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Elbon CE, Stewart FJ, Glass JB. Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone. Appl Environ Microbiol 2024; 90:e0209923. [PMID: 38445905 PMCID: PMC11022542 DOI: 10.1128/aem.02099-23] [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: 11/20/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (nod) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed nod genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria, rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe nod, but at lower relative abundance than UBA11136 in the upper ODZ. The nod-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named ptd) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.IMPORTANCEIn marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world's largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (nod) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe nod at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.
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Affiliation(s)
- Claire E. Elbon
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Frank J. Stewart
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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2
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Clements CS, Pratte ZA, Stewart FJ, Hay ME. Removal of detritivore sea cucumbers from reefs increases coral disease. Nat Commun 2024; 15:1338. [PMID: 38409274 PMCID: PMC10897328 DOI: 10.1038/s41467-024-45730-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 08/21/2023] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
Coral reefs are in global decline with coral diseases playing a significant role. This is especially true for Acroporid corals that represent ~25% of all Pacific coral species and generate much of the topographic complexity supporting reef biodiversity. Coral diseases are commonly sediment-associated and could be exacerbated by overharvest of sea cucumber detritivores that clean reef sediments and may suppress microbial pathogens as they feed. Here we show, via field manipulations in both French Polynesia and Palmyra Atoll, that historically overharvested sea cucumbers strongly suppress disease among corals in contact with benthic sediments. Sea cucumber removal increased tissue mortality of Acropora pulchra by ~370% and colony mortality by ~1500%. Additionally, farmerfish that kill Acropora pulchra bases to culture their algal gardens further suppress disease by separating corals from contact with the disease-causing sediment-functioning as mutualists rather than parasites despite killing coral bases. Historic overharvesting of sea cucumbers increases coral disease and threatens the persistence of tropical reefs. Enhancing sea cucumbers may enhance reef resilience by suppressing disease.
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Affiliation(s)
- Cody S Clements
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Zoe A Pratte
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Mark E Hay
- School of Biological Sciences and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
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3
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Bertagnolli AD, Maritan AJ, Tumolo BB, Fritz SF, Oakland HC, Mohr EJ, Poole GC, Albertson LK, Stewart FJ. Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome. ISME Commun 2023; 3:111. [PMID: 37848489 PMCID: PMC10582121 DOI: 10.1038/s43705-023-00315-8] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
| | - Andrew J Maritan
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Benjamin B Tumolo
- Department of Ecology, Montana State University, Bozeman, MT, 59717, USA
| | - Samuel F Fritz
- Department of Ecology, Montana State University, Bozeman, MT, 59717, USA
| | - Hayley C Oakland
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Elizabeth J Mohr
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Geoffrey C Poole
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
- Montana Institute on Ecosystems, Montana State University, Bozeman, MT, 59717, USA
| | | | - Frank J Stewart
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, 59717, USA
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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4
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Graciette AGC, Hoopes LA, Clauss T, Stewart FJ, Pratte ZA. The microbiome of African penguins (Spheniscus demersus) under managed care resembles that of wild marine mammals and birds. Sci Rep 2023; 13:16679. [PMID: 37794122 PMCID: PMC10551019 DOI: 10.1038/s41598-023-43899-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/29/2023] [Indexed: 10/06/2023] Open
Abstract
Animals under managed care in zoos and aquariums are ideal surrogate study subjects for endangered species that are difficult to obtain in the wild. We compared the fecal and oral microbiomes of healthy, managed African penguins (Spheniscus demersus) to those of other domestic and wild vertebrate hosts to determine how host identity, diet, and environment shape the penguin microbiome. The African penguin oral microbiome was more similar to that of piscivorous marine mammals, suggesting that diet and a marine environment together play a strong role in shaping the oral microbiome. Conversely, the penguin cloaca/fecal microbiome was more similar to that of other birds, suggesting that host phylogeny plays a significant role in shaping the gut microbiome. Although the penguins were born under managed care, they had a gut microbiome more similar to that of wild bird species compared to domesticated (factory-farmed) birds, suggesting that the managed care environment and diet resemble those experienced by wild birds. Finally, the microbiome composition at external body sites was broadly similar to that of the habitat, suggesting sharing of microbes between animals and their environment. Future studies should link these results to microbial functional capacity and host health, which will help inform conservation efforts.
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Affiliation(s)
- Ana G Clavere Graciette
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Frank J Stewart
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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5
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Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Sci Data 2023; 10:332. [PMID: 37244914 DOI: 10.1038/s41597-023-02222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
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Affiliation(s)
- Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alvaro M Plominsky
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Alyse Kiesser
- School of Engineering, The University of British Columbia, Kelowna, BC, Canada
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, 4070386, Concepción, Chile
- Instituto Milenio de Oceanografía, Casilla 1313, 4070386, Concepción, Chile
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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Clavere-Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Anim Microbiome 2022; 4:34. [PMID: 35606841 PMCID: PMC9128078 DOI: 10.1186/s42523-022-00187-8] [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: 08/24/2021] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.
Results Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.
Conclusion For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00187-8.
