Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome.
archaea
microbial diversity
microscale
phycosphere
thalassohaline ecosystem
Journal
Molecular ecology
ISSN: 1365-294X
Titre abrégé: Mol Ecol
Pays: England
ID NLM: 9214478
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
revised:
18
09
2023
received:
05
06
2023
accepted:
09
10
2023
medline:
7
12
2023
pubmed:
30
10
2023
entrez:
30
10
2023
Statut:
ppublish
Résumé
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6824-6838Subventions
Organisme : MITI CNRS Origines
ID : Oracle
Organisme : MITI CNRS X-Life
ID : Cabman
Informations de copyright
© 2023 John Wiley & Sons Ltd.
Références
Adam, P. S., Borrel, G., Brochier-Armanet, C., & Gribaldo, S. (2017). The growing tree of archaea: New perspectives on their diversity, evolution and ecology. The ISME Journal, 11(11), 2407-2425. https://doi.org/10.1038/ismej.2017.122
Allison, S. D., & Martiny, J. B. H. (2008). Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 105(Supplement 1), 11512-11519. https://doi.org/10.1073/pnas.0801925105
Amin, S. A., Green, D. H., Hart, M. C., Küpper, F. C., Sunda, W. G., & Carrano, C. J. (2009). Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism. Proceedings of the National Academy of Sciences of the United States of America, 106(40), 17071-17076. https://doi.org/10.1073/pnas.0905512106
Amin, S. A., Hmelo, L. R., van Tol, H. M., Durham, B. P., Carlson, L. T., Heal, K. R., Morales, R. L., Berthiaume, C. T., Parker, M. S., Djunaedi, B., Ingalls, A. E., Parsek, M. R., Moran, M. A., & Armbrust, E. V. (2015). Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature, 522(7554), 98-101. https://doi.org/10.1038/nature14488
Angel, R., Matthies, D., & Conrad, R. (2011). Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One, 6(5), e20453. https://doi.org/10.1371/journal.pone.0020453
Ashraf, N., Ahmad, F., & Lu, Y. (2023). Synergy between microalgae and microbiome in polluted waters. Trends in Microbiology, 31(1), 9-21. https://doi.org/10.1016/j.tim.2022.06.004
Bell, W., & Mitchell, R. (1972). Chemotactic and growth responses of marine bacteria to algal extracellular products. The Biological Bulletin, 143(2), 265-277. https://doi.org/10.2307/1540052
Bernard, C., Escalas, A., Villeriot, N., Agogué, H., Hugoni, M., Duval, C., Carré, C., Got, P., Sarazin, G., Jézéquel, D., Leboulanger, C., Grossi, V., Ader, M., & Troussellier, M. (2019). Very low phytoplankton diversity in a tropical saline-alkaline lake, with co-dominance of Arthrospira fusiformis (cyanobacteria) and Picocystis salinarum (Chlorophyta). Microbial Ecology, 78(3), 603-617. https://doi.org/10.1007/s00248-019-01332-8
Bizic, M. (2021). Phytoplankton photosynthesis: An unexplored source of biogenic methane emission from oxic environments. Journal of Plankton Research, 43(6), 822-830. https://doi.org/10.1093/plankt/fbab069
Bižić, M., Klintzsch, T., Ionescu, D., Hindiyeh, M. Y., Günthel, M., Muro-Pastor, A. M., Eckert, W., Urich, T., Keppler, F., & Grossart, H.-P. (2020). Aquatic and terrestrial cyanobacteria produce methane. Science Advances, 6(3), eaax5343. https://doi.org/10.1126/sciadv.aax5343
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., Mills, D. A., & Caporaso, J. G. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10(1), 57-59. https://doi.org/10.1038/nmeth.2276
