An introduction to and a reflection on the “ecogenomics promise”

References

• Azam , F and Worden , A Z . 2004 . Oceanography: microbes, molecules, and marine ecosystems . Science , 303 : 1622 – 1624 .
   PubMed Web of Science ®Google Scholar
• Barke , J , Seipke , R F , Grüschow , S , Heavens , D , Drou , N , Bibb , M J , Goss , R JM , Yu , D W and Hutchings , M I . 2010 . A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant. Acromyrmex octospinosus . BMC Biol , 8 : 109
   PubMed Web of Science ®Google Scholar
• Béjà , O . 2004 . To BAC or not to BAC: marine ecogenomics . Curr Opin Biotechnol , 15 : 187 – 190 .
   PubMed Web of Science ®Google Scholar
• Béjà , O , Aravind , L , Koonin , E V , Suzuki , M T , Hadd , A , Nguyen , L P , Jovanovich , S B , Gates , C M , Feldman , R A Spudich , J L . 2000 . Bacterial rhodopsin: evidence for a new type of phototrophy in the sea . Science , 289 : 1902 – 1906 .
   PubMed Web of Science ®Google Scholar
• Bijlsma , R and Loeschcke , V . 2005 . Environmental stress, adaptation and evolution: an overview . J Evol Biol , 18 : 744 – 749 .
   PubMed Web of Science ®Google Scholar
• Brune , A . 2007 . Woodworker's digest . Nature , 450 : 487 – 488 .
   PubMedGoogle Scholar
• Chapman , R W . 2001 . EcoGenomics – a consilience for comparative immunology? . Dev Comp Immunol , 25 : 549 – 551 .
   PubMedGoogle Scholar
• Chariton , A A , Court , L N , Hartley , D M , Colloff , M J and Hardy , C M . 2010 . Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA . Front Ecol Environ , 8 ( 5 ) : 233 – 238 .
   Google Scholar
• Daniel , R . 2004 . The soil metagenome – a rich resource for the discovery of novel natural products . Curr Opin Biotechnol , 15 : 199 – 204 .
   PubMed Web of Science ®Google Scholar
• DeLong , E F . 2002 . Microbial population genomics and ecology . Curr Opin Microbiol , 5 : 520 – 524 .
   PubMedGoogle Scholar
• DeLong , E F . 2004 . Microbial population genomics and ecology: the road ahead . Environ Microbiol , 6 : 875 – 878 .
   PubMedGoogle Scholar
• Demain , A. Adrio J . 2008 . Contributions of microorganisms to industrial biotechnology . Mol Biotechnol , 38 : 41 – 55 .
   PubMed Web of Science ®Google Scholar
• Dexter , K G , Pennington , T D and Cunningham , C W . 2010 . Using DNA to assess errors in tropical tree identifications . How often are ecologists wrong and when does it matter? Ecol Monogr , 80 ( 2 ) : 267 – 286 .
   Google Scholar
• Dicke , M , Van Loon , JJA and De Jong , PW . 2004 . Ecogenomics benefits community ecology . Science , 305 : 618 – 619 .
   PubMedGoogle Scholar
• Doney , S C , Abbott , M R , Cullen , J J , Karl , D M and Rothstein , L . 2004 . From genes to ecosystems: the ocean's new frontier . Front Ecol Environ , 2 : 457 – 466 .
   Web of Science ®Google Scholar
• Falkowski , P G and de , Vargas C . 2004 . Shotgun sequencing in the sea: a blast from the past? . Science , 304 : 58 – 60 .
   PubMedGoogle Scholar
• Feder , M E and Mitchell-Olds , T . 2003 . Evolutionary and ecological functional genomics . Nat Rev Genet , 4 : 649 – 655 .
   Web of Science ®Google Scholar
• Ficetola , G F , Miaud , C , Pompanon , F and Taberlet , P . 2008 . Species detection using environmental DNA from water samples . Biol Lett , 4 : 423 – 425 .
