1
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Reed JM, Wolfe BE, Romero LM. Is resilience a unifying concept for the biological sciences? iScience 2024; 27:109478. [PMID: 38660410 PMCID: PMC11039332 DOI: 10.1016/j.isci.2024.109478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
There is increasing interest in applying resilience concepts at different scales of biological organization to address major interdisciplinary challenges from cancer to climate change. It is unclear, however, whether resilience can be a unifying concept consistently applied across the breadth of the biological sciences, or whether there is limited capacity for integration. In this review, we draw on literature from molecular biology to community ecology to ascertain commonalities and shortcomings in how resilience is measured and interpreted. Resilience is studied at all levels of biological organization, although the term is often not used. There is a suite of resilience mechanisms conserved across biological scales, and there are tradeoffs that affect resilience. Resilience is conceptually useful to help diverse researchers think about how biological systems respond to perturbations, but we need a richer lexicon to describe the diversity of perturbations, and we lack widely applicable metrics of resilience.
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Affiliation(s)
- J. Michael Reed
- Department of Biology, Tufts University, Medford 02155, MA, USA
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2
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Clark CS, Ohstrom A, Rolon ML, Smith M, Wolfe BE, Wee J, Van Buiten CB. Sourdough starter culture microbiomes influence physical and chemical properties of wheat bread. J Food Sci 2024; 89:1414-1427. [PMID: 38328986 DOI: 10.1111/1750-3841.16957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/23/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Sourdough fermentation is an ancient leavening method that uses wild yeasts to produce carbon dioxide, contributing to bread rise, and bacteria which produce organic acids. Sourdough starter cultures are known to be diverse in terms of the microorganisms they comprise and while specific genera and species of microorganisms have been identified from starters and associated with specific attributes, overarching relationships between sourdough starter culture microbiomes and bread quality are not well understood. The objective of this study was to characterize differences in the physical and chemical properties of breads produced with sourdough starter cultures with unique microbiomes. Sourdough starter cultures (n = 20) of known microbial populations were used to produce wheat-based dough and bread, which were analyzed for chemical and physical properties then compared to their microbial populations in order to identify relationships between microbial profiles and dough/bread qualities. All samples were also compared to bread produced only with Saccharomyces cerevisiae (baker's yeast). Significant differences among pH, titratable acidity, loaf volume, crumb firmness, crust color, free amino acids, and organic acids were observed when comparing sourdough breads to the yeast-only control (p ≤ 0.05). Furthermore, bacterial diversity of sourdough starter cultures was correlated with lactic acid and free amino acid in the dough and loaf volume and crumb firmness of baked breads. No significant correlations were found between fungal diversity and measured outcomes. These data demonstrate the importance of considering sourdough starter microbiomes as an ingredient in baked goods and they contribute to quality and safety outcomes in bread production. PRACTICAL APPLICATION: Sourdough starter cultures have diverse and dynamic populations of bacteria and yeasts, which contribute to the production of bread products. These populations can influence the physical and chemical properties of sourdough fermentation and final breads. Understanding of the relationship between sourdough starter microbiomes and bread quality parameters can lead to targeted development of sourdough bread products with specific physical and chemical properties.
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Affiliation(s)
- Caitlin S Clark
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, Colorado, USA
| | - Ashley Ohstrom
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - M Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Molly Smith
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, Colorado, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Josephine Wee
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Charlene B Van Buiten
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, Colorado, USA
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3
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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4
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Louw NL, Wolfe BE, Uricchio LH. A phylogenomic perspective on interspecific competition. Ecol Lett 2024; 27:e14359. [PMID: 38332550 DOI: 10.1111/ele.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/30/2023] [Accepted: 11/16/2023] [Indexed: 02/10/2024]
Abstract
Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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5
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Abstract
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Kasturi Lele
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Collin B Edwards
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
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6
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Cosetta CM, Niccum B, Kamkari N, Dente M, Podniesinski M, Wolfe BE. Bacterial-fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species. ISME J 2023; 17:1504-1516. [PMID: 37524910 PMCID: PMC10432416 DOI: 10.1038/s41396-023-01462-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 08/02/2023]
Abstract
Experimental studies of microbial evolution have largely focused on monocultures of model organisms, but most microbes live in communities where interactions with other species may impact rates and modes of evolution. Using the cheese rind model microbial community, we determined how species interactions shape the evolution of the widespread food- and animal-associated bacterium Staphylococcus xylosus. We evolved S. xylosus for 450 generations alone or in co-culture with one of three microbes: the yeast Debaryomyces hansenii, the bacterium Brevibacterium aurantiacum, and the mold Penicillium solitum. We used the frequency of colony morphology mutants (pigment and colony texture phenotypes) and whole-genome sequencing of isolates to quantify phenotypic and genomic evolution. The yeast D. hansenii strongly promoted diversification of S. xylosus. By the end of the experiment, all populations co-cultured with the yeast were dominated by pigment and colony morphology mutant phenotypes. Populations of S. xylosus grown alone, with B. aurantiacum, or with P. solitum did not evolve novel phenotypic diversity. Whole-genome sequencing of individual mutant isolates across all four treatments identified numerous unique mutations in the operons for the SigB, Agr, and WalRK global regulators, but only in the D. hansenii treatment. Phenotyping and RNA-seq experiments highlighted altered pigment and biofilm production, spreading, stress tolerance, and metabolism of S. xylosus mutants. Fitness experiments revealed antagonistic pleiotropy, where beneficial mutations that evolved in the presence of the yeast had strong negative fitness effects in other biotic environments. This work demonstrates that bacterial-fungal interactions can have long-term evolutionary consequences within multispecies microbiomes by facilitating the evolution of strain diversity.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Brittany Niccum
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Nick Kamkari
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Michael Dente
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | | | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
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7
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Ye R, Tomo C, Chan N, Wolfe BE. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere 2023; 8:e0004723. [PMID: 37219436 PMCID: PMC10449494 DOI: 10.1128/msphere.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Christopher Tomo
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Neal Chan
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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8
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. Analyst 2023. [PMID: 37259951 DOI: 10.1039/d3an00408b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
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.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612, USA
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Celine A Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, 02155, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
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9
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Tannous J, Cosetta CM, Drott MT, Rush TA, Abraham PE, Giannone RJ, Keller NP, Wolfe BE. LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly. mBio 2023:e0076923. [PMID: 37162223 DOI: 10.1128/mbio.00769-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions in nature are often unknown. Using an antibacterial Penicillium isolate and a cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, confirming the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how global regulators of fungal transcription can control the assembly of bacterial communities and highlights an ecological role for a widespread class of fungal specialized metabolites. IMPORTANCE Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and microbiomes in general are largely unknown. Our study highlights how specialized metabolites secreted by a Penicillium species can mediate cheese rind development via differential inhibition of bacterial community members. Because LaeA regulates specialized metabolites and other ecologically relevant traits in a wide range of filamentous fungi, this global regulator may have similar impacts in other fungus-dominated microbiomes.
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Affiliation(s)
- Joanna Tannous
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Milton T Drott
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Tomás A Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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10
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. bioRxiv 2023:2023.03.13.532449. [PMID: 36993360 PMCID: PMC10054941 DOI: 10.1101/2023.03.13.532449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
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 molecule mediated 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 spp. 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 their role in complex communities should continue to be a priority.
