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For: Zhao Z, Baltar F, Herndl GJ. Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Sci Adv 2020;6. [PMID: 32494615 PMCID: PMC7159927 DOI: 10.1126/sciadv.aaz4354] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Number Cited by Other Article(s)
1
Zhang Y, Liu H, Jing H. Community differences and potential function along the particle size spectrum of microbes in the twilight zone. MICROBIOME 2025;13:121. [PMID: 40369676 PMCID: PMC12076831 DOI: 10.1186/s40168-025-02116-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 04/15/2025] [Indexed: 05/16/2025]
2
Hou L, Zhao Z, Steger-Mähnert B, Jiao N, Herndl GJ, Zhang Y. Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach. MICROBIOME 2025;13:114. [PMID: 40329386 PMCID: PMC12054258 DOI: 10.1186/s40168-025-02097-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 03/19/2025] [Indexed: 05/08/2025]
3
Sher D, George EE, Wietz M, Gifford S, Zoccarato L, Weissberg O, Koedooder C, Valiya Kalladi WB, Barreto Filho MM, Mireles R, Malavin S, Liddor Naim M, Idan T, Shrivastava V, Itelson L, Sade D, Abu Hamoud A, Soussan-Farhat Y, Barak N, Karp P, Moore LR. Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126. PLoS One 2025;20:e0321141. [PMID: 40273159 PMCID: PMC12021255 DOI: 10.1371/journal.pone.0321141] [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: 04/25/2024] [Accepted: 02/28/2025] [Indexed: 04/26/2025]  Open
4
Gong JC, Li BH, Liu CY, Li PF, Hu JW, Yang GP. Impact of salinity gradients on nitric oxide emissions and functional microbes in estuarine wetland sediments. WATER RESEARCH 2025;273:123046. [PMID: 39894607 DOI: 10.1016/j.watres.2024.123046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 12/18/2024] [Accepted: 12/24/2024] [Indexed: 02/04/2025]
5
Zaragoza-Solas A, Baltar F. Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome. Nat Commun 2025;16:2793. [PMID: 40118827 PMCID: PMC11928666 DOI: 10.1038/s41467-025-57974-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/03/2025] [Indexed: 03/24/2025]  Open
6
Ren Z, Luo W, Li H, Ding H, Zhang Y. Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow. ISME COMMUNICATIONS 2025;5:ycaf003. [PMID: 39866751 PMCID: PMC11765414 DOI: 10.1093/ismeco/ycaf003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 01/02/2025] [Accepted: 01/08/2025] [Indexed: 01/28/2025]
7
Li Y, Zhang C, Zhong M, Hu S, Cui Y, Fang J, Yu X. Revealing the metabolic potential and environmental adaptation of nematophagous fungus, Purpureocillium lilacinum, derived from hadal sediment. Front Microbiol 2024;15:1474180. [PMID: 39569000 PMCID: PMC11576294 DOI: 10.3389/fmicb.2024.1474180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 10/09/2024] [Indexed: 11/22/2024]  Open
8
Liu S, Chen Q, Liu L, Dong C, Qiu X, Tang K. Organic matter composition fluctuations disrupt free-living bacterial communities more than particle-associated bacterial communities in coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;949:174845. [PMID: 39053558 DOI: 10.1016/j.scitotenv.2024.174845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
9
Quan Q, Liu J, Li C, Ke Z, Tan Y. Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep. mSphere 2024;9:e0054924. [PMID: 39269181 PMCID: PMC11524163 DOI: 10.1128/msphere.00549-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/13/2024] [Indexed: 09/15/2024]  Open
10
Sun F, Yang H, Zhang X, Tan F, Wang G, Shi Q. Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching. MARINE ENVIRONMENTAL RESEARCH 2024;201:106694. [PMID: 39163656 DOI: 10.1016/j.marenvres.2024.106694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/12/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024]
11
Russo DA, Oliinyk D, Pohnert G, Meier F, Zedler JAZ. EXCRETE workflow enables deep proteomics of the microbial extracellular environment. Commun Biol 2024;7:1189. [PMID: 39322645 PMCID: PMC11424642 DOI: 10.1038/s42003-024-06910-2] [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: 03/27/2024] [Accepted: 09/17/2024] [Indexed: 09/27/2024]  Open