   PubMed Web of Science ®Google Scholar
• Fonseca , V G , Carvalho , G R , Sung , W , Johnson , H F , Power , D M , Neill , S P , Packer , M , Blaxter , M L , Lambshead , J D Thomas , W K . 2010 . Second-generation environmental sequencing unmasks marine metazoan biodiversity . Nat Comm , 1 : 1 – 8 .
   PubMedGoogle Scholar
• Fuhrman , J A . 2009 . Microbial community structure and its functional implications . Nature , 459 : 193 – 198 .
   PubMed Web of Science ®Google Scholar
• Galperin , M Y and Koonin , E V . 2010 . From complete genomics sequence to ‘complete’ understanding? . Trends Biotechnol , 28 : 398 – 406 .
   PubMed Web of Science ®Google Scholar
• Handelsman , J . 2004 . Metagenomics: application of genomics to uncultured microorganisms . Microbiol Mol Biol Rev , 68 ( 4 ) : 669 – 685 .
   PubMed Web of Science ®Google Scholar
• Handelsman , J , Rondon , M R , Brady , S F , Clardy , J and Goodman , R M . 1998 . Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products . Chem Biol , 5 : R245 – R249 .
   PubMed Web of Science ®Google Scholar
• Head , I M , Jones , D M and Röling , W FM . 2006 . Marine microorganisms make a meal of oil . Nat Rev Microbiol , 4 : 173 – 182 .
   PubMed Web of Science ®Google Scholar
• Hofmann , GE , Burnaford , J L and Fielman , K T . 2005 . Genomics-fueled approaches to current challenges in marine ecology . Trends Ecol Evol , 20 : 305 – 311 .
   PubMedGoogle Scholar
• Holterman , M , Rybarczyk , K , Van , den Elsen S , Van , Megen H , Mooyman , P , Santiago , R P , Bongers , T OM , Bakker , J and Helder , J . 2008 . A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats . Mol Ecol Resour , 8 : 23 – 34 .
   PubMed Web of Science ®Google Scholar
• Kakirde , K S , Parsley , L C and Liles , M R . 2010 . Size does matter: application-driven approaches for soil metagenomics . Soil Biol Biochem , 42 : 1911 – 1923 .
   PubMed Web of Science ®Google Scholar
• Kloet , R R , De , Cock Buning T and Bunders , J FG . 2010 . Applying the multi-level perspective to understand research program dynamics . Submitted to Sci Pub Pol ,
   Google Scholar
• Kowalchuk , G A , Speksnijder , A GCL , Zhang , K , Goodman , R M and Van Veen , JA. 2007 . Finding the needles in the metagenome haystack . Microb Ecol , 53 : 475 – 485 .
   PubMed Web of Science ®Google Scholar
• Landry , C R , Townsend , J P , Hartl , D L and Cavalieri , D . 2006 . Ecological and evolutionary genomics of Saccharomyces cerevisiae . Mol Ecol , 15 : 575 – 591 .
   PubMed Web of Science ®Google Scholar
• Langer , M , Gabor , E M , Liebeton , K , Meurer , G , Niehaus , F , Schulze , R , Eck , J and Lorenz , P . 2006 . Metagenomics: an inexhaustible access to nature's diversity . Biotechnol J , 1 : 815 – 821 .
   PubMedGoogle Scholar
• Lefevre , F , Robe , P , Jarrin , C , Ginolhac , A , Zago , C , Auriol , D , Vogel , T M , Simonet , P and Nalin , R . 2008 . Drugs from hidden bugs: their discovery via untapped resources . Res Microbiol , 159 : 153 – 161 .
   PubMed Web of Science ®Google Scholar
• Leveau , J . 2007 . The magic and menace of metagenomics: prospects for the study of plant growth-promoting rhizobacteria . Eur J Plant Pathol , 119 : 279 – 300 .
