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Ladau J, Brodie EL, Falco N, Bansal I, Hoffman EB, Joachimiak MP, Mora AM, Walker AM, Wainwright HM, Wu Y, Pavicic M, Jacobson D, Hess M, Brown JB, Abuabara K. Estimating geographic variation of infection fatality ratios during epidemics. Infect Dis Model 2024; 9:634-643. [PMID: 38572058 PMCID: PMC10990719 DOI: 10.1016/j.idm.2024.02.009] [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] [Received: 11/10/2023] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Objectives We aim to estimate geographic variability in total numbers of infections and infection fatality ratios (IFR; the number of deaths caused by an infection per 1,000 infected people) when the availability and quality of data on disease burden are limited during an epidemic. Methods We develop a noncentral hypergeometric framework that accounts for differential probabilities of positive tests and reflects the fact that symptomatic people are more likely to seek testing. We demonstrate the robustness, accuracy, and precision of this framework, and apply it to the United States (U.S.) COVID-19 pandemic to estimate county-level SARS-CoV-2 IFRs. Results The estimators for the numbers of infections and IFRs showed high accuracy and precision; for instance, when applied to simulated validation data sets, across counties, Pearson correlation coefficients between estimator means and true values were 0.996 and 0.928, respectively, and they showed strong robustness to model misspecification. Applying the county-level estimators to the real, unsimulated COVID-19 data spanning April 1, 2020 to September 30, 2020 from across the U.S., we found that IFRs varied from 0 to 44.69, with a standard deviation of 3.55 and a median of 2.14. Conclusions The proposed estimation framework can be used to identify geographic variation in IFRs across settings.
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Affiliation(s)
- Joshua Ladau
- Departments of Computational Precision Health and Dermatology, University of California, San Francisco, CA, 94115, USA
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nicola Falco
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ishan Bansal
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Elijah B. Hoffman
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Graduate Group in Biostatistics, University of California, Berkeley, CA, 94720, USA
| | - Marcin P. Joachimiak
- Biosystems Data Science, Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ana M. Mora
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Angelica M. Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Haruko M. Wainwright
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Boston, MA, 02139, USA
| | - Yulun Wu
- Graduate Group in Biostatistics, University of California, Berkeley, CA, 94720, USA
| | - Mirko Pavicic
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | | | - James B. Brown
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Statistics Department, University of California, Berkeley, CA, 94720, USA
| | - Katrina Abuabara
- Departments of Computational Precision Health and Dermatology, University of California, San Francisco, CA, 94115, USA
- Division of Epidemiology and Biostatistics, University of California Berkeley School of Public Health, 2121 Berkeley Way, Berkeley, CA, 94720, USA
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2
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Ladau J, Ramirez KS. A global catalogue of plant-beneficial bacteria. Nat Food 2023; 4:933-934. [PMID: 37904025 DOI: 10.1038/s43016-023-00877-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Affiliation(s)
- Joshua Ladau
- Department of Computational Precision Health, University of California, San Francisco, CA, USA.
| | - Kelly S Ramirez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
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3
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Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. Author Correction: A genomic catalog of Earth's microbiomes. Nat Biotechnol 2021; 39:521. [PMID: 33795890 PMCID: PMC8041621 DOI: 10.1038/s41587-021-00898-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - Dongying Wu
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - I-Min Chen
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - T B K Reddy
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | | | - Sean P Jungbluth
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dylan Chivian
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paramvir Dehal
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Axel Visel
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
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4
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Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. A genomic catalog of Earth's microbiomes. Nat Biotechnol 2021; 39:499-509. [PMID: 33169036 PMCID: PMC8041624 DOI: 10.1038/s41587-020-0718-6] [Citation(s) in RCA: 307] [Impact Index Per Article: 102.3] [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: 12/24/2019] [Accepted: 09/28/2020] [Indexed: 01/02/2023]
Abstract
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
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Affiliation(s)
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - Dongying Wu
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - I-Min Chen
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | - T B K Reddy
- DOE Joint Genome Institute, Berkeley, CA, USA
| | | | | | | | | | | | - Sean P Jungbluth
- DOE Joint Genome Institute, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dylan Chivian
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paramvir Dehal
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Axel Visel
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
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5
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Roque BM, Brooke CG, Ladau J, Polley T, Marsh LJ, Najafi N, Pandey P, Singh L, Kinley R, Salwen JK, Eloe-Fadrosh E, Kebreab E, Hess M. Correction to: Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage. Anim Microbiome 2019. [PMCID: PMC7803119 DOI: 10.1186/s42523-019-0005-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Větrovský T, Kohout P, Kopecký M, Machac A, Man M, Bahnmann BD, Brabcová V, Choi J, Meszárošová L, Human ZR, Lepinay C, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Morais D, Navrátilová D, Odriozola I, Štursová M, Švec K, Tláskal V, Urbanová M, Wan J, Žifčáková L, Howe A, Ladau J, Peay KG, Storch D, Wild J, Baldrian P. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat Commun 2019; 10:5142. [PMID: 31723140 PMCID: PMC6853883 DOI: 10.1038/s41467-019-13164-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [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: 08/23/2018] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa. The authors assemble and analyse previously generated mycobiome data linked to geographical locations across the world. They describe the distribution of fungal taxa and show that climate is an important driver of fungal biogeography and that fungal diversity appears to be concentrated at high latitudes.
