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For: Armitage DW, Jones SE. How sample heterogeneity can obscure the signal of microbial interactions. ISME J 2019;13:2639-2646. [PMID: 31249391 PMCID: PMC6794314 DOI: 10.1038/s41396-019-0463-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 11/08/2022]
Number Cited by Other Article(s)
1
Feng Z, Li N, Deng Y, Yu Y, Gao Q, Wang J, Chen S, Xing R. Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China. Ecol Evol 2024;14:e11001. [PMID: 38352203 PMCID: PMC10862184 DOI: 10.1002/ece3.11001] [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: 05/07/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]  Open
2
Wang M, Zhao K, Li X, Xie BB. Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains. Front Microbiol 2023;14:1308767. [PMID: 38098661 PMCID: PMC10719935 DOI: 10.3389/fmicb.2023.1308767] [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: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]  Open
3
Deng T, He Z, Xu M, Dong M, Guo J, Sun G, Huang H. Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning. mBio 2023;14:e0156723. [PMID: 37702500 PMCID: PMC10653917 DOI: 10.1128/mbio.01567-23] [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: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023]  Open
4
Fujiyoshi S, Yarimizu K, Fuenzalida G, Campos M, Rilling JI, Acuña JJ, Miranda PC, Cascales EK, Perera I, Espinoza-González O, Guzmán L, Jorquera MA, Maruyama F. Monitoring bacterial composition and assemblage in the Gulf of Corcovado, southern Chile: Bacteria associated with harmful algae. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023;4:100194. [PMID: 37346179 PMCID: PMC10279789 DOI: 10.1016/j.crmicr.2023.100194] [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: 06/23/2023]  Open
5
Bickel S, Or D. Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria. Commun Biol 2023;6:322. [PMID: 36966207 PMCID: PMC10039866 DOI: 10.1038/s42003-023-04703-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023]  Open
6
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Habitats Within the Plant Root Differ in Bacterial Network Topology and Taxonomic Assortativity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023;36:165-175. [PMID: 36463399 DOI: 10.1094/mpmi-09-22-0188-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
7
Chen W, Sang S, Shao L, Li Y, Li T, Gan L, Liu L, Wang D, Zhou L. Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China. Microbiol Spectr 2023;11:e0368322. [PMID: 36507672 PMCID: PMC9927264 DOI: 10.1128/spectrum.03683-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]  Open
8
Bove CB, Ingersoll MV, Davies SW. Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions. Integr Comp Biol 2022;62:1756-1769. [PMID: 36099871 DOI: 10.1093/icb/icac141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/24/2022] [Accepted: 09/05/2022] [Indexed: 01/05/2023]  Open
9
Pacheco AR, Pauvert C, Kishore D, Segrè D. Toward FAIR Representations of Microbial Interactions. mSystems 2022;7:e0065922. [PMID: 36005399 PMCID: PMC9599284 DOI: 10.1128/msystems.00659-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
10
Fleishman SM, Eissenstat DM, Bell TH, Centinari M. Functionally-explicit sampling can answer key questions about the specificity of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2022;17:51. [PMID: 36221138 PMCID: PMC9555203 DOI: 10.1186/s40793-022-00445-x] [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: 02/11/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
11
Historical contingencies and phage induction diversify bacterioplankton communities at the microscale. Proc Natl Acad Sci U S A 2022;119:e2117748119. [PMID: 35862452 PMCID: PMC9335236 DOI: 10.1073/pnas.2117748119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
12
Chen L, Zhao B, Palomo A, Sun Y, Cheng Z, Zhang M, Xia Y. Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations. WATER RESEARCH 2022;220:118640. [PMID: 35661503 DOI: 10.1016/j.watres.2022.118640] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
13
