82
McFall-Ngai M, Hadfield MG, Bosch TCG et al (2013) Animals in a
bacterial world, a new imperative for the life sciences. Proc Natl
Acad Sci U S A 110:3229–3236
McNutt MK, Camilli R, Crone TJ et al (2012) Review of flow rate estimates of the Deepwater Horizon oil spill. Proc Natl Acad Sci U S
A 109:20260–20267
Moran MA (2015) The global ocean microbiome. Science
347:aac8455
Nirenberg M (2004) Historical review: deciphering the genetic code – a
personal account. Trends Biochem Sci 29:46–54
Noguera-Solano R, Ruiz-Gutierrez R, Rodriguez-Caso JM (2013)
Genome: twisting stories with DNA. Endeavour 37:213–219
O’Leary NA, Wright MW, Brister JR et al (2016) Reference sequence
(RefSeq) database at NCBI: current status, taxonomic expansion,
and functional annotation. Nucleic Acids Res 44:D733–D745
Olsen JL, Rouzé P, Verhelst B et al (2016) The genome of the seagrass
Zostera marina reveals angiosperm adaptation to the sea. Nature
530:331–335
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA et al (2016)
Uncovering Earth’s virome. Nature 536:425–430
Park JJ, Wang H, Gargouri M et al (2015) The response of
Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis. Plant J 81:611–624
Pascault N, Loux V, Derozier S et al (2015) Technical challenges in
metatranscriptomic studies applied to the bacterial communities of
freshwater ecosystems. Genetica 143:157–167
Patti GJ, Yanes O, Siuzdak G (2012) Metabolomics: the apogee of the
omics trilogy. Int J Pharm Pharm Sci 13:263–269
Pedrós-Alió C (2012) The rare bacterial biosphere. Annu Rev Mar Sci
4:449–466
Pheasant M, Mattick JS (2007) Raising the estimate of functional
human sequences. Genome Res 17:1245–1253
Pimm SL, Jenkins CN, Abell R et al (2014) The biodiversity of species
and their rates of extinction, distribution, and protection. Science
344:1246752
Pogoreutz C, Rädecker N, Cárdenas A et al (2017) Nitrogen fixation
aligns with nifH abundance and expression in two coral trophic
functional groups. Front Microbiol 8:1187
Rhoads A, Au KF (2015) PacBio sequencing and its applications.
Genomics Proteomics Bioinformatics 13:278–289
Ritchie KB (2006) Regulation of microbial populations by coral surface
mucus and mucus associated bacteria. Mar Ecol Prog Ser 322:1–14
Rohwer F, Seguritan V, Azam F et al (2002) Diversity and distribution
of coral-associated bacteria. Mar Ecol Prog Ser 243:1–10
Röthig T, Costa RM, Simona F et al (2016) Distinct bacterial communities associated with the coral model Aiptasia in Aposymbiotic and
symbiotic states with Symbiodinium. Front Mar Sci 3:234
Ruggles KV, Krug K, Wang X et al (2017) Methods, tools and
current perspectives in proteogenomics. Mol Cell Proteomics
16:959–981
Sampson TR, Mazmanian SK (2015) Control of brain development,
function, and behavior by the microbiome. Cell Host Microbe
17:565–576
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Schuster SC (2008) Next-generation sequencing transforms today’s
biology. Nat Methods 5:16–18
Selbach M, Schwanhäusser B, Thierfelder N et al (2008) Widespread
changes in protein synthesis induced by microRNAs. Nature
455:58–63
Shnit-Orland M, Sivan A, Kushmaro A (2012) Antibacterial activity of Pseudoalteromonas in the coral Holobiont. Microb Ecol
64:851–859
Simmonds P, Adams MJ, Benkö M et al (2017) Consensus statement:
virus taxonomy in the age of metagenomics. Nat Rev Microbiol
15:161–168
Stackebrandt E, Frederiksen W, Garrity GM et al (2002) Report of the
ad hoc comittee for the re-evaluation of the species definition in
bacteriology. Int J Syst Evol Microbiol 52:1043–1047
Taberlet P, Coissac E, Hajibabaei M et al (2012) Environmental
DNA. Mol Ecol 21:1789–1793
Teeling H, Fuchs BM, Becher D et al (2012) Substrate-controlled succesion of marine Bacterioplankton populations induced by a phytoplankton bloom. Science 336:608–611
The Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261
The Gene Ontology Consortium (2017) Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium.