Buchan, A., LeCleir, G. R., Gulvik, C. A., & González, J. M. (2014). Master recyclers: Features and functions of bacteria associated with phytoplankton blooms. Nature Reviews Microbiology, 12(10), 686-698. https://doi.org/10.1038/nrmicro3326
Cadeau, P., Jezequel, D., Leboulanger, C., Fouilland, E., Le Floc'h, E., Chaduteau, C., Milesi, V., Guelard, J., Sarazin, G., Katz, A., d'Amore, S., Bernard, C., & Ader, M. (2020). Carbon isotope evidence for large methane emissions to the Proterozoic atmosphere. Scientific Reports, 10, Article 18186. https://doi.org/10.1038/s41598-020-75100-x
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471-2105-10-421
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., & Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America, 108(Suppl 1), 4516-4522. https://doi.org/10.1073/pnas.1000080107
Castelle, C. J., Brown, C. T., Anantharaman, K., Probst, A. J., Huang, R. H., & Banfield, J. F. (2018). Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nature Reviews Microbiology, 16(10), 629-645. https://doi.org/10.1038/s41579-018-0076-2
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., Taylor, R. C., Williams, K. H., & Banfield, J. F. (2015). Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Current Biology, 25(6), 690-701. https://doi.org/10.1016/j.cub.2015.01.014
Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17(4), 540-552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Cellamare, M., Duval, C., Drelin, Y., Djediat, C., Touibi, N., Agogué, H., Leboulanger, C., Ader, M., & Bernard, C. (2018). Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean). FEMS Microbiology Ecology, 94(8), fiy108. https://doi.org/10.1093/femsec/fiy108
Christian, J. R., & Anderson, T. R. (2002). Chapter 16-Modeling DOM Biogeochemistry. In D. A. Hansell & C. A. Carlson (Eds.), Biogeochemistry of marine dissolved organic matter (pp. 717-755). Academic Press. https://doi.org/10.1016/B978-012323841-2/50018-X
Cordero, O. X., & Datta, M. S. (2016). Microbial interactions and community assembly at microscales. Current Opinion in Microbiology, 31, 227-234. https://doi.org/10.1016/j.mib.2016.03.015
Croft, M. T., Lawrence, A. D., Raux-Deery, E., Warren, M. J., & Smith, A. G. (2005). Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature, 438(7064), 90-93. https://doi.org/10.1038/nature04056
Dadheech, P. K., Glöckner, G., Casper, P., Kotut, K., Mazzoni, C. J., Mbedi, S., & Krienitz, L. (2013). Cyanobacterial diversity in the hot spring, pelagic and benthic habitats of a tropical soda lake. FEMS Microbiology Ecology, 85(2), 389-401. https://doi.org/10.1111/1574-6941.12128
Dal Co, A., van Vliet, S., Kiviet, D. J., Schlegel, S., & Ackermann, M. (2020). Short-range interactions govern the dynamics and functions of microbial communities. Nature Ecology & Evolution, 4(3), 366-375. https://doi.org/10.1038/s41559-019-1080-2
Dombrowski, N., Lee, J.-H., Williams, T. A., Offre, P., & Spang, A. (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiology Letters, 366(2), fnz008. https://doi.org/10.1093/femsle/fnz008
Dombrowski, N., Williams, T. A., Sun, J., Woodcroft, B. J., Lee, J. H., Minh, B. Q., Rinke, C., & Spang, A. (2020). Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications, 11(1), 3939. https://doi.org/10.1038/s41467-020-17408-w