Cai YJ, Liu ZA, Zhang S, Liu H, Nicol GW, Chen Z. Microbial community structure is stratified at the millimeter-scale across the soil-water interface. ISME COMMUNICATIONS 2022;2:53. [PMID: 37938662 PMCID: PMC9723559 DOI: 10.1038/s43705-022-00138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 08/09/2023]
14
Guseva K, Darcy S, Simon E, Alteio LV, Montesinos-Navarro A, Kaiser C. From diversity to complexity: Microbial networks in soils. SOIL BIOLOGY & BIOCHEMISTRY 2022;169:108604. [PMID: 35712047 PMCID: PMC9125165 DOI: 10.1016/j.soilbio.2022.108604] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/07/2023]
15
Hughes DJ, Raina JB, Nielsen DA, Suggett DJ, Kühl M. Disentangling compartment functions in sessile marine invertebrates. Trends Ecol Evol 2022;37:740-748. [PMID: 35570130 DOI: 10.1016/j.tree.2022.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 01/01/2023]
16
Gleich SJ, Cram JA, Weissman JL, Caron DA. NetGAM: Using generalized additive models to improve the predictive power of ecological network analyses constructed using time-series data. ISME COMMUNICATIONS 2022;2:23. [PMID: 37938660 PMCID: PMC9723797 DOI: 10.1038/s43705-022-00106-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 05/26/2023]
17
It's the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science. mSystems 2022;7:e0103321. [PMID: 35014875 PMCID: PMC8751381 DOI: 10.1128/msystems.01033-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
18
Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
19
Faust K. Open challenges for microbial network construction and analysis. THE ISME JOURNAL 2021;15:3111-3118. [PMID: 34108668 PMCID: PMC8528840 DOI: 10.1038/s41396-021-01027-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/03/2023]
20
Schagen M, Bosch J, Johnson J, Duker R, Lebre P, Potts AJ, Cowan DA. The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket). PeerJ 2021;9:e12176. [PMID: 34707927 PMCID: PMC8501999 DOI: 10.7717/peerj.12176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/29/2021] [Indexed: 01/04/2023]  Open
21
Zou K, Wang R, Xu S, Li Z, Liu L, Li M, Zhou L. Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence. WATER RESEARCH 2021;200:117294. [PMID: 34102388 DOI: 10.1016/j.watres.2021.117294] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
22
Swain A, Devereux M, Fagan WF. Deciphering trophic interactions in a mid-Cambrian assemblage. iScience 2021;24:102271. [PMID: 33817576 PMCID: PMC8010449 DOI: 10.1016/j.isci.2021.102271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/07/2020] [Accepted: 03/02/2021] [Indexed: 11/23/2022]  Open
23
Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front Microbiol 2021;11:618373. [PMID: 33633695 PMCID: PMC7901896 DOI: 10.3389/fmicb.2020.618373] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022]  Open
24
Dini-Andreote F, Kowalchuk GA, Prosser JI, Raaijmakers JM. Towards meaningful scales in ecosystem microbiome research. Environ Microbiol 2020;23:1-4. [PMID: 33047413 DOI: 10.1111/1462-2920.15276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
25
Furey PC, Lee SS, Clemans DL. Substratum-associated microbiota. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020;92:1629-1648. [PMID: 33463854 DOI: 10.1002/wer.1410] [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: 04/30/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 06/12/2023]
26
Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. FEMS Microbiol Lett 2020;366:5513995. [PMID: 31187139 PMCID: PMC6610204 DOI: 10.1093/femsle/fnz125] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]  Open
27
Centler F, Günnigmann S, Fetzer I, Wendeberg A. Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining. Microorganisms 2020;8:microorganisms8020190. [PMID: 32019172 PMCID: PMC7074749 DOI: 10.3390/microorganisms8020190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 01/03/2023]  Open
28
Coller E, Cestaro A, Zanzotti R, Bertoldi D, Pindo M, Larger S, Albanese D, Mescalchin E, Donati C. Microbiome of vineyard soils is shaped by geography and management. MICROBIOME 2019;7:140. [PMID: 31699155 PMCID: PMC6839268 DOI: 10.1186/s40168-019-0758-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/09/2019] [Indexed: 05/12/2023]
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