Les picocyanobactéries marines Synechococcus sont les seconds organismes photosynthétiques les plus abondants sur Terre. Elles présentent une grande diversité pigmentaire du fait de différences dans la composition de leur antenne collectrice de lumière (phycobilisome), ce qui leur permet d'utiliser efficacement une grande partie du spectre lumineux. Cependant, l'évolution, l'écologie et les bases moléculaires de cette diversité restent mal comprises. La comparaison d'une région génomique impliquée dans la synthèse des phycobilisomes de 54 souches et de populations naturelles m'a permis de proposer un scénario pour l'évolution des différents types pigmentaires et de montrer que cette diversité pigmentaire précède la diversification des Synechococcus marins. J'ai ensuite développé une procédure bioinformatique pour quantifier l'abondance relative de tous les types pigmentaires connus à partir de métagénomes. Appliquée aux données de Tara Oceans, cela m'a permis de décrire leur répartition à l'échelle mondiale, révélant que l'acclimatation chromatique de type IV, qui permet aux cellules de modifier leur spectre d'absorption en fonction de la couleur de la lumière, domine les populations naturelles de Synechococcus, et que des mutants naturels de l'acclimatation chromatique prévalent dans les étendues oligotrophes de l'océan Pacifique sud. Enfin, la caractérisation génétique de deux membres d'une famille d'enzymes liant les pigments à la phycoérythrine II, constituant majeur des phycobilisomes, a apporté de nouvelles perspectives sur les bases moléculaires de l'acclimatation chromatique et révélé l'importance des variations alléliques dans la diversité des types pigmentaires. / Marine Synechococcus are the second most abundant photosynthetic organisms on the planet. These picocyanobacteria present very diverse pigmentations due to differences in the composition of their light-harvesting antenna (phycobilisome), allowing them to efficiently exploit a wide range of spectral niches. Yet, the evolution, ecology and molecular bases of the different Synechococcus pigment types are not well understood. By comparing the genomic regions involved in the synthesis of phycobilisome rods from 54 sequenced isolates spanning all cultured pigment types and from natural Synechococcus populations, I proposed a scenario for the evolution of the different pigment types and showed that the pigment diversity of marine Synechococcus predates the diversification of this genus. Then, I developed a bioinformatic pipeline for reliably quantifying all known Synechococcus pigment types from metagenomes. Applying it to the Tara Oceans dataset allowed me to describe for the first time their distribution in the global ocean and revealed that type IV chromatic acclimation, a process by which cells can match their absorption properties to the ambient light colour, is widespread and constitutes the dominant pigmentation in Synechococcus populations. It also showed that natural chromatic acclimation mutants prevail in wide oligotrophic areas of the southern Pacific Ocean. Finally, I genetically characterized two members of an enzyme family binding chromophores to phycoerythrin-II, a major component of phycobilisomes. This provided new insights into the molecular bases of chromatic acclimation and revealed the importance of allelic variation for the diversity of pigment types.