Escalas, A., Troussellier, M., Melayah, D., Bruto, M., Nicolas, S., Bernard, C., Ader, M., Leboulanger, C., Agogué, H., & Hugoni, M. (2021). Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiology Ecology, 97(12), fiab163. https://doi.org/10.1093/femsec/fiab163
Escudié, F., Auer, L., Bernard, M., Mariadassou, M., Cauquil, L., Vidal, K., Maman, S., Hernandez-Raquet, G., Combes, S., & Pascal, G. (2017). FROGS: Find, rapidly, OTUs with galaxy solution. Bioinformatics, 34(8), 1287-1294. https://doi.org/10.1093/bioinformatics/btx791
Fu, H., Uchimiya, M., Gore, J., & Moran, M. A. (2020). Ecological drivers of bacterial community assembly in synthetic phycospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(7), 3656-3662. https://doi.org/10.1073/pnas.1917265117
Golyshina, O. V., Toshchakov, S. V., Makarova, K. S., Gavrilov, S. N., Korzhenkov, A. A., La Cono, V., Arcadi, E., Nechitaylo, T. Y., Ferrer, M., Kublanov, I. V., Wolf, Y. I., Yakimov, M. M., & Golyshin, P. N. (2017). “ARMAN” archaea depend on association with euryarchaeal host in culture and in situ. Nature Communications, 8(1), 60. https://doi.org/10.1038/s41467-017-00104-7
Günthel, M., Donis, D., Kirillin, G., Ionescu, D., Bizic, M., McGinnis, D. F., Grossart, H.-P., & Tang, K. W. (2019). Contribution of oxic methane production to surface methane emission in lakes and its global importance. Nature Communications, 10(1), 5497. https://doi.org/10.1038/s41467-019-13320-0
Haichar, F., El, Z., Marol, C., Berge, O., Rangel-Castro, J. I., Prosser, J. I., Balesdent, J., Heulin, T., & Achouak, W. (2008). Plant host habitat and root exudates shape soil bacterial community structure. The ISME Journal, 2(12), 1221-1230. https://doi.org/10.1038/ismej.2008.80
Halary, S., Duperron, S., Demay, J., Duval, C., Hamlaoui, S., Piquet, B., Reinhardt, A., Bernard, C., & Marie, B. (2022). Metagenome-based exploration of bacterial communities associated with cyanobacteria strains isolated from thermal muds. Microorganisms, 10(12), 2337. https://doi.org/10.3390/microorganisms10122337
Hamm, J. N., Erdmann, S., Eloe-Fadrosh, E. A., Angeloni, A., Zhong, L., Brownlee, C., Williams, T. J., Barton, K., Carswell, S., Smith, M. A., Brazendale, S., Hancock, A. M., Allen, M. A., Raftery, M. J., & Cavicchioli, R. (2019). Unexpected host dependency of Antarctic Nanohaloarchaeota. Proceedings of the National Academy of Sciences of the United States of America, 116(29), 14661-14670. https://doi.org/10.1073/pnas.1905179116
Huang, W. C., Liu, Y., Zhang, X., Zhang, C. J., Zou, D., Zheng, S., Xu, W., Luo, Z., Liu, F., & Li, M. (2021). Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. Nature Communications, 12, 5281. https://doi.org/10.1038/s41467-021-25565-9
Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C., & Stetter, K. O. (2002). A new phylum of archaea represented by a nanosized hyperthermophilic symbiont. Nature, 417(6884), 63-67. https://doi.org/10.1038/417063a
Hugoni, M., Domaizon, I., Taib, N., Biderre-Petit, C., Agogué, H., Galand, P. E., Debroas, D., & Mary, I. (2015). Temporal dynamics of active archaea in oxygen-depleted zones of two deep lakes. Environmental Microbiology Reports, 7(2), 321-329. https://doi.org/10.1111/1758-2229.12251
Hugoni, M., Escalas, A., Bernard, C., Nicolas, S., Jézéquel, D., Vazzoler, F., Sarazin, G., Leboulanger, C., Bouvy, M., Got, P., Ader, M., Troussellier, M., & Agogué, H. (2018). Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Molecular Ecology, 27, 4775-4786.