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Affiliation(s)
- Gordon T. Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Jessica C. Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612
| | - Emily C. Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Celine A. Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
- Tufts University Sensory and Science Center, Medford Massachusetts, 02155
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607
| | - Rachel J. Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
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11
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Wolfe BE. Are fermented foods an overlooked reservoir and vector of antimicrobial resistance? Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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12
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Madden AA, Oliverio AM, Kearns PJ, Henley JB, Fierer N, Starks PTB, Wolfe BE, Romero LM, Lattin CR. Chronic stress and captivity alter the cloacal microbiome of a wild songbird. J Exp Biol 2022; 225:274791. [DOI: 10.1242/jeb.243176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
There are complex interactions between an organism's microbiome and its response to stressors, often referred to as the “gut-brain axis;” however, the ecological relevance of this axis in wild animals remains poorly understood. Here, we used a chronic mild stress protocol to induce stress in wild-caught house sparrows (Passer domesticus), and compared microbial communities among stressed animals, those recovering from stress, captive controls (unstressed), and a group not brought into captivity. We assessed changes in microbial communities and abundance of shed microbes by culturing cloacal samples on multiple media to select for aerobic and anaerobic bacteria and fungi. We complemented this with cultivation-independent 16S and ITS rRNA gene amplification and sequencing, pairing these results with host physiological and immune metrics, including body mass change, relative spleen mass, and plasma corticosterone concentrations. We found significant effects of stress and captivity on the house sparrow microbiomes, with stress leading to an increased relative abundance of endotoxin-producing bacteria— a possible mechanism for the hyperinflammatory response observed in captive avians. While we found evidence that the microbiome community partially recovers after stress cessation, animals may lose key taxa, and the abundance of endotoxin-producing bacteria persists. Our results suggest an overall link between chronic stress, host immune system, and the microbiome, with the loss of potentially beneficial taxa (e.g., lactic acid bacteria), and an increase in endotoxin-producing bacteria due to stress and captivity. Ultimately, consideration of the host's microbiome may be useful when evaluating the impact of stressors on individual and population health.
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Affiliation(s)
- Anne A. Madden
- Department of Biology, Tufts University, Medford, MA 02155, USA
- The Microbe Institute, Everett, MA, 02149, USA
| | - Angela M. Oliverio
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
- Yale School of the Environment, Yale University, 195 Prospect St., New Haven, CT, 06511, USA
| | | | - Jessica B. Henley
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | | | | | | | - Christine R. Lattin
- Department of Biology, Tufts University, Medford, MA 02155, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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13
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Ellis JL, Karl JP, Oliverio AM, Fu X, Soares JW, Wolfe BE, Hernandez CJ, Mason JB, Booth SL. Dietary vitamin K is remodeled by gut microbiota and influences community composition. Gut Microbes 2022; 13:1-16. [PMID: 33651646 PMCID: PMC7928036 DOI: 10.1080/19490976.2021.1887721] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Vitamins have well-established roles in bacterial metabolism. Menaquinones (MKn, n = prenyl units in sidechain) are bacterially produced forms of vitamin K produced by the gut microbiota and consumed in the diet. Little is known about the influence of dietary vitamin K quinones on gut microbial composition and MKn production. Here, male and female C57BL6 mice were fed a vitamin K deficient diet or vitamin K sufficient diets containing phylloquinone (PK, plant-based vitamin K form), MK4, and/or MK9. DNA was extracted from cecal contents and 16S sequencing conducted to assess microbial composition. Cecal microbial community composition was significantly different in vitamin K deficient female mice compared to females on vitamin K sufficient diets (all p < .007). Parallel trends were seen in male mice, but were not statistically significant (all p > .05 but <0.1). Next, stable isotope-labeled vitamin K quinones were supplemented to male and female C57BL6 mice (2H7PK, 13C11MK4, 2H7MK7, 2H7MK9) and to an in vitro fermentation model inoculated with human stool (2H7PK, 2H7MK4, 2H7MK9, or vitamin K precursor 2H8-menadione). Vitamin K quinones in feces and culture aliquots were measured using LC-MS. In vivo, supplemented vitamin K quinones were remodeled to other MKn (2H7- or 13C6-labeled MK4, MK10, MK11, and MK12), but in vitro only the precursor 2H8-menadione was remodeled to 2H7MK4, 2H7MK9, 2H7MK10, and 2H7MK11. These results suggest that dietary vitamin K deficiency alters the gut microbial community composition. Further studies are needed to determine if menadione generated by host metabolism may serve as an intermediate in dietary vitamin K remodeling in vivo.
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Affiliation(s)
- Jessie L. Ellis
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,The Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA, USA
| | - J. Philip Karl
- Military Nutrition Division, US Army Research Institute of Environmental Medicine, Natick, MA, USA
| | - Angela M. Oliverio
- Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, CO, USA
| | - Xueyan Fu
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Jason W. Soares
- Soldier Effectiveness Directorate, US Army Combat Capabilities Developmental Command Soldier Center, Natick, MA, USA
| | | | - Christopher J. Hernandez
- Schools of Mechanical and Aerospace Engineering & Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joel B. Mason
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,The Friedman School of Nutrition Science & Policy, Tufts University, Boston, MA, USA
| | - Sarah L. Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA,CONTACT Sarah L. Booth 711 Washington Street, Boston, MA 02111, USA
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14
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Cosetta CM, Wolfe BE. Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution. ACTA ACUST UNITED AC 2021; 56:e95. [PMID: 31891451 DOI: 10.1002/cpmc.95] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts
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15
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Biango-Daniels MN, Wolfe BE. American artisan cheese quality and spoilage: A survey of cheesemakers' concerns and needs. J Dairy Sci 2021; 104:6283-6294. [PMID: 33888221 DOI: 10.3168/jds.2020-19345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022]
Abstract
Production of artisan cheeses, including surface-ripened cheeses, has increased in the United States over the past 2 decades. Although many of these cheesemakers report unique quality and spoilage problems during production, a systematic assessment of the quality concerns facing this sector of specialty cheese production has not been conducted. Here we report the effects of microbial spoilage and quality issues on US artisan cheese production. In a survey of 61 cheesemakers, the most common issues reported were undesirable surface molds (71%) and incorrect or unexpected colors or pigments on rinds (54%). When asked, 18% of participants indicated that they were extremely concerned about quality and spoilage problems, and they indicated that their quality standards are frequently not met, either annually (39%) or monthly (33%). Although most of the respondents (62%) said that just 0 to 5% of their cheese was lost or rendered less valuable due to quality issues annually, a small number (7% combined) reported large losses of 20 to 30% or >30% of their product lost or rendered less valuable. Almost all respondents (95%) agreed that improved quality would reduce waste, increase profits, and improve production. The survey respondents indicated in open response questions that they want access to more online resources related to quality issues and digital forums to discuss issues with experts and peers when problems arise. These findings represent the first attempt to document and estimate the effect of quality and spoilage on the American artisan cheese industry. Future work should investigate what technologies, interventions, or information could reduce losses from these problems.