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Affiliation(s)
| | - Mary E McWhirt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lisa A Hoopes
- Department of Research and Conservation, Georgia Aquarium, Atlanta, GA, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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7
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Steinsdóttir HGR, Gómez Ramírez E, Mhatre S, Schauberger C, Bertagnolli AD, Pratte ZA, Stewart FJ, Thamdrup B, Bristow LA. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environ Microbiol 2022; 24:2361-2379. [PMID: 35415879 PMCID: PMC9323439 DOI: 10.1111/1462-2920.16003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations, and 16S rRNA gene sequencing over three consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 μmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water, respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Eddy Gómez Ramírez
- CIMAR, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Snehit Mhatre
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Anthony D Bertagnolli
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Zoe A Pratte
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana.,School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA
| | - Bo Thamdrup
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Department of Biology, University of Southern Denmark, Odense, Denmark
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8
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Pratte ZA, Perry C, Dove ADM, Hoopes LA, Ritchie KB, Hueter RE, Fischer C, Newton AL, Stewart FJ. Microbiome structure in large pelagic sharks with distinct feeding ecologies. Anim Microbiome 2022; 4:17. [PMID: 35246276 PMCID: PMC8895868 DOI: 10.1186/s42523-022-00168-x] [Citation(s) in RCA: 4] [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: 09/01/2021] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Background Sharks play essential roles in ocean food webs and human culture, but also face population declines worldwide due to human activity. The relationship between sharks and the microbes on and in the shark body is unclear, despite research on other animals showing the microbiome as intertwined with host physiology, immunity, and ecology. Research on shark-microbe interactions faces the significant challenge of sampling the largest and most elusive shark species. We leveraged a unique sampling infrastructure to compare the microbiomes of two apex predators, the white (Carcharodon carcharias) and tiger shark (Galeocerdo cuvier), to those of the filter-feeding whale shark (Rhincodon typus), allowing us to explore the effects of feeding mode on intestinal microbiome diversity and metabolic function, and environmental exposure on the diversity of microbes external to the body (on the skin, gill). Results The fecal microbiomes of white and whale sharks were highly similar in taxonomic and gene category composition despite differences in host feeding mode and diet. Fecal microbiomes from these species were also taxon-poor compared to those of many other vertebrates and were more similar to those of predatory teleost fishes and toothed whales than to those of filter-feeding baleen whales. In contrast, microbiomes of external body niches were taxon-rich and significantly influenced by diversity in the water column microbiome. Conclusions These results suggest complex roles for host identity, diet, and environmental exposure in structuring the shark microbiome and identify a small, but conserved, number of intestinal microbial taxa as potential contributors to shark physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00168-x.
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Affiliation(s)
- Zoe A Pratte
- Department of Microbiology & Cell Biology, Montanta State University, 621 Leon Johnson Hall, Bozeman, MT, 59717, USA.
| | - Cameron Perry
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Kim B Ritchie
- University of South Carolina Beaufort, Beaufort, SC, USA
| | - Robert E Hueter
- OCEARCH, 1790 Bonanza Drive, Park City, UT, USA.,Center for Shark Research, Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, USA
| | | | - Alisa L Newton
- Disney's Animals, Science and Environment, 1200 N. Savannah Circle East, Bay Lake, FL, USA
| | - Frank J Stewart
- Department of Microbiology & Cell Biology, Montanta State University, 621 Leon Johnson Hall, Bozeman, MT, 59717, USA.,Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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9
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Perry CT, Pratte ZA, Clavere-Graciette A, Ritchie KB, Hueter RE, Newton AL, Fischer GC, Dinsdale EA, Doane MP, Wilkinson KA, Bassos-Hull K, Lyons K, Dove ADM, Hoopes LA, Stewart FJ. Elasmobranch microbiomes: emerging patterns and implications for host health and ecology. Anim Microbiome 2021; 3:61. [PMID: 34526135 PMCID: PMC8444439 DOI: 10.1186/s42523-021-00121-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/04/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.
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Affiliation(s)
- Cameron T Perry
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Robert E Hueter
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,OCEARCH, Park City, UT, USA
| | - Alisa L Newton
- Disney's Animals, Science and Environment, Orlando, FL, USA
| | - G Christopher Fischer
- OCEARCH, Park City, UT, USA.,Marine Science Research Institute, Jacksonville University, Jacksonville, FL, USA
| | - Elizabeth A Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program ℅ Mote Marine Laboratory, Sarasota, FL, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA
| | - Kady Lyons
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Alistair D M Dove
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Lisa A Hoopes
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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10
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. ISME J 2021; 15:2206-2232. [PMID: 33612832 PMCID: PMC8319197 DOI: 10.1038/s41396-021-00917-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 08/01/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.
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Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
- Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
- Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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11
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Patin NV, Dietrich ZA, Stancil A, Quinan M, Beckler JS, Hall ER, Culter J, Smith CG, Taillefert M, Stewart FJ. Correction: Gulf of Mexico blue hole harbors high levels of novel microbial lineages. ISME J 2021; 15:2490. [PMID: 34035445 DOI: 10.1038/s41396-021-00996-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA. .,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA. .,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA. .,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
| | | | - A Stancil
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - M Quinan
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - J S Beckler
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Ft. Pierce, FL, USA
| | - E R Hall
- Mote Marine Laboratory, Sarasota, FL, USA
| | - J Culter
- Mote Marine Laboratory, Sarasota, FL, USA
| | - C G Smith
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL, USA
| | - M Taillefert
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - F J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
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12
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Glass JB, Ranjan P, Kretz CB, Nunn BL, Johnson AM, Xu M, McManus J, Stewart FJ. Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments. Environ Microbiol 2021; 23:4646-4660. [PMID: 34190392 DOI: 10.1111/1462-2920.15656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
Gas hydrates harbour gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential. Atribacteria sequences generally increased in relative sequence abundance with increasing sediment depth. Most Atribacteria ASVs belonged to JS-1-Genus 1 and clustered with other sequences from gas hydrate-bearing sediments. We recovered 21 metagenome-assembled genomic bins spanning three geochemical zones in the sediment core: the sulfate-methane transition zone, the metal (iron/manganese) reduction zone, and the gas hydrate stability zone. We found evidence for bacterial fermentation as a source of acetate for aceticlastic methanogenesis and as a driver of iron reduction in the metal reduction zone. In multiple zones, we identified a Ni-Fe hydrogenase-Na+ /H+ antiporter supercomplex (Hun) in Atribacteria and Firmicutes bins and in other deep subsurface bacteria and cultured hyperthermophiles from the Thermotogae phylum. Atribacteria expressed tripartite ATP-independent transporters downstream from a novel regulator (AtiR). Atribacteria also possessed adaptations to survive extreme conditions (e.g. high salt brines, high pressure and cold temperatures) including the ability to synthesize the osmolyte di-myo-inositol-phosphate as well as expression of K+ -stimulated pyrophosphatase and capsule proteins.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Abigail M Johnson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Manlin Xu
