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An investigation into the potential impacts of ocean acidification and ocean fertilisation on the genetic diversity of marine bacterial assemblages

By John Woolven-Allen


Based on the increase of 16S rRNA gene sequences in databases it is possible\ud to design improved oligonucleotide primers for this gene. Primers were designed in\ud silico to specifically amplify fragments of the gene from the Alpha, Beta and Gamma\ud subgroups of the Proteobacteria, as well as from Bacteroidetes, Firmicutes,\ud Cyanobacteria and Planctomycetes and tested in silico and in vitro.\ud The aim was to investigate bacterioplankton diversity and reveal greater\ud fingerprint diversity within these groups than is possible using primers specific for the\ud entire domain Bacteria, and also to reduce clone library redundancy. It was then\ud aimed to investigate the potential impacts of increased pCO2 and ocean fertilisation\ud with iron (Fe) and phosphorus (P), on bacterioplankton diversity. Group-specific\ud clone libraries representing contrasting marine regions were analysed, and the\ud usefulness and specificity of the primers validated. The clone libraries showed\ud members of the oligotrophic marine group (OMG) to be present in an in situ coastal\ud mesocosm supplemented with nutrients.\ud The newly-developed group-specific primers were used in combination with\ud an improved method of denaturing gradient gel electrophoresis (DGGE) to profile in\ud detail bacterial communities in mesocosms, which were maintained at 750 ppm of\ud pCO2, the level projected for the global surface ocean in the year 3000, and 380 ppm\ud of CO2, the present level. Increased pCO2 correlated with a decrease in abundance of\ud some members of the Gammaproteobacteria. Otherwise there was little impact on\ud diversity due to raised pCO2.\ud The same DGGE protocol was applied to samples from an ocean Fe and P\ud fertilisation experiment. Diversity change due to Fe was not evident. However in\ud seawater amended with P there was an explosive growth of some cells with 16S\ud rRNA genes similar to those of the SAR86 clade, and others with similarity to\ud Gammaproteobacteria with large genomes such as Oceanospirillum sp. and\ud Psychromonas sp

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  8. (1991). 16S ribosomal DNA amplification for phylogenetic study.
  9. (1996). 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria.
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  15. (2005). 4.1.2 Effects of seawater acidification on bacteria There has been little investigation into the effects of ocean acidification on pelagic bacteria. In
  16. (1999). 4.1.4 Use of DGGE to study marine microbial communities A small sample of previous work on marine microbial communities using DGGE includes community biogeographical distribution in the Arctic Ocean by Ferrari and Hollibaugh
  17. (2007). 4.5.1 Experimental Setting The Large Scale Facility located in the Raunefjord used here, belonging to the University of Bergen, has been used before for large-scale mesocosm (> 12,000 L) studies (for example Grossart et al., 2006; Riebesell et al.,
  18. (2008). Microbial productivity Net primary production and chlorophyll a biomass are limited by N and P in the oligotrophic northeast Atlantic Ocean, both increasing as a result of the addition of Fe (Dixon,
  19. (2005). 71Table 3.3. Comparison of 16S rRNA gene group-specific primers developed in this study with those used in previous studies by Blackwood
  20. (2002). 733.3.2.1 Alphaproteobacteria The forward primer (28f) used to amplify the Alphaproteobacteria was taken from a molecular probe designed by Ashelford
  21. (1996). 914.1.3 Measuring the effects of elevated CO2 using mesocosm enclosure studies Work with bacterial cultures in vitro enables specific genetic, metabolic and physiological questions to be addressed. Stretton and colleagues
  22. (1997). a Comparison is based on the mixture of primers CYA781R(a) and CYA781R(b) (Nübel et al.,
  23. (2005). A comparison of DNAand RNA-based clone libraries from the same marine bacterioplankton community.
  24. (2007). A drop in the ocean: Can dumping tonnes of fertiliser into the oceans really turn back the tide of global warming?
  25. (1989). A halophilic denitrifier, Bacillus halodenitrificans sp.
  26. (1998). A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples.
  27. (1996). A massive phytoplankton bloom induced by an ecosystem-scale iron fertilisation experiment in the equatorial Pacific Ocean.
  28. (2000). A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilisation.
  29. (1997). A molecular view of microbial diversity and the biosphere.
  30. (1988). A novel free-living prochlorophyte abundant in the oceanic euphotic zone.
