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1. Spatial distribution and biogeochemistry of redox active species in arctic sedimentary porewaters and seeps

   https://doi.org/10.1039/d1em00505g  

   Hudson, Jeffrey M.; Michaud, Alexander B.; Emerson, David; Chin, Yu-Ping (March 2022, Environmental Science: Processes & Impacts)

   Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn( ii ), Fe( ii ), O 2 , and Fe( iii )-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe( ii ) oxidation and reductive dissolution of Fe( iii ) and Mn( iv ) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe( iii ) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe( ii ) and soluble Fe( iii ) in a highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle. 

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2. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

   https://doi.org/10.1186/s40168-021-01187-7  

   Rolando, Jose L.; Kolton, Max; Song, Tianze; Kostka, Joel E. (December 2022, Microbiome)

   Abstract Background Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. Results A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora . Conclusions The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. 

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3. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora

   https://doi.org/10.1038/s41467-024-47646-1  

   Rolando, J. L.; Kolton, M.; Song, T.; Liu, Y.; Pinamang, P.; Conrad, R.; Morris, J. T.; Konstantinidis, K. T.; Kostka, J. E. (April 2024, Nature Communications)

   Abstract Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plantSpartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from theCandidatusThiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizingdsrAand nitrogen-fixingnifKtranscripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis betweenS. alternifloraand sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes. 

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4. Unraveling Fe(II)-Oxidizing Mechanisms in a Facultative Fe(II) Oxidizer, Sideroxydans lithotrophicus Strain ES-1, via Culturing, Transcriptomics, and Reverse Transcription-Quantitative PCR

   https://doi.org/10.1128/AEM.01595-21  

   Zhou, Nanqing; Keffer, Jessica L.; Polson, Shawn W.; Chan, Clara S. (January 2022, Applied and Environmental Microbiology)

   Buan, Nicole R. (Ed.)

   ABSTRACT Sideroxydans lithotrophicus ES-1 grows autotrophically either by Fe(II) oxidation or by thiosulfate oxidation, in contrast to most other isolates of neutrophilic Fe(II)-oxidizing bacteria (FeOB). This provides a unique opportunity to explore the physiology of a facultative FeOB and constrain the genes specific to Fe(II) oxidation. We compared the growth of S. lithotrophicus ES-1 on Fe(II), thiosulfate, and both substrates together. While initial growth rates were similar, thiosulfate-grown cultures had higher yield with or without Fe(II) present, which may give ES-1 an advantage over obligate FeOB. To investigate the Fe(II) and S oxidation pathways, we conducted transcriptomics experiments, validated with reverse transcription-quantitative PCR (RT-qPCR). We explored the long-term gene expression response at different growth phases (over days to a week) and expression changes during a short-term switch from thiosulfate to Fe(II) (90 min). The dsr and sox sulfur oxidation genes were upregulated in thiosulfate cultures. The Fe(II) oxidase gene cyc2 was among the top expressed genes during both Fe(II) and thiosulfate oxidation, and addition of Fe(II) to thiosulfate-grown cells caused an increase in cyc2 expression. These results support the role of Cyc2 as the Fe(II) oxidase and suggest that ES-1 maintains readiness to oxidize Fe(II), even in the absence of Fe(II). We used gene expression profiles to further constrain the ES-1 Fe(II) oxidation pathway. Notably, among the most highly upregulated genes during Fe(II) oxidation were genes for alternative complex III, reverse electron transport, and carbon fixation. This implies a direct connection between Fe(II) oxidation and carbon fixation, suggesting that CO 2 is an important electron sink for Fe(II) oxidation. IMPORTANCE Neutrophilic FeOB are increasingly observed in various environments, but knowledge of their ecophysiology and Fe(II) oxidation mechanisms is still relatively limited. Sideroxydans isolates are widely observed in aquifers, wetlands, and sediments, and genome analysis suggests metabolic flexibility contributes to their success. The type strain ES-1 is unusual among neutrophilic FeOB isolates, as it can grow on either Fe(II) or a non-Fe(II) substrate, thiosulfate. Almost all our knowledge of neutrophilic Fe(II) oxidation pathways comes from genome analyses, with some work on metatranscriptomes. This study used culture-based experiments to test the genes specific to Fe(II) oxidation in a facultative FeOB and refine our model of the Fe(II) oxidation pathway. We gained insight into how facultative FeOB like ES-1 connect Fe, S, and C biogeochemical cycling in the environment and suggest a multigene indicator would improve understanding of Fe(II) oxidation activity in environments with facultative FeOB. 