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Affiliation(s)
- Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.,Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic
| | - Martin Kopecký
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521, Praha 6, Czech Republic
| | - Antonin Machac
- Faculty of Science, Charles University, Albertov 6, 12844, Praha 2, Czech Republic.,Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark.,Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T 1Z4, Canada
| | - Matěj Man
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Lenka Meszárošová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Zander Rainier Human
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Diana Navrátilová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Joe Wan
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA, 50011, USA
| | - Joshua Ladau
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | | | - David Storch
- Center for Theoretical Study, Charles University and the Czech Academy of Sciences, Jilská 1, 11000, Praha 1, Czech Republic.,Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Jan Wild
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243, Průhonice, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Ladau J, Eloe-Fadrosh EA. Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology. Trends Microbiol 2019; 27:662-669. [PMID: 31000488 DOI: 10.1016/j.tim.2019.03.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023]
Abstract
Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.
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Roque BM, Brooke CG, Ladau J, Polley T, Marsh LJ, Najafi N, Pandey P, Singh L, Kinley R, Salwen JK, Eloe-Fadrosh E, Kebreab E, Hess M. Effect of the macroalgae Asparagopsis taxiformis on methane production and rumen microbiome assemblage. Anim Microbiome 2019; 1:3. [PMID: 33499933 PMCID: PMC7803124 DOI: 10.1186/s42523-019-0004-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [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: 09/19/2018] [Accepted: 01/17/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH4) production from beef cattle by up to ~ 99% when added to Rhodes grass hay; a common feed in the Australian beef industry. These experiments have shown significant reductions in CH4 without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California, the largest milk producing state in the US. RESULTS Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome consistent with the Anna Karenina hypothesis, with increased β-diversity, over time scales of approximately 3 days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of CH4 in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed. CONCLUSIONS The methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy for dairy cattle. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.
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Affiliation(s)
- Breanna Michell Roque
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Charles Garrett Brooke
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Joshua Ladau
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Tamsen Polley
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Lyndsey Jean Marsh
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Negeen Najafi
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Pramod Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, One Shields Avenue, Davis, CA 95616 USA
| | - Latika Singh
- Department of Population Health and Reproduction, School of Veterinary Medicine, One Shields Avenue, Davis, CA 95616 USA
| | - Robert Kinley
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Building 145 James Cook Drive, James Cook University, Townsville, QLD 4811 Australia
| | - Joan King Salwen
- Department of Earth System Science, Stanford University, 450 Serra Mall, Stanford, CA 94305 USA
| | - Emiley Eloe-Fadrosh
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ermias Kebreab
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Matthias Hess
- Department of Animal Science, University of California, 2251 Meyer Hall, Davis, CA 95616 USA
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Lloyd KG, Steen AD, Ladau J, Yin J, Crosby L. Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes. mSystems 2018; 3:e00055-18. [PMID: 30273414 PMCID: PMC6156271 DOI: 10.1128/msystems.00055-18] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [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: 04/16/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029 (81%) and 2.2 × 1029 (25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems. IMPORTANCE In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called "microbial dark matter," are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions. Author Video: An author video summary of this article is available.
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Affiliation(s)
- Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Andrew D. Steen
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Joshua Ladau
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
| | - Junqi Yin
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Lonnie Crosby
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, USA
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10
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1219] [Impact Index Per Article: 174.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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11
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Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Urban greenness influences airborne bacterial community composition. Sci Total Environ 2016; 571:680-7. [PMID: 27418518 DOI: 10.1016/j.scitotenv.2016.07.037] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [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: 05/17/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/06/2023]
Abstract
Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing neighborhoods and open space systems that foster better human health.