12
Li X, Cheng X, Xu J, Wu J, Chan LL, Cai Z, Zhou J. Dynamic patterns of carbohydrate metabolism genes in bacterioplankton during marine algal blooms. Microbiol Res 2024;286:127785. [PMID: 38851011 DOI: 10.1016/j.micres.2024.127785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/01/2024] [Accepted: 05/25/2024] [Indexed: 06/10/2024]
13
Zhao Z, Amano C, Reinthaler T, Baltar F, Orellana MV, Herndl GJ. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat Commun 2024;15:6411. [PMID: 39080340 PMCID: PMC11289388 DOI: 10.1038/s41467-024-50867-z] [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: 07/14/2023] [Accepted: 07/24/2024] [Indexed: 08/02/2024]  Open
14
Chen S, Xie ZX, Yan KQ, Chen JW, Li DX, Wu PF, Peng L, Lin L, Dong CM, Zhao Z, Fan GY, Liu SQ, Herndl GJ, Wang DZ. Functional vertical connectivity of microbial communities in the ocean. SCIENCE ADVANCES 2024;10:eadj8184. [PMID: 38781332 PMCID: PMC11114224 DOI: 10.1126/sciadv.adj8184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
15
Zhao Z, Amano C, Reinthaler T, Orellana MV, Herndl GJ. Substrate uptake patterns shape niche separation in marine prokaryotic microbiome. SCIENCE ADVANCES 2024;10:eadn5143. [PMID: 38748788 PMCID: PMC11095472 DOI: 10.1126/sciadv.adn5143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
16
Zhao Z, Baltar F, Herndl GJ. Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes. Microbiol Spectr 2024;12:e0303623. [PMID: 38511953 PMCID: PMC11210215 DOI: 10.1128/spectrum.03036-23] [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: 08/04/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]  Open
17
Dang YR, Cha QQ, Liu SS, Wang SY, Li PY, Li CY, Wang P, Chen XL, Tian JW, Xin Y, Chen Y, Zhang YZ, Qin QL. Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench. MICROBIOME 2024;12:77. [PMID: 38664737 PMCID: PMC11044484 DOI: 10.1186/s40168-024-01789-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
18
Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. mSystems 2024;9:e0006724. [PMID: 38380923 PMCID: PMC10949469 DOI: 10.1128/msystems.00067-24] [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: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]  Open
19
Guider JT, Yoshimura KM, Block KR, Biddle JF, Shah Walter SR. Archaeal blooms and busts in an estuarine time series. Environ Microbiol 2024;26:e16584. [PMID: 38372423 DOI: 10.1111/1462-2920.16584] [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: 08/11/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
20
Khan T, Song W, Nappi J, Marzinelli EM, Egan S, Thomas T. Functional guilds and drivers of diversity in seaweed-associated bacteria. FEMS MICROBES 2023;5:xtad023. [PMID: 38213395 PMCID: PMC10781435 DOI: 10.1093/femsmc/xtad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]  Open
21
Li F, Burger A, Eppley JM, Poff KE, Karl DM, DeLong EF. Planktonic microbial signatures of sinking particle export in the open ocean's interior. Nat Commun 2023;14:7177. [PMID: 37935690 PMCID: PMC10630432 DOI: 10.1038/s41467-023-42909-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]  Open
22
Xiong M, Jiang W, Zou S, Kang D, Yan X. Microbial carbohydrate-active enzymes influence soil carbon by regulating the of plant- and fungal-derived biomass decomposition in plateau peat wetlands under differing water conditions. Front Microbiol 2023;14:1266016. [PMID: 37731925 PMCID: PMC10507343 DOI: 10.3389/fmicb.2023.1266016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]  Open
23
Breyer E, Baltar F. The largely neglected ecological role of oceanic pelagic fungi. Trends Ecol Evol 2023;38:870-888. [PMID: 37246083 DOI: 10.1016/j.tree.2023.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
24
Debeljak P, Bayer B, Sun Y, Herndl GJ, Obernosterer I. Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean. MICROBIOME 2023;11:187. [PMID: 37596690 PMCID: PMC10439609 DOI: 10.1186/s40168-023-01600-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/16/2023] [Indexed: 08/20/2023]