  31. (1998). A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater.
  32. (2002). A technique whose time has come.
  33. (2008). Abundance and diversity of microbial life in ocean crust.
  34. (1982). Achromopeptidase for lysis of anaerobic Grampositive cocci.
  35. (2007). Actively growing bacteria in the Inland Sea of Japan, identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis.
  36. (2003). An efficient strategy for screening large cloned libraries of amplified 16S rDNA sequences from complex environmental communities.
  37. (2001). an OIF experiment, SEEDS, was conducted in the northwest sub Arctic Pacific Ocean primarily to investigate phytoplankton response (Tsuda and Takeda,
  38. (2003). Anthropogenic carbon and ocean pH.
  39. (2008). Application of a novel rpoC1-RFLP approach reveals that marine Prochlorococcus populations in the Atlantic gyres are composed of greater microdiversity than previously described.
  40. (2001). Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques.
  41. (2004). ARB: A software environment for sequence data.
  42. (2006). Assessment of microbial phylogenetic diversity based on environmental nucleic acids.
  43. (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies.
  44. (2000). Atmospheric carbon dioxide concentrations over the past 60 million years.
  45. (1989). Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.
  46. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.
  47. (2004). b Hours elapsed since deployment of P patch c Time of day that samples were taken d Sampling position relative to the P patch; P, prior to patch being laid; I, in patch; O, out of patch
  48. (2005). Bacillus alveayuensis sp. nov., a thermophilic bacterium isolated from deep-sea sediments of the Ayu Trough.
  49. (2002). Bacteria of the γ-subclass Proteobacteria associated with zooplankton in Chesapeake Bay.
  50. (1999). Bacterial community composition during two consecutive NE Monsoon periods in the Arabian Sea studied by denaturing gradient gel electrophoresis (DGGE) of rRNA genes. Deep-Sea Research. Part II -
  51. (2006). Bacterial community diversity associated with four marine sponges from the South China Sea based on 16S rDNADGGE fingerprinting.
  52. (1997). Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.
  53. (2003). Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: Effects of virus infection, containment, and nutrient enrichment.
  54. (2006). Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas).
  55. (2005). Bacterial diversity promotes community stability and functional resilience after perturbation.
  56. (1987). Bacterial evolution.
  57. (1959). Bacterial populations in seawater as determined by different methods of enumeration.
  58. (1976). Bacterial substrates and productivity in marine ecosystems.
  59. (1999). Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization.
  60. (2006). Bias in the PCR can distort the DGGE ribotype profile relative to the bacterial community structure in the environment (Mary et al.,
  61. (1908). Binary profiles are related according to a similarity matrix. This is constructed using the Jaccard coefficient (Jaccard,
  62. (1990). Biogeochemical significance of bacterial biomass in the ocean's euphotic zone.
  63. (2000). Biogeographical diversity among marine bacterioplankton.
  64. (2005). Bizionia paragorgiae gen. nov., sp. no., a novel member of the family Flavobacteriaceae isolated from the soft coral Paragorgia arborea.
  65. BLASTn analysis of the sequence from band 10 matched it to the thermophilic Bacillus alveayuensis, a marine sediment dweller (Bae et al.,
  66. (2000). Capturing greenhouse gases.
  67. (2003). Carbon acquisition of bloom-forming marine phytoplankton.
  68. (2007). Carbon sequestration technology roadmap and program plan.
  69. (2003). Carbonate deposition, climate stability, and neoproterozoic ice ages.
  70. (2002). Cell-specific detection of phosphorus stress in Trichodesmium from the western North Atlantic.
  71. (2001). Change in marine communities: an approach to statistical analysis and interpretation, 2 nd Edition,
  72. (2002). Changes in primary productivity and chlorophyll a in response to iron fertilisation in the southern Polar Frontal Zone.
  73. (1996). Characterisation of carbon dioxide-inducible genes of the marine bacterium, Pseudomonas sp.
  74. (1997). Characteristics of the deep ocean carbon system during the past 150,000 years: ΣCO2 distributions, deep water flow patterns, and abrupt climate change.
  75. (1997). Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
  76. (2007). Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high Arctic.
  77. (1979). Chroococcoid cyanobacteria in the sea: A ubiquitous and diverse phototrophic biomass.
  78. (2003). Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea.