   Google Scholar
• Li , Y , Ãlvarez , O A , Gutteling , E W , Tijsterman , M , Fu , J , Riksen , J AG , Hazendonk , E , Prins , P , Plasterk , R HA Jansen , R C . 2006 . Mapping determinants of gene expression plasticity by genetical genomics in C. elegans . PLoS Genet , 2 : e222
   PubMed Web of Science ®Google Scholar
• Lorenz , P and Eck , J . 2005 . Metagenomics and industrial applications . Nat Rev Microbiol , 3 : 510 – 516 .
   PubMed Web of Science ®Google Scholar
• Maphosa , F , de , Vos WM and Smidt , H . 2010 . Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria . Trends Biotechnol , 28 : 308 – 316 .
   PubMed Web of Science ®Google Scholar
• Medinger , R , Nolte , V , Pandey , R V , Jost , S , Ottenwälder , B , Schlötterer , C and Boenigk , J . 2010 . Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms . Mol Ecol , 19 : 32 – 40 .
   PubMed Web of Science ®Google Scholar
• Nota , B , Timmermans , M J , Franken , O , Montagne-Wajer , K , Mariën , J , De Boer , ME , De Boer , TE , Ylstra , B , Van Straalen , NM and Roelofs , D . 2008 . Gene expression analysis of collembola in cadmium containing soil . Environ Sci Technol , 42 ( 21 ) : 8152 – 8157 .
   PubMedGoogle Scholar
• Oh , D C , Poulsen , M , Currie , C R and Clardy , J . 2009 . Dentigerumycin: a bacterial mediator of an ant fungus symbiosis . Nat Chem Biol , 5 ( 6 ) : 391 – 393 .
   PubMed Web of Science ®Google Scholar
• Ouborg , N J , Angeloni , F and Vergeer , P . 2010 . An essay on the necessity and feasibility of conservation genomics . Conserv Genet , 11 : 643 – 653 .
   Google Scholar
• Ouborg , N J and Kammenga , J E . Ecogenomics in the Netherlands: exploration of opportunities and necessities. Vision document of the Netherlands Ecogenomics Research Organisation (NERO) . Paper presented at: First National Ecogenomics Day . February 29 2008 , Ede, The Netherlands. Paper and more information available via the corresponding author
   Google Scholar
• Ouborg , N J and Vriezen , W H . 2007 . An ecologist's guide to ecogenomicsSoil DNA libraries for anticancer drug discovery . J. Ecol , 95 : 8 – 16 .
   Web of Science ®Google Scholar
• Pettit , R K . 2004 . Soil DNA libraries for anticancer drug discovery . Cancer Chemother Pharmacol , 54 : 1 – 6 .
   PubMed Web of Science ®Google Scholar
• Pieterse , C MJ and Dicke , M . 2007 . Plant interactions with microbes and insects: from molecular mechanisms to ecology . Trends Plant Sci , 12 : 564 – 569 .
   PubMed Web of Science ®Google Scholar
• Porazinska , D L , Giblin-Davis , R M , Faller , L , Farmerie , W , Kanzaki , N , Morris , K , Powers , T O , Tucker , A E , Sung , W and Thomas , W K . 2009 . Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity . Mol Ecol Res , 9 : 1439 – 1450 .
   PubMed Web of Science ®Google Scholar
• Poynton , H C , Varshavsky , J R , Chang , B , Cavigiolio , G , Chan , S , Holman , P S , Loguinov , A V , Bauer , D J , Komachi , K Theil , E C . 2007 . Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity . Environ Sci Technol , 41 : 1044 – 1050 .
   PubMed Web of Science ®Google Scholar
• Raaijmakers , J M , Paulitz , T C , Steinberg , C , Alabouvette , C and Moënne-Loccoz , Y . 2009 . The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms . Plant Soil , 321 : 341 – 361 .
   Web of Science ®Google Scholar
• Riesenfeld , C S , Goodman , R M and Handelsman , J . 2004 . Uncultured soil bacteria are a reservoir of new antibiotic resistance genes . Environ Microbiol , 6 : 981 – 989 .