Thesis (Ph.D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Extensive genetic diversity has been discovered in the microbial world, yet mechanisms that shape and maintain this diversity remain poorly understood. This thesis investigates to what extent populations of the gamma-proteobacterial family, Vibrionaceae, are ecologically specialized by investigating the distribution across a wide range of environmental categories, such as marine invertebrates or particles in the water column. Additionally, it seeks to determine whether in situ population distributions directly result from a competitive advantage over other Vibrio populations. This was investigated by in vitro competition assays on mixtures of native, sterilized particles. Generalist populations were found to dominate the associations with marine invertebrates, consistent with a model of high migration dominated population assembly. A majority of populations occurred broadly within and among the different types of invertebrates sampled, with one population being a near perfect generalist with regard to seasons, host taxa and body regions. High variability across host individuals, consistent with a scenario of stochastic clonal expansion, was especially pronounced in crab and zooplankton samples. Specialization, demonstrated by specific and reproducible association with different particle types in the water column, is more common than specialization within invertebrate hosts. / (cont.) Co-existing Vibrio species show strong preferences for different types of particulate matter in the water column suggesting that competition for limited resources influences their evolution. While populations show different growth profiles on particle derived substrates, relative growth advantages of specialist populations in competition with other Vibrio populations on native particles may not be sufficient to explain observed environmental distributions. Instead, populations may gain an advantage on these particles by colonizing the living plant or zooplankton prior to death and degradation into particulate matter. In summary, although vibrios are known commensals of marine invertebrates, evidence suggests that population structure within animals is fairly weak compared to suspended particles in the water column. This highlights the importance of comparing multiple environmental categories and migration among them to investigate population structure and adaptation. / by Sarah Pacocha Preheim. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The distribution and magnitude of marine primary production helps determine the ocean's role in global carbon cycling. Constraining factors that impact this productivity and elucidating selective pressures that drive the composition of marine microbial communities are thus essential aspects of marine biogeochemistry. Vitamin B₁₂, also known as cobalamin, is a cobalt containing organometallic micronutrient produced by some bacteria and archaea and required by many eukaryotic phytoplankton for methionine biosynthesis and regeneration. Although the potential for vitamin B₁₂ availability to impact primary production and phytoplankton species composition has long been recognized, the lack of molecular-level tools for studying B₁₂ production, use and acquisition has limited inquiry into the role of the vitamin in marine biogeochemical processes. This thesis describes the development of such tools and implements them for the study of B₁₂ dynamics in an Antarctic shelf ecosystem. Nucleic acid probes for B₁₂ biosynthesis genes were designed and used to identify a potentially dominant group of B₁₂ producers in the Ross Sea. The activity of this group was then verified by mass spectrometry-based peptide measurements. Then, possible interconnections between iron and B₁₂ dynamics in this region were identified using field-based bottle incubation experiments and vitamin uptake measurements, showing that iron availability may impact both B₁₂ production and consumption. Changes in diatom proteomes induced by low B₁₂ and low iron availability were then examined and used to identify a novel B₁₂ acquisition protein, CBA1, in diatoms. This represents the first identification of a B₁₂ acquisition protein in eukaryotic phytoplankton. Transcripts encoding CBA 1 were detected in natural phytoplankton communities, confirming that B₁₂ acquisition is an important part of phytoplankton molecular physiology. Selected reaction monitoring mass spectrometry was used to measure the abundance of CBA1 and methionine synthase proteins in diatoms cultures, revealing distinct protein abundance patterns as a function of B₁₂ availability. These peptide measurements were implemented to quantify methionine synthase proteins in McMurdo Sound, revealing that there is both B₁₂ utilization and starvation in natural diatom communities and that these peptide measurements hold promise for revealing the metabolic status of marine ecosystems with respect to vitamin B₁₂. / by Erin Marie Bertrand. / Ph.D.

Thesis (Ph.D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Biological activity has shaped the surface of the earth in numerous ways, but life's most pervasive and persistent global impact has been the secular oxidation of the surface environment. Through primary production - the biochemical reduction of carbon dioxide to synthesize biomass - large amounts of oxidants such as molecular oxygen, sulfate and ferric iron have accumulated in the ocean, atmosphere and crust, fundamentally altering the chemical environment of the earth's surface. This thesis addresses aspects of the role of marine microorganisms in driving this process. In the first section of the thesis, biomarkers (hydrocarbon molecular fossils) are used to investigate the early history of microbial diversity and biogeochemistry. Molecular fossils from the Transvaal Supergroup, South Africa, document the presence in the oceans of a diverse microbiota, including eukaryotes, as well as oxygenic photosynthesis and aerobic biochemistry, by ca. 2.7Ga. Experimental study of the oxygen requirements of steroid biosynthesis suggests that sterane biomarkers in late Archean rocks are consistent with the persistence of microaerobic surface ocean environments long before the initial oxygenation of the atmosphere. In the second part, using Prochlorococcus (a marine cyanobacterium that is the most abundant primary producer on earth today) as a model system, we explored how microbes use the limited nutrient resources available in the marine environment to make the protein catalysts that enable primary production. Quantification of the Prochlorococcus proteome over the diel cell-division cycle reveals that protein abundances are distinct from transcript-level dynamics, and that small temporal shifts in enzyme levels can redirect metabolic fluxes. This thesis illustrates how molecular techniques can contribute to a systems-level understanding of biogeochemical processes, which will aid in reconstructing the past of, and predicting future change in, earth surface environment / by Jacob Richard Waldbauer. / Ph.D.