  79. (2001). Climate change 2001: the scientific basis. Contribution of Working Group I to the Third Assessment Report of the International Panel on Climate Change. Cambridge:
  80. (2003). Climate-driven changes to the atmospheric CO2 sink in the subtropical North Pacific Ocean.
  81. (2001). CO2 and HCO3 -uptake in marine diatoms acclimated to different CO2 concentrations.
  82. (2000). Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization.
  83. (2006). Community genomics among stratified microbial assemblages in the ocean's interior.
  84. (2003). Community structure of ammonia-oxidizing bacteria within anoxic marine sediments.
  85. (2006). Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea.
  86. (2004). Composition of estuarine bacterial communities assessed by denaturing gradient gel electrophoresis and fluorescence in situ hybridization. Limnology and Oceanography:
  87. (1993). Consumption of dissolved organic carbon by marine bacteria and demand for inorgainc nutrients.
  88. (2000). Control of bacterial growth in idealised food webs.
  89. (2001). Control of phytoplankton growth by iron and silicic acid availability in the subantarctic Southern Ocean: Experimental results from the SAZ project.
  90. (2005). Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series.
  91. (2002). Critical issues in bacterial phylogeny.
  92. (2004). Cultivation and growth characteristics of a diverse group of oligotrophic marine gammaproteobacteria.
  93. (2006). Cyanobacterial community richness is low in high CO2 and ambient CO2 mesocosms, 16S rRNA gene fragment band total counts being stable at between eight and ten. Neither treatment supports a richer population (Figure 4.9). (a) (b)
  94. (2003). Decadal variation of the surface water pCO2 in the western and central equatorial Pacific.
  95. (2006). Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
  96. (2001). Decreasing marine biogenic calcification: a negative feedback on rising atmospheric pCO2.
  97. (2005). Deep-ocean, sediment-dwelling animals are sensitive to sequestered carbon dioxide.
  98. (2005). Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes.
  99. (1998). Denaturing gradient gel electrophoresis (DGGE) in microbial ecology.
  100. (2001). Denaturing gradient gel electrophoresis in marine microbial ecology.
  101. (2007). Depth-specific distribution of Bacteroidetes in the oligotrophic eastern Mediterranean Sea.
  102. (2003). Design and evaluation of PCR primers for analysis of bacterial populations in wine by denaturing gradient gel electrophoresis.
  103. (1998). Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA.
  104. (2006). Detection and quantification of Vibrio populations using denaturant gradient gel electrophoresis.
  105. (1997). Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis.
  106. (2004). Development and application of a real-time PCR approach for quantification of uncultured bacteria in the central Baltic Sea.
  107. (2006). Development and evaluation of specific 16S rDNA primers for marine Cytophaga-Flavobacteria cluster.
  108. (1997). Development of a new semi-nested PCR method for detection of Legionella species and its application to surveillance of legionellae in hospital cooling tower water.
  109. (2004). Different SAR86 subgroups harbour divergent proteorhodopsins.
  110. (1999). Direct effects of CO2 concentration on growth and isotopic composition of marine plankton.
  111. (2004). Discovery of the novel candidate phylum "Poribacteria" in marine sponges.
  112. (2001). Discrediting ocean fertilisation.
  113. (1995). Discussion 5.4.1 Experimental background In oligotrophic pelagic marine environments, which constitute roughly 30 % of the area of the world’s oceans, bacterial biomass often exceeds phytoplankton biomass (Cho and Azam,
  114. (1999). Distribution of microbial assemblages in the Central Arctic Ocean Basin studied by PCR/DGGE: Analysis of a large data set.
  115. (1997). Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.
  116. (2003). Diversity and structure of bacterial communities in Arctic and Antarctic pack ice.
  117. (2005). Diversity of bacteria associated with the coral Pocillopora Damicornis from the Great Barrier Reef.
  118. (1999). Diversity of free-living and attached bacteria in offshore western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA.
  119. (1983). DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: Correspondence with melting theory.
  120. (1977). DNA sequencing with chainterminating inhibitors.
  121. (1992). Dual staining of natural bacterioplankton with 4',6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences.
  122. (2005). Dynamics of autotrophic picoplankton and heterotrophic bacteria in the East China Sea.
  123. (2000). Ecological resilience - in theory and application.
  124. (2004). Ecological significance of microdiversity: Identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies.
  125. (1999). Effect of CO2 concentration on C:N:P ratio in marine phytoplankton: A species comparison.