   PubMed Web of Science ®Google Scholar
• Roelofs , D , Aarts , M GM , Schat , H and Van Straalen , NM . 2008 . Functional ecological genomics to demonstrate general and specific responses to abiotic stress . Funct Ecol , 22 : 8 – 18 .
   Google Scholar
• Roelofsen , A , Broerse , J EW , De Cock , Buning T and Bunders , J FG . 2008 . Exploring the future of ecological genomics: integrating CTA with vision assessment . Technol Forecast Soc Change , 75 : 334 – 355 .
   Web of Science ®Google Scholar
• Rondon , M R , August , P R , Bettermann , A D , Brady , S F , Grossman , T H , Liles , M R , Loiacono , K A , Lynch , B A , MacNeil , I A Minor , C . 2000 . Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms . Appl Environ Microbiol , 66 : 2541 – 2547 .
   PubMed Web of Science ®Google Scholar
• Roossinck , M J , Saha , P , Wiley , G B , Quan , J , White , J D , Lai , H , Chavarria , F , Shen , G and Roe , B A . 2010 . Ecogenomics: using massively parallel pyrosequencing to understand virus ecology . Mol Ecol , 19 : 81 – 88 .
   PubMedGoogle Scholar
• Schmeisser , C , Steele , H and Streit , W . 2007 . Metagenomics, biotechnology with non-culturable microbes . Appl Microbiol Biotechnol , 75 : 955 – 962 .
   PubMed Web of Science ®Google Scholar
• Shaw , J , Colbourne , J , Davey , J , Glaholt , S , Hampton , T , Chen , C , Folt , C and Hamilton , J . 2007 . Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins . BMC Genomics , 8 : 477
   Google Scholar
• Shimizu , K K and Purugganan , M D . 2005 . Evolutionary and ecological genomics of arabidopsis . Plant Physiol , 138 : 578 – 584 .
   PubMedGoogle Scholar
• Snape , J R , Maund , S J , Pickford , D B and Hutchinson , T H . 2004 . Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology . Aquat Toxicol , 67 : 143 – 154 .
   PubMed Web of Science ®Google Scholar
• Snoeren , T AL , De Jong , PW and Dicke , M . 2007 . Ecogenomic approach to the role of herbivore-induced plant volatiles in community ecology – essay review . J Ecol , 95 : 17 – 26 .
   Google Scholar
• Suen , G , Scott , J J , Aylward , F O , Adams , S M , Tringe , S G , Pinto-Tomas , A A , Foster , C E , Pauly , M , Weimer , P J Barry , K W . 2010 . An insect-herbivore microbiome with high plant biomass-degrading capacity . PLoS Genet , 6 ( 9 ) : e1001129
   PubMed Web of Science ®Google Scholar
• Thakur , N L , Jain , R , Natalio , F , Hamer , B , Thakur , A N and Müller , W EG . 2008 . Marine molecular biology: an emerging field of biological sciences . Biotechnol Adv , 26 : 233 – 245 .
   PubMed Web of Science ®Google Scholar
• Thomas , M A and Klaper , R . 2004 . Genomics for the ecological toolbox . Trends Ecol. Evol , 19 : 439 – 445 .
   PubMed Web of Science ®Google Scholar
• Timmermans , M , Roelofs , D , Marien , J and Van Straalen , NM. 2008 . Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers . BMC Evol Biol , 8 : 83
   PubMedGoogle Scholar
• Timmermans , M J , De Boer , ME , Nota , B , De Boer , TE , Marien , J , Klein-Lankhorst , R M , Van Straalen , NM and Roelofs , D . 2007 . Collembase: a repository for springtail genomics and soil quality assessment . BMC Genomics , 8 : 341
   PubMedGoogle Scholar
• Torsten , T , Suhelen , E , Dominic , B , Charmaine , N , Lily , T and Ricardo , C . 2007 . Integration of genomics and proteomics in marine microbial ecology . Mar Ecol Prog Ser , 332 : 291 – 299 .