Bacterioplankton is characterized by high diversity, short generation times and rapid turnover. Despite their small size, these numerous microorganisms are a fundamental piece of aquatic ecosystems by channeling carbon to higher trophic levels through dissolved organic matter utilization. Yet, several gaps remain in our knowledge and understanding of bacterioplankton populations regarding detailed temporal dynamics, and mechanisms determining biogeographical patterns and potential responses to climate change. The aim of this thesis was to examine responses in bacterioplankton community composition and function when challenged by natural and anthropogenically-induced change in environmental conditions. High temporal resolution analysis of bacterioplankton population dynamics in the Baltic Sea indicated detailed seasonal responses. It also showed a similar but wide spectrum of niche differentiation patterns within several major bacterial groups. Analysis of geographic distributions of marine bacterial populations revealed bimodal occupancy-frequency patterns in bacterial communities, indicating that the presence of many locally rare taxa along with a few locally abundant taxa were explained by stochastic variation in colonization and extinction rates. Experimental manipulations with natural marine bacterioplankton assemblages revealed both specialist and generalist strategies in utilizing specific dissolved organic carbon compounds. When subjected to experimentally increased sea surface temperatures, lowered pH and additions of terrigenous carbon, some populations decreased in relative abundance while others were stable; concomitantly, many populations increased in relative abundance. Shifts in bacterial community composition were shown to correlate with changes in community functioning, but detection of such correlations depended largely on the detail of phylogenetic analysis and successional stage of the communities. The results in this thesis suggest that both natural and anthropogenically-induced changes in environmental conditions promote simultaneous adjustment and replacement of bacterial populations tightly linked with metabolic plasticity. These trade-offs play a significant role for understanding the relationship between bacterioplankton population dynamics and potential shifts in carbon cycling properties. We also show the importance of regional effects in shaping bacterial community composition, crucial for interpreting bacterioplankton distribution patterns. In conclusion, this thesis emphasizes the critical importance of connecting analysis of bacterioplankton population dynamics with examination of ecological mechanisms to improve our understanding of factors that regulate the distribution and activity of distinct bacterioplankton populations. / Hälften av all fotosyntes på vår planet utförs av växtplankton. De producerar organiskt material som utgör grunden för näringskedjan i havet. Ungefär hälften av det organiska material som produceras av växtplankton utnyttjas inte direkt, utan omsätts istället av bakterieplankton som lever och växer fritt i vattenmassan eller på olika partiklar. Bakterieplankton spelar därmed en nyckelroll i ekosystemet genom sin konsumtion av organiskt kol som för energi högre upp i näringskedjan. Trots deras nyckelroll i akvatiska miljöer vet vi fortfarande mycket lite om bakteriernas detaljerade säsongsmönster, mekanismer bakom rumsliga mönster och hur olika populationer kan komma att svara på klimatförändringar. Målet med denna avhandling var att undersöka hur specifika populationers dynamik och ekosystemfunktion påverkas av naturliga eller klimatorsakade förändringar i havsmiljön. Våra resultat av högupplöst säsongsbunden dynamik i Östersjöns bakteriesamhälle avslöjar en liknande bred uppdelning av ekologiska strategier inom varje större grupp av bakterier, både i relativ abundans och temporal fördelning. Utbredning i rum och tid av många lokalt ovanliga populationer jämfört med få lokalt vanliga populationer förklarades genom stokastisk variation i kolonisations- och utdöendehastigheter. Vidare tyder experimentella studier med tillsatser av