• 4D imaging reveals mechanisms of clay-carbon protection and release

    Judy Q. Yang; Xinning Zhang; Ian C. Bourg; Howard A. Stone
    Journal Article

    Soil absorbs about 20% of anthropogenic carbon emissions annually, and clay is one of the key carbon-capture materials. Although sorption to clay is widely assumed to strongly retard the microbial decomposition of soil organic matter, enhanced degradation of clay-associated organic carbon has been observed under certain conditions. The...

  • Alternative nitrogenase activity in the environment and nitrogen cycle implications

    Xinning Zhang; Darcy L. McRose; Romain Darnajoux; J. P. Bellenger; François M.M. Morel; Anne M.L. Kraepiel
    Journal Article

    Biological nitrogen fixation, the main natural input of fixed nitrogen into the biosphere, is catalyzed by Mo-, V-, or Fe-only nitrogenase metalloenzymes. Although “alternative” V- and Fe-only nitrogenase genes are found in many environments, the contribution of these isoenzymes to N2 fixation is unknown. Here we present a new method (ISARA,...

  • Biological nitrogen fixation by alternative nitrogenases in boreal cyanolichens: importance of molybdenum availability and implications for current biological nitrogen fixation estimates

    Romain Darnajoux; Xinning Zhang; Darcy L. McRose; Jolanta Miadlikowska; François Lutzoni; Anne M.L. Kraepiel; Jean-Philippe Bellenger
    Journal Article

    Summary Cryptogamic species and their associated cyanobacteria have attracted the attention of biogeochemists because of their critical roles in the nitrogen cycle through symbiotic and asymbiotic biological fixation of nitrogen (BNF). BNF is mediated by the nitrogenase enzyme, which, in its most common form, requires molybdenum at its active...

  • Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review

    Romain * Darnajoux; J. P. Bellenger; X. Zhang; A.M. Kraepiel
    Journal Article

    Biological nitrogen fixation (BNF), a key reaction of the nitrogen cycle, is catalyzed by the enzyme nitrogenase. The best studied isoform of this metalloenzyme requires molybdenum (Mo) at its active center to reduce atmospheric dinitrogen (N2) into bioavailable ammonium. The Mo-dependent nitrogenase is found in all diazotrophs and is the only...

  • Carbon substrate re-orders relative growth of a bacterium using Mo-, V-, or Fe-nitrogenase for nitrogen fixation.

    K. E.* Luxem; A. M.L. Kraepiel; L. Zhang; J. R. Waldbauer; X. Zhang
    Journal Article

    Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron (Fe)-only nitrogenase metalloenzymes. Studies with purified enzymes have found that the ‘alternative’ V- and Fe-nitrogenases generally reduce N2 more slowly and produce more byproduct H2 than the Mo-nitrogenase, leading to an assumption that their usage...

  • Critical inundation level for methane emissions from wetlands

    Salvatore Calabrese; Alicia Garcia; Jared L. Wilmoth; Xinning Zhang; Amilcare Porporato
    Journal Article

    Global methane (CH4) emissions have reached approximately 600 Tg per year, 20-40% of which are from wetlands. Of the primary factors affecting these emissions, the water table level is among the most uncertain. Here we conduct a global meta-analysis of chamber and flux-tower observations of CH4 emissions and employ a mechanistic model to show...

  • Crochelins: Siderophores with an Unprecedented Iron-Chelating Moiety from the Nitrogen-Fixing Bacterium Azotobacter chroococcum

    O. Baars; X. Zhang; M. I. Gibson; A. T. Stone; F. M.M. Morel; M. R. Seyedsayamdost
    Journal Article

    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...

  • Diversity and activity of alternative nitrogenases in sequenced genomes and coastal environments

    D. L. McRose; X. Zhang; A.M. L. Kraepiel; F. M.M. Morel
    Journal Article

    © 2017 McRose, Zhang, Kraepiel and Morel. The nitrogenase enzyme, which catalyzes the reduction of N2 gas to NH4+, occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient 'canonical' Mo-nitrogenase, whereas Fe-only and V-('alternative') nitrogenases are often...

