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Shiryev SA, Agarwala R. Indexing and searching petabase-scale nucleotide resources. Nat Methods 2024; 21:994-1002. [PMID: 38755321 PMCID: PMC11166510 DOI: 10.1038/s41592-024-02280-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024]
Abstract
Searching vast and rapidly growing nucleotide content in resources, such as runs in the Sequence Read Archive and assemblies for whole-genome shotgun sequencing projects in GenBank, is currently impractical for most researchers. Here we present Pebblescout, a tool that navigates such content by providing indexing and search capabilities. Indexing uses dense sampling of the sequences in the resource. Search finds subjects (runs or assemblies) that have short sequence matches to a user query, with well-defined guarantees and ranks them using informativeness of the matches. We illustrate the functionality of Pebblescout by creating eight databases that index over 3.7 petabases. The web service of Pebblescout can be reached at https://pebblescout.ncbi.nlm.nih.gov . We show that for a wide range of query lengths, Pebblescout provides a data-driven way for finding relevant subsets of large nucleotide resources, reducing the effort for downstream analysis substantially. We also show that Pebblescout results compare favorably to MetaGraph and Sourmash.
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Affiliation(s)
- Sergey A Shiryev
- Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Richa Agarwala
- Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Huang Z, Shu L, He Z, Yan Q. Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits. ENVIRONMENTAL RESEARCH 2024; 257:119272. [PMID: 38823613 DOI: 10.1016/j.envres.2024.119272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.
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Affiliation(s)
- Zhenyu Huang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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Jin R, Pradal MA, Hantsoo K, Gnanadesikan A, St-Laurent P, Bjerrum CJ. Constructing a model including the cryptic sulfur cycle in Chesapeake Bay requires judicious choices for key processes and parameters. MethodsX 2023; 11:102253. [PMID: 38098778 PMCID: PMC10719513 DOI: 10.1016/j.mex.2023.102253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/10/2023] [Indexed: 12/17/2023] Open
Abstract
A new biogeochemical model for Chesapeake Bay has been developed by merging two published models - the ECB model of Da et al. (2018) that has been calibrated for the Bay but only simulates nitrogen, carbon and oxygen and the BioRedoxCNPS model of al Azhar et al. (2014) and Hantsoo et al. (2018) that includes cryptic sulfur cycling. Comparison between these models shows that judicious choices are required for key processes and parameters. This manuscript documents the sources of differences between the two published models in order to select the most realistic configuration for our new model.•This study focuses on three sets of differences-processes only included in ECB (burial and dissolved organic matter), processes only included in BioRedoxCNPS (explicit dynamics for hydrogen sulfide, sulfate and nitrite, light attenuation that does not include CDOM or sediments), and differences in parameters common to the two codes.•Sensitivity studies that highlight particular choices (absorption by dissolved organic matter, nitrification rates, stoichiometric ratios) are also shown.•The new model includes sulfur cycling and has comparable skill in predicting oxygen as ECB, but also has improved simulation of nitrogen species compared with both original codes.
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Affiliation(s)
- Rui Jin
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Marie-Aude Pradal
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Kalev Hantsoo
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Anand Gnanadesikan
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Pierre St-Laurent
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, United States
| | - Christian J. Bjerrum
- Department of Geoscience and Natural Resource Management, University of Copenhagen, Copenhagen 1165, Denmark
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Pérez Castro S, Peredo EL, Mason OU, Vineis J, Bowen JL, Mortazavi B, Ganesh A, Ruff SE, Paul BG, Giblin AE, Cardon ZG. Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Appl Environ Microbiol 2023; 89:e0098823. [PMID: 37882526 PMCID: PMC10686091 DOI: 10.1128/aem.00988-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.
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Affiliation(s)
- Sherlynette Pérez Castro
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Crop and Soil Sciences, University of Georgia, Athens, USA
| | - Elena L. Peredo
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Olivia U. Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Joseph Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
| | - Jennifer L. Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
| | - Behzad Mortazavi
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - S. Emil Ruff
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Blair G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Anne E. Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Zoe G. Cardon
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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