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16
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Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 2021; 18:196-208. [PMID: 33398112 PMCID: PMC7925329 DOI: 10.1038/s41575-020-00390-5] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
Abstract
An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.
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Affiliation(s)
- Maria L Marco
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| | - Michael Gänzle
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Edmonton, Canada
| | - Marie Claire Arrieta
- Department of Physiology and Pharmacology, International Microbiome Center, University of Calgary, Calgary, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Wilhelm Holzapfel
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang, Gyeongbuk, South Korea
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Dan Merenstein
- Department of Family Medicine, Georgetown University, Washington, DC, USA
| | - Gregor Reid
- Lawson Health Research Institute, and Departments of Microbiology & Immunology and Surgery, University of Western Ontario, London, Ontario, Canada
| | | | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA.
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17
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Landis EA, Oliverio AM, McKenney EA, Nichols LM, Kfoury N, Biango-Daniels M, Shell LK, Madden AA, Shapiro L, Sakunala S, Drake K, Robbat A, Booker M, Dunn RR, Fierer N, Wolfe BE. The diversity and function of sourdough starter microbiomes. eLife 2021; 10:e61644. [PMID: 33496265 PMCID: PMC7837699 DOI: 10.7554/elife.61644] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.
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Affiliation(s)
| | - Angela M Oliverio
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- North Carolina Museum of Natural SciencesRaleighUnited States
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Nicole Kfoury
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | | | - Leonora K Shell
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | - Lori Shapiro
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
| | | | - Kinsey Drake
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Albert Robbat
- Department of Chemistry, Tufts UniversityMedfordUnited States
| | - Matthew Booker
- Department of History, North Carolina State UniversityRaleighUnited States
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State UniversityRaleighUnited States
- Danish Natural History Museum, University of CopenhagenCopenhagenDenmark
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulderUnited States
- Cooperative Institute for Research in Environmental Sciences, University of ColoradoBoulderUnited States
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18
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Pierce EC, Morin M, Little JC, Liu RB, Tannous J, Keller NP, Pogliano K, Wolfe BE, Sanchez LM, Dutton RJ. Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. Nat Microbiol 2021; 6:87-102. [PMID: 33139882 PMCID: PMC8515420 DOI: 10.1038/s41564-020-00800-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/16/2020] [Indexed: 11/09/2022]
Abstract
Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial-fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial-fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.
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Affiliation(s)
- Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Manon Morin
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jessica C Little
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roland B Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Joanna Tannous
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Food Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Laura M Sanchez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA.
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19
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Fulcher MR, Bolton ML, Millican MD, Michalska-Smith MJ, Dundore-Arias JP, Handelsman J, Klassen JL, Milligan-Myhre KC, Shade A, Wolfe BE, Kinkel LL. Broadening Participation in Scientific Conferences during the Era of Social Distancing. Trends Microbiol 2020; 28:949-952. [PMID: 32978058 PMCID: PMC7507981 DOI: 10.1016/j.tim.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/03/2022]
Abstract
Virtual conferences can offer significant benefits but require considerable planning and creativity to be successful. Here we describe the successes and failures of a hybrid in-person/virtual conference model. The COVID-19 epidemic presents the scientific community with an opportunity to pioneer novel models that effectively engage virtual participants to advance conference goals.
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Affiliation(s)
- Michael R Fulcher
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Marian L Bolton
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Michael D Millican
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA
| | - Matthew J Michalska-Smith
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA; Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA
| | | | - Jo Handelsman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Kathryn C Milligan-Myhre
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Department of Biological Sciences, University of Alaska, Anchorage, AK, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.
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20
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Cosetta CM, Kfoury N, Robbat A, Wolfe BE. Fungal volatiles mediate cheese rind microbiome assembly. Environ Microbiol 2020; 22:4745-4760. [PMID: 32869420 DOI: 10.1111/1462-2920.15223] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022]
Abstract
In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe-microbe or microbe-host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community-level dynamics. We used the notoriously volatile cheese rind microbiome to identify bacteria responsive to volatiles produced by five widespread cheese fungi. Vibrio casei had the strongest growth stimulation when exposed to all fungi. In multispecies community experiments, fungal volatiles caused a shift to a Vibrio-dominated community, potentially explaining the widespread occurrence of Vibrio in surface-ripened cheeses. RNA sequencing identified activation of the glyoxylate shunt as a possible mechanism underlying volatile-mediated growth promotion and community assembly. Our study demonstrates how airborne chemicals could be used to control the composition of microbiomes and illustrates how volatiles may impact the development of cheese rinds.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
| | - Nicole Kfoury
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Albert Robbat
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
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21
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Williams KB, Bischof J, Lee FJ, Miller KA, LaPalme JV, Wolfe BE, Levin M. Regulation of axial and head patterning during planarian regeneration by a commensal bacterium. Mech Dev 2020; 163:103614. [DOI: 10.1016/j.mod.2020.103614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
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22
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Niccum BA, Kastman EK, Kfoury N, Robbat A, Wolfe BE. Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function. mSystems 2020; 5:e00149-20. [PMID: 32546667 PMCID: PMC7300356 DOI: 10.1128/msystems.00149-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury).IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
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Affiliation(s)
- Brittany A Niccum
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Erik K Kastman
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Nicole Kfoury
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Albert Robbat
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, Massachusetts, USA
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23
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Miller ER, O'Mara Schwartz J, Cox G, Wolfe BE. A Gnotobiotic System for Studying Microbiome Assembly in the Phyllosphere and in Vegetable Fermentation. J Vis Exp 2020. [PMID: 32568237 DOI: 10.3791/61149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The phyllosphere, the above ground portion of the plant that can be colonized by microbes, is a useful model system to identify processes of microbial community assembly. This protocol outlines a system for studying microbial community dynamics in the phyllosphere of Napa cabbage plants. It describes how to grow germ-free plants in test tubes with a calcined clay and nutrient broth substrate. Inoculation of germ-free plants with specific microbial cultures provides opportunities to measure microbial growth and community dynamics in the phyllosphere. Through the use of sterile vegetable extract produced from cabbages shifts in microbial communities that occur during fermentation can also be assessed. This system is relatively simple and inexpensive to set up in the lab and can be used to address key ecological questions in microbial community assembly. It also provides opportunities to understand how phyllosphere community composition can impact the microbial diversity and quality of vegetable fermentations. This approach for developing gnotobiotic cabbage phyllosphere communities could be applied to other wild and agricultural plant species.
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Affiliation(s)
| | | | - Grace Cox
- Department of Biology, Tufts University
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24
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Cosetta CM, Wolfe BE. Causes and consequences of biotic interactions within microbiomes. Curr Opin Microbiol 2019; 50:35-41. [PMID: 31627129 DOI: 10.1016/j.mib.2019.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/20/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes.
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Affiliation(s)
- Casey M Cosetta
- Tufts University, Department of Biology, Medford, MA 02155, United States
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, MA 02155, United States.
