Bioprospecting from Marine Sediments of New Brunswick, Canada: Exploring the Relationship between Total Bacterial Diversity and Actinobacteria Diversity

2005, Bioactive microbial metabolites, J. Antibiot. (Tokyo), 58, 1, 10.1038/ja.2005.1

Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F., and Hopwood, D.A. (2000). Practical Streptomyces Genetics, John Innes Foundation. [2nd ed.].

Fischbach, 2009, Antibiotics for emerging pathogens, Science, 325, 1089, 10.1126/science.1176667

Koehn, 2005, Rediscovering natural products as a source of new drugs, Discov. Med., 5, 159

Bredholt, 2008, Actinomycetes from sediments in the Trondheim Fjord, Norway: Diversity and biological activity, Mar. Drugs, 6, 12, 10.3390/md6010012

Stach, 2006, Diversity of actinomycetes isolated from challenger deep sediment (10,898 M) from the Mariana Trench, Extremophiles, 10, 181, 10.1007/s00792-005-0482-z

Jensen, 2007, Species-Specific secondary metabolite production in marine actinomycetes of the genus Salinispora, Appl. Environ. Microbiol., 73, 1146, 10.1128/AEM.01891-06

Maldonado, 2009, Actinobacterial diversity from marine sediments collected in Mexico, Antonie Van Leeuwenhoek, 95, 111, 10.1007/s10482-008-9294-3

Ravenschlag, 1999, High bacterial diversity in permanently cold marine sediments, Appl. Environ. Microbiol., 65, 3982, 10.1128/AEM.65.9.3982-3989.1999

Feling, 2003, Salinosporamide A: A highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora, Angew. Chem., 42, 355, 10.1002/anie.200390115

Kwon, 2006, Marinomycins A–D, antitumor-antibiotics of a new structure class from a marine actinomycete of the recently discovered genus “Marinispora”, J. Am. Chem. Soc., 128, 1622, 10.1021/ja0558948

Olano, 2009, Antitumor compounds from marine actinomycetes, Mar. Drugs, 7, 210, 10.3390/md7020210

Hughes, 2008, The marinopyrroles, antibiotics of an unprecedented structure class from a marine Streptomyces sp., Org. Lett., 10, 629, 10.1021/ol702952n

Fenical, 1993, Chemical studies of marine bacteria: Developing a new resource, Chem. Rev., 93, 1673, 10.1021/cr00021a001

Liu, 2010, Bioprospecting microbial natural product libraries from the marine environment for drug discovery, J. Antibiot. (Tokyo), 63, 415, 10.1038/ja.2010.56

Freel, 2012, Microdiversity and evidence for high dispersal rates in the marine actinomycete ‘Salinispora pacifica’, Environ. Microbiol., 14, 480, 10.1111/j.1462-2920.2011.02641.x

Jensen, 1991, Distribution of actinomycetes in near-shore tropical marine sediments, Appl. Environ. Microbiol., 57, 1102, 10.1128/aem.57.4.1102-1108.1991

Jorgensen, 2012, Correlating microbial community profiles with geochemical data in highly stratified sediments from the arctic mid-ocean ridge, Proc. Natl. Acad. Sci. USA, 109, E2846, 10.1073/pnas.1207574109

Fu, 2011, Cytotoxic bipyridines from the marine-derived actinomycete Actinoalloteichus cyanogriseus WH1-2216-6, J. Nat. Prod., 74, 1751, 10.1021/np200258h

Jensen, 1995, The relative abundance and seawater requirements of gram-positive bacteria in near-shore tropical marine samples, Microb. Ecol., 29, 249, 10.1007/BF00164888

Ward, 2006, Diversity and biogeography of marine actinobacteria, Curr. Opin. Microbiol., 9, 279, 10.1016/j.mib.2006.04.004

Jensen, 2005, Culturable marine actinomycete diversity from tropical pacific ocean sediments, Environ. Microbiol., 7, 1039, 10.1111/j.1462-2920.2005.00785.x

Lim, 2011, Analysis of the microbial community and geochemistry of a sediment core from Great Slave Lake, Canada, Antonie Van Leeuwenhoek, 99, 423, 10.1007/s10482-010-9500-y

Forschner, 2009, Microbial diversity in cenozoic sediments recovered from the Lomonosov Ridge in the central arctic basin, Environ. Microbiol., 11, 630, 10.1111/j.1462-2920.2008.01834.x

Turley, 2000, Bacteria in the cold deep-sea benthic boundary layer and sediment-water interface of the NE Atlantic, FEMS Microbiol. Ecol., 33, 89

Burzynski, M. (1985). A Guide to Fundy National Park, Douglas & McIntyre.