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5. Iron cycling and isotopic fractionation in a ferruginous, seasonally ice-covered lake

   https://doi.org/10.1016/j.gca.2024.07.037  

   Heard, Andy W; Ostrander, Chadlin M; Swanner, Elizabeth D; Rico, Kathryn; Nielsen, Sune G (October 2024, Geochimica et Cosmochimica Acta)

   Ferruginous conditions, defined by anoxia and abundant dissolved ferrous iron (Fe2+aq), dominated the Precambrian oceans but are essentially non-existent in a modern, oxygenated world. Ferruginous meromictic lakes represent natural laboratories to ground truth our understanding of the stable Fe isotope proxy, which has been used extensively in interpreting the origins of Fe-rich sedimentary rocks like iron formations (IFs) and the interactions of early life with high-Fe2+aq conditions. Here we report comprehensive geochemical and Fe isotopic analyses of samples collected in May and August 2022, and March 2023, from Deming Lake, Minnesota, a ferruginous meromictic lake that undergoes surface freezing in winter and never becomes euxinic. Through chemical and Fe isotopic analyses of different putative Fe sources to Deming Lake; including eolian input trapped in winter ice cover, nearby bogs, and regional groundwaters sampled at surface springs; we find that a groundwater source provides the best chemical and Fe isotopic match for Deming Lake and can support Fe2+aq-rich waters at depth that maintain a permanent chemocline at ~12 m. The ice-free Deming Lake water column can be split into three layers dominated by distinct Fe cycling regimes. Layer (I) extends from the lake surface to the base of the oxycline at ~6 m, and its Fe cycling is dominated by isotopically light Fe uptake into biomass, likely from stabilized dissolved Fe3+, with variable eolian lithogenic influences. Layer (II) extends between the oxycline and the chemocline at ~12 m and is dominated by partial Fe2+aq oxidation on approach to the oxycline, with the formation of variably isotopically heavy Fe3+-bearing particles. Layer (III) underlies the chemocline and is defined by Fe2+ phosphate (vivianite) and carbonate saturation and precipitation under anoxic, Fe2+aq-rich conditions with little Fe isotopic fractionation. The ice-covered winter water column features more homogenous Fe chemistry above the chemocline, which we attribute to seasonal homogenization of Layers (I) and (II), with suppressed ferric particle formation. Authigenic Fe minerals with non-crustal (light) Fe isotopic compositions only appreciably accumulate in sediments in Deming Lake underlying the chemocline. All sediments deposited above 12 m appear crustal in their Fe isotopic, Mn/Fe, and Fe/Al ratios, likely revealing efficient reductive dissolution of Fe3+-bearing lake precipitates and remineralization of Fe-bearing biomass. We find limited fractionation of Fe isotopes in the ice-covered water column and suggest this provides evidence that substantial delivery of oxidants is required to generate highly fractionated Fe isotopic compositions in Sturtian Snowball era IFs. By comparing Fe isotopic and Mn/Fe fractionation trends in the different Deming Lake layers, we also suggest that correlations between these two parameters in giant early Paleoproterozoic IFs requires the simultaneous deposition of multiple authigenic phases on the ancient seafloor. Finally, high-precision triple Fe isotopic analyses of dissolved Fe impacted by extensive oxidation near the Deming Lake oxycline reveal that the slope of the mass fractionation law for natural, O2-mediated Fe2+aq oxidation is identical to those previously defined for both UV photo-oxidation, and for an array of highly fractionated Paleoproterozoic IFs. 

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