  126. (2002). Effect of CO2 concentration on the PIC/POC ratio in the coccolithophore Emiliania huxleyi grown under light-limiting conditions and different daylengths.
  127. (2007). Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis.
  128. (2001). Effect of primers hybridising to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling.
  129. (2004). Effects of CO2 enrichment on marine phytoplankton.
  130. (2007). Effects of phytoplankton bloom in a coastal ecosystem on the composition of bacterial communities.
  131. (2005). Efficient export of carbon to the deep ocean through dissolved organic matter.
  132. (2003). Elemental composition of marine Prochlorococcus and Synechococcus: Implications for the ecological stoichiometry of the sea.
  133. (2007). Enhanced biological carbon consumption in a high CO2 ocean.
  134. (1999). Enhanced carbonate dissolution: a means of sequestering waste CO2 as ocean bicarbonate.
  135. (2006). Environmental biology of the marine Roseobacter lineage.
  136. (2004). Environmental genome shotgun sequencing of the Sargasso Sea.
  137. (1990). Essentials of Oceanography.
  138. (2004). Estimating bacterial diversity from clone libraries with flat rank abundance distributions.
  139. (2002). Estimating prokaryotic diversity and its limits.
  140. (1994). Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi seamount,
  141. (2002). Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.
  142. (1993). Evidence from Aeromonas for genetic crossing-over in ribosomal sequences.
  143. (2004). Evidence from massive siderite beds for a CO2-rich atmosphere before ~1.8 billion years ago.
  144. (2000). Evolution, diversity, and molecular ecology of marine prokaryotes.
  145. (2002). f 684r e Alphaproteobacteria
  146. (2002). f These primers were suggested for use as FISH probes by Ashelford
  147. (2005). Fate of heterotrophic microbes in pelagic habitats: Focus on populations.
  148. (2004). Fine-scale phylogenetic architecture of a complex bacterial community.
  149. (2006). Firmicutes community development. (a) DGGE of PCR products amplified from DNA extracted from mesocosms 1 (high CO2) and 6 (ambient CO2). Profiles are labelled according to the sample date in
  150. (2001). Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes.
  151. (2006). Functional annotation of a diversity inventory is always desirable. As well as reverse transcription of 16S rRNA, methods using labelled nucleotide incorporation into genomic DNA, such as DNA-based (Friedrich,
  152. (2004). GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis.
  153. (1979). Generic assignments, strain histories and properties of pure cultures of cyanobacteria.
  154. (1990). Genetic diversity in Sargasso Sea bacterioplankton.
  155. (2002). Genetic diversity of "satellite" bacteria present in cultures of marine diatoms.
  156. (2005). Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton.
  157. (2005). Genome streamlining in a cosmopolitan oceanic bacterium.
  158. (2005). Genomic insights that advance the species definition for prokaryotes.
  159. (1934). Geobiologie of inleiding tot de milieukunde.
  160. (1997). Global air-sea flux of CO2: An estimate 239based on measurements of sea-air pCO2 difference.
  161. (2002). Global dispersal of free-living microbial eukaryote species.
  162. (2006). Global patterns of diversity and community structure in marine bacterioplankton.
  163. (1985). Growth of bacteria in seawater filtered through 0.2 m nucleopore membranes: implications for dilution experiments.
  164. (2003). High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters.
  165. (2006). High resolution genetic diversity studies of marine Synechococcus isolates using rpoC1-based restriction fragment length polymorphism.
  166. (2002). High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates.
  167. (2002). Identification of bacteria associated with dinoflagellates (Dinophyceae) Alexandrium spp. using tyramide signal amplification-fluorescent in situ hybridization and confocal microscopy.
  168. (2007). Improved groupspecific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities.
  169. In Figure 5.14 there is no obvious Firmicutes-specific profile change correlating with treatment.
  170. In keeping with the lack of variation between the Bacteria DGGE profiles (Figure 5.6), the corresponding MDS plot (Figure 5.7) shows little evidence of treatment-specific clustering.
  171. (2004). Increase of atmospheric CO2 promotes phytoplankton productivity.
  172. (2006). Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic.
  173. (2003). Influence of CO2, nitrate, phosphate, and silicate limitation on intracellular dimethylsulfoniopropionate in batch cultures of the coastal diatom Thalassiosira pseudonana.
  174. (1997). Inorganic nutrient limitation of oceanic bacterioplankton.