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Affiliation(s)
- Gwynne Mhuireach
- Department of Landscape Architecture, University of Oregon, Eugene, OR, United States; Institute for a Sustainable Environment, University of Oregon, Eugene, OR, United States; Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States; Energy Studies in Buildings Laboratory, Department of Architecture, University of Oregon, Eugene, OR, United States.
| | - Bart R Johnson
- Department of Landscape Architecture, University of Oregon, Eugene, OR, United States; Institute for a Sustainable Environment, University of Oregon, Eugene, OR, United States
| | - Adam E Altrichter
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Joshua Ladau
- Gladstone Institutes, University of California, San Francisco, CA, United States
| | - James F Meadow
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Katherine S Pollard
- Gladstone Institutes, University of California, San Francisco, CA, United States; Division of Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, United States
| | - Jessica L Green
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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12
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Maurice CF, Knowles SCL, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. ISME J 2015; 9:2423-34. [PMID: 26023870 PMCID: PMC4611506 DOI: 10.1038/ismej.2015.53] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 02/10/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022]
Abstract
Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.
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Affiliation(s)
- Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Sarah C L Knowles
- Centre for Immunity, Infection and Evolution (CIIE), School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, UK
| | | | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.,Institute for Human Genetics and Division of Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, UK
| | - Amy B Pedersen
- Centre for Immunity, Infection and Evolution (CIIE), School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Peter J Turnbaugh
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA.,Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California San Francisco, San Francisco, CA, USA
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Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 2013; 342:621-4. [PMID: 24179225 DOI: 10.1126/science.1243768] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.
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Affiliation(s)
- Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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14
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Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Global marine bacterial diversity peaks at high latitudes in winter. ISME J 2013; 7:1669-77. [PMID: 23514781 PMCID: PMC3749493 DOI: 10.1038/ismej.2013.37] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/25/2013] [Accepted: 01/31/2013] [Indexed: 11/17/2022]
Abstract
Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms.
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Affiliation(s)
- Joshua Ladau
- The Gladstone Institutes, University of California, San Francisco, CA 94158, USA.
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15
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16
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Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol 2011; 7:e1001061. [PMID: 21283775 PMCID: PMC3024254 DOI: 10.1371/journal.pcbi.1001061] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [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: 07/22/2010] [Accepted: 12/17/2010] [Indexed: 12/30/2022] Open
Abstract
Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
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Affiliation(s)
- Thomas J Sharpton
- The J. David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America.
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Ladau J, Schwager SJ. Robust hypothesis tests for independence in community assembly. J Math Biol 2008; 57:537-55. [DOI: 10.1007/s00285-008-0176-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 02/26/2008] [Indexed: 11/24/2022]
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20
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Bezzerides A, Yong TH, Bezzerides J, Husseini J, Ladau J, Eisner M, Eisner T. Plant-derived pyrrolizidine alkaloid protects eggs of a moth (Utetheisa ornatrix) against a parasitoid wasp (Trichogramma ostriniae). Proc Natl Acad Sci U S A 2004; 101:9029-32. [PMID: 15173598 PMCID: PMC428467 DOI: 10.1073/pnas.0402480101] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [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] [Indexed: 11/18/2022] Open
Abstract
Pyrrolizidine alkaloid (PA), sequestered by the moth Utetheisa ornatrix from its larval food plant, is transmitted by both males and females to the eggs. Males confer PA on the female by seminal infusion, and females pass this gift, together with PA that they themselves procured as larvae, to the eggs. Here we show that PA protects the eggs against parasitization by the chalcidoid wasp, Trichogramma ostriniae. Eggs laid subsequent to a first mating of an Utetheisa female receive most of their PA from the female. The amount they receive from the male is insufficient to provide for full protection. However, female Utetheisa are promiscuous and therefore likely to receive PA on a cumulative basis from their male partners.
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Abstract
Gonatista grisea (Fabricius) is one of many arboreal arthropods and reptiles that orient downwards to ambush prey. To investigate if orienting downwards increases hunting success, a 2 × 2 factorial experiment was performed using mantid orientation (upwards, downwards) and direction of prey approach (posterior, anterior) as factors and prey capture success as the response variable. The results indicated that the mantid captures prey equally well when oriented upwards or downwards but that it is less effective when the prey approaches posteriorly. Because prey likely climb upwards more frequently than downwards, these findings suggest that G. grisea increases its hunting success with its downwards orientation.
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