   Google Scholar
• Torsvik , V and Ovreas , L . 2002 . Microbial diversity and function in soil: from genes to ecosystems . Curr Opin Microbiol , 5 : 240 – 245 .
   PubMed Web of Science ®Google Scholar
• Travers , S E , Smith , M D , Bai , J , Hulbert , S H , Leach , J E , Schnable , P S , Knapp , A K , Milliken , G A , Fay , P A Saleh , A . 2007 . Ecological genomics: making the leap from model systems in the lab to native populations in the field . Front Ecol Environ , 5 : 19 – 24 .
   Web of Science ®Google Scholar
• Tringe , S G , Von Mering , C , Kobayashi , A , Salamov , A A , Chen , K , Chang , H W , Podar , M , Short , J M , Mathur , E J Detter , J C . 2005 . Comparative metagenomics of microbial communities . Science , 308 : 554 – 557 .
   PubMed Web of Science ®Google Scholar
• Tyson , G W , Chapman , J , Hugenholtz , P , Allen , E E , Ram , R J , Richardson , P M , Solovyev , V V , Rubin , E M , Rokhsar , D S and Banfield , J F . 2004 . Community structure and metabolism through reconstruction of microbial genomes from the environment . Nature , 428 : 37 – 43 .
   PubMed Web of Science ®Google Scholar
• Van Boxtel , AL , Kamstra , J H , Cenijn , P H , Pieterse , B , Wagner , M J , Antink , M , Krab , K , Van der Burg , B , Marsh , G Brouwer , A . 2008 . Microarray analysis reveals a mechanism of phenolic polybrominated diphenylether toxicity in zebrafish . Environ Sci Technol , 42 : 1773 – 1779 .
   PubMed Web of Science ®Google Scholar
• Van Loon , L. 2007 . Plant responses to plant growth-promoting rhizobacteria . Eur J Plant Pathol , 119 : 243 – 254 .
   Web of Science ®Google Scholar
• Van Straalen , NM and Roelofs , D . 2006 . An introduction to ecological genomics , 1st ed. , Oxford : Oxford University Press .
   Google Scholar
• Venter , J C , Remington , K , Heidelberg , J F , Halpern , A L , Rusch , D , Eisen , J A , Wu , D Y , Paulsen , I , Nelson , K E Nelson , W . 2004 . Environmental genome shotgun sequencing of the Sargasso Sea . Science , 304 : 66 – 74 .
   PubMed Web of Science ®Google Scholar
• Ward , N . 2006 . New directions and interactions in metagenomics research . FEMS Microbiol Ecol , 55 : 331 – 338 .
   PubMed Web of Science ®Google Scholar
• Warnecke , F , Luginbuhl , P , Ivanova , N , Ghassemian , M , Richardson , T H , Stege , J T , Cayouette , M , McHardy , A C , Djordjevic , G Aboushadi , N . 2007 . Metagenomics and functional analysis of hindgut microbiota of a wood-feeding higher termite . Nature , 450 : 560 – 565 .
   PubMed Web of Science ®Google Scholar
• Wilson , K , Thorndyke , M , Nilsen , F , Rogers , A and Martinez , P . 2005 . Marine systems: moving into the genomics era . Mar Ecol , 26 : 3 – 16 .
   Google Scholar
• Woon Roh , S , Abell , G CJ , Kim , K H , Nam , Y D and Bae , J W . 2010 . Comparing microarrays and next-generation sequencing technologies for microbial ecology research . Trends Biotechnol , 28 : 291 – 299 .
   PubMedGoogle Scholar
• Xu , J . 2006 . Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances . Mol Ecol , 15 : 1713 – 1731 .
   PubMed Web of Science ®Google Scholar
• Young , I M and Crawford , J W . 2004 . Interactions and self-organization in the soil-microbe complex . Science , 304 : 1634 – 1637 .
   PubMed Web of Science ®Google Scholar