olika kolkällor på att marina bakterier har olika ekologiska strategier, där populationer är specialister eller generalister i utnyttjandet av enskilda kolkällor. Med hjälp av experiment med naturliga bakteriesamhällen bekräftade vi tydliga temperatureffekter på bakteriesamhällets sammansättning, och en mindre effekt av lägre pH - som dock tillsammans med förhöjd temperatur bidrog till en tydlig synergistisk effekt på artsammansättningen. Ökad temperatur tillsammans med tillsats av terrestert kol gav också en stor effekt på bakteriesamhällets struktur och ekosystemfunktion och pekar på en potentiellt viktig påverkan av ökad framtida nederbörd och avrinning från vattendrag till havet. Samtliga tre experiment med fokus på klimatpåverkan bekräftade förekomsten av populationer som försvann eller minskade i relativ abundans vid klimatpåverkan (känslighet), medan andra var stabila (resistens). Samtidigt svarade många populationer positivt på klimatorsakade förändringar i havsmiljön och ökade i relativ abundans (respons) samtidigt som bakteriernas ekosystemfunktion påverkades positivt. Sammanfattningsvis visar denna avhandling att vissa nya bakteriepopulationer kan etablera sig och ersätta andra samtidigt som vissa befintliga populationer anpassar sin livsstrategi och ekologi till förändringar i havsmiljön. Vi visar också vikten av regionala effekter, d.v.s. kolonisation och utdöende, för bakteriesamhällets struktur, viktigt för tolkningen av biogeografiska mönster och den genomiska potentialen hos specifika populationer. Denna avhandling poängterar därmed betydelsen av att koppla studier av ekologiska mekanismer till både rumsliga och temporala spridningsmönster hos bakterier och till populationers kapacitet att svara på och anpassa sig till förändringar i havsmiljön.

Made available in DSpace on 2016-08-17T18:39:35Z (GMT). No. of bitstreams: 1 3286.pdf: 1985838 bytes, checksum: e5ef56af190be032fb21c75bb7198227 (MD5) Previous issue date: 2010-06-01 / Universidade Federal de Sao Carlos / Studies of marine natural products in 20 years of research have revealed a wide variety of molecules with complex structures and hitherto unknown, and potent biological activities. The aims of this study were to isolate microbial strains associated with Didemnum granulatum, to fermentate such strains for the production of crude extracts and the screening of these extracts for bioactive secondary metabolites. For the isolation of the strains, six different culture media were prepared with artificial sea water: malt extract 2% and 3%, carrot/potato, corn, oat and GPY. The strains were cultivated for 30 days in 250mL of the same culture media. The crude extracts were obtained by partition with ethyl acetate. The extracts were sent for the cytotoxic activity bioassay and analyzed by thin layer chromatography (TLC) on silica gel plate (with absorption in UV-vis). Among the 26 extracts, samples DG (M3) 6'C and DG (M3) 5'C showed potent cytotoxic activity, samples DG (B) 13, DG (M3) 1 and DG (G) 2B a moderate activity. The analysis by TLC indicated the presence of bioactive secondary metabolites in the extracts. The strains were identified as bioactive three fungal: DG (M 3) 6'C (Penicillium sp.) DG (M3) 5'C (Cladosporium sp.) DG (M3) 1 (Aspergillus sp.) And two bacterial: DG (B) 13 (Aurantimonas sp.) DG (G) 2B (Nocardiopsis sp.). These were grown on a larger scale of broth (500 mL) and extracted after 7, 14, 21 and 30 days of incubation. We carried out a cleaning process of these extracts by solid phase extraction (SPE) column of silica gel derivatized with C18 (35 mL of eluent: 100% H2O, MeOH/H2O 1:1 and MeOH 100%). The fractions generated were analyzed by HPLC-UV-MS trying to find characteristic profiles of secondary metabolites. From the DG sample (M3) 6'C (A + B), was isolated and identified the compound 13- deoxy-fomenona previously obtained by Tirilly et al. in 1983. Although this compound is not unheard of, no literature reports of studies involving bioassays cytotoxic against tumor cells and even this compound has been isolated from other species of microorganisms other than the fungus Dicyma pulvinata. / Os