Jirsová, D., Füssy, Z., Richtová, J., Gruber, A., & Oborník, M. (2019). Morphology, ultrastructure, and mitochondrial genome of the marine non-photosynthetic Bicosoecid Cafileria marina gen. Et Sp. Nov. Microorganisms, 7(8), 240. https://doi.org/10.3390/microorganisms7080240
Kadnikov, V. V., Savvichev, A. S., Mardanov, A. V., Beletsky, A. V., Chupakov, A. V., Kokryatskaya, N. M., Pimenov, N. V., & Ravin, N. V. (2020). Metabolic diversity and evolutionary history of the archaeal phylum “Candidatus Micrarchaeota” uncovered from a freshwater lake metagenome. Applied and Environmental Microbiology, 86(23), 02199-20. https://doi.org/10.1128/AEM.02199-20
Klintzsch, T., Langer, G., Nehrke, G., Wieland, A., Lenhart, K., & Keppler, F. (2019). Methane production by three widespread marine phytoplankton species: Release rates, precursor compounds, and potential relevance for the environment. Biogeosciences, 16(20), 4129-4144. https://doi.org/10.5194/bg-16-4129-2019
Krienitz, L., Dadheech, P. K., & Kotut, K. (2013). Mass developments of the cyanobacteria Anabaenopsis and Cyanospira (Nostocales) in the soda lakes of Kenya: Ecological and systematic implications. Hydrobiologia, 703(1), 79-93. https://doi.org/10.1007/s10750-012-1346-z
Kuraku, S., Zmasek, C. M., Nishimura, O., & Katoh, K. (2013). ALeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Research, 41(Web Server issue), W22-W28. https://doi.org/10.1093/nar/gkt389
Leboulanger, C., Agogué, H., Bernard, C., Bouvy, M., Carré, C., Cellamare, M., Duval, C., Fouilland, E., Got, P., Intertaglia, L., Lavergne, C., Le Floc'h, E., Roques, C., & Sarazin, G. (2017). Microbial diversity and cyanobacterial production in Dziani Dzaha crater lake, a unique tropical thalassohaline environment. PLoS One, 12(1), e0168879. https://doi.org/10.1371/journal.pone.0168879
Lefort, V., Desper, R., & Gascuel, O. (2015). FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program: Table 1. Molecular Biology and Evolution, 32(10), 2798-2800. https://doi.org/10.1093/molbev/msv150
Lepère, C., Domaizon, I., Hugoni, M., Vellet, A., & Debroas, D. (2016). Diversity and dynamics of active small microbial eukaryotes in the anoxic zone of a freshwater meromictic lake (Pavin, France). Frontiers in Microbiology, 7, 130. https://doi.org/10.3389/fmicb.2016.00130
Li, J., Gu, L., Bai, S., Wang, J., Su, L., Wei, B., Zhang, L., & Fang, J. (2021). Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea. Biogeosciences, 18(1), 113-133. https://doi.org/10.5194/bg-18-113-2021
Liu, J., Meng, Z., Liu, X., & Zhang, X.-H. (2019). Microbial assembly, interaction, functioning, activity and diversification: A review derived from community compositional data. Marine Life Science & Technology, 1(1), 112-128. https://doi.org/10.1007/s42995-019-00004-3
Louati, I., Nunan, N., Tambosco, K., Bernard, C., Humbert, J. F., & Leloup, J. (2023). The phyto-bacterioplankton couple in a shallow freshwater ecosystem: Who leads the dance? Harmful Algae, 126, 102436. https://doi.org/10.1016/j.hal.2023.102436
Mahé, F., Rognes, T., Quince, C., De Vargas, C., & Dunthorn, M. (2014). Swarm: Robust and fast clustering method for amplicon-based studies. PeerJ, 2, e593.