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25
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Bodinaku I, Shaffer J, Connors AB, Steenwyk JL, Biango-Daniels MN, Kastman EK, Rokas A, Robbat A, Wolfe BE. Rapid Phenotypic and Metabolomic Domestication of Wild Penicillium Molds on Cheese. mBio 2019; 10:e02445-19. [PMID: 31615965 PMCID: PMC6794487 DOI: 10.1128/mbio.02445-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 02/05/2023] Open
Abstract
Fermented foods provide novel ecological opportunities for natural populations of microbes to evolve through successive recolonization of resource-rich substrates. Comparative genomic data have reconstructed the evolutionary histories of microbes adapted to food environments, but experimental studies directly demonstrating the process of domestication are lacking for most fermented food microbes. Here, we show that during adaptation to cheese, phenotypic and metabolomic traits of wild Penicillium molds rapidly change to produce domesticated phenotypes with properties similar to those of the industrial cultures used to make Camembert and other bloomy rind cheeses. Over a period of just a few weeks, populations of wild Penicillium strains serially passaged on cheese had reduced pigment, spore, and mycotoxin production. Domesticated strains also had a striking change in volatile metabolite production, shifting from production of earthy or musty volatile compounds (e.g., geosmin) to fatty and cheesy volatiles (e.g., 2-nonanone, 2-undecanone). RNA sequencing demonstrated a significant decrease in expression of 356 genes in domesticated strains, with an enrichment of many secondary metabolite production pathways in these downregulated genes. By manipulating the presence of neighboring microbial species and overall resource availability, we demonstrate that the limited competition and high nutrient availability of the cheese environment promote rapid trait evolution of Penicillium molds.IMPORTANCE 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 traits and quickly shift toward producing desirable aroma compounds. In addition to experimentally demonstrating a putative domestication pathway for P. camemberti, our work suggests that wild Penicillium isolates could be rapidly domesticated to produce new flavors and aesthetics in fermented foods.
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Affiliation(s)
- Ina Bodinaku
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Jason Shaffer
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Allison B Connors
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Jacob L Steenwyk
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, USA
| | | | - Erik K Kastman
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, USA
| | - Albert Robbat
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, Massachusetts, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, USA
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26
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Lee FJ, Williams KB, Levin M, Wolfe BE. The Bacterial Metabolite Indole Inhibits Regeneration of the Planarian Flatworm Dugesia japonica. iScience 2018; 10:135-148. [PMID: 30521984 PMCID: PMC6280633 DOI: 10.1016/j.isci.2018.11.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023] Open
Abstract
Planarian flatworms have been used for over a century as models for regeneration. Planarians live in aquatic environments with constant exposure to microbes, but the mechanisms by which bacteria may mediate planarian regeneration are largely unknown. We characterized the microbiome of laboratory populations of the planarian Dugesia japonica and determined how individual bacteria impact D. japonica regeneration. Eight to ten taxa in the phyla Bacteroidetes and Proteobacteria consistently occur across planarian colonies housed in different research laboratories. Individual members of the D. japonica microbiome can delay regeneration including the development of eye spots and blastema formation. The microbial metabolite indole is produced in significant quantities by two bacteria that are consistently found in the D. japonica microbiome and contributes to delays in regeneration. Collectively, these results provide a baseline understanding of the bacteria associated with the planarian D. japonica and demonstrate how metabolite production by host-associated microbes can affect regeneration. The planarian worm Dugesia japonica is colonized by Bacteroidetes and Proteobacteria Many of these bacteria can be cultured and experimentally manipulated Some bacteria can inhibit regeneration, including eye and blastema formation Indole produced by planarian-associated bacteria contributes to regeneration delays
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Affiliation(s)
- Fredrick J Lee
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA.
| | | | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Benjamin E Wolfe
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA.
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Kamelamela N, Zalesne M, Morimoto J, Robbat A, Wolfe BE. Indigo- and indirubin-producing strains of Proteus and Psychrobacter are associated with purple rind defect in a surface-ripened cheese. Food Microbiol 2018; 76:543-552. [PMID: 30166186 DOI: 10.1016/j.fm.2018.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/17/2018] [Accepted: 07/19/2018] [Indexed: 01/28/2023]
Abstract
The rinds of surface-ripened cheeses have expected aesthetic properties, including distinct colors, that contribute to overall quality and consumer acceptance. Atypical rind pigments are frequently reported in small-scale cheese production, but the causes of these color defects are largely unknown. We provide a potential microbial explanation for a striking purple rind defect in a surface-ripened cheese. A cheese producer in the United States reported to us several batches of a raw-milk washed-rind cheese with a distinctly purple rind. We isolated a Proteus species from samples with purple rind defect, but not from samples with typical rind pigments, suggesting that this strain of Proteus could be causing the defect. When provided tryptophan, a precursor in the indigo and indirubin biosynthesis pathway, the isolated strain of Proteus secreted purple-red pigments. A Psychrobacter species isolated from both purple and normal rinds also secreted purple-red pigments. Using thin-layer chromatography and liquid chromatography-mass spectrometry, we confirmed that these bacteria produced indigo and indirubin from tryptophan just as closely related bacteria make these compounds in purple urine bag syndrome in medical settings. Experimental cheese communities with or without Proteus and Psychrobacter confirmed that these Proteobacteria cause purple pigmentation of cheese rinds. Reports of purple rinds in two other cheeses from Europe and the observation of pigment production by Proteus and Psychrobacter strains isolated from other cheese rinds suggest that purple rind defect has the potential to be widespread in surface-ripened cheeses.
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Affiliation(s)
- Noelani Kamelamela
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA
| | - Michael Zalesne
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA
| | - Joshua Morimoto
- Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA; Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Albert Robbat
- Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA; Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, 200 Boston Ave., Medford, MA, 02155, USA; Tufts University Sensory and Science Center, Tufts University, 200 Boston Ave., Medford, MA 02155, USA.
