the position of frontal systems and covary with primary productivity and total dissolved Mn and Fe concentrations. These covariations agree with potential local changes in phytoplankton Cd uptake rates, resulting from differences in the availability of Cd, Zn, Mn, and Fe. A band of negative Cd* values is associated with formation of Subantarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW). In contrast to SAMW, which may export low Cd : P ratios from the Southern Ocean, the Cd : P ratios in AAIW increase by mixing with underlying Upper Circumpolar Deep Water before being exported from the Southern Ocean. Deep waters show constant Cd : P ratios, and both elements behave conservatively with end‐member mixing between deep waters of the Weddell Gyre, the Antarctic Circumpolar Current, and inflowing North Atlantic Deep Water. Overall, our results support the hypothesis that the kink in the global Cd vs. P relation is largely caused by high Cd : P uptake ratios in the trace‐nutrient—limited Southern Ocean.}, number={2}, journal={Limnology and Oceanography}, publisher={Wiley-Blackwell}, author={Baars, Oliver and Abouchami, Wafa and Galer, Stephen J. G. and Boye, Marie and Croot, Peter L.}, year={2014}, month={Jan}, pages={385–399} }
 @article{baars_croot_2011, title={Comparison of Alternate Reactants for pM Level Cobalt Analysis in Seawater by the Use of Catalytic Voltammetry}, volume={23}, url={http://oceanrep.geomar.de/12442/}, DOI={10.1002/elan.201100003}, abstractNote={The analysis of Cobalt (Co) at low pM concentrations in seawater with Adsorptive Cathodic Stripping Voltammetry involves high concentrations of sodium nitrite (NaNO2) to enhance the signal in an electrocatalytic reaction. In this study we found three substitutes for NaNO2 that critically affected the sensitivity. Optimisation of a method with potassium bromate (KBrO3) resulted in an excellent detection limit (0.9 pM) after a 90 s adsorption period. Reactant concentration and consumption were 10× reduced compared to protocols with NaNO2 and reagent blanks were lower. Accuracy and precision were verified with SAFe intercalibration standards and the method was applied using open ocean seawater samples. The reaction mechanism is discussed and differences to NaNO2 are shown.}, number={7}, journal={Electroanalysis}, publisher={Wiley-Blackwell}, author={Baars, Oliver and Croot, Peter L.}, year={2011}, month={May}, pages={1663–1670} }
 @article{baars_2011, title={Distribution and speciation of zinc,cadmium and cobalt in the Southern Ocean}, url={http://oceanrep.geomar.de/13499/}, author={Baars, Oliver}, year={2011} }
 @article{croot_baars_streu_2011, title={The distribution of dissolved zinc in the Atlantic sector of the Southern Ocean}, volume={58}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80054718835&partnerID=MN8TOARS}, DOI={10.1016/j.dsr2.2010.10.041}, abstractNote={The distribution of dissolved zinc (Zn) was investigated in the Atlantic sector of the Southern Ocean in the austral autumn of 2008 as part of the IPY GEOTRACES expedition ZERO & DRAKE. Research focused on transects across the major frontal systems along the Zero Meridian and across the Drake Passage. There was a strong gradient in surface zinc concentrations observed across the Antarctic Polar Front along both transects and high zinc levels were found in surface waters throughout the Southern Ocean. Vertical profiles for dissolved Zinc showed the presence of local minima and maxima in the upper 200 m consistent with significant uptake by phytoplankton and release by zooplankton grazing, respectively. Highest deep water zinc concentrations were found in the centre of the Weddell Gyre associated with Central Intermediate Water (CIW), a water mass which is depleted in O2, elevated in CO2 and is regionally a CFC minimum. Our data suggests that the remineralization of sinking particles is a key control on the distribution of Zn in the Southern Ocean. Disappearance ratios of zinc to phosphate (Zn:P) in the upper water column increased southwards along both transects and based on laboratory studies they suggest slower growth rates of phytoplankton due to iron or light limitation. Zinc and silicate were strongly correlated throughout the study region but the disappearance ratio (Zn:Si) was relatively uniform overall except for the region close to the ice edge on the Zero Meridian.}, number={25-26}, journal={Deep-Sea Research Part II: Topical Studies in Oceanography}, author={Croot, P.L. and Baars, O. and Streu, P.}, year={2011}, pages={2707–2719} }