Nucleic Acids Res 45:D331–D338
Thiele S, Richter M, Balestra C et al (2017) Taxonomic and functional
diversity of a coastal planktonic bacterial community in a riverinfluenced marine area. Mar Genomics 32:61–69
Turnbaugh PJ, Ley RE, Hamady M et al (2007) The human microbiome
project. Nature 449:804–810
Valentini A, Taberlet P, Miaud C et al (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol 25:929–942
Voolstra CR, Miller DJ, Ragan MA et al (2015) The ReFuGe 2020 consortium—using “omics” approaches to explore the adaptability and
resilience of coral holobionts to environmental change. Front Mar
Sci 2:68
Wilmes P, Simmons SL, Denef VJ et al (2009) The dynamic genetic
repertoire of microbial communities. FEMS Microbiol Rev
33:109–132
Zanta MA, Belguise-Valladier P, Behr JP (1999) Gene delivery: a single
nuclear localization signal peptide is sufficient to carry DNA to the
cell nucleus. Proc Natl Acad Sci U S A 96:91–96
Ziegler M, Seneca FO, Yum LK et al (2017) Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat
Commun 8:14213
Open Access This chapter is licensed under the terms of the Creative
Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link
to the Creative Commons license and indicate if changes were made.
The images or other third party material in this chapter are included
in the chapter’s Creative Commons license, unless indicated otherwise
in a credit line to the material. If material is not included in the chapter’s
Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to
obtain permission directly from the copyright holder.
J. D. Brüwer and H. Buck-Wiese
McFall-Ngai M, Hadfield MG, Bosch TCG et al (2013) Animals in a
bacterial world, a new imperative for the life sciences. Proc Natl
Acad Sci U S A 110:3229–3236
McNutt MK, Camilli R, Crone TJ et al (2012) Review of flow rate estimates of the Deepwater Horizon oil spill. Proc Natl Acad Sci U S
A 109:20260–20267
Moran MA (2015) The global ocean microbiome. Science
347:aac8455
Nirenberg M (2004) Historical review: deciphering the genetic code – a
personal account. Trends Biochem Sci 29:46–54
Noguera-Solano R, Ruiz-Gutierrez R, Rodriguez-Caso JM (2013)
Genome: twisting stories with DNA. Endeavour 37:213–219
O’Leary NA, Wright MW, Brister JR et al (2016) Reference sequence
(RefSeq) database at NCBI: current status, taxonomic expansion,
and functional annotation. Nucleic Acids Res 44:D733–D745
Olsen JL, Rouzé P, Verhelst B et al (2016) The genome of the seagrass
Zostera marina reveals angiosperm adaptation to the sea. Nature
530:331–335
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA et al (2016)
Uncovering Earth’s virome. Nature 536:425–430
Park JJ, Wang H, Gargouri M et al (2015) The response of
Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis. Plant J 81:611–624
Pascault N, Loux V, Derozier S et al (2015) Technical challenges in
metatranscriptomic studies applied to the bacterial communities of
freshwater ecosystems. Genetica 143:157–167
Patti GJ, Yanes O, Siuzdak G (2012) Metabolomics: the apogee of the
omics trilogy. Int J Pharm Pharm Sci 13:263–269
Pedrós-Alió C (2012) The rare bacterial biosphere. Annu Rev Mar Sci
4:449–466
Pheasant M, Mattick JS (2007) Raising the estimate of functional
human sequences. Genome Res 17:1245–1253
Pimm SL, Jenkins CN, Abell R et al (2014) The biodiversity of species
and their rates of extinction, distribution, and protection. Science
344:1246752
Pogoreutz C, Rädecker N, Cárdenas A et al (2017) Nitrogen fixation
aligns with nifH abundance and expression in two coral trophic
functional groups. Front Microbiol 8:1187
Rhoads A, Au KF (2015) PacBio sequencing and its applications.