25
Zhu XY, Li Y, Xue CX, Lidbury IDEA, Todd JD, Lea-Smith DJ, Tian J, Zhang XH, Liu J. Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems. MICROBIOME 2023;11:175. [PMID: 37550707 PMCID: PMC10405439 DOI: 10.1186/s40168-023-01618-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
26
Tinta T, Zhao Z, Bayer B, Herndl GJ. Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria. MICROBIOME 2023;11:156. [PMID: 37480075 PMCID: PMC10360251 DOI: 10.1186/s40168-023-01598-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/13/2023] [Indexed: 07/23/2023]
27
Sun CC, Zhao WJ, Yue WZ, Cheng H, Sun FL, Wang YT, Wu ML, Engel A, Wang YS. Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China. Front Microbiol 2023;14:1180321. [PMID: 37425997 PMCID: PMC10322874 DOI: 10.3389/fmicb.2023.1180321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]  Open
28
Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023;11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
29
Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023;15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
30
Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas. mSystems 2022;7:e0086422. [PMID: 36342154 PMCID: PMC9765461 DOI: 10.1128/msystems.00864-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
31
Fadeev E, Carpaneto Bastos C, Hennenfeind JH, Biller SJ, Sher D, Wietz M, Herndl GJ. Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle. MICROLIFE 2022;4:uqac025. [PMID: 37223730 PMCID: PMC10117737 DOI: 10.1093/femsml/uqac025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 05/25/2023]
32
Global Distribution of Carbohydrate Utilization Potential in the Prokaryotic Tree of Life. mSystems 2022;7:e0082922. [PMID: 36413015 PMCID: PMC9765126 DOI: 10.1128/msystems.00829-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
33
Bioprospecting for Novel Bacterial Sources of Hydrolytic Enzymes and Antimicrobials in the Romanian Littoral Zone of the Black Sea. Microorganisms 2022;10:microorganisms10122468. [PMID: 36557721 PMCID: PMC9780896 DOI: 10.3390/microorganisms10122468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]  Open
34
Amano C, Zhao Z, Sintes E, Reinthaler T, Stefanschitz J, Kisadur M, Utsumi M, Herndl GJ. Limited carbon cycling due to high-pressure effects on the deep-sea microbiome. NATURE GEOSCIENCE 2022;15:1041-1047. [PMID: 36504693 PMCID: PMC9726642 DOI: 10.1038/s41561-022-01081-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
35
Yan Z, Kang E, Zhang K, Hao Y, Wang X, Li Y, Li M, Wu H, Zhang X, Yan L, Zhang W, Li J, Yang A, Niu Y, Kang X. Asynchronous responses of microbial CAZymes genes and the net CO2 exchange in alpine peatland following 5 years of continuous extreme drought events. ISME COMMUNICATIONS 2022;2:115. [PMID: 37938678 PMCID: PMC9723601 DOI: 10.1038/s43705-022-00200-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2023]
36
Wietz M, López-Pérez M, Sher D, Biller SJ, Rodriguez-Valera F. Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium. MICROBIOLOGY (READING, ENGLAND) 2022;168. [PMID: 36748580 DOI: 10.1099/mic.0.001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
37
Lloyd CC, Brown S, Balmonte JP, Hoarfrost A, Ghobrial S, Arnosti C. Particles act as ‘specialty centers’ with expanded enzymatic function throughout the water column in the western North Atlantic. Front Microbiol 2022;13:882333. [PMID: 36246226 PMCID: PMC9553992 DOI: 10.3389/fmicb.2022.882333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022]  Open
38
Arandia-Gorostidi N, Berthelot H, Calabrese F, Stryhanyuk H, Klawonn I, Iversen M, Nahar N, Grossart HP, Ploug H, Musat N. Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups. Sci Rep 2022;12:14949. [PMID: 36056039 PMCID: PMC9440002 DOI: 10.1038/s41598-022-18915-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022]  Open
39