Malfatti, F., & Azam, F. (2009). Atomic force microscopy reveals microscale networks and possible symbioses among pelagic marine bacteria. Aquatic Microbial Ecology, 58, 1-14. https://doi.org/10.3354/ame01355
Orland, C., Yakimovich, K. M., Mykytczuk, N. C. S., Basiliko, N., & Tanentzap, A. J. (2020). Think global, act local: The small-scale environment mainly influences microbial community development and function in lake sediment. Limnology and Oceanography, 65(S1), S88-S100. https://doi.org/10.1002/lno.11370
Pálmai, T., Szabó, B., Kotut, K., Krienitz, L., & Padisák, J. (2020). Ecophysiology of a successful phytoplankton competitor in the African flamingo lakes: The green alga Picocystis salinarum (Picocystophyceae). Journal of Applied Phycology, 32(3), 1813-1825. https://doi.org/10.1007/s10811-020-02092-6
Park, J. S., & Simpson, A. G. B. (2015). Diversity of heterotrophic protists from extremely hypersaline habitats. Protist, 166(4), 422-437. https://doi.org/10.1016/j.protis.2015.06.001
Pascault, N., Rué, O., Loux, V., Pédron, J., Martin, V., Tambosco, J., Bernard, C., Humbert, J., & Leloup, J. (2021). Insights into the cyanosphere: Capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions? Environmental Microbiology Reports, 13(3), 364-374. https://doi.org/10.1111/1758-2229.12944
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007). SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35(21), 7188-7196. https://doi.org/10.1093/nar/gkm864
Ramette, A. (2007). Multivariate analyses in microbial ecology. FEMS Microbiology Ecology, 62(2), 142-160. https://doi.org/10.1111/j.1574-6941.2007.00375.x
Ritchie, R. J. (2006). Consistent sets of spectrophotometric chlorophyll equations for acetone, methanol and ethanol solvents. Photosynthesis Research, 89(1), 27-41. https://doi.org/10.1007/s11120-006-9065-9
Roesler, C. (2002). Distribution, production, and ecophysiology of Picocystis strain ML in mono Lake, California. Limnology and Oceanography, 47(2), 440-452.
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584. https://doi.org/10.7717/peerj.2584
Rybarski, A. E., Nitsche, F., Soo Park, J., Filz, P., Schmidt, P., Kondo, R., GB Simpson, A., & Arndt, H. (2021). Revision of the phylogeny of Placididea (Stramenopiles): Molecular and morphological diversity of novel placidid protists from extreme aquatic environments. European Journal of Protistology, 81, 125809. https://doi.org/10.1016/j.ejop.2021.125809
Sapp, M., Schwaderer, A. S., Wiltshire, K. H., Hoppe, H.-G., Gerdts, G., & Wichels, A. (2007). Species-specific bacterial communities in the phycosphere of microalgae? Microbial Ecology, 53(4), 683-699. https://doi.org/10.1007/s00248-006-9162-5
Sarazin, G., Jézéquel, D., Leboulanger, C., Fouilland, E., Floc'h, E. L., Bouvy, M., Gérard, E., Agogué, H., Bernard, C., Hugoni, M., Grossi, V., Troussellier, M., & Ader, M. (2021). Geochemistry of an endorheic thalassohaline ecosystem: The Dziani Dzaha crater lake (Mayotte archipelago, Indian Ocean). Comptes Rendus. Géoscience, 0(0), 1-19. https://doi.org/10.5802/crgeos.43
Schuurman, T., de Boer, R. F., Kooistra-Smid, A. M. D., & van Zwet, A. A. (2004). Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical setting. Journal of Clinical Microbiology, 42(2), 734-740. https://doi.org/10.1128/JCM.42.2.734-740.2004
Schwank, K., Bornemann, T. L. V., Dombrowski, N., Spang, A., Banfield, J. F., & Probst, A. J. (2019). An archaeal symbiont-host association from the deep terrestrial subsurface. The ISME Journal, 13(8), 2135-2139. https://doi.org/10.1038/s41396-019-0421-0
Seyedsayamdost, M. R., Wang, R., Kolter, R., & Clardy, J. (2014). Hybrid biosynthesis of roseobacticides from algal and bacterial precursor molecules. Journal of the American Chemical Society, 136(43), 15150-15153. https://doi.org/10.1021/ja508782y
Seymour, J., Ahmed, T., Durham, W., & Stocker, R. (2010). Chemotactic response of marine bacteria to the extracellular products of Synechococcus and Prochlorococcus. Aquatic Microbial Ecology, 59, 161-168. https://doi.org/10.3354/ame01400