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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13
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Abdelrahman SM, Patin NV, Hanora A, Aboseidah A, Desoky S, Desoky SG, Stewart FJ, Lopanik NB. The natural product biosynthetic potential of Red Sea nudibranch microbiomes. PeerJ 2021; 9:e10525. [PMID: 33604161 PMCID: PMC7868072 DOI: 10.7717/peerj.10525] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/18/2020] [Indexed: 01/21/2023] Open
Abstract
Background Antibiotic resistance is a growing problem that can be ameliorated by the discovery of novel drug candidates. Bacterial associates are often the source of pharmaceutically active natural products isolated from marine invertebrates, and thus, important targets for drug discovery. While the microbiomes of many marine organisms have been extensively studied, microbial communities from chemically-rich nudibranchs, marine invertebrates that often possess chemical defences, are relatively unknown. Methods We applied both culture-dependent and independent approaches to better understand the biochemical potential of microbial communities associated with nudibranchs. Gram-positive microorganisms isolated from nudibranchs collected in the Red Sea were screened for antibacterial and antitumor activity. To assess their biochemical potential, the isolates were screened for the presence of natural product biosynthetic gene clusters, including polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, using PCR. The microbiomes of the nudibranchs were investigated by high-throughput sequencing of 16S rRNA amplicons. Results In screens against five model microorganisms, 51% of extracts displayed antimicrobial activity against more than one organism, and 19% exhibited antitumor activity against Ehrlich’s ascites carcinoma. Sixty-four percent of isolates contained PKS and NRPS genes, suggesting their genomes contain gene clusters for natural product biosynthesis. Thirty-five percent were positive for more than one class of biosynthetic gene. These strains were identified as belonging to the Firmicutes and Actinobacteria phyla via 16S rRNA gene sequencing. In addition, 16S rRNA community amplicon sequencing revealed all bacterial isolates were present in the uncultured host-associated microbiome, although they were a very small percentage of the total community. Taken together, these results indicate that bacteria associated with marine nudibranchs are potentially a rich source of bioactive compounds and natural product biosynthetic genes.
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Affiliation(s)
- Samar M Abdelrahman
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Faculty of Science, Suez University, Suez, Egypt
| | - Nastassia V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Amro Hanora
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | | | | | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Nicole B Lopanik
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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14
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Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst Appl Microbiol 2021; 44:126185. [PMID: 33676264 DOI: 10.1016/j.syapm.2021.126185] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, One Cyclotron Road, Mail Stop 91R0183, Berkeley, CA 94720, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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15
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Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. Corrigendum: Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Front Microbiol 2021; 11:619943. [PMID: 33424821 PMCID: PMC7793716 DOI: 10.3389/fmicb.2020.619943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Cecilia B Kretz
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
| | - Sherry L Seston
- Department of Biology, Alverno College, Milwaukee, WI, United States
| | - Kristen N Buck
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States
| | - William M Landing
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, United States
| | - Peter L Morton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, United States
| | - James W Moffett
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Stephen J Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kevin L Vergin
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Frank J Stewart
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,School of Biology, Georgia Institute of Technology, Atlanta, GA, United States
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16
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Bertagnolli AD, Konstantinidis KT, Stewart FJ. Non-denitrifier nitrous oxide reductases dominate marine biomes. Environ Microbiol Rep 2020; 12:681-692. [PMID: 33459515 DOI: 10.1111/1758-2229.12879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 06/12/2023]
Abstract
Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N2O). To understand the enzymatic basis of N2O cycling in the ocean, we mined metagenomes to characterize genes encoding bacterial nitrous oxide reductase (NosZ) catalyzing N2O reduction to N2. We examined data sets from diverse biomes but focused primarily on those from oxygen minimum zones where N2O levels are often elevated. With few exceptions, marine nosZ data sets were dominated by 'atypical' clade II gene variants. Atypical nosZ has been associated with low oxygen, enhanced N2O affinity, and organisms lacking enzymes for complete denitrification, i.e., non-denitrifiers. Atypical nosZ often occurred in metagenome-assembled genomes (MAGs) with nitrate or nitrite respiration genes, although MAGs with genes for complete denitrification were rare. We identified atypical nosZ in several taxa not previously associated with N2O consumption, in addition to known N2O-associated groups. The data suggest that marine environments generally select for high N2O-scavenging ability across diverse taxa and have implications for how N2O concentration may affect N2O removal rates.
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Affiliation(s)
- Anthony D Bertagnolli
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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17
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Clements CS, Burns AS, Stewart FJ, Hay ME. Parasite-host ecology: the limited impacts of an intimate enemy on host microbiomes. Anim Microbiome 2020; 2:42. [PMID: 33499998 PMCID: PMC7807496 DOI: 10.1186/s42523-020-00061-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/11/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Impacts of biotic stressors, such as consumers, on coral microbiomes have gained attention as corals decline worldwide. Corallivore feeding can alter coral microbiomes in ways that contribute to dysbiosis, but feeding strategies are diverse - complicating generalizations about the nature of consumer impacts on coral microbiomes. RESULTS In field experiments, feeding by Coralliophila violacea, a parasitic snail that suppresses coral growth, altered the microbiome of its host, Porites cylindrica, but these impacts were spatially constrained. Alterations in microbial community composition and variability were largely restricted to snail feeding scars; basal or distal areas ~ 1.5 cm or 6-8 cm away, respectively, were largely unaltered. Feeding scars were enriched in taxa common to stressed corals (e.g. Flavobacteriaceae, Rhodobacteraceae) and depauperate in putative beneficial symbionts (e.g. Endozoicomonadaceae) compared to locations that lacked feeding. CONCLUSIONS Previous studies that assessed consumer impacts on coral microbiomes suggested that feeding disrupts microbial communities, potentially leading to dysbiosis, but those studies involved mobile corallivores that move across and among numerous individual hosts. Sedentary parasites like C. violacea that spend long intervals with individual hosts and are dependent on hosts for food and shelter may minimize damage to host microbiomes to assure continued host health and thus exploitation. More mobile consumers that forage across numerous hosts should not experience these constraints. Thus, stability or disruption of microbiomes on attacked corals may vary based on the foraging strategy of coral consumers.