 @article{baars_croot_2011, title={The speciation of dissolved zinc in the Atlantic sector of the Southern Ocean}, volume={58}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80054741749&partnerID=MN8TOARS}, DOI={10.1016/j.dsr2.2011.02.003}, abstractNote={The speciation of dissolved zinc (Zn) was investigated by voltammetry in the Atlantic sector of the Southern Ocean along two transects across the major frontal systems: along the Zero Meridian and across the Drake Passage. In the Southern Ocean south of the APF we found detectable labile inorganic Zn throughout the surface waters in contrast to studies from lower latitudes. Using a combination of ASV titrations and pseudopolarography revealed the presence of significant concentration of electrochemically inert Zn ligands throughout the Southern Ocean. These ligands however were nearly always saturated due to the presence of excess concentrations of dissolved Zn that were associated with the high nutrient waters south of the Antarctic Polar Front (APF). Only in surface waters did the concentration of Zn complexing ligands exceed the dissolved Zn concentrations suggesting a biological source for these ligands. Our findings have clear implications for the biogeochemical cycling of Zn and for the interpretation of paleo records utilizing Zn in opal as a tracer of Zn speciation in the water column.}, number={25-26}, journal={Deep-Sea Research Part II: Topical Studies in Oceanography}, author={Baars, O. and Croot, P.L.}, year={2011}, pages={2720–2732} }
 @article{klingele_klingele_baars_lozan_buchholz_leibeling_plass_meyer_kersting_2007, title={Tetranuclear nickel(II) complexes composed of pairs of dinuclear LNi <inf>2</inf> fragments linked by acetylenedicarboxylate, terephthalate, and isophthalate dianions: Synthesis, structures and magnetic properties}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-36549051163&partnerID=MN8TOARS}, DOI={10.1002/ejic.200700748}, abstractNote={The tetranuclear nickel(II) complexes [(LNi II 2 ) 2 (acetylene-dicarboxylate)][BPh4]2 (2[BPh 4 ) 2 ), [(LNi"2)2(terephthalate)]- ]-[BPh 4 ) 2 (3[BPh 4 ) 2 ), and [(LNi"2)2(isophthalate)][BPh 4 ] 2 (4[BPh 4 ] 2 ), where L 2- represents a macrocyclic hexaaza-dithiophenolate ligand, have been synthesized and characterised by UV/Vis spectroscopy, IR spectroscopy, X-ray crystallography, and magnetic susceptibility measurements. Each dicarboxylate dianion acts as a quadridentate bridging ligand linking two bioctahedral LNi 2 units via μ 1,3 -bridging carboxylate functions to generate discrete [(LNi II 2 ) 2 (dicarb-oxylate)] 2+ dications with a central LNi 2 (O 2 C-R-CO 2 )Ni 2 L core. The structures differ mainly in the distance between the center of the Ni...Ni axes of the isostructural LNi 2 units (8.841(1) A in 2[BPh 4 ) 2 , 10.712(1) in 3[BPh 4 ] 2 , and 9.561(1) in 4[BPh 4 ] 2 ) and the tilting angle between the two Ni 2 O 2 planes (86.3° in 2[BPh 4 ] 2 , 58.2° in 3[BPh 4 ] 2 , 20.9° in 4[BPh 4 ] 2 ). Magnetic susceptibility measurements on the complexes over the range 2.0-295 K reveal the presence of weak ferromagnetic exchange interactions between the Ni II ions within the dinuclear subunits with values for the magnetic exchange constant J 1 of 23.1(5), 18.1(5), and 14.2(5) cm -1 for 2[BPh 4 ] 2 , 3[BPh 4 ] 2 , and 4[BPh 4 ] 2 , respectively (H = -2JS 1 S 2 ). The magnitude of the exchange interaction J 2 across the dicarboxylate bridges is in all cases less than 0.1 cm -1 , suggesting that no significant interdimer exchange coupling occurs in 2[BPh 4 ] 2 -4[BPh 4 ] 2 .}, number={33}, journal={European Journal of Inorganic Chemistry}, author={Klingele, J. and Klingele, M.H. and Baars, O. and Lozan, V. and Buchholz, A. and Leibeling, G. and Plass, W. and Meyer, F. and Kersting, B.}, year={2007}, pages={5277–5285} }