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Applied and Environmental Science

  • Open Access
    Bottom-Up Fabrication of Protein Nanowires via Controlled Self-Assembly of Recombinant <em>Geobacter</em> Pilins
    Editor's Pick Research Article | Applied and Environmental Science
    Bottom-Up Fabrication of Protein Nanowires via Controlled Self-Assembly of Recombinant Geobacter Pilins

    The discovery in 2005 of conductive protein appendages (pili) in the metal-reducing bacterium Geobacter sulfurreducens challenged our understanding of biological electron transfer and pioneered studies in electromicrobiology that revealed the electronic basis of many microbial metabolisms and interactions. The protein nature of the pili afforded opportunities for...

    K. M. Cosert, Angelines Castro-Forero, Rebecca J. Steidl, Robert M. Worden, G. Reguera
  • Open Access
    Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers
    Research Article | Applied and Environmental Science
    Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers

    Fungi dominate the turnover of wood, Earth’s largest pool of aboveground terrestrial carbon. Fungi first evolved this capacity by degrading lignin to access and hydrolyze embedded carbohydrates (white rot). Multiple lineages, however, adapted faster reactive oxygen species (ROS) pretreatments to loosen lignocellulose and selectively extract sugars (brown rot). This brown rot “shortcut” often coincided with losses (>60%) of...

    Jiwei Zhang, Kevin A. T. Silverstein, Jesus David Castaño, Melania Figueroa, Jonathan S. Schilling
  • Open Access
    Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community
    Research Article | Applied and Environmental Science
    Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community

    CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks...

    Christian M. K. Sieber, Blair G. Paul, Cindy J. Castelle, Ping Hu, Susannah G. Tringe, David L. Valentine, Gary L. Andersen, Jillian F. Banfield
  • Open Access
    DNA- and RNA-SIP Reveal <em>Nitrospira</em> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
    Research Article | Applied and Environmental Science
    DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

    With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3− uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer...

    Arda Gülay, S. Jane Fowler, Karolina Tatari, Bo Thamdrup, Hans-Jørgen Albrechtsen, Waleed Abu Al-Soud, Søren J. Sørensen, Barth F. Smets
  • Open Access
    Photoferrotrophs Produce a PioAB Electron Conduit for Extracellular Electron Uptake
    Research Article | Applied and Environmental Science
    Photoferrotrophs Produce a PioAB Electron Conduit for Extracellular Electron Uptake

    Some anoxygenic phototrophs use soluble iron, insoluble iron minerals (such as rust), or their proxies (poised electrodes) as electron donors for photosynthesis. However, the underlying electron uptake mechanisms are not well established. Here, we show that these phototrophs use a protein complex made of an outer membrane porin and a periplasmic decaheme cytochrome (electron transfer protein) to harvest electrons from both soluble iron...

    Dinesh Gupta, Molly C. Sutherland, Karthikeyan Rengasamy, J. Mark Meacham, Robert G. Kranz, Arpita Bose
  • Open Access
    The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets
    Research Article | Applied and Environmental Science
    The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets

    β-Defensins are host defense peptides controlling infections in species ranging from humans to invertebrates. However, the antimicrobial activity of most human β-defensins is impaired at physiological salt concentrations. We explored the properties of big defensins, the β-defensin ancestors, which have been conserved in a number of marine organisms, mainly mollusks. By focusing on a big defensin from oyster (Cg-BigDef1), we...

    Karine Loth, Agnès Vergnes, Cairé Barreto, Sébastien N. Voisin, Hervé Meudal, Jennifer Da Silva, Albert Bressan, Nawal Belmadi, Evelyne Bachère, Vincent Aucagne, Chantal Cazevielle, Hélène Marchandin, Rafael Diego Rosa, Philippe Bulet, Lhousseine Touqui, Agnès F. Delmas, Delphine Destoumieux-Garzón
  • Open Access
    Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression
    Research Article | Applied and Environmental Science
    Antibiotics and Host-Tailored Probiotics Similarly Modulate Effects on the Developing Avian Microbiome, Mycobiome, and Host Gene Expression

    Alternative approaches are greatly needed to reduce the need for antibiotic use in food animal production. This study utilized a pipeline for the development of a host-tailored probiotic to enhance performance in commercial turkeys and modulate their microbiota, similar to the effects of low-dose antibiotic administration. We determined that a host-tailored probiotic, developed in the context of the commercial turkey gut microbiome, was...

    Tonya L. Ward, Bonnie P. Weber, Kristelle M. Mendoza, Jessica L. Danzeisen, Katharine Llop, Kevin Lang, Jonathan B. Clayton, Elicia Grace, Jeanine Brannon, Igor Radovic, Mai Beauclaire, Timothy J. Heisel, Dan Knights, Carol Cardona, Mike Kogut, Casey Johnson, Sally L. Noll, Ryan Arsenault, Kent M. Reed, Timothy J. Johnson
  • Open Access
    Rapid Phenotypic and Metabolomic Domestication of Wild <em>Penicillium</em> Molds on Cheese
    Editor's Pick Research Article | Applied and Environmental Science
    Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese

    Industrial cultures of filamentous fungi are used to add unique aesthetics and flavors to cheeses and other microbial foods. How these microbes adapted to live in food environments is generally unknown as most microbial domestication is unintentional. Our work demonstrates that wild molds closely related to the starter culture Penicillium camemberti can readily lose...

    Ina Bodinaku, Jason Shaffer, Allison B. Connors, Jacob L. Steenwyk, Megan N. Biango-Daniels, Erik K. Kastman, Antonis Rokas, Albert Robbat, Benjamin E. Wolfe
  • Open Access
    Emergent Properties in <span class="named-content genus-species" id="named-content-1">Streptococcus mutans</span> Biofilms Are Controlled through Adhesion Force Sensing by Initial Colonizers
    Research Article | Applied and Environmental Science
    Emergent Properties in Streptococcus mutans Biofilms Are Controlled through Adhesion Force Sensing by Initial Colonizers

    A new concept in biofilm science is introduced: “adhesion force sensitivity of genes,” defining the degree up to which expression of different genes in adhering bacteria is controlled by the environmental adhesion forces they experience. Analysis of gene expression as a function of height in a biofilm showed that the information about the substratum surface to which initially adhering bacteria adhere is passed up to a biofilm height of...

    Can Wang, Jiapeng Hou, Henny C. van der Mei, Henk J. Busscher, Yijin Ren
  • Open Access
    Anaerobic Degradation of Non-Methane Alkanes by “<em>Candidatus</em> Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico
    Research Article | Applied and Environmental Science
    Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico

    Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming “Candidatus Argoarchaeum” and “Candidatus Syntrophoarchaeum” are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. “Ca. Methanoliparia” occurs as single cells associated with oil droplets. These archaea...

    Rafael Laso-Pérez, Cedric Hahn, Daan M. van Vliet, Halina E. Tegetmeyer, Florence Schubotz, Nadine T. Smit, Thomas Pape, Heiko Sahling, Gerhard Bohrmann, Antje Boetius, Katrin Knittel, Gunter Wegener

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