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Affiliation(s)
- Cody S Clements
- Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332-0230, USA.
| | - Andrew S Burns
- Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332-0230, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Frank J Stewart
- Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332-0230, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, 59717-3520, USA
| | - Mark E Hay
- Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332-0230, USA
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18
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 6:136. [PMID: 33184503 PMCID: PMC7752755 DOI: 10.1038/s41564-020-00827-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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19
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Szeinbaum N, Nunn BL, Cavazos AR, Crowe SA, Stewart FJ, DiChristina TJ, Reinhard CT, Glass JB. Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn(III) reduction. Environ Microbiol Rep 2020; 12:583-593. [PMID: 32613749 PMCID: PMC7775658 DOI: 10.1111/1758-2229.12867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 05/23/2023]
Abstract
Soluble ligand-bound Mn(III) can support anaerobic microbial respiration in diverse aquatic environments. Thus far, Mn(III) reduction has only been associated with certain Gammaproteobacteria. Here, we characterized microbial communities enriched from Mn-replete sediments of Lake Matano, Indonesia. Our results provide the first evidence for the biological reduction of soluble Mn(III) outside the Gammaproteobacteria. Metagenome assembly and binning revealed a novel betaproteobacterium, which we designate 'Candidatus Dechloromonas occultata.' This organism dominated the enrichment and expressed a porin-cytochrome c complex typically associated with iron-oxidizing Betaproteobacteria and a novel cytochrome c-rich protein cluster (Occ), including an undecaheme putatively involved in extracellular electron transfer. This occ gene cluster was also detected in diverse aquatic bacteria, including uncultivated Betaproteobacteria from the deep subsurface. These observations provide new insight into the taxonomic and functional diversity of microbially driven Mn(III) reduction in natural environments.
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Affiliation(s)
- Nadia Szeinbaum
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Brook L. Nunn
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Amanda R. Cavazos
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sean A. Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Christopher T. Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- NASA Astrobiology Institute, Alternative Earths Team, Mountain View, CA, USA
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20
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Patin NV, Brown E, Chebli G, Garfield C, Kubanek J, Stewart FJ. Microbial and chemical dynamics of a toxic dinoflagellate bloom. PeerJ 2020; 8:e9493. [PMID: 33240577 PMCID: PMC7676380 DOI: 10.7717/peerj.9493] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/27/2020] [Accepted: 06/17/2020] [Indexed: 01/10/2023] Open
Abstract
Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.
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Affiliation(s)
- Nastassia V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Emily Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Gabriella Chebli
- Department of Chemistry, Agnes Scott College, Decatur, GA, United States of America
| | - Claire Garfield
- School of Arts and Sciences, State University of New York at Stony Brook, Stony Brook, NY, United States of America
| | - Julia Kubanek
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, United States of America.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States of America
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21
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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22
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Clements CS, Burns AS, Stewart FJ, Hay ME. Seaweed-coral competition in the field: effects on coral growth, photosynthesis and microbiomes require direct contact. Proc Biol Sci 2020; 287:20200366. [PMID: 32453990 DOI: 10.1098/rspb.2020.0366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A number of tropical reefs have transitioned from coral to macroalgal dominance, but the role of macroalgal competition in coral decline is debated. There is a need to understand the relative roles of direct coral-algal effects versus indirect, microbially mediated effects shaping these interactions, as well as the relevant scales at which interactions operate under natural field, as opposed to laboratory, conditions. We conducted a manipulative field experiment investigating how direct contact versus close proximity (approx. 1.5 cm) with macroalgae (Galaxaura rugosa, Sargassum polycystum) impacted the growth, photosynthetic efficiency, and prokaryotic microbiome of the common Indo-Pacific coral Acropora millepora. Both coral growth and photosynthetic efficiency were suppressed when in direct contact with algae or their inert mimics--but not when in close proximity to corals without direct contact. Coral microbiomes were largely unaltered in composition, variability, or diversity regardless of treatment, although a few uncommon taxa differed in abundance among treatments. Negative impacts of macroalgae were contact dependent, accounted for by physical structure alone and had minimal effects on coral microbiomes. The spatial constraints of these interactions have important implications for understanding and predicting benthic community dynamics as reefs degrade.
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Affiliation(s)
- Cody S Clements
- School of Biological Sciences, Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Andrew S Burns
- School of Biological Sciences, Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.,NIAID Microbiome Program, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Stewart
- School of Biological Sciences, Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717-3520, USA
| | - Mark E Hay
- School of Biological Sciences, Aquatic Chemical Ecology Center, and Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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23
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Bray MS, Wu J, Padilla CC, Stewart FJ, Fowle DA, Henny C, Simister RL, Thompson KJ, Crowe SA, Glass JB. Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes. Environ Microbiol Rep 2020; 12:49-57. [PMID: 31701641 PMCID: PMC7779115 DOI: 10.1111/1758-2229.12809] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/14/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
Electroactive type IV pili, or e-pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e-pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22-aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e-pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e-pilins were diverse in length and phylogeny, and included truncated e-pilins in Geobacter spp., as well as longer putative e-pilins in Fe(II)-oxidizing Betaproteobacteria and Zetaproteobacteria.