Das, 2006, Marine microbial diversity and ecology: Importance and future perspectives, Curr. Sci., 90, 1325

Wang, 2012, Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags, Appl. Environ. Microbiol., 78, 8264, 10.1128/AEM.01821-12

Babalola, 2009, Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils, Environ. Microbiol., 11, 566, 10.1111/j.1462-2920.2008.01809.x

Tringe, 2005, Metagenomics: DNA sequencing of environmental samples, Nat. Rev. Gen., 6, 805, 10.1038/nrg1709

Sogin, 2006, Microbial diversity in the deep sea and the underexplored “rare biosphere”, Proc. Natl. Acad. Sci. USA, 103, 12115, 10.1073/pnas.0605127103

Wang, 2007, Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07

Bull, 2000, Search and discovery strategies for biotechnology: The paradigm shift, Microbiol. Mol. Biol. Rev., 64, 573, 10.1128/MMBR.64.3.573-606.2000

Chao, 1992, Estimating the number of classes via sample coverage, J. Am. Stat. Assoc., 87, 210, 10.1080/01621459.1992.10475194

Chao, 1984, Nonparametric estimation of the number of classes in a population, Scand. J. Stat., 11, 265

Schloss, 2005, Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness, Appl. Environ. Microbiol., 71, 1501, 10.1128/AEM.71.3.1501-1506.2005

Kemp, 2004, Bacterial diversity in aquatic and other environments: What 16S rDNA libraries can tell us, FEMS Microbiol. Ecol., 47, 161, 10.1016/S0168-6496(03)00257-5

Nacke, 2011, Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils, PLoS One, 6, 1, 10.1371/journal.pone.0017000

Fierer, 2006, The diversity and biogeography of soil bacterial communities, Proc. Natl. Acad. Sci. USA, 103, 626, 10.1073/pnas.0507535103

Ewers, 2012, Bacterial community profiles from sediments of the Anacostia River using metabolic and molecular analyses, Environ. Sci. Pollut. Res., 19, 1271, 10.1007/s11356-011-0656-4

Duncan, K. (2013). Unpublished work.

Glazer, 2007, Spatial structure of the microbial community in sandy carbonate sediment, Mar. Ecol. Prog. Ser., 346, 61, 10.3354/meps06996

Musat, 2006, Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea, Syst. Appl. Microbiol., 29, 333, 10.1016/j.syapm.2005.12.006

Gobet, 2012, Diversity and dynamics of rare and of resident bacterial populations in coastal sands, ISME J., 6, 542, 10.1038/ismej.2011.132

Hollister, 2010, Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments, ISME J., 4, 829, 10.1038/ismej.2010.3

Certini, 2004, Rock fragments in soil support a different microbial community from the fine earth, Soil Biol. Biochem., 36, 1119, 10.1016/j.soilbio.2004.02.022

Kirchman, 2010, The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes, Environ. Microbiol., 12, 1132, 10.1111/j.1462-2920.2010.02154.x

Giovannoni, 2005, Molecular diversity and ecology of microbial plankton, Nature, 437, 343, 10.1038/nature04158

Ghiglione, 2012, Pole-to-pole biogeography of surface and deep marine bacterial communities, Proc. Natl. Acad. Sci. USA, 109, 17633, 10.1073/pnas.1208160109

Mincer, 2005, Culture-dependent and culture-independent diversity within the obligate marine actinomycete genus Salinispora, Appl. Environ. Microbiol., 71, 7019, 10.1128/AEM.71.11.7019-7028.2005

Bull, 2005, Marine actinobacteria: Perspectives, challenges, future directions, Antonie Van Leeuwenhoek, 87, 65, 10.1007/s10482-004-6562-8

Eccleston, 2008, The occurrence of bioactive Micromonosporae in aquatic habitats of the sunshine coast in Australia, Mar. Drugs, 6, 243, 10.3390/md6020243

Maldonado, 2008, Characterisation of micromonosporae from aquatic environments using molecular taxonomic methods, Antonie van Leeuwenhoek, 94, 289, 10.1007/s10482-008-9244-0

Schwientek, 2011, Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology, J. Biotechnol., 155, 68, 10.1016/j.jbiotec.2011.04.010

Jensen, 2008, An assessment of actinobacterial diversity in the marine environment, Antonie Van Leeuwenhoek, 94, 51, 10.1007/s10482-008-9239-x

Newman, 2006, New drugs from marine microbes: The tide is turning, J. Ind. Microbiol. Biotechnol., 33, 539, 10.1007/s10295-006-0115-2

Guo, 2008, A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: Use of multilocus sequence analysis for streptomycete systematics, Int. J. Syst. Evol. Microbiol., 58, 149, 10.1099/ijs.0.65224-0

Wawrik, 2007, Biogeography of actinomycete communities and type II polyketide synthase genes in soils collected in New Jersey and Central Asia, Appl. Environ. Microbiol., 73, 2982, 10.1128/AEM.02611-06

Gontang, 2007, Phylogenetic diversity of gram-positive bacteria cultured from marine sediments, Appl. Environ. Microbiol., 73, 3272, 10.1128/AEM.02811-06

Takizawa, 1993, Isolation and diversity of actinomycetes in the Chesapeake Bay, Appl. Environ. Microbiol., 59, 997, 10.1128/aem.59.4.997-1002.1993

France, B. (1986). Actinomycetes of the Bottom Sediments of Various Sea, Actes de colloques.