Breyer E, Zhao Z, Herndl GJ, Baltar F. Global contribution of pelagic fungi to protein degradation in the ocean. MICROBIOME 2022;10:143. [PMID: 36050758 PMCID: PMC9434897 DOI: 10.1186/s40168-022-01329-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/19/2022] [Indexed: 05/31/2023]
40
Zhang X, Liu Z, Xu W, Pan J, Huang Y, Cai M, Luo Z, Li M. Genomic insights into versatile lifestyle of three new bacterial candidate phyla. SCIENCE CHINA. LIFE SCIENCES 2022;65:1547-1562. [PMID: 35060074 DOI: 10.1007/s11427-021-2037-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/01/2021] [Indexed: 05/28/2023]
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Liu H, Liao C, Wu L, Tang J, Chen J, Lei C, Zheng L, Zhang C, Liu YY, Xavier J, Dai L. Ecological dynamics of the gut microbiome in response to dietary fiber. THE ISME JOURNAL 2022;16:2040-2055. [PMID: 35597888 PMCID: PMC9296629 DOI: 10.1038/s41396-022-01253-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 12/19/2022]
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Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column. mBio 2022;13:e0156922. [PMID: 35862780 PMCID: PMC9426571 DOI: 10.1128/mbio.01569-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
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Malfertheiner L, Martínez-Pérez C, Zhao Z, Herndl GJ, Baltar F. Phylogeny and Metabolic Potential of the Candidate Phylum SAR324. BIOLOGY 2022;11:599. [PMID: 35453798 PMCID: PMC9031357 DOI: 10.3390/biology11040599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
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Xie ZX, He YB, Zhang SF, Lin L, Wang MH, Wang DZ. Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior. Front Microbiol 2022;13:749874. [PMID: 35250917 PMCID: PMC8889253 DOI: 10.3389/fmicb.2022.749874] [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: 07/30/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022]  Open
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Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord. mSystems 2021;6:e0057521. [PMID: 34904860 PMCID: PMC8670421 DOI: 10.1128/msystems.00575-21] [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] [Indexed: 11/20/2022]  Open
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Cathalot C, Roussel EG, Perhirin A, Creff V, Donval JP, Guyader V, Roullet G, Gula J, Tamburini C, Garel M, Godfroy A, Sarradin PM. Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production. Nat Commun 2021;12:6861. [PMID: 34824206 PMCID: PMC8617075 DOI: 10.1038/s41467-021-26877-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/19/2021] [Indexed: 11/09/2022]  Open
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Fadeev E, Rogge A, Ramondenc S, Nöthig EM, Wekerle C, Bienhold C, Salter I, Waite AM, Hehemann L, Boetius A, Iversen MH. Sea ice presence is linked to higher carbon export and vertical microbial connectivity in the Eurasian Arctic Ocean. Commun Biol 2021;4:1255. [PMID: 34732822 PMCID: PMC8566512 DOI: 10.1038/s42003-021-02776-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 10/09/2021] [Indexed: 01/04/2023]  Open
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Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 2021;4:604. [PMID: 34021239 PMCID: PMC8139981 DOI: 10.1038/s42003-021-02112-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/16/2021] [Indexed: 02/04/2023]  Open
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Baltar F, Zhao Z, Herndl GJ. Potential and expression of carbohydrate utilization by marine fungi in the global ocean. MICROBIOME 2021;9:106. [PMID: 33975640 PMCID: PMC8114511 DOI: 10.1186/s40168-021-01063-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/29/2021] [Indexed: 05/26/2023]
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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020;11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022]  Open
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