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Affiliation(s)
- Marcus S. Bray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jieying Wu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cory C. Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - David A. Fowle
- Department of Geology, University of Kansas, Lawrence, KS, USA
| | - Cynthia Henny
- Research Center for Limnology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Rachel L. Simister
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Katharine J. Thompson
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Sean A. Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Division of Earth and Planetary Sciences, School of Biological Sciences, and Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Jennifer B. Glass
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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24
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Beatty DS, Valayil JM, Clements CS, Ritchie KB, Stewart FJ, Hay ME. Variable effects of local management on coral defenses against a thermally regulated bleaching pathogen. Sci Adv 2019; 5:eaay1048. [PMID: 31616794 PMCID: PMC6774716 DOI: 10.1126/sciadv.aay1048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/05/2019] [Indexed: 05/05/2023]
Abstract
Bleaching and disease are decimating coral reefs especially when warming promotes bleaching pathogens, such as Vibrio coralliilyticus. We demonstrate that sterilized washes from three common corals suppress V. coralliilyticus but that this defense is compromised when assays are run at higher temperatures. For a coral within the ecologically critical genus Acropora, inhibition was 75 to 154% greater among colonies from coral-dominated marine protected areas versus adjacent fished areas that were macroalgae-dominated. Acropora microbiomes were more variable within fished areas, suggesting that reef degradation may also perturb coral microbial communities. Defenses of a robust poritid coral and a weedy pocilloporid coral were not affected by reef degradation, and microbiomes were unaltered for these species. For some ecologically critical, but bleaching-susceptible, corals such as Acropora, local management to improve reef state may bolster coral resistance to global change, such as bacteria-induced coral bleaching during warming events.
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Affiliation(s)
- Deanna S. Beatty
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, 311 Ferst Dr., Atlanta, GA 30332, USA
| | - Jinu Mathew Valayil
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, 311 Ferst Dr., Atlanta, GA 30332, USA
| | - Cody S. Clements
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, 311 Ferst Dr., Atlanta, GA 30332, USA
| | - Kim B. Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret St., Beaufort, SC 29902, USA
| | - Frank J. Stewart
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, 311 Ferst Dr., Atlanta, GA 30332, USA
| | - Mark E. Hay
- School of Biological Sciences and Aquatic Chemical Ecology Center, Georgia Institute of Technology, 311 Ferst Dr., Atlanta, GA 30332, USA
- Corresponding author.
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25
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Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists' warning to humanity: microorganisms and climate change. Nat Rev Microbiol 2019; 17:569-586. [PMID: 31213707 PMCID: PMC7136171 DOI: 10.1038/s41579-019-0222-5] [Citation(s) in RCA: 623] [Impact Index Per Article: 124.6] [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] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Abstract
In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Antje Boetius
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, and The Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | | | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Christine M Foreman
- Center for Biofilm Engineering, and Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - David A Hutchins
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science & Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David S Reay
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia I Rich
- Microbiology Department, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Department of Microbiology, and Department of Civil, Environmental and Geodetic Engineering, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Scott C Weaver
- Department of Microbiology and Immunology, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
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26
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Abstract
In the ocean's major oxygen minimum zones (OMZs), oxygen is effectively absent from sea water and life is dominated by microorganisms that use chemicals other than oxygen for respiration. Recent studies that combine advanced genomic and chemical detection methods are delineating the different metabolic niches that microorganisms can occupy in OMZs. Understanding these niches, the microorganisms that inhabit them, and their influence on marine biogeochemical cycles is crucial as OMZs expand with increasing seawater temperatures.
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Affiliation(s)
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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27
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Beinart RA, Luo C, Konstantinidis KT, Stewart FJ, Girguis PR. The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. Front Microbiol 2019; 10:1818. [PMID: 31474946 PMCID: PMC6702916 DOI: 10.3389/fmicb.2019.01818] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 04/08/2019] [Accepted: 07/23/2019] [Indexed: 12/29/2022] Open
Abstract
Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.
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Affiliation(s)
- Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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28
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Lau E, Frame CH, Nolan EJ, Stewart FJ, Dillard ZW, Lukich DP, Mihalik NE, Yauch KE, Kinker MA, Waychoff SL. Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone. PLoS One 2019; 14:e0217136. [PMID: 31112557 PMCID: PMC6529010 DOI: 10.1371/journal.pone.0217136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 09/19/2018] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2-) and NO2- to nitrate (NO3-), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). We characterized the distribution of nitrifiers at 5 depths spanning the oxic to hypoxic zone of the offshore Benguela upwelling system above the continental slope off Namibia. Based on 16S rRNA gene amplicon sequencing, the proportional abundance of nitrifiers (ammonia and nitrite oxidizers) increased with depth, driven by an increase in ammonia-oxidizing archaea (AOA; Thaumarchaeota) to up to 33% of the community at hypoxic depths where O2 concentrations fell to ~25 μM. The AOA community transitioned from being dominated by a few members at oxic depths to a more even representation of taxa in the hypoxic zone. In comparison, the community of NO2--oxidizing bacteria (NOB), composed primarily of Nitrospinae, was far less abundant and exhibited higher evenness at all depths. The AOA:NOB ratio declined with depth from 41:1 in the oxic zone to 27:1 under hypoxia, suggesting potential variation in the balance between NO2- production and consumption via nitrification. Indeed, in contrast to prior observations from more O2-depleted sites closer to shore, NO2- did not accumulate at hypoxic depths near this offshore site, potentially due in part to a tightened coupling between AOA and NOB.
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Affiliation(s)
- Evan Lau
- Department of Biology, Menlo College, Atherton, California, United States of America
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
- * E-mail:
| | - Caitlin H. Frame
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - E. Joseph Nolan
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zachary W. Dillard
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Daniel P. Lukich
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Nicole E. Mihalik
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Katelyn E. Yauch
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Marcus A. Kinker
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
| | - Samantha L. Waychoff
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America
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29
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Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, Könneke M, Littmann S, Mooshammer M, Niggemann J, Petrov S, Richter A, Stewart FJ, Wagner M, Kuypers MMM, Bristow LA. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol 2018; 4:234-243. [PMID: 30531977 DOI: 10.1038/s41564-018-0316-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 10/30/2018] [Indexed: 02/01/2023]
Abstract
Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4-6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7-10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean.
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Affiliation(s)
- Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Abiel T Kidane
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin Könneke
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Maria Mooshammer
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Jutta Niggemann
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Sandra Petrov
- Marine Archaea Group, MARUM - Center for Marine Environmental Sciences & Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Laura A Bristow
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
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30
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Abstract
In Figure 3, 'Candidatus Scalindua' and Thaumarchaeota were erroneously shown to produce nitrous oxide (N2O). As neither group directly produces N2O, the arrows and products have been removed both online and in the pdf. The authors apologize for any confusion caused.