  175. (1993). Interaction of iron and major nutrients controls phytoplankton growth and species composition in the tropical Pacific Ocean.
  176. (2004). Interactions among dissolved organic carbon, microbial processes, and community structure in the mesopelagic zone of the northwestern Sargasso Sea.
  177. (2006). Interactions between marine snow and heterotrophic bacteria: aggregate formation and microbial dynamics.
  178. (2007). Interactions of planktonic algae and bacteria: effects on algal growth and organic matter dynamics.
  179. (2004). Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic.
  180. (1988). Iron deficiency limits phytoplankton growth in the northeast Pacific subarctic.
  181. (1990). Iron in Antarctic waters.
  182. (1996). Iron stimulation of Antarctic bacteria.
  183. (1995). IronEx II seeded an HNLC region in the eastern tropical Pacific Ocean with Fe (Coale
  184. (2002). Is ocean fertilisation credible and creditable?
  185. (2002). Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment.
  186. (2001). Isolation of novel pelagic bacteria from the German Bight and their seasonal contributions to surface picoplankton.
  187. (1993). Isolation of typical marine bacteria by dilution culture: growth, maintenance, and characteristics of isolates under laboratory conditions.
  188. (2006). Isotopes as tools for microbial ecologists.
  189. (1998). Kinetic bias in estimate of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicaon length heterogeneity.
  190. (2002). Life and the evolution of Earth's atmosphere.
  191. (1995). Limits to growth and respiration of bacterioplankton
  192. (2008). Macro and micro nutrient limitation of microbial productivity in oligotrophic subtropical Atlantic waters.
  193. (2008). Major differences of bacterial diversity and activity inside and outside of a natural iron-fertilised phytoplankton bloom in the Southern Ocean.
  194. (2005). Marine diatom species harbour distinct bacterial communities.
  195. (2004). Marine Microbiology, Ecology and Applications. London: Bios Scientific Publishers.
  196. (1985). Measurements of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats.
  197. (2007). Mesoscale iron enrichment experiments 1993-2005: Synthesis and future directions.
  198. (2007). Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.
  199. (2004). Metagenomics: Application of genomics to uncultured microorganisms.
  200. (2007). Microbes and the marine phosphorus cycle.
  201. (2001). Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition.
  202. (2001). Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: Changes in the genetic diversity of bacterial populations.
  203. (2006). Microbial community related to volatile organic compound (VOC) emission in household biowaste.
  204. (2006). Microbial diversity in the deep sea and the underexplored "rare biosphere".
  205. (2008). Microbial food web structure in a naturally iron-fertilised area in the Southern Ocean (Kerguelen Plateau). Deep-Sea Research. Part II -
  206. (2002). Microbial Life. Sunderland: Sinauer Associates.
  207. (2007). Microbial population structures in the deep marine biosphere.
  208. (2002). Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations.
  209. (1994). Minimal effect of iron fertilisation on sea-surface carbon dioxide concentrations.
  210. (2002). Minimising effects of CO2 storage in oceans.
  211. (1994). Molecular analysis of enrichment cultures of marine ammonia oxidisers.
  212. (2000). Molecular analysis of microbial communities in mobile deltaic muds of southeastern Papua New Guinea.
  213. (2005). Molecular and morphological characterisation of ten polar and near-polar strains within the Oscillatoriales.
  214. (2003). Molecular diversity among marine picophytoplankton as revealed by psbA analyses.
  215. (2007). Molecular dynamics of Emiliania huxleyi and cooccurring viruses during two separate mesocosm studies.
  216. (2002). Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus.
  217. (2005). Molecular phylogeny of bacteria based on comparative sequence analysis of conserved genes.
  218. (2004). Molecular sequence analysis of prokaryotic diversity in the middle and outer sections of the Portuguese estuary Ria de Aveiro.
  219. (1965). Molecules as documents of evolutionary history.
  220. (1998). Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNAtargeted probes.
  221. (2001). Most studies of bacterial response to OIF experiments have measured gross ecological parameters such as changes to bacterial abundance and production. Within OIF patches, relative to HNLC areas outside, the former has risen between three-fold (Cochlan,
  222. (2005). Nature of phosphorus limitation in the ultraoligotrophic eastern Mediterranean.
  223. (2005). Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities.
  224. (1999). Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean.
  225. (1908). Nouvelles recherches sur la distribution florale.
  226. (2005). Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester.
  227. (2005). Nucleic acid recovery from complex environmental samples.