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28
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Schaeffer RN, Wilson CM, Radville L, Barrett M, Whitney E, Roitman S, Miller ER, Wolfe BE, Thornber CS, Orians CM, Preisser EL. Individual and non‐additive effects of exotic sap‐feeders on root functional and mycorrhizal traits of a shared conifer host. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Claire M. Wilson
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | - Laura Radville
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Department of Ecosystem Science and Management and Ecology Intercollege Graduate Degree Program Pennsylvania State University University Park PA USA
| | - Mauri Barrett
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- USDA‐APHIS Buzzards Bay MA USA
| | - Elizabeth Whitney
- Department of Biological Sciences University of Rhode Island Kingston RI USA
| | - Sofia Roitman
- Department of Biological Sciences Tufts University Medford MA USA
| | - Esther R. Miller
- Department of Biological Sciences Tufts University Medford MA USA
| | | | - Carol S. Thornber
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Department of Natural Resources Science University of Rhode Island Kingston RI USA
| | - Colin M. Orians
- Department of Biological Sciences Tufts University Medford MA USA
| | - Evan L. Preisser
- Department of Biological Sciences University of Rhode Island Kingston RI USA
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Abstract
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities. DOI:http://dx.doi.org/10.7554/eLife.22144.001 From the depths of the ocean to the lining of the human gut, almost every environment on Earth is home to a unique community of microorganisms referred to as a microbiome. Within these communities, unrelated microorganisms can exchange genetic information through a process known as horizontal gene transfer. For example, genes linked to antibiotic resistance are often transferred between different microorganisms, which can create increasingly drug resistant microbes and has important implications for human health. Horizontal gene transfer has been studied for almost 100 years, but examining it directly is challenging because, almost by definition, it requires studying a community of microbes rather than one microbe in isolation. As such, researchers are looking for simple models of microbial communities that can be easily manipulated in experiments. Bonham et al. have now turned to the outer surface of cheese, also known as cheese rind, to better understand horizontal gene transfer. As a model system, the cheese rind microbiome is relatively simple to work with because cheese rind is easy to replicate in the laboratory, and the microbes growing on cheese can be grown on their own or in combinations with other microbes. By comparing the genetic material of 165 cheese-associated bacteria to one another, Bonham et al. identified over 4,000 genes that were shared between the bacteria, including several large clusters of genes that were shared by many species. Many of the identified genes (about 23% to be precise) appear to help the microorganisms acquire nutrients that are known to be in short supply on the surface of cheese surface, including iron. Bacteria typically use specialized molecules called siderophores to scavenge for iron and uptake systems to carry the iron-bound siderophore back into the cell. Notably, only the genes associated with the uptake systems were found in some of the shared gene clusters. This finding suggests that horizontal gene transfer has allowed some microbes to “cheat” and take up iron-bound siderophores without expending energy to produce the siderophores themselves. Using the cheese rind microbiome as a model system, it becomes possible to explore how horizontal gene transfer works in more detail than before. A better understanding of this process can then be applied to other important microbiomes, including those where genes conferring antibiotic resistance are commonly exchanged. DOI:http://dx.doi.org/10.7554/eLife.22144.002
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Affiliation(s)
- Kevin S Bonham
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | | | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, San Diego, United States.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, San Diego, United States
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Morokuma J, Durant F, Williams KB, Finkelstein JM, Blackiston DJ, Clements T, Reed DW, Roberts M, Jain M, Kimel K, Trauger SA, Wolfe BE, Levin M. Planarian regeneration in space: Persistent anatomical, behavioral, and bacteriological changes induced by space travel. ACTA ACUST UNITED AC 2017; 4:85-102. [PMID: 28616247 PMCID: PMC5469732 DOI: 10.1002/reg2.79] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/27/2017] [Accepted: 04/21/2017] [Indexed: 12/14/2022]
Abstract
Regeneration is regulated not only by chemical signals but also by physical processes, such as bioelectric gradients. How these may change in the absence of the normal gravitational and geomagnetic fields is largely unknown. Planarian flatworms were moved to the International Space Station for 5 weeks, immediately after removing their heads and tails. A control group in spring water remained on Earth. No manipulation of the planaria occurred while they were in orbit, and space‐exposed worms were returned to our laboratory for analysis. One animal out of 15 regenerated into a double‐headed phenotype—normally an extremely rare event. Remarkably, amputating this double‐headed worm again, in plain water, resulted again in the double‐headed phenotype. Moreover, even when tested 20 months after return to Earth, the space‐exposed worms displayed significant quantitative differences in behavior and microbiome composition. These observations may have implications for human and animal space travelers, but could also elucidate how microgravity and hypomagnetic environments could be used to trigger desired morphological, neurological, physiological, and bacteriomic changes for various regenerative and bioengineering applications.
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Affiliation(s)
- Junji Morokuma
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Fallon Durant
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Katherine B Williams
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Joshua M Finkelstein
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Douglas J Blackiston
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Twyman Clements
- Kentucky Space LLC, 200 West Vine St., Suite 420 Lexington KY 40507 USA
| | - David W Reed
- NASA Kennedy Space Center Space Station Processing Facility Building M7-0360, Kennedy Space Center FL 32899 USA
| | - Michael Roberts
- Center for the Advancement of Science in Space (CASIS) 6905 N. Wickham Rd., Suite 500 Melbourne FL 32940 USA
| | - Mahendra Jain
- Kentucky Space LLC, 200 West Vine St., Suite 420 Lexington KY 40507 USA
| | - Kris Kimel
- Exomedicine Institute 200 West Vine St. Lexington KY 40507 USA
| | - Sunia A Trauger
- Harvard University Small Molecule Mass Spectrometry Facility 52 Oxford St. Cambridge MA 02138 USA
| | - Benjamin E Wolfe
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
| | - Michael Levin
- Allen Discovery Center at Tufts University Biology Department Tufts University 200 Boston Ave., Suite 4600 Medford MA 02155-4243 USA
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Fu X, Harshman SG, Shen X, Haytowitz DB, Karl JP, Wolfe BE, Booth SL. Multiple Vitamin K Forms Exist in Dairy Foods. Curr Dev Nutr 2017; 1:e000638. [PMID: 29955705 PMCID: PMC5998353 DOI: 10.3945/cdn.117.000638] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/15/2017] [Accepted: 05/31/2017] [Indexed: 01/07/2023] Open
Abstract
Background: The plant-based form of vitamin K (phylloquinone, vitamin K-1) has been well quantified in the US diet. Menaquinones (vitamin K-2) are another class of vitamin K compounds that differ from phylloquinone in the length and saturation of their side chain, but they have not been well characterized in foods. Objectives: The objectives of this study were to 1) quantify phylloquinone and the different forms of menaquinones [menaquinone (MK) 4-MK13] in milk, yogurt, Greek yogurt, creams, and cheeses and 2) compare the menaquinone contents of full-fat, reduced-fat, and nonfat dairy products. Methods: All dairy samples were either obtained from the USDA National Food and Nutrient Analysis Program or purchased from retail outlets. Phylloquinone and menaquinone concentrations in these dairy products were quantified by mass spectrometry technology. Results: Full-fat dairy products contained appreciable amounts of menaquinones, primarily in the forms of MK9, MK10, and MK11. We also measured modest amounts of phylloquinone, MK4, MK8, and MK12 in these products. In contrast, there was little MK5-7 or MK13 detected in the majority of dairy products. The total vitamin K contents of soft cheese, blue cheese, semi-soft cheese, and hard cheese were (means ± SEMs): 506 ± 63, 440 ± 41, 289 ± 38, and 282 ± 5.0 µg/100 g, respectively. Nonfermented cheeses, such as processed cheese, contained lower amounts of vitamin K (98 ± 11 µg/100 g). Reduced-fat or fat-free dairy products contained ∼5-22% of the vitamin K found in full-fat equivalents. For example, total vitamin K contents of full-fat milk (4% fat), 2%-fat milk, 1%-fat milk, and nonfat milk were 38.1 ± 8.6, 19.4 ± 7.7, 12.9 ± 2.0, and 7.7 ± 2.9 µg/100 g, respectively. Conclusions: To the best of our knowledge, this is the first report of menaquinone contents of US dairy products. Findings indicate that the amount of vitamin K contents in dairy products is high and proportional to the fat content of the product.