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Affiliation(s)
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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31
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Ganesh S, Bertagnolli AD, Bristow LA, Padilla CC, Blackwood N, Aldunate M, Bourbonnais A, Altabet MA, Malmstrom RR, Woyke T, Ulloa O, Konstantinidis KT, Thamdrup B, Stewart FJ. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME J 2018; 12:2706-2722. [PMID: 29991764 DOI: 10.1038/s41396-018-0223-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/20/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.
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Affiliation(s)
- Sangita Ganesh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.,Radiant Genomics, Emeryville, 94608, CA, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Laura A Bristow
- Biogeochemistry Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Nigel Blackwood
- Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, Faculty of Natural Sciences and Oceanography, University of Concepción, Casilla 160-C, Concepción, Chile.,Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | - Annie Bourbonnais
- Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, 02543, MA, USA.,School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Mark A Altabet
- School for Marine Science and Technology, University of Massachusetts Dartmouth, 706 Rodney French Blvd, New Bedford, 02744, MA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, 94598, CA, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, 4070386, Chile
| | | | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA.
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32
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Fareed S, Sarode N, Stewart FJ, Malik A, Laghaie E, Khizer S, Yan F, Pratte Z, Lewis J, Immergluck LC. Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children. PeerJ 2018; 6:e4663. [PMID: 29868248 PMCID: PMC5984579 DOI: 10.7717/peerj.4663] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 12/10/2017] [Accepted: 04/02/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fecal Microbiota Transplantation (FMT) is an innovative means of treating recurrent Clostridium difficile infection (rCDI), through restoration of gut floral balance. However, there is a lack of data concerning the efficacy of FMT and its impact on the gut microbiome among pediatric patients. This study analyzes clinical outcomes and microbial community composition among 15 pediatric patients treated for rCDI via FMT. METHODS This is a prospective, observational, pilot study of 15 children ≤18 years, who presented for rCDI and who met inclusion criteria for FMT at a pediatric hospital and pediatric gastroenterology clinic. Past medical history and demographics were recorded at enrollment and subsequent follow-up. Specimens of the donors' and the patients' pre-FMT and post-FMT fecal specimen were collected and used to assess microbiome composition via 16S rRNA gene sequencing. RESULTS FMT successfully prevented rCDI episodes for minimum of 3 months post-FMT in all patients, with no major adverse effects. Three patients reported continued GI bleeding; however, all three also had underlying Inflammatory Bowel Disease (IBD). Our analyses confirm a significant difference between pre-and post-FMT gut microbiome profiles (Shannon diversity index), whereas no significant difference was observed between post-FMT and donor microbiome profiles. At the phyla level, post-FMT profiles showed significantly increased levels of Bacteroidetes and significantly decreased levels of Proteobacteria. Subjects with underlying IBD showed no difference in their pre-and post-FMT profiles. CONCLUSION The low rate of recurrence or re-infection by C. difficile, coupled with minimal adverse effects post-FMT, suggests that FMT is a viable therapeutic means to treat pediatric rCDI. Post-FMT microbiomes are different from pre-FMT microbiomes, and similar to those of healthy donors, suggesting successful establishment of a healthier microbiome.
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Affiliation(s)
- Shaaz Fareed
- Department of Microbiology/Biochemistry/Immunology, Morehouse School of Medicine, Atlanta, GA, United States of America
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Neha Sarode
- Department of Organismic & Evolutionary Biology, Harvard University, Boston, MA, United States of America
| | - Frank J. Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Aneeq Malik
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Elham Laghaie
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Saadia Khizer
- Clinical Research, Children’s Healthcare of Atlanta, Atlanta, GA, United States of America
| | - Fengxia Yan
- Department of Community Health & Preventive Medicine, Morehouse School of Medicine, Atlanta, GA, United States of America
| | - Zoe Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Jeffery Lewis
- Pediatric Gastroenterology, Children’s Center for Digestive Health Care, LLC, Atlanta, GA, United States of America
| | - Lilly Cheng Immergluck
- Department of Microbiology/Biochemistry/Immunology, Morehouse School of Medicine, Atlanta, GA, United States of America
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, United States of America
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33
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Beatty DS, Clements CS, Stewart FJ, Hay ME. Intergenerational effects of macroalgae on a reef coral: major declines in larval survival but subtle changes in microbiomes. Mar Ecol Prog Ser 2018; 589:97-114. [PMID: 30505048 PMCID: PMC6261492 DOI: 10.3354/meps12465] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Tropical reefs are shifting from coral to macroalgal dominance, with macroalgae suppressing coral recovery, potentially via effects on coral microbiomes. Understanding how macroalgae affect corals and their microbiomes requires comparing algae- versus coral-dominated reefs without confounding aspects of time and geography. We compared survival, settlement, and post-settlement survival of larvae, as well as the microbiomes of larvae and adults, of the Pacific coral Pocillopora damicornis between an Marine Protected Area (MPA) dominated by corals versus an adjacent fished area dominated by macroalgae. Microbiome composition in adult coral, larval coral, and seawater did not differ between the MPA and fished area. However, microbiomes of adult coral were more variable in the fished area and Vibrionaceae bacteria, including strains most closely related to the pathogen Vibrio shilonii, were significantly enriched, but rare, in adult and larval coral from the fished area. Larvae from the macroalgae-dominated area exhibited higher pre-settlement mortality and reduced settlement compared to those from the coral-dominated area. Juveniles planted into a coral-dominated area survived better than those placed into a fished area dominated by macroalgae. Differential survival depended on whether macroalgae were immediately adjacent to juvenile coral rather than on traits of the areas per se. Contrary to our expectations, coral microbiomes were relatively uniform at the community level despite dramatic differences in macroalgal cover between the MPA (~2% cover) and fished (~90%) area. Reducing macroalgae may elicit declines in rare but potentially harmful microbes in coral and their larvae, as well as positive intergenerational effects on offspring survival.
