in

Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations

  • 1.

    Kislyuk AO, Haegeman B, Bergman NH, Weitz JS. Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genom. 2011;12:1–10.

    Google Scholar 

  • 2.

    Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008;11:472–7.

    CAS 

    Google Scholar 

  • 3.

    Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci USA. 2005;102:13950–5.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 4.

    Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15:589–94.

    CAS 

    Google Scholar 

  • 5.

    Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol. 2015;23:148–54.

    CAS 
    PubMed 

    Google Scholar 

  • 6.

    Caro-Quintero A, Konstantinidis KT. Bacterial species may exist, metagenomics reveal. Environ Microbiol. 2012;14:347–55.

    CAS 
    PubMed 

    Google Scholar 

  • 7.

    Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, et al. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. ISME J. 2018;12:742–55.

    CAS 
    PubMed 

    Google Scholar 

  • 8.

    Olm MR, Crits-Christoph A, Diamond S, Lavy A, Matheus Carnevali PB, Banfield JF. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems. 2020;5:e00731–19.

  • 9.

    Konstantinidis KT, DeLong EF. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J. 2008;2:1052–65.

    CAS 
    PubMed 

    Google Scholar 

  • 10.

    Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 2016;10:1589–601.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 11.

    Johnston ER, Rodriguez RL, Luo C, Yuan MM, Wu L, He Z, et al. Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem. Front Microbiol. 2016;7:579.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 12.

    Meziti A, Tsementzi D, Rodriguez RL, Hatt JK, Karayanni H, Kormas KA, et al. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. ISME J. 2019;13:767–79.

    PubMed 

    Google Scholar 

  • 13.

    Orellana LH, Ben Francis T, Kruger K, Teeling H, Muller MC, Fuchs BM, et al. Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. ISME J. 2019;13:3024–36.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 14.

    Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Shapiro BJ, Polz MF. Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol. 2014;22:235–47.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 16.

    Andreani NA, Hesse E, Vos M. Prokaryote genome fluidity is dependent on effective population size. ISME J. 2017;11:1719–21.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 17.

    Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc B 2006;361:1929–40.

    Google Scholar 

  • 18.

    McInerney JO, McNally A, O’Connell MJ. Why prokaryotes have pangenomes. Nat Microbiol. 2017;2:17040.

    CAS 
    PubMed 

    Google Scholar 

  • 19.

    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 20.

    Tully BJ, Graham ED, Heidelberg JF. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data. 2018;5:170203.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 21.

    Chen LX, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Res. 2020;30:315–33.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 22.

    Shaiber A, Eren AM. Composite metagenome-assembled genomes reduce the quality of public genome repositories. mBio. 2019;10:e00725–19.

  • 23.

    Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048.

    CAS 

    Google Scholar 

  • 24.

    Meziti A, Rodriguez-R LM, Hatt JK, Peña-Gonzalez A, Levy K, Konstantinidis KT. The reliability of metagenome-assembled genomes (MAGs) in representing natural populations: Insights from comparing MAGs against isolate genomes derived from the same fecal sample. Appl Environ Microbiol. 2021;87:e02593–20.

  • 25.

    Meziti A, Tsementzi D, Ar Kormas K, Karayanni H, Konstantinidis KT. Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics. Environ Microbiol. 2016;18:4640–52.

    PubMed 

    Google Scholar 

  • 26.

    Arevalo P, VanInsberghe D, Elsherbini J, Gore J, Polz MF. A reverse ecology approach based on a biological definition of microbial populations. Cell. 2019;178:820–34.e14.

    CAS 
    PubMed 

    Google Scholar 

  • 27.

    Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ. 2018;6:e4320.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 28.

    Delmont TO, Kiefl E, Kilinc O, Esen OC, Uysal I, Rappe MS, et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. Elife. 2019;8:e46497.

  • 29.

    Berube PM, Biller SJ, Hackl T, Hogle SL, Satinsky BM, Becker JW, et al. Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Sci Data. 2018;5:1–11.

    Google Scholar 

  • 30.

    Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014;344:416–20.

    CAS 
    PubMed 

    Google Scholar 

  • 31.

    Viver T, Orellana LH, Diaz S, Urdiain M, Ramos-Barbero MD, Gonzalez-Pastor JE, et al. Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities. Environ Microbiol. 2019;21:4300–15.

    CAS 
    PubMed 

    Google Scholar 

  • 32.

    Viver T, Cifuentes A, Diaz S, Rodriguez-Valdecantos G, Gonzalez B, Anton J, et al. Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: evidence that unexplored sites constitute sources of cultivable novelty. Syst Appl Microbiol. 2015;38:266–75.