Genomics Proteomics Bioinformatics 13:278–289
Ritchie KB (2006) Regulation of microbial populations by coral surface
mucus and mucus associated bacteria. Mar Ecol Prog Ser 322:1–14
Rohwer F, Seguritan V, Azam F et al (2002) Diversity and distribution
of coral-associated bacteria. Mar Ecol Prog Ser 243:1–10
Röthig T, Costa RM, Simona F et al (2016) Distinct bacterial communities associated with the coral model Aiptasia in Aposymbiotic and
symbiotic states with Symbiodinium. Front Mar Sci 3:234
Ruggles KV, Krug K, Wang X et al (2017) Methods, tools and
current perspectives in proteogenomics. Mol Cell Proteomics
16:959–981
Sampson TR, Mazmanian SK (2015) Control of brain development,
function, and behavior by the microbiome. Cell Host Microbe
17:565–576
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chainterminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467
Schuster SC (2008) Next-generation sequencing transforms today’s
biology. Nat Methods 5:16–18
Selbach M, Schwanhäusser B, Thierfelder N et al (2008) Widespread
changes in protein synthesis induced by microRNAs. Nature
455:58–63
Shnit-Orland M, Sivan A, Kushmaro A (2012) Antibacterial activity of Pseudoalteromonas in the coral Holobiont. Microb Ecol
64:851–859
Simmonds P, Adams MJ, Benkö M et al (2017) Consensus statement:
virus taxonomy in the age of metagenomics. Nat Rev Microbiol
15:161–168
Stackebrandt E, Frederiksen W, Garrity GM et al (2002) Report of the
ad hoc comittee for the re-evaluation of the species definition in
bacteriology. Int J Syst Evol Microbiol 52:1043–1047
Taberlet P, Coissac E, Hajibabaei M et al (2012) Environmental
DNA. Mol Ecol 21:1789–1793
Teeling H, Fuchs BM, Becher D et al (2012) Substrate-controlled succesion of marine Bacterioplankton populations induced by a phytoplankton bloom. Science 336:608–611
The Gene Ontology Consortium (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261
The Gene Ontology Consortium (2017) Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium.
Nucleic Acids Res 45:D331–D338
Thiele S, Richter M, Balestra C et al (2017) Taxonomic and functional
diversity of a coastal planktonic bacterial community in a riverinfluenced marine area. Mar Genomics 32:61–69
Turnbaugh PJ, Ley RE, Hamady M et al (2007) The human microbiome
project. Nature 449:804–810
Valentini A, Taberlet P, Miaud C et al (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol 25:929–942
Voolstra CR, Miller DJ, Ragan MA et al (2015) The ReFuGe 2020 consortium—using “omics” approaches to explore the adaptability and
resilience of coral holobionts to environmental change. Front Mar
Sci 2:68
Wilmes P, Simmons SL, Denef VJ et al (2009) The dynamic genetic
repertoire of microbial communities. FEMS Microbiol Rev
33:109–132
Zanta MA, Belguise-Valladier P, Behr JP (1999) Gene delivery: a single
nuclear localization signal peptide is sufficient to carry DNA to the
cell nucleus. Proc Natl Acad Sci U S A 96:91–96
Ziegler M, Seneca FO, Yum LK et al (2017) Bacterial community dynamics are linked to patterns of coral heat tolerance. Nat
Commun 8:14213
Open Access This chapter is licensed under the terms of the Creative
Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link
to the Creative Commons license and indicate if changes were made.
The images or other third party material in this chapter are included
in the chapter’s Creative Commons license, unless indicated otherwise
in a credit line to the material. If material is not included in the chapter’s
Creative Commons license and your intended use is not permitted by
statutory regulation or exceeds the permitted use, you will need to
obtain permission directly from the copyright holder.
J. D. Brüwer and H. Buck-Wiese