  228. (1995). Nucleotide sequences of streptomycete 16S ribosomal DNA—towards a specific identification system for streptomycetes using PCR.
  229. (2001). Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns.
  230. (1995). Nutrient limitation of bacterial growth and rates of bacterivory in lakes and oceans: A comparative study.
  231. (1936). Observations on the multiplication of bacteria in different volumes of stored sea water and the influence of oxygen tension and solid surfaces.
  232. (2005). Ocean acidification due to increasing atmospheric carbon dioxide. In: The Royal Society.
  233. (2002). Ocean storage of CO2, 2nd Edition.
  234. (2001). Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity.
  235. (2004). Oligotrophic bacterioplankton with a novel singlecell life strategy.
  236. (2005). On the origin and evolution of plastids.
  237. (2005). On the other hand documented effects of OPF experiments on pelagic bacterial community structures could not be found, although bacteria are known to be P-limited in oligotrophic environments (Cotner et al., 1997; Thingstad et al., 1998; Thingstad et al.,
  238. (1999). Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis.
  239. (2005). Overview of the marine Roseobacter lineage.
  240. (1998). P-limitation of both phytoplankton and heterotrophic bacteria in NW Mediterranean summer surface waters.
  241. (1997). PCR primers to amplify 16S rRNA genes from cyanobacteria.
  242. (1993). PCR-DGGE application of group-specific primers The technique of PCR-DGGE (Muyzer et al.,
  243. (2001). PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods.
  244. (1991). PCR-SSCP: a simple and sensitive method for the detection of mutations in genomic DNA.
  245. (2004). Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga.
  246. (2006). Phenotypic diversity and phylogeny of picocyanobacteria in mesotrophic and eutrophic reservoirs investigated by a cultivation-dependent polyphasic approach. In Depatment of Faculty of Biological Sciences. Ceske Budejovice:
  247. (1998). Phisiology and molecular phylogeny of coexisting Prochlorococcus ecotypes.
  248. (1991). phosphorus fertilisation experiments Several studies have shown a lack of P to limit the growth of oceanic phytoplankton (Krom et al.,
  249. (1991). Phosphorus limitation of primary productivity
  250. (1997). Phosphoruslimited bacterioplankton growth in the Sargasso Sea.
  251. (1983). Photosynthesis of picoplankton in the oligotrophic ocean.
  252. (2008). Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific subtropical gyre.
  253. (2004). Phylogenetic and functional diversity of the culturable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum.
  254. (2000). Phylogenetic comparisons of a coastal bacterioplankton community with its counterparts in open ocean and freshwater systems.
  255. (1993). Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans.
  256. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
  257. (1993). Phylogenetic relationships of marine bacteria, mainly members of the family Vibrionaceae, determined on the basis of 16S rRNA sequences.
  258. (2004). Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay.
  259. (2005). Phylum- and class-specific PCR primers for general microbial community analysis.
  260. (2006). Polymerase chain reaction-based denaturing gradient gel electrophoresis in the evaluation of oral microbiota.
  261. (1991). Possible biogeochemical consequenses of ocean fertilisation.
  262. (2000). Potential limits on the efficiency of ocean fertilisation as a carbon sequestration strategy: the importance of circulation. In American Geophysical Union Fall Meeting.
  263. (2002). Primers 359f and 682r (Table 3.1) were identical to two of those suggested by Ashelford
  264. (2002). PRIMROSE: A computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database.
  265. (1999). Prochlorococcus, a marine photosynthetic prokaryote of global significance.
  266. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
  267. (1998). Prokaryotes: The unseen majority.
  268. (2001). Pseudomonas stutzeri nitrate reductase gene abundance in environmental samples measured by real-time PCR.
  269. (2004). Quantification of Gram-negative sulphate-reducing bacteria in rice field soil by 16S rRNA gene-targeted real-time PCR.
  270. (2000). Quantitative analysis of smallsubunit rRNA genes in mixed microbial populations via 5'-nuclease assays.
  271. (2005). Rapid acidification of the ocean during the Paleocene-Eocene thermal maximum.
  272. (1998). Rapid diversification of marine picophytoplankton with dissimilar light-harvesting structures inferred from sequences of Prochlorococcus and Synechococcus (Cyanobacteria).
  273. (2000). Reduced calcification of marine plankton in response to increased atmospheric CO2.