    CAS 
    PubMed 

    Google Scholar 

  • 33.

    Viver T, Conrad RE, Orellana LH, Urdiain M, González-Pastor JE, Hatt JK, et al. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps. ISME J. 2020:15:1–14.

  • 34.

    Konstantinidis KT, Tiedje JM. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA. 2004;101:3160–5.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 35.

    Rodriguez‐R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol. 2020;22:3394–412.

    PubMed 

    Google Scholar 

  • 36.

    Pena A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverria J, et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J. 2010;4:882–95.

    CAS 
    PubMed 

    Google Scholar 

  • 37.

    Maistrenko OM, Mende DR, Luetge M, Hildebrand F, Schmidt TSB, Li SS, et al. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity. ISME J. 2020;14:1247–59.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 38.

    Anton J, Lucio M, Pena A, Cifuentes A, Brito-Echeverria J, Moritz F, et al. High metabolomic microdiversity within co-occurring isolates of the extremely halophilic bacterium Salinibacter ruber. PLOS ONE. 2013;8:e64701.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Luley-Goedl C, Nidetzky B. Glycosides as compatible solutes: biosynthesis and applications. Nat Prod Rep. 2011;28:875–96.

    CAS 
    PubMed 

    Google Scholar 

  • 40.

    Antón J, Oren A, Benlloch S, Rodríguez-Valera F, Amann R, Rosselló-Mora R. Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the bacteria from saltern crystallizer ponds. IJSEM. 2002;52:485–91.

    PubMed 

    Google Scholar 

  • 41.

    Antón J, Rosselló-Mora R, Rodríguez-Valera F, Amann R. Extremely halophilic bacteria in crystallizer ponds from solar salterns. Appl Environ Microbiol. 2000;66:3052–7.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 42.

    Viver T, Orellana L, Gonzalez-Torres P, Diaz S, Urdiain M, Farias ME, et al. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. Syst Appl Microbiol. 2018;41:198–212.

    PubMed 

    Google Scholar 

  • 43.

    Oren A, Rodríguez-Valera F. The contribution of halophilic Bacteria to the red coloration of saltern crystallizer ponds. FEMS Microbiol Ecol. 2001;36:123–30.

    CAS 
    PubMed 

    Google Scholar 

  • 44.

    Santos F, Moreno-Paz M, Meseguer I, Lopez C, Rossello-Mora R, Parro V, et al. Metatranscriptomic analysis of extremely halophilic viral communities. ISME J. 2011;5:1621–33.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 45.

    Kuo CH, Ochman H. Deletional bias across the three domains of life. Genome Biol Evol. 2009;1:145–52.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 46.

    Lane N, Martin W. The energetics of genome complexity. Nature. 2010;467:929–34.

    CAS 
    PubMed 

    Google Scholar 

  • 47.

    Vos M, Hesselman MC, Te Beek TA, van Passel MWJ, Eyre-Walker A. Rates of lateral gene transfer in prokaryotes: high but why? Trends Microbiol. 2015;23:598–605.

    CAS 
    PubMed 

    Google Scholar 

  • 48.

    Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 2005;3:679–87.

    CAS 
    PubMed 

    Google Scholar 

  • 49.

    Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Droge J, et al. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods. 2017;14:1063–71.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 50.

    Munoz R, Lopez-Lopez A, Urdiain M, Moore ER, Rossello-Mora R. Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments. Syst Appl Microbiol. 2011;34:69–75.

    CAS 
    PubMed 

    Google Scholar 

  • 51.

    Urdiain M, López-López A, Gonzalo C, Busse H-J, Langer S, Kämpfer P, et al. Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense. Syst Appl Microbiol. 2008;31:339–51.

    CAS 
    PubMed 

    Google Scholar 

  • 52.

    Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge, United Kingdom: Babraham Bioinformatics, Babraham Institute; 2010.

  • 53.

    Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 54.

    Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.

    Google Scholar 

  • 55.

    Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res. 2018;46:W282–8.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 56.

    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.

  • 57.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLOS ONE. 2010;5:e9490.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 59.

    Rambaut A. FigTree v1.4.4. http://tree.bio.ed.ac.uk/software/figtree/ 2018.

  • 60.

    Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23:127–8.

    CAS 
    PubMed 

    Google Scholar 

  • 61.

    Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 62.

    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421.

    Google Scholar 

  • 63.

    Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36:2251–2.

    CAS 
    PubMed 

    Google Scholar 

  • 64.

    Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 


  • Source: Ecology - nature.com

    A constraint on historic growth in global photosynthesis due to increasing CO2

    A tool to speed development of new solar cells