Omura, 1977, A new alkaloid AM-2282 of Streptomyces origin taxonomy, fermentation, isolation and preliminary characterization, J. Antibiot., 30, 275, 10.7164/antibiotics.30.275

Schleissner, 2011, Antitumor actinopyranones produced by Streptomyces albus POR-04-15-053 isolated from a marine sediment, J. Nat. Prod., 74, 1590, 10.1021/np200196j

Jensen, 2010, Linking species concepts to natural product discovery in the post-genomic era, J. Ind. Microbiol. Biotechnol., 37, 219, 10.1007/s10295-009-0683-z

Watve, 2001, How many antibiotics are produced by the genus Streptomyces?, Arch. Microbiol., 176, 386, 10.1007/s002030100345

Magarvey, 2004, Isolation and characterization of novel marine-derived actinomycete taxa rich in bioactive metabolites, Appl. Environ. Microbiol., 70, 7520, 10.1128/AEM.70.12.7520-7529.2004

Newman, 2007, Natural products as sources of new drugs over the last 25 years, J. Nat. Prod., 70, 461, 10.1021/np068054v

Hou, 2012, Microbial strain prioritization using metabolomics tools for the discovery of natural products, Anal. Chem., 84, 4277, 10.1021/ac202623g

Penn, 2009, Genomic islands link secondary metabolism to functional adaptation in marine actinobacteria, Int. J. Syst. Evol. Microbiol., 3, 1193

Donadio, 2007, Polyketide synthases and nonribosomal peptide synthetases: The emerging view from bacterial genomics, Nat. Prod. Rep., 24, 1073, 10.1039/b514050c

Burzynski, M., and Marceau, A. (1984). Fundy Bay of the Giant Tides, Fundy Guild Inc.

Tiessen, 1981, An improved method for the determination of carbon in soils and soil extracts by dry combustion, Commun. Soil Sci. Plant Anal., 12, 211, 10.1080/00103628109367142

Mehlich, 1984, Mehlich 3 soil test extractant: A modification of Mehlich 2 extractant, Commun. Soil Sci. Plant Anal., 15, 1409, 10.1080/00103628409367568

Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, Cold Springs Harbour Laboratory Press. [2nd ed.].

Dowd, 2008, Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP), BMC Microbiol., 8, 1, 10.1186/1471-2180-8-125

Research and Testing Laboratory Homepage. Available online:http://www.researchandtesting.com.

Dowd, 2008, Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use, Soil Biol. Biochem., 40, 2762, 10.1016/j.soilbio.2008.07.022

Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537, 10.1128/AEM.01541-09

Schloss, 2011, Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies, PLoS One, 6, e2731, 10.1371/journal.pone.0027310

Schloss Mothur Wiki SOP. Available online:http://Www.Mothur.Org/Wiki/454_SOP.

Mothur. Available online:http://www.mothur.org/wiki/Silva_reference.

Clarke, K.R., and Gorley, R.N. (2006). PRIMER (Plymouth Routines in Multivariate Ecological Research) V6: User Manual/Tutorial, PRIMER-E Ltd.

Warwick, R.M., and Clarke, K.R. (2001). Changes in Marine Communities: An Approach to Statistical Analysis and Interpretation, PRIMER-E Ltd.. [2nd ed.].

Mincer, 2002, Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments, Appl. Environ. Microbiol., 68, 5005, 10.1128/AEM.68.10.5005-5011.2002

Maldonado, 2005, Diversity of cultivable actinobacteria in geographically widespread marine sediments, Antonie Van Leeuwenhoek, 87, 11, 10.1007/s10482-004-6525-0

Atlas, R.M., and Parks, L.C. (1993). Handbook of Microbiological Media, CRC Press.

Shirling, 1966, Methods for characterization of Streptomyces species, Int. J. Syst. Evol. Microbiol., 16, 313

Hopwood, D.A. (1986). Genetic Manipulation of Streptomyces: A Laboratory Manual, The John Innes Foundation.

Weisburg, 1991, 16S ribosomal DNA amplification for phylogenetic study, J. Bacteriol., 173, 697, 10.1128/jb.173.2.697-703.1991

Kaplan, 2001, 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM, Appl. Environ. Microbiol., 67, 1935, 10.1128/AEM.67.4.1935-1939.2001

Basic Local Alignment Search tool. Available online:http://blast.ncbi.nlm.nih.gov/Blast.cgi.

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2

ClustalW2. Available online:http://www.ebi.ac.uk/tools/clustalw2.

Saitou, 1987, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406

Felsenstein, 1985, Confidence limits on phylogenies: An approach using the bootstrap, Evolution, 39, 783, 10.2307/2408678