  274. (1997). Regulation of bacterial growth rates by dissolved organic carbon and temperature in the equatorial Pacific Ocean.
  275. (2000). Reidentification of facultatively alkaliphilic Bacillus firmus OF4. Extremophiles 4:
  276. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics.
  277. (2002). Representing key phytoplankton functional groups in ocean carbon cycle models: Coccolithophorids.
  278. (2002). Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences.
  279. (2004). Response of bacterioplankton to iron fertilisation in the Southern Ocean.
  280. (2003). Response of coccolithophorid Emiliania huxleyi to elevated partial pressure of CO2 under nitrogen limitation.
  281. (2001). Response of marine bacterial community composition to iron additions in three ironlimited regimes.
  282. (2005). Response of pico-, nano-, and microphytoplankton during the Southern Ocean iron fertilization experiment EIFEX.
  283. (2005). Responses of phytoplankton and heterotrophic bacteria in the northwest subarctic Pacific to in situ iron fertilisation as estimated by HPLC pigmant analysis and flow cytometry.
  284. (2005). Results from the sub Arctic Pacific iron experiment for ecosystem dynamics study (SEEDS).
  285. (2003). Review and re-analysis of domainspecific 16S primers.
  286. (2000). Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology.
  287. (2002). RNA stable isotope probing, a novel means of linking microbial community function to phylogeny.
  288. (1990). Role of sub-micrometre particles in the ocean.
  289. (2000). rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity.
  290. rRNA gene fragment profiles (Figure 5.16) were obtained for the Planctomycetes using the specific protocol listed in Sections 2.2.2 and 3.2.2. (a) Experiment One (b) Experiment Two
  291. (1998). Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales.
  292. (2006). Seasonal dynamics of bacterioplankton community structure at a coastal station in the western English Channel.
  293. (2000). Seasonal succession in marine bacterioplankton.
  294. (2007). Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH.
  295. (1979). Secrets of the Sea. London: Reader's Digest
  296. (1995). Sequestering atmospheric carbon dioxide by increasing ocean alkalinity. Energy -
  297. (2004). Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities.
  298. (2005). Serial analysis of V6 ribosomal sequence tags (SARST-V6): A method for efficient, high-throughput analysis of microbial community composition.
  299. (1996). showed bacteria took up 20 % to 45 % of bio-available iron. This indicated also a significant role for bacteria in global oceanic Fe cycling, and carbon flux with the atmosphere.
  300. (2000). Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products.
  301. (2004). Southern Ocean iron enrichment experiment: Carbon cycling in high- and low-Si waters.
  302. (1992). sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b.
  303. (1987). Specific synthesis of DNA in vitro via a polymerase catalyzed chain reaction.
  304. (2007). Specificity and sensitivity of eubacterial primers utilised for molecular profiling of bacteria within complex microbial ecosystems.
  305. (2001). Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment.
  306. (2006). Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes.
  307. stage MDS analysis A comparison of bacterial communities from high CO2 and ambient CO2 mesocosms has been done already using DGGE (see
  308. (2001). stage MDS In Section two second stage MDS analyses are performed using PRIMER-E (for method see Clarke and Warwick,
  309. (2006). Subsequent performance of a nested PCR on this template necessarily reduced the size of ribotype sequences for DGGE. However there is a balance to be struck, as both PCR and DGGE are compromised with longer sequences (Neufeld and Mohn,
  310. (2006). Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments.
  311. (2005). Synthesis of iron fertilisation experiments: From the Iron Age in the Age of Enlightenment.
  312. (1935). T.H. Huxley's diary of the voyage of H.M.S. Rattlesnake. London: Chatto and Windus.
  313. (2003). Taxonomic outline of the procaryotes.
  314. (2001). Taxonomic outline of the prokaryotic genera: Bergey's manual of systematic bacteriology.
  315. (2005). Temporal distribution of viruses, bacteria and phytoplankton throughout the water column in a freshwater hypereutrophic lake.
  316. (2000). Temporal trends in deep ocean Redfield ratios.
  317. (2006). Testing the effect of CO2 concentration on the dynamics of marine heterotrophic bacterioplankton.
  318. (1994). Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean.
  319. (2006). The Atlantic Meridional Transect Programme (AMT): a contextual view 1995–2005. Deep-Sea Research. Part II -
  320. (1998). The Crucible of Creation.