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Affiliation(s)
- Xueyan Fu
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Stephanie G Harshman
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Xiaohua Shen
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - David B Haytowitz
- Beltsville Human Nutrition Research Center, USDA–Agricultural Research Service, Beltsville, MD
| | - J Philip Karl
- Military Nutrition Division, US Army Research Institute of Environmental Medicine, Natick, MA
| | | | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
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32
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Karl JP, Fu X, Wang X, Zhao Y, Shen J, Zhang C, Wolfe BE, Saltzman E, Zhao L, Booth SL. Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota-targeted dietary intervention. Am J Clin Nutr 2015; 102:84-93. [PMID: 26016865 DOI: 10.3945/ajcn.115.109496] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Emerging evidence supports novel roles for vitamin K in cardiometabolic health, some of which may be unique to the bacterially synthesized vitamin K forms known as menaquinones. However, factors influencing menaquinone biosynthesis by the gut microbiota and associations with cardiometabolic health have not been examined. OBJECTIVE The objective of this study was to identify associations between fecal menaquinone profiles, gut microbiota composition, and biomarkers of cardiometabolic health. DESIGN The menaquinone profile and gut microbiota structure were periodically measured in fecal samples collected from 77 overweight Chinese adults who consumed a prescribed diet previously shown to alter gut microbiota composition and to improve cardiometabolic biomarkers. RESULTS Covariance among menaquinones within individual fecal samples partitioned individuals into 2 distinct groups, herein introduced as menaquinotypes of the human gut. Menaquinotypes were characterized by differences in menaquinone (MK) 5 and MK9-MK13 and differences in the relative abundance of several operational taxonomic units (OTUs) delineated at the species level, predominantly within the genera Prevotella spp. and Bacteroides spp. Fecal MK4, MK6, and MK8 decreased during the intervention (P < 0.05); and longitudinal changes in the relative abundance of >100 OTUs were associated with altered fecal content of ≥1 individual menaquinone. The strongest and most consistent relations were between Prevotella spp. and MK5 and MK11-MK13, between Bacteroides spp. and MK9 and MK10, and between Escherichia/Shigella spp. and MK8. Neither individual menaquinones nor menaquinotypes were longitudinally associated with markers of glycemia, insulin resistance, or inflammation. CONCLUSIONS These findings suggest that variability in fecal menaquinone content is predominantly determined by relatively few genera within the gut microbiota and that diet-mediated alterations in gut microbiota composition may provide a feasible approach for altering gut menaquinone content. This trial was registered at the Chinese Clinical Trials Registry as ChiCTR-TRC-09000353.
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Affiliation(s)
- J Philip Karl
- Vitamin K Laboratory and Energy Metabolism Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | | | - Xiaoxin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yufeng Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Shen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Edward Saltzman
- Energy Metabolism Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China; and
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Abstract
Microbial communities of fermented foods have provided humans with tools for preservation and flavor development for thousands of years. These simple, reproducible, accessible, culturable, and easy-to-manipulate systems also provide opportunities for dissecting the mechanisms of microbial community formation. Fermented foods can be valuable models for processes in less tractable microbiota.
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Affiliation(s)
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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Wolfe BE, Button JE, Santarelli M, Dutton RJ. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 2014; 158:422-433. [PMID: 25036636 DOI: 10.1016/j.cell.2014.05.041] [Citation(s) in RCA: 373] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/07/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.
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Affiliation(s)
- Benjamin E Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Julie E Button
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Marcela Santarelli
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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35
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Hess J, Skrede I, Wolfe BE, LaButti K, Ohm RA, Grigoriev IV, Pringle A. Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi. Genome Biol Evol 2014; 6:1564-78. [PMID: 24923322 PMCID: PMC4122921 DOI: 10.1093/gbe/evu121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.
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Affiliation(s)
- Jaqueline Hess
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Inger Skrede
- Department of Organismic and Evolutionary Biology, Harvard UniversitySection for Genetics and Evolutionary Biology, University of Oslo, Norway
| | - Benjamin E Wolfe
- Department of Organismic and Evolutionary Biology, Harvard UniversityFAS Center for Systems Biology, Harvard University
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California
| | - Robin A Ohm
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California
| | - Anne Pringle
- Department of Organismic and Evolutionary Biology, Harvard University
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David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2013; 505:559-63. [PMID: 24336217 PMCID: PMC3957428 DOI: 10.1038/nature12820] [Citation(s) in RCA: 5986] [Impact Index Per Article: 544.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022]
Abstract
Long-term diet influences the structure and activity of the trillions of
microorganisms residing in the human gut1–5, but it
remains unclear how rapidly and reproducibly the human gut microbiome responds
to short-term macronutrient change. Here, we show that the short-term
consumption of diets composed entirely of animal or plant products alters
microbial community structure and overwhelms inter-individual differences in
microbial gene expression. The animal-based diet increased the abundance of
bile-tolerant microorganisms (Alistipes, Bilophila, and
Bacteroides) and decreased the levels of Firmicutes that
metabolize dietary plant polysaccharides (Roseburia, Eubacterium
rectale, and Ruminococcus bromii). Microbial
activity mirrored differences between herbivorous and carnivorous
mammals2, reflecting
trade-offs between carbohydrate and protein fermentation. Foodborne microbes
from both diets transiently colonized the gut, including bacteria, fungi, and
even viruses. Finally, increases in the abundance and activity of
Bilophila wadsworthia on the animal-based diet support a
link between dietary fat, bile acids, and the outgrowth of microorganisms
capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the
gut microbiome can rapidly respond to altered diet, potentially facilitating the
diversity of human dietary lifestyles.
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Affiliation(s)
- Lawrence A David
- 1] FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] Society of Fellows, Harvard University, Cambridge, Massachusetts 02138, USA [3] Molecular Genetics & Microbiology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
| | - Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Rachel N Carmody
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - David B Gootenberg
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Julie E Button
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Benjamin E Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alisha V Ling
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - A Sloan Devlin
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Yug Varma
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Michael A Fischbach
- Department of Bioengineering & Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94158, USA
| | - Sudha B Biddinger
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Hsu CC, ElNaggar MS, Peng Y, Fang J, Sanchez LM, Mascuch SJ, Møller A, Alazzeh EK, Pikula J, Quinn RA, Zeng Y, Wolfe BE, Dutton RJ, Gerwick L, Zhang L, Liu X, Månsson M, Dorrestein PC. Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Anal Chem 2013; 85:7014-8. [PMID: 23819546 PMCID: PMC3890442 DOI: 10.1021/ac401613x] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microorganisms such as bacteria and fungi produce a variety of specialized metabolites that are invaluable for agriculture, biological research, and drug discovery. However, the screening of microbial metabolic output is usually a time-intensive task. Here, we utilize a liquid microjunction surface sampling probe for electrospray ionization-mass spectrometry to extract and ionize metabolite mixtures directly from living microbial colonies grown on soft nutrient agar in Petri-dishes without any sample pretreatment. To demonstrate the robustness of the method, this technique was applied to observe the metabolic output of more than 30 microorganisms, including yeast, filamentous fungi, pathogens, and marine-derived bacteria, that were collected worldwide. Diverse natural products produced from different microbes, including Streptomyces coelicolor , Bacillus subtilis , and Pseudomonas aeruginosa are further characterized.