  • Effect of iron limitation on the isotopic composition of cellular and released fixed nitrogen in Azotobacter vinelandii

    D.L. McRose; A. Lee; S.H. Kopf; O. Baars; A.M.L. Kraepiel; D.M. Sigman; F.M.M. Morel; X. Zhang
    Journal Article

    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...

  • Evidence for Cascades of Perturbation and Adaptation in the Metabolic Genes of Higher Termite Gut Symbionts

    Xinning Zhang; Jared R. Leadbetter
    Journal Article

    Termites and their gut microbes engage in fascinating dietary mutualisms. Less is known about how these complex symbioses have evolved after first emerging in an insect ancestor over 120 million years ago. Here we examined a bacterial gene, formate dehydrogenase (fdhF), that is key to the mutualism in 8 species of “higher” termite (members of...

  • Fate of DTPA, EDTA, and EDDS in Hydroponic Media and Effects on Plant Mineral Nutrition

    T. M. Vadas; X. Zhang; A. M. Curran; B. A. Ahner
    Journal Article

    Synthetic chelators are commonly used in hydroponic media to solubilize iron (Fe); however, the fate of these chelators is unknown. This study examined the persistence of three synthetic chelators, ethylenediaminetetraacetate (EDTA), diethylenetriaminepentaacetate (DTPA), and ethylenediaminedisuccinate (EDDS) in a bench-scale lettuce production...

  • Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood-feeding termites and a wood-feeding roach

    Xinning Zhang; Eric G. Matson; Jared R. Leadbetter
    Journal Article

    Summary The bacterial Wood?Ljungdahl pathway for CO2-reductive acetogenesis is important for the nutritional mutualism occurring between wood-feeding insects and their hindgut microbiota. A key step in this pathway is the reduction of CO2 to formate, catalysed by the enzyme formate dehydrogenase (FDH). Putative selenocysteine- (Sec) and...

  • Genetic, structural, and functional diversity of low and high-affinity siderophores in strains of nitrogen fixing: Azotobacter chroococcum

    X. Zhang; O. Baars; F. M.M. Morel
    Journal Article

    © 2019 The Royal Society of Chemistry. 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...

  • Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

    Eric G. Matson; Adam Z. Rosenthal; Xinning Zhang; Jared R. Leadbetter
    Journal Article

    When prokaryotic cells acquire mutations, encounter translation-inhibiting substances, or experience adverse environmental conditions that limit their ability to synthesize proteins, transcription can become uncoupled from translation. Such uncoupling is known to suppress transcription of protein-encoding genes in bacteria. Here we show that...

  • Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics

    X. Zhang; B. B. Ward; D. M. Sigman
    Journal Article

    Nitrogen (N) is used in many of life’s fundamental biomolecules, and it is also a participant in environmental redox chemistry. Biogeochemical processes control the amount and form of N available to organisms (“fixed” N). These interacting processes result in N acting as the proximate limiting nutrient in most surface environments. Here, we...

  • Large D/H variations in bacterial lipids reflect central metabolic pathways

    Xinning Zhang; Aimee L. Gillespie; Alex L. Sessions
    Journal Article

    Large hydrogen-isotopic (D/H) fractionations between lipids and growth water have been observed in most organisms studied to date. These fractionations are generally attributed to isotope effects in the biosynthesis of lipids, and are frequently assumed to be approximately constant for the purpose of reconstructing climatic variables. Here, we...

  • Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy

    Adam Z. Rosenthal; Xinning Zhang; Kaitlyn S. Lucey; Elizabeth A. Ottesen; Vikas Trivedi; Harry M.T. Choi; Niles A. Pierce; Jared R. Leadbetter
    Journal Article

    Most environments host a poorly understood microbial diversity. In recent years, work on gene inventories and metagenomics has revealed much about the microbial species and metabolic genes that may be present in situ; however, connecting microbial species with environmental function has lagged. Here a combination of emerging single-cell and...

  • Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

    Falk Warnecke; Peter Luginbühl; Natalia Ivanova; Majid Ghassemian; Toby H. Richardson; Justin T. Stege; Michelle Cayouette; Alice C. McHardy; Gordana Djordjevic; Nahla Aboushadi; Rotem Sorek; Susannah G. Tringe; Mircea Podar; Hector Garcia Martin; Victor Kunin; Daniel Dalevi; Julita Madejska; Edward Kirton; Darren Platt; Ernest Szeto; Asaf Salamov; Kerrie Barry; Natalia Mikhailova; Nikos C. Kyrpides; Eric G. Matson; Elizabeth A. Ottesen; Xinning Zhang; Myriam Hernández; Catalina Murillo; Luis G. Acosta; Isidore Rigoutsos; Giselle Tamayo; Brian D. Green; Cathy Chang; Edward M. Rubin; Eric J. Mathur; Dan E. Robertson; Philip Hugenholtz; Jared R. Leadbetter
    Journal Article

    From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms...

  • Molybdenum threshold for ecosystem-scale alternative vanadium nitrogenase activity in boreal forests

    Romain* Darnajoux; Nicolas Magain; Marie Renaudin; François Lutzoni; Jean-Philippe Bellenger; Xinning Zhang
    Journal Article

    Biological nitrogen fixation (BNF) by microorganisms associated with cryptogamic covers, such as cyanolichens and bryophytes, is a primary source of fixed nitrogen in pristine, high-latitude ecosystems. On land, low molybdenum (Mo) availability has been shown to limit BNF by the most common form of nitrogenase (Nase), which requires Mo in its...

  • Nitrogen isotope fractionation by alternative nitrogenases and past ocean anoxia

    Xinning Zhang; Daniel M. Sigman; François M.M. Morel; Anne M.L. Kraepiel
    Journal Article

    Biological nitrogen fixation is the main route by which nitrogen enters the biosphere. This reaction is catalyzed by nitrogenase, a metalloenzyme that exists in forms containing molybdenum, vanadium, or iron only. The contribution of the “alternative” vanadium and iron-only nitrogenases to nitrogen fixation in the present and the past is...

  • Possible contribution of alternative nitrogenases to nitrogen fixation by asymbiotic N2-fixing bacteria in soils

    J.-P. Bellenger; Y. Xu; X. Zhang; F. M.M. Morel; A.M. L. Kraepiel
    Journal Article

    The relative contributions of the alternative (V- and Fe-only) and canonical (Mo-) nitrogenases to N2 fixation in natural environments are still largely unknown. Here we combine chemical and molecular approaches to examine their role in terrestrial ecosystems. Pure-culture studies show that while the R ratio (defined as R = ...

  • The purple non-sulfur bacterium Rhodopseudomonas palustris produces novel petrobactin related siderophores under aerobic and anaerobic conditions

    O. Baars; F. M.M. Morel; X. Zhang
    Journal Article

    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...

  • The role of oxygen in stimulating methane production in wetlands

    Jared L. Wilmoth; Jeffra K. Schaefer; Danielle R. Schlesinger; Spencer W. Roth; Patrick G. Hatcher; Julie K. Shoemaker; Xinning Zhang
    Journal Article

    Methane (CH4), a potent greenhouse gas, is the second most important greenhouse gas contributor to climate change after carbon dioxide (CO2). The biological emissions of CH4 from wetlands are a major uncertainty in CH4 budgets. Microbial methanogenesis by Archaea is an anaerobic process accounting for most biological CH4 production in nature,...

  • Selenium controls transcription of paralogous formate dehydrogenase genes in the termite gut acetogen, Treponema primitia

    Eric G. Matson; X. Zhang; Jared R. Leadbetter
    Journal Article

    The termite gut spirochete,Treponema primitia,isaCO2-reductive acetogen that is phylogeneticallydistinct from other distantly related and moreextensively studied acetogens such asMoorella ther-moacetica. Research onT. primitiahas revealeddetails about the role of spirochetes in CO2-reductiveacetogenesis, a process important to the...

  • The Siderophore Metabolome of Azotobacter vinelandii

    O. Baars; X. Zhang; F. M.M. Morel; M. R. Seyedsayamdost
    Journal Article

    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...