Seymour, J. R., Amin, S. A., Raina, J.-B., & Stocker, R. (2017). Zooming in on the phycosphere: The ecological interface for phytoplankton-bacteria relationships. Nature Microbiology, 2(7), 17065. https://doi.org/10.1038/nmicrobiol.2017.65
Shibl, A. A., Isaac, A., Ochsenkühn, M. A., Cárdenas, A., Fei, C., Behringer, G., Arnoux, M., Drou, N., Santos, M. P., Gunsalus, K. C., Voolstra, C. R., & Amin, S. A. (2020). Diatom modulation of select bacteria through use of two unique secondary metabolites. Proceedings of the National Academy of Sciences of the United States of America, 117(44), 27445-27455. https://doi.org/10.1073/pnas.2012088117
Sorokin, D. Y., Berben, T., Melton, E. D., Overmars, L., Vavourakis, C. D., & Muyzer, G. (2014). Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles, 18(5), 791-809. https://doi.org/10.1007/s00792-014-0670-9
Suzuki, A., Kaneko, R., Kodama, T., Hashihama, F., Suwa, S., Tanita, I., Furuya, K., & Hamasaki, K. (2017). Comparison of community structures between particle-associated and free-living prokaryotes in tropical and subtropical Pacific Ocean surface waters. Journal of Oceanography, 73, 383-395. https://doi.org/10.1007/s10872-016-0410-0
Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56(4), 564-577. https://doi.org/10.1080/10635150701472164
Teeling, H., Fuchs, B. M., Becher, D., Klockow, C., Gardebrecht, A., Bennke, C. M., Kassabgy, M., Huang, S., Mann, A. J., Waldmann, J., Weber, M., Klindworth, A., Otto, A., Lange, J., Bernhardt, J., Reinsch, C., Hecker, M., Peplies, J., Bockelmann, F. D., … Amann, R. (2012). Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science (New York, N.Y.), 336(6081), 608-611. https://doi.org/10.1126/science.1218344
Uroz, S., Courty, P. E., & Oger, P. (2019). Plant symbionts are engineers of the plant-associated microbiome. Trends in Plant Science, 24(10), 905-916. https://doi.org/10.1016/j.tplants.2019.06.008
Vigneron, A., Cruaud, P., Lovejoy, C., & Vincent, W. F. (2022). Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia. ISME Communications, 2(1), 4. https://doi.org/10.1038/s43705-022-00088-6
Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., & Knight, R. (2016). Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems, 1(1), e00009-e00015. https://doi.org/10.1128/mSystems.00009-15
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16), 5261-5267. https://doi.org/10.1128/AEM.00062-07
Woodhouse, J. N., Kinsela, A. S., Collins, R. N., Bowling, L. C., Honeyman, G. L., Holliday, J. K., & Neilan, B. A. (2016). Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake. The ISME Journal, 10(6), 1337-1351. https://doi.org/10.1038/ismej.2015.218
Yang, C., Wang, Q., Simon, P. N., Liu, J., Liu, L., Dai, X., Zhang, X., Kuang, J., Igarashi, Y., Pan, X., & Luo, F. (2017). Distinct network interactions in particle-associated and free-living bacterial communities during a Microcystis aeruginosa bloom in a plateau lake. Frontiers in Microbiology, 8, 1202. https://doi.org/10.3389/fmicb.2017.01202
Youssef, N. H., Rinke, C., Stepanauskas, R., Farag, I., Woyke, T., & Elshahed, M. S. (2015). Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites.’. The ISME Journal, 9(2), 447-460. https://doi.org/10.1038/ismej.2014.141
Zhang, W., Ding, W., Li, Y.-X., Tam, C., Bougouffa, S., Wang, R., Pei, B., Chiang, H., Leung, P., Lu, Y., Sun, J., Fu, H., Bajic, V. B., Liu, H., Webster, N. S., & Qian, P.-Y. (2019). Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature Communications, 10(1), 517. https://doi.org/10.1038/s41467-019-08463-z
Zhou, J., Chen, G. F., Ying, K. Z., Jin, H., Song, J. T., & Cai, Z. H. (2019). Phycosphere microbial succession patterns and assembly mechanisms in a marine dinoflagellate bloom. Applied and Environmental Microbiology, 85(15), e00349-19. https://doi.org/10.1128/AEM.00349-19