Publications List
36 Publications
Journal Article
Shifts in the hydrogen stable isotopic composition (2H/1H ratio) of lipids relative to water (lipid/water 2H-fractionation) at natural abundances reflect different sources of the central cellular reductant, NADPH, in bacteria. Here, we demonstrate that lipid/water 2H-fractionation (2εfattyacid/water) can also constrain the relative importance of…
Journal Article
Abstract Microorganisms have evolved diverse strategies to acquire the vital element nitrogen (N) from the environment. Ecological and physiological controls on the distribution of these strategies among microbes remain unclear. In this study, we examine the distribution of 10 major N acquisition strategies in taxonomically and metabolically…
Journal Article
Sulfate reducing bacteria (SRB) comprise one of the few prokaryotic groups in which biological…
Journal Article
Biological nitrogen fixation (BNF) by canonical molybdenum and complementary vanadium, and iron-only nitrogenase isoforms is the primary natural source of newly fixed nitrogen. Understanding controls on global nitrogen cycling requires knowledge of the isoform responsible for environmental BNF. The isotopic acetylene reduction assay (ISARA),…
Journal Article
Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as…
Journal Article
New bioavailable nitrogen (N) from biological nitrogen fixation (BNF) is critical for the N budget and productivity of marine ecosystems. Nitrogen-fixing organisms typically inactivate BNF when less metabolically costly N sources, like ammonium (NH 4 +), are available. Yet, several studies have observed BNF in benthic…
Journal Article
Hydrogen (H2) gas is an obligatory byproduct of nitrogen (N2) reduction during biological nitrogen fixation by the metalloenzyme nitrogenase. Despite significant efforts, diazo- trophic H2 production rates remain too low to compete with fossil fuel-derived H2. Here, we investigate the role of temperature (14, 19, 30 C), carbon metabolism …
Journal Article
Introduction After publication of this work, it was brought to our attention that it has not been tested whether R. palustris CGA009 and its derivative strains can use dimethyl sulfoxide (DMSO) as an electron sink (Luxem et al., 2020). Here, we report the results of additional bioinformatic, physiological, and chemical experiments to test…
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 conditions…
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, yet…
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 novel mechanistic model to…
Journal Article
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V)-and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here, we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions…
Journal Article
(Figure Presented) Figure 4. Cycle of biologically driven N transformations that occur in natural and human-influenced terrestrial and marine environments. Nitrogen (N2) fixation (step 1) and N assimilation (from ammonium, nitrate, or organic N, step 2) are anabolic processes, whereas mineralization (step 3), nitrification (steps 4−6), DNRA (steps 7,…
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 review…
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…
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 results…
Molybdenum threshold for ecosystem scale alternative vanadium nitrogenase activity in boreal forests
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…
Journal Article
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,…
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…
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 molecules…
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 and…
Journal Article
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 considered backup enzymes, used when Mo is…
Journal Article
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 site…
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,…
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…
Journal Article
Biological nitrogen fixation constitutes the main input of fixed nitrogen to Earth s ecosystems, and its isotope effect is a key parameter in isotope-based interpretations of the N cycle. The nitrogen isotopic composition (δ15N) of newly fixed N is currently believed to be∼-10/00, based on measurements of organic matter from diazotrophs using…
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=acetylene reduction rate…
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 the…
Journal Article
Identifying microbes responsible for particular environmental functions is challenging, given that most environments contain an uncultivated microbial diversity. Here we combined approaches to identify bacteria expressing genes relevant to catabolite flow and to locate these genes within their environment, in this case the gut of a "lower," wood…
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 the…
Journal Article
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 cysteine- (Cys)…
Journal Article
The termite gut spirochete, Treponema primitia, is a CO 2-reductive acetogen that is phylogenetically distinct from other distantly related and more extensively studied acetogens such as Moorella thermoacetica. Research on T. primitia has revealed details about the role of spirochetes in CO 2-reductive acetogenesis, a process important to the…
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…
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 1 and are therefore important both for their roles…
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…