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Affiliation(s)
- Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Yao Peng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jinshu Fang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laura M. Sanchez
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Amalie Møller
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | - Jiri Pikula
- University of Veterinary and Pharmaceutical Sciences, Palackeho 1/3, 612 42 Brno, Czech Republic
| | - Robert A. Quinn
- Biology Department, San Diego State University, San Diego, CA 92182, USA
| | - Yi Zeng
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin E. Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachel J. Dutton
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lena Gerwick
- Scripps Institute of Oceanography, La Jolla, CA 92037, USA
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Maria Månsson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Pieter C. Dorrestein
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA 92093, USA
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Abstract
PURPOSE The purpose of this study was to investigate gender differences in binge eating and associated behavioral correlates in college students. METHODS A webbased survey was conducted with 2073 students (mean age 19.8 yr; range 18-23 yr). Multiple logistic regression was used to calculate odds ratios and 95% confidence intervals for the factors associated with binge eating. RESULTS Twenty-nine percent of students reported recent bingeing. Factors associated with binge eating included being female, having a higher body mass index, current tobacco use, and exercising to lose weight. Women were more likely to binge eat (73.8%; χ(2)=32.3; p≤0.001), report loss of control (45%; χ(2)=16.3; p≤0.001), self induced vomiting (20.7%; χ(2)=15.9; p≤0.001), and laxative use (6.7%; χ(2)=8.93; p≤0.001). CONCLUSIONS Results generated from this study suggest that gender-disparate behaviors are potential targets for future tailored interventions.
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Affiliation(s)
- S Kelly-Weeder
- William F. Connell School of Nursing, Boston College, Chestnut Hill, MA 02467, USA.
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Wolfe BE, Tulloss RE, Pringle A. The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis. PLoS One 2012; 7:e39597. [PMID: 22815710 PMCID: PMC3399872 DOI: 10.1371/journal.pone.0039597] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/28/2012] [Indexed: 11/19/2022] Open
Abstract
Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms.
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Affiliation(s)
- Benjamin E Wolfe
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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Wolfe BE, Pringle A. Geographically structured host specificity is caused by the range expansions and host shifts of a symbiotic fungus. ISME J 2012; 6:745-55. [PMID: 22134645 PMCID: PMC3309363 DOI: 10.1038/ismej.2011.155] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/12/2011] [Accepted: 09/15/2011] [Indexed: 11/09/2022]
Abstract
The inability to associate with local species may constrain the spread of mutualists arriving to new habitats, but the fates of introduced, microbial mutualists are largely unknown. The deadly poisonous ectomycorrhizal fungus Amanita phalloides (the death cap) is native to Europe and introduced to the East and West Coasts of North America. By cataloging host associations across the two continents, we record dramatic changes in specificity among the three ranges. On the East Coast, where the fungus is restricted in its distribution, it associates almost exclusively with pines, which are rarely hosts of A. phalloides in its native range. In California, where the fungus is widespread and locally abundant, it associates almost exclusively with oaks, mirroring the host associations observed in Europe. The most common host of the death cap in California is the endemic coast live oak (Quercus agrifolia), and the current distribution of A. phalloides appears constrained within the distribution of Q. agrifolia. In California, host shifts to native plants are also associated with a near doubling in the resources allocated to sexual reproduction and a prolonged fruiting period; mushrooms are twice as large as they are elsewhere and mushrooms are found throughout the year. Host and niche shifts are likely to shape the continuing range expansion of A. phalloides and other ectomycorrhizal fungi introduced across the world.
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Affiliation(s)
- Benjamin E Wolfe
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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Abstract
Although most species in the genus Amanita form ectomycorrhizal associations, a few are reported to be saprotrophs living in grassland habitats. Little is known about the ecology and distribution of these free-living Amanita species. We describe the ecology of Amanita thiersii, a species commonly collected in lawns throughout the Mississippi River Basin. Stable isotopes of carbon, transcriptomic sequences and patterns of growth on complex carbon sources provide evidence for A. thiersii as a saprotrophic species. Sporocarps of A. thiersii are less depleted in (13)C compared to published data for ectomycorrhizal fungi, supporting a saprotrophic mode of carbon acquisition in the field. Orthologs of cellulase genes known to play key roles in the decomposition of cellulose in other basidiomycetes were identified in a transcriptome of A. thiersii, establishing that this species has the genetic potential to degrade cellulose. Amanita thiersii also can use artificial cellulose or sterile grass litter as a sole carbon source. DNA sequences of three nuclear gene regions and banding patterns from four inter-simple sequence repeat markers were identical across 31 populations from throughout the known range of the species, which suggests the genetic diversity of A. thiersii populations is low. Maps of A. thiersii collections made from the 1950s until present suggest this species is experiencing a range expansion. It was reported first in 1952 in Texas and now occurs in nine states north to Illinois. These data provide an ecological context for interpreting the genome of A. thiersii, currently being sequenced at the United States Department of Energy's Joint Genome Institute.
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Affiliation(s)
- Benjamin E Wolfe
- Harvard University, FAS Center for Systems Biology, Cambridge, MA 02138, USA.
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Wolfe BE, Richard F, Cross HB, Pringle A. Distribution and abundance of the introduced ectomycorrhizal fungus Amanita phalloides in North America. New Phytol 2010; 185:803-816. [PMID: 20002314 DOI: 10.1111/j.1469-8137.2009.03097.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Despite a growing awareness of the global reach of ectomycorrhizal (EM) fungal introductions, little is known about the fate of introduced EM fungi in novel ranges. Using herbarium specimens, species distribution models, and field collections of sporocarps, root tips and extramatrical mycelia, we assessed the distribution and abundance of the European species Amanita phalloides in North America. There are two distinct ranges of the fungus, one along the West Coast (California to British Columbia) and the second on the East Coast (Maryland to Maine). As predicted by a species distribution model, the West Coast range is larger. Amanita phalloides is more frequently found in native forests on the West Coast than on the East Coast. At Point Reyes Peninsula in California, A. phalloides dominates community sporocarp biomass, and is frequent as root tips. In individual soil cores at Point Reyes, root tips of A. phalloides make up 50% of total root tip biomass. Hyphae of A. phalloides are frequent, but make up only 2% of total hyphal biomass. The contrasting patterns of the distribution and abundance of A. phalloides on the East and West Coasts of North America may influence both its future spread and its impacts.
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Affiliation(s)
- Benjamin E Wolfe
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Abstract
Plants have often been moved across the globe with intact root systems. These roots are likely to have housed symbiotic ectomycorrhizal (EM) fungi and the movement of plants may have facilitated the introduction of EM fungi.Here, we report data compiled from a newly created database of EM fungal introductions.We estimate the magnitude of EM fungal introductions around the world and examine patterns associated with these introductions. We also use the data to develop a framework for understanding the invasion biology of EM fungi.At least 200 species of basidiomycete and ascomycete EM fungi have been moved from native ranges to novel habitats. The majority of recorded introductions are associated with Pinus or Eucalyptus plantations in the southern hemisphere. Most introduced species appear to be constrained from spreading in novel habitats and associate only with their introduced hosts. Aspects of life history, including host range, may influence the ability of EM species to establish or invade. Human-caused introductions of EM fungi are a common and global phenomenon.The mechanisms controlling EM fungi in novel habitats and potential impacts of EM fungal introductions are almost entirely unknown.
