1 Genomics in the Discovery and Monitoring
25
as priorities for managing marine biodiversity in the future: first, elucidating the
link between diversity and ecosystem function, and second, undertaking empirical
studies that demonstrate that increased biodiversity can enhance simultaneously and
stabilize various measures of ecosystem functioning (Worm et al. 2006, Danovaro
et al. 2008). Our belief is that genomics will play a pivotal role in both elements of
such activity.
References
Adachi M, Kanno T, Okamoto R, Itakura S, Yamaguchi M, Nishijima T (2003) Population structure
of Alexandrium (Dinophyceae) cyst formation-promoting bacteria in Hiroshima Bay, Japan.
Appl Environ Microbiol 69:6560–6568
Allen EE, Banfield JF (2005) Community genomics and microbial ecology and evolution. Nat Rev
Genet 3:489–498
Allen MJ, Martinez-Martinez J et al (2007) Use of microarrays to assess viral diversity: from
genotype to phenotype. Environ Microbiol Apr 9(4):971–982
Allen MJ, Wilson WH (2008) Aquatic virus diversity accessed through omic techniques: a route
map to function. Curr Opin Microbiol 11(3):226–232
Amann RI, Binder, BJ, Olson, RJ et al (1990) Combination of 16S rRNA-targeted oligonucleotide
probes with flow cytometry for analysing mixed microbial populations. Appl Environ Microbiol
56:1919–1925
Angel M (1992) Managing biodiversity in the oceans. In: Peterson M (ed) Diversity of oceanic
life. CSIS, Washington
Angly FE, Felts B et al (2006) The marine viromes of four oceanic regions. PLoS Biol
4(11):e368
Arnold WS, Hitchcock GL, Frischer ME, Wanninkhof R, Sheng P (2005) Dispersal of an induced
larval cohort in a coastal lagoon. Limnol Oceanogr 50:587–597
Arise JC (2004) Molecular Markers, Natural History, and Evolution 2nd ed. Sinauer Assoc Inc,
Sunderland, Massachusetts
Babcock DA, Wawrik B et al (2007) Rapid screening of a large insert BAC library for specific 16S
rRNA genes using TRFLP. J Microbiol Methods 71(2):156–161
Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through
DNA barcoding of stomatopod larvae. Proc R Soc B 273:2053–2061
Barki Y, Douek J, Graur D, Gateno D, Rinkevich B (2000) Polymorphism in soft coral larvae
revealed by amplified fragment-length polymorphism (AFLP) markers. Mar Biol 136:37–41
Beja O (2004) To BAC or not to BAC: marine ecogenomics. Curr Opin Biotechnol 15(3):187–190
Beja O, Aravind L et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the
sea. Science 289(5486):1902–1906
Bellwood DR, Hughes TP, Folke C, Nystro M (2004) Confronting the coral reef crisis. Nature
429:827–833
Bench SR, Hanson TE et al (2007) Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73(23):7629–7641
Bhadury P, Austen MC et al (2006) Development and evaluation of a DNA-barcoding approach
for the rapid identification of nematodes. Mar Ecol Prog Ser 320:1–9
Biddle JF, Fitz-Gibbon S et al (2008) Metagenomic signatures of the Peru Margin subseafloor
biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105(30):
10583–10588
Biegala IC, Not F, Vaulot D, Simon N (2003) Quantitative assessment of picoeukaryotes in the
natural environment by using taxon-specific oligonucleotide probes in association with tyramide signal amplification, fluorescence-in-situ-hybridization and flow cytometry. Appl Environ
Microbiol 69:5519–5529
25
as priorities for managing marine biodiversity in the future: first, elucidating the
link between diversity and ecosystem function, and second, undertaking empirical
studies that demonstrate that increased biodiversity can enhance simultaneously and
stabilize various measures of ecosystem functioning (Worm et al. 2006, Danovaro
et al. 2008). Our belief is that genomics will play a pivotal role in both elements of
such activity.
References
Adachi M, Kanno T, Okamoto R, Itakura S, Yamaguchi M, Nishijima T (2003) Population structure
of Alexandrium (Dinophyceae) cyst formation-promoting bacteria in Hiroshima Bay, Japan.
Appl Environ Microbiol 69:6560–6568
Allen EE, Banfield JF (2005) Community genomics and microbial ecology and evolution. Nat Rev
Genet 3:489–498
Allen MJ, Martinez-Martinez J et al (2007) Use of microarrays to assess viral diversity: from
genotype to phenotype. Environ Microbiol Apr 9(4):971–982
Allen MJ, Wilson WH (2008) Aquatic virus diversity accessed through omic techniques: a route
map to function. Curr Opin Microbiol 11(3):226–232
Amann RI, Binder, BJ, Olson, RJ et al (1990) Combination of 16S rRNA-targeted oligonucleotide
probes with flow cytometry for analysing mixed microbial populations. Appl Environ Microbiol
56:1919–1925
Angel M (1992) Managing biodiversity in the oceans. In: Peterson M (ed) Diversity of oceanic
life. CSIS, Washington
Angly FE, Felts B et al (2006) The marine viromes of four oceanic regions. PLoS Biol
4(11):e368
Arnold WS, Hitchcock GL, Frischer ME, Wanninkhof R, Sheng P (2005) Dispersal of an induced
larval cohort in a coastal lagoon. Limnol Oceanogr 50:587–597
Arise JC (2004) Molecular Markers, Natural History, and Evolution 2nd ed. Sinauer Assoc Inc,
Sunderland, Massachusetts
Babcock DA, Wawrik B et al (2007) Rapid screening of a large insert BAC library for specific 16S
rRNA genes using TRFLP. J Microbiol Methods 71(2):156–161
Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through
DNA barcoding of stomatopod larvae. Proc R Soc B 273:2053–2061
Barki Y, Douek J, Graur D, Gateno D, Rinkevich B (2000) Polymorphism in soft coral larvae
revealed by amplified fragment-length polymorphism (AFLP) markers. Mar Biol 136:37–41
Beja O (2004) To BAC or not to BAC: marine ecogenomics. Curr Opin Biotechnol 15(3):187–190
Beja O, Aravind L et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the
sea. Science 289(5486):1902–1906
Bellwood DR, Hughes TP, Folke C, Nystro M (2004) Confronting the coral reef crisis. Nature
429:827–833
Bench SR, Hanson TE et al (2007) Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73(23):7629–7641
Bhadury P, Austen MC et al (2006) Development and evaluation of a DNA-barcoding approach
for the rapid identification of nematodes. Mar Ecol Prog Ser 320:1–9
Biddle JF, Fitz-Gibbon S et al (2008) Metagenomic signatures of the Peru Margin subseafloor
biosphere show a genetically distinct environment. Proc Natl Acad Sci USA 105(30):
10583–10588
Biegala IC, Not F, Vaulot D, Simon N (2003) Quantitative assessment of picoeukaryotes in the
natural environment by using taxon-specific oligonucleotide probes in association with tyramide signal amplification, fluorescence-in-situ-hybridization and flow cytometry. Appl Environ
Microbiol 69:5519–5529