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Affiliation(s)
- Deanna S. Beatty
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Cody S. Clements
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Frank J. Stewart
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Mark E. Hay
- School of Biological Sciences and Aquatic Chemical Ecology Center Georgia Institute of Technology, Atlanta, GA 30332-0230
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34
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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35
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Sharp KH, Pratte ZA, Kerwin AH, Rotjan RD, Stewart FJ. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. Microbiome 2017; 5:120. [PMID: 28915923 PMCID: PMC5603060 DOI: 10.1186/s40168-017-0329-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [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: 03/27/2017] [Accepted: 08/20/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition. RESULTS Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density. CONCLUSIONS Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore help to identify basic principles of coral microbiome assembly, as well as functional relationships among holobiont members.
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Affiliation(s)
- Koty H. Sharp
- Department of Biology, Marine Biology and Environmental Science, Roger Williams University, 1 Old Ferry Road, Bristol, RI 02809 USA
| | | | | | - Randi D. Rotjan
- Boston University, Boston, USA
- New England Aquarium, Boston, USA
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36
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Garcia-Robledo E, Padilla CC, Aldunate M, Stewart FJ, Ulloa O, Paulmier A, Gregori G, Revsbech NP. Cryptic oxygen cycling in anoxic marine zones. Proc Natl Acad Sci U S A 2017; 114:8319-8324. [PMID: 28716941 PMCID: PMC5547588 DOI: 10.1073/pnas.1619844114] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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
Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.
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Affiliation(s)
- Emilio Garcia-Robledo
- Microbiology Section, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark;
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, 4070386 Concepcion, Chile
- Departamento de Oceanografía, Instituto Milenio de Oceanografía, Universidad de Concepción, 4070386 Concepción, Chile
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Instituto Milenio de Oceanografía, Universidad de Concepción, 4070386 Concepción, Chile
| | - Aurélien Paulmier
- Laboratoire d'Etudes en Géophysique et Océanographie Spatiales, Institut de Recherche pour le Développement, CNRS, Centre National d'Etudes Spatiales, University of Toulouse, 31400 Toulouse, France
| | - Gerald Gregori
- Aix Marseille Université, Université de Toulon, CNRS, Institut pour la Recherche et le Développement, Mediterranean Institute of Oceanography UM 110, 13288 Marseille, France
| | - Niels Peter Revsbech
- Microbiology Section, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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Abstract
Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce "MArVD", for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset. Application of MArVD to 10 viral metagenomes from two depth profiles in the Eastern Tropical North Pacific (ETNP) oxygen minimum zone revealed 43 new putative archaeal virus genomes and large genome fragments ranging in size from 10 to 31 kb. Network-based classifications, which were consistent with marker gene phylogenies where available, suggested that these putative archaeal virus contigs represented six novel candidate genera. Ecological analyses, via fragment recruitment and ordination, revealed that the diversity and relative abundances of these putative archaeal viruses were correlated with oxygen concentration and temperature along two OMZ-spanning depth profiles, presumably due to structuring of the host Archaea community. Peak viral diversity and abundances were found in surface waters, where Thermoplasmata 16S rRNA genes are prevalent, suggesting these archaea as hosts in the surface habitats. Together these findings provide a baseline for identifying archaeal viruses in sequence datasets, and an initial picture of the ecology of such viruses in non-extreme environments.
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Affiliation(s)
- Dean R Vik
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Jennifer R Brum
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Joanne B Emerson
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Cory C Padilla
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Frank J Stewart
- Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
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Parris DJ, Brooker RM, Morgan MA, Dixson DL, Stewart FJ. Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement. PeerJ 2016; 4:e2412. [PMID: 27635360 PMCID: PMC5012416 DOI: 10.7717/peerj.2412] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 05/09/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022] Open
Abstract
The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.
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Affiliation(s)
- Darren J Parris
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
| | - Rohan M Brooker
- School of Marine Science and Policy, University of Delaware , Newark , DE , United States
| | - Michael A Morgan
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
| | - Danielle L Dixson
- School of Marine Science and Policy, University of Delaware , Newark , DE , United States
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology , Atlanta , GA , United States
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Tsementzi D, Wu J, Deutsch S, Nath S, Rodriguez-R LM, Burns AS, Ranjan P, Sarode N, Malmstrom RR, Padilla CC, Stone BK, Bristow LA, Larsen M, Glass JB, Thamdrup B, Woyke T, Konstantinidis KT, Stewart FJ. SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 2016; 536:179-83. [PMID: 27487207 PMCID: PMC4990128 DOI: 10.1038/nature19068] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/30/2016] [Indexed: 01/25/2023]
Abstract
Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.
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Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes. Front Microbiol 2016; 7:1074. [PMID: 27486438 PMCID: PMC4949241 DOI: 10.3389/fmicb.2016.01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022] Open
Abstract
Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
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Affiliation(s)
| | - Roxanne A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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41
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Glass JB, Kretz CB, Ganesh S, Ranjan P, Seston SL, Buck KN, Landing WM, Morton PL, Moffett JW, Giovannoni SJ, Vergin KL, Stewart FJ. Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones. Front Microbiol 2015; 6:998. [PMID: 26441925 PMCID: PMC4585252 DOI: 10.3389/fmicb.2015.00998] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 07/10/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.