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Affiliation(s)
- Else C Vellinga
- Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Benjamin E Wolfe
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Anne Pringle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Abstract
BACKGROUND Recent studies suggest that purging disorder (PD) may be a common eating disorder that is associated with clinically significant levels of distress and high levels of psychiatric co-morbidity. However, no study has established evidence of disorder-related impairment or whether distress is specifically related to PD rather than to co-morbid disorders. METHOD Three groups of normal-weight women [non-eating disorder controls (n=38), with PD (n=24), and with bulimia nervosa (BN)-purging subtype (n=57)] completed structured clinical interviews and self-report assessments. RESULTS Both PD and BN were associated with significant co-morbidity and elevations on indicators of distress and impairment compared to controls. Compared to BN, PD was associated with lower rates of current and lifetime mood disorders but higher rates of current anxiety disorders. Elevated distress and impairment were maintained in PD and BN after controlling for Axis I and Axis II disorders. CONCLUSIONS PD is associated with elevated distress and impairment and should be considered for inclusion as a provisional disorder in nosological schemes such as the Diagnostic and Statistical Manual to facilitate much-needed research on this clinically significant syndrome.
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Affiliation(s)
- P K Keel
- Department of Psychology, The University of Iowa, Iowa City, IA, USA.
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Peterson CN, Day S, Wolfe BE, Ellison AM, Kolter R, Pringle A. A keystone predator controls bacterial diversity in the pitcher-plant (Sarracenia purpurea) microecosystem. Environ Microbiol 2008; 10:2257-66. [DOI: 10.1111/j.1462-2920.2008.01648.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wolfe BE, Mummey DL, Rillig MC, Klironomos JN. Small-scale spatial heterogeneity of arbuscular mycorrhizal fungal abundance and community composition in a wetland plant community. Mycorrhiza 2007; 17:175-183. [PMID: 17186281 DOI: 10.1007/s00572-006-0089-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Accepted: 10/19/2006] [Indexed: 05/13/2023]
Abstract
Although it has become increasingly clear that arbuscular mycorrhizal fungi (AMF) play important roles in population, community, and ecosystem ecology, there is limited information on the spatial structure of the community composition of AMF in the field. We assessed small-scale spatial variation in the abundance and molecular diversity of AMF in a calcareous fen, where strong underlying environmental gradients such as depth to water table may influence AMF. Throughout an intensively sampled 2 x 2 m plot, we assessed AMF inoculum potential at a depth of 0-6 and 6-12 cm and molecular diversity of the AMF community using terminal restriction fragment length polymorphism of 18S rDNA. Inoculum potential was only significantly spatially autocorrelated at a depth of 6-12 cm and was significantly positively correlated with depth to water table at both depths. Molecular diversity of the AMF community was highly variable within the plot, ranging from 2-14 terminal restriction fragments (T-RFs) per core, but the number of T-RFs did not relate to water table or plant species richness. Plant community composition was spatially autocorrelated at small scales, but AMF community composition showed no significant spatial autocorrelation. Saturated soils of calcareous fens contain many infective AMF propagules and the abundance and diversity of AMF inoculum is patchy over small spatial scales.
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Affiliation(s)
- Benjamin E Wolfe
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02130, USA.
| | - Daniel L Mummey
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA
| | - Matthias C Rillig
- Division of Biological Sciences, The University of Montana, Missoula, MT, 59812, USA
| | - John N Klironomos
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Stinson KA, Campbell SA, Powell JR, Wolfe BE, Callaway RM, Thelen GC, Hallett SG, Prati D, Klironomos JN. Invasive plant suppresses the growth of native tree seedlings by disrupting belowground mutualisms. PLoS Biol 2006. [PMID: 16623597 DOI: 10.1371/journalpbio.0040140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
The impact of exotic species on native organisms is widely acknowledged, but poorly understood. Very few studies have empirically investigated how invading plants may alter delicate ecological interactions among resident species in the invaded range. We present novel evidence that antifungal phytochemistry of the invasive plant, Alliaria petiolata, a European invader of North American forests, suppresses native plant growth by disrupting mutualistic associations between native canopy tree seedlings and belowground arbuscular mycorrhizal fungi. Our results elucidate an indirect mechanism by which invasive plants can impact native flora, and may help explain how this plant successfully invades relatively undisturbed forest habitat.
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Stinson KA, Campbell SA, Powell JR, Wolfe BE, Callaway RM, Thelen GC, Hallett SG, Prati D, Klironomos JN. Invasive plant suppresses the growth of native tree seedlings by disrupting belowground mutualisms. PLoS Biol 2006; 4:e140. [PMID: 16623597 PMCID: PMC1440938 DOI: 10.1371/journal.pbio.0040140] [Citation(s) in RCA: 325] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/01/2006] [Indexed: 12/05/2022] Open
Abstract
The impact of exotic species on native organisms is widely acknowledged, but poorly understood. Very few studies have empirically investigated how invading plants may alter delicate ecological interactions among resident species in the invaded range. We present novel evidence that antifungal phytochemistry of the invasive plant, Alliaria petiolata, a European invader of North American forests, suppresses native plant growth by disrupting mutualistic associations between native canopy tree seedlings and belowground arbuscular mycorrhizal fungi. Our results elucidate an indirect mechanism by which invasive plants can impact native flora, and may help explain how this plant successfully invades relatively undisturbed forest habitat.
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Affiliation(s)
- Kristina A Stinson
- 1Harvard Forest, Harvard University, Petersham, Massachusetts, United States of America
| | - Stuart A Campbell
- 2Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jeff R Powell
- 2Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Benjamin E Wolfe
- 2Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ragan M Callaway
- 3Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Giles C Thelen
- 3Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Steven G Hallett
- 4Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daniel Prati
- 5Department of Community Ecology, UFZ Centre for Environmental Research, Halle, Germany
| | - John N Klironomos
- 2Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Klironomos JN, Allen MF, Rillig MC, Piotrowski J, Makvandi-Nejad S, Wolfe BE, Powell JR. Abrupt rise in atmospheric CO2 overestimates community response in a model plant–soil system. Nature 2005; 433:621-4. [PMID: 15703744 DOI: 10.1038/nature03268] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Accepted: 12/09/2004] [Indexed: 11/09/2022]
Abstract
Attempts to understand the ecological effect of increasing atmospheric CO2 concentration, [CO2], usually involve exposing today's ecosystems to expected future [CO2] levels. However, a major assumption of these approaches has not been tested--that exposing ecosystems to a single-step increase in [CO2] will yield similar responses to those of a gradual increase over several decades. We tested this assumption on a mycorrhizal fungal community over a period of six years. [CO2] was either increased abruptly, as is typical of most [CO2] experiments, or more gradually over 21 generations. The two approaches resulted in different structural and functional community responses to increased [CO2]. Some fungi were sensitive to the carbon pulse of the abrupt [CO2] treatment. This resulted in an immediate decline in fungal species richness and a significant change in mycorrhizal functioning. The magnitude of changes in fungal diversity and functioning in response to gradually increasing [CO2] was smaller, and not significantly different to those with ambient [CO2]. Our results suggest that studies may overestimate some community responses to increasing [CO2] because biota may be sensitive to ecosystem changes that occur as a result of abrupt increases.
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Affiliation(s)
- John N Klironomos
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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