  321. (1979). The Cyanobacteria classification, by Greengenes, into numbered families and groups follows that of Rippka
  322. (2004). The effect of iron fertilization on carbon sequestration in the Southern Ocean.
  323. (1876). The etiology of anthrax, based on the life history of Bacillus anthracis.
  324. (2001). The heterotrophic bacterial response during a mesoscale iron enrichment experiment (IronEx II) in the eastern equitorial Pacific Ocean.
  325. (2004). The heterotrophic bacterial response during the Southern Ocean Iron Experiment (SOFeX).
  326. (2001). The impact of in situ Fe fertilisation on the microbial food web in the Southern Ocean. Deep-Sea Research. Part II -
  327. (2002). The in silico analysis was carried out using the PRIMROSE program (Ashelford et al.,
  328. (1999). the mesoscale OIF experiment SOIREE targeted the HNLC region of the polar Southern Ocean, looking at all aspects of the composition and dynamics of the microbial food web (Boyd et al.,
  329. (2008). The metabolic balance at two contrasting sites in the Southern Ocean: The iron-fertilised Kerguelen area and HNLC waters. Deep-Sea Research. Part II -
  330. (2001). The microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates.
  331. (2007). The microbial loop.
  332. (1987). The neighbour-joining method: A new method for reconstructing phylogenetic trees.
  333. (1974). The ocean's food web, a changing paradigm.
  334. (2004). The oceanic gel phase: a bridge in the DOM-POM continuum.
  335. (2004). The oceanic sink for anthropogenic CO2.
  336. (1970). The Open Sea: Its Natural History, Part 1: The World of Plankton: Collins Fontana.
  337. (1996). The role of heterotrophic bacteria in iron-limited ocean ecosystems.
  338. (2007). The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin.
  339. (1981). The seasonal abundance, vertical distribution, and relative microbial biomass of chroococcoid cyanobacteria at a station in southern California coastal waters.
  340. (2002). The single, ancient origin of chromist plastids.
  341. (2004). The Southern Ocean was again the site of Fe fertilisation in the 2000 EisenEx experiment (Gervais et al., 2002; Arrieta et al.,
  342. (2003). The uncultured microbial majority.
  343. (2004). The use of DGGE analyses to explore eastern Mediterranean and Red Sea marine picophytoplankton assemblages.
  344. (1999). This band occurs faintly in every profile of the Planctomycetes gel in Figure 5.16. Prochlorococcus sp. cells make up the bulk of primary producing biomass in the oligotrophic subtropical oceans (Partensky et al.
  345. This sequence aligns well with Winogradskyella, a member of the Bacteroidetes.
  346. (2003). Three mesocosms were bubbled with CO2 gas until the dissolved gas’s partial pressure in the water was ~ 750 ppm, equivalent to that estimated for the global ocean surface for the year 2100 (Caldeira and Wickett,
  347. (2003). To investigate specifically the diversity of Gram-positive bacteria in the oceans, specific primers for the Firmicutes (350f/814r) were designed. Actinobacteria-specific primers are already available and proved to be successful for marine samples
  348. (2004). Transparent exopolymer particles and dissolved organic production by Emiliania huxleyi exposed to different CO2 concentrations: A mesocosm experiment.
  349. (1999). Two distinct mechanisms cause heterogeneity of 16S rRNA.
  350. (2006). Unlocking the "microbial black box" using RNA-based stable isotope probing technologies.
  351. (1995). Unravelling the extent of diversity within the order Planctomycetales.
  352. (2001). Upper ocean carbon export and the biological pump.
  353. (2000). Uptake and regeneration of inorganic nutrients by marine heterotrophic bacteria.
  354. (2002). Use of 16S ribosomal DNA for delineation of marine bacterioplankton species.
  355. (2007). Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.
  356. (1993). Use of 16S rRNA-targeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria.
  357. (2004). Use of ammoniaoxidizing bacterial-specific phylogenetic probe Nso1225 as a primer for fingerprint analysis of ammonia-oxidizer communities.
  358. (2001). Variations in bacterial community structure during a dinoflagellate bloom analysed by DGGE and 16S rDNA sequencing.
  359. (1993). Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results.
  360. (2008). was the most abundant autotroph (Dixon,
  361. (2002). What are bacterial species?
  362. (2002). While OIF as a strategy to mitigate global warming has its advocates
  363. (1979). Widespread occurrence of a unicellular, marine, planktonic cyanobacterium.

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