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Affiliation(s)
- Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Cecilia B Kretz
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | | | - Kristen N Buck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - William M Landing
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - Peter L Morton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University Tallahassee, FL, USA
| | - James W Moffett
- Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | | | - Kevin L Vergin
- Department of Microbiology, Oregon State University Corvallis, OR, USA
| | - Frank J Stewart
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology Atlanta, GA, USA ; School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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42
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Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ. Standard filtration practices may significantly distort planktonic microbial diversity estimates. Front Microbiol 2015; 6:547. [PMID: 26082766 PMCID: PMC4451414 DOI: 10.3389/fmicb.2015.00547] [Citation(s) in RCA: 30] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 02/01/2023] Open
Abstract
Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05–0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
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Affiliation(s)
- Cory C Padilla
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Shelby Gantt
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Alex Huhman
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Darren J Parris
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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43
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Duret MT, Pachiadaki MG, Stewart FJ, Sarode N, Christaki U, Monchy S, Srivastava A, Edgcomb VP. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone. FEMS Microbiol Ecol 2015; 91:fiv037. [DOI: 10.1093/femsec/fiv037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2015] [Indexed: 11/14/2022] Open
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Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off northern Chile. mBio 2014; 5:e01966. [PMID: 25352619 PMCID: PMC4217175 DOI: 10.1128/mbio.01966-14] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [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] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2 at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N2 and N2O production by denitrification was achieved at 205 and 297 nM O2, respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O2. This O2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O2 inhibition kinetics but strongly stimulated N2O production by denitrification. These results identify new O2 thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses. IMPORTANCE The removal of fixed nitrogen via anammox and denitrification associated with low O2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O2 are poorly known. The present study elucidated how nanomolar O2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art (15)N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O2, but denitrification was more O2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O2, although expression of some of these genes decreased. Quantifying O2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur.
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Affiliation(s)
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Loreto De Brabandere
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | | | - Osvaldo Ulloa
- Departamento de Oceanografía & Instituto Mileno de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Don E Canfield
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
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Parris DJ, Ganesh S, Edgcomb VP, DeLong EF, Stewart FJ. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Front Microbiol 2014; 5:543. [PMID: 25389417 PMCID: PMC4211540 DOI: 10.3389/fmicb.2014.00543] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 08/22/2014] [Accepted: 09/29/2014] [Indexed: 02/02/2023] Open
Abstract
Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2–1.6 μm, >1.6 μm) from seven depths through the anoxic oxygen minimum zone (OMZ) off northern Chile. Sequencing of >154,000 amplicons revealed contrasting patterns of phylogenetic diversity across size fractions and depths. Protist and total eukaryote diversity in the >1.6 μm fraction peaked at the chlorophyll maximum in the upper photic zone before declining by ~50% in the OMZ. In contrast, diversity in the 0.2–1.6 μm fraction, though also elevated in the upper photic zone, increased four-fold from the lower oxycline to a maximum at the anoxic OMZ core. Dinoflagellates of the Dinophyceae and endosymbiotic Syndiniales clades dominated the protist assemblage at all depths (~40–70% of sequences). Other protist groups varied with depth, with the anoxic zone community of the larger size fraction enriched in euglenozoan flagellates and acantharean radiolarians (up to 18 and 40% of all sequences, respectively). The OMZ 0.2–1.6 μm fraction was dominated (11–99%) by Syndiniales, which exhibited depth-specific variation in composition and total richness despite uniform oxygen conditions. Metazoan sequences, though confined primarily to the 1.6 μm fraction above the OMZ, were also detected within the anoxic zone where groups such as copepods increased in abundance relative to the oxycline and upper OMZ. These data, compared to those from other low-oxygen sites, reveal variation in OMZ microeukaryote composition, helping to identify clades with potential adaptations to oxygen-depletion.
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Affiliation(s)
- Darren J Parris
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | | | - Edward F DeLong
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Parsons Laboratory 48 Cambridge, UK ; Center for Microbial Ecology, Research and Education Hawaii, HI, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 2014; 15:924. [PMID: 25342549 PMCID: PMC4287430 DOI: 10.1186/1471-2164-15-924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [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: 04/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. RESULTS Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. CONCLUSIONS The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Eisen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA.
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Lee FJ, Rusch DB, Stewart FJ, Mattila HR, Newton ILG. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environ Microbiol 2014; 17:796-815. [PMID: 24905222 DOI: 10.1111/1462-2920.12526] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/30/2022]
Abstract
The honey bee, the world's most important agricultural pollinator, relies exclusively on plant-derived foods for nutrition. Nectar and pollen collected by honey bees are processed and matured within the nest through the activities of honey bee-derived microbes and enzymes. In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome. The function of the microbial community in the honey bee, as revealed by metatranscriptome sequencing, resembles that of other animal guts and food-processing environments. We identified three major bacterial classes that are active in the gut (γ-Proteobacteria, Bacilli and Actinobacteria), all of which are predicted to participate in the breakdown of complex macromolecules (e.g. polysaccharides and polypeptides), the fermentation of component parts of these macromolecules, and the generation of various fermentation products, such as short-chain fatty acids and alcohol. The ability of the microbial community to metabolize these carbon-rich food sources was confirmed through the use of community-level physiological profiling. Collectively, these findings suggest that the gut microflora of the honey bee harbours bacterial members with unique roles, which ultimately can contribute to the processing of plant-derived food for colonies.
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Affiliation(s)
- Fredrick J Lee
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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Lin Y, Cradick TJ, Brown MT, Deshmukh H, Ranjan P, Sarode N, Wile BM, Vertino PM, Stewart FJ, Bao G. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res 2014; 42:7473-85. [PMID: 24838573 PMCID: PMC4066799 DOI: 10.1093/nar/gku402] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [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: 12/18/2013] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed to minimize off-target cleavage in large mammalian genomes. Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions ('DNA bulge') or deletions ('RNA bulge') compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. Variants of single-guide RNAs (sgRNAs) for four endogenous loci were used as model systems, and their cleavage activities were quantified at different positions with 1- to 5-bp bulges. We further investigated 114 putative genomic off-target loci of 27 different sgRNAs and confirmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the guide strand. Our results strongly indicate the need to perform comprehensive off-target analysis related to DNA and sgRNA bulges in addition to base mismatches, and suggest specific guidelines for reducing potential off-target cleavage.
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Affiliation(s)
- Yanni Lin
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Thomas J Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Matthew T Brown
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Harshavardhan Deshmukh
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brian M Wile
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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Abstract
Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.
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Affiliation(s)
- Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Concepción 4070386, Chile.
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