estudos sobre produtos naturais marinhos, durante os ultimos 20 anos de pesquisa, revelaram uma grande variedade de moleculas com estruturas complexas e ate entao desconhecidas, alem de potentes atividades biologicas. Assim, os objetivos deste trabalho foram isolar linhagens de micro-organismos associadas a ascidia Didemnum granulatum, sua posterior fermentacao para a producao de extratos brutos e a analise destes extratos na busca por metabolitos secundarios bioativos. Para o isolamento das linhagens foram utilizados os seguintes meios de cultura preparados com agua do mar artificial: extrato de malte 2% e 3%, cenoura/batata, fuba, aveia e GPY. A fermentacao das linhagens foi feita em 250 mL dos mesmos meios de cultura sem agar, durante 30 dias. Os extratos brutos foram obtidos por particao com acetato de etila. Estes extratos foram enviados para bioensaio de atividade citotoxica contra celulas tumorais e analisados por cromatografia em camada delgada (CCD) em placa de silica gel (com diferentes reveladores). Dentre os 26 extratos, as amostras DG(M3) 6 C e DG(M3) 5 C apresentaram potente atividade citotoxica, as amostras DG(B)13, DG(M3)1 e DG(G)2B uma atividade moderada. As analises por CCD indicaram a presenca de metabolitos secundarios nos extratos bioativos. As linhagens bioativas foram identificadas como sendo tres fungicas: DG(M3)6 C (Penicilium sp.); DG(M3)5 C (Cladosporium sp.); DG(M3)1 (Aspergillus sp.) e duas bacterianas: DG(B)13 (Aurantimonas sp.); DG(G)2B (Nocardiopsis sp.). Estas foram cultivadas em escala maior de meio liquido (500 mL) e extraidas apos 7, 14, 21 e 30 dias de incubacao. Realizou-se um processo de limpeza destes extratos por extracao em fase solida (SPE) em coluna de silica-gel derivatizada com C18 (35 mL dos eluentes: H2O 100%, MeOH/H2O 1:1 e MeOH 100%). As fracoes geradas foram analisadas por CLAE-UV-EM buscando-se encontrar perfis caracteristicos de metabolitos secundarios. A partir da amostra DG(M3) 6 C (A+B), foi isolado e identificado o composto 13-desoxi-fomenona, previamente obtido por Tirilly et al. em 1983. Apesar deste composto nao ser inedito, nao ha relatos na literatura de estudos envolvendo bioensaios citotoxicos contra celulas tumorais e nem mesmo deste composto ter sido isolado de outras especies de microrganismos que nao seja do fungo Dicyma pulvinata.

Oceans are powered by active, metabolically diverse microorganisms, which are important in regulating biogeochemical cycles on Earth. Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. Bacterial adaptation to fluctuating environmental conditions involves extensive reprogramming, and redirection of bacterial metabolism and physiology. In this thesis, I investigated the molecular mechanisms of bacterial adaptation strategies to sustain their growth and survival, focusing on the regulation of gene and protein expression in heterotrophic marine bacteria. Comparative proteomics analyses of the growth and non-growth conditions, uncovered central adaptations that marine bacteria employ to allow them to change their metabolism to support exponential growth in response to nutrients and to readjust to stationary phase under nutrient limitation. Our results highlight that during nutrient rich conditions three distinct bacteria lineages have great similarities in their proteome. On the other hand, we observed pronounced differences in behavior between taxa during stationary phase. Analyses of the proteorhodopsin containing bacterium Vibrio sp. AND4 during starvation showed that significantly improved survival in the light compared to darkness. Notably, proteins involved in promoting cell vitality and survival had higher relative abundance under light. In contrast, cells in the dark need to degrade their endogenous resources to support their basic cellular demands under starvation. Thus, light strongly influences how PR-containing bacteria organize their molecular composition in response to starvation. Study of alternative energy generation metabolisms in the Alphaproteobacteria Phaeobacter sp. MED193 showed that the addition of thiosulfate enhanced the bacterial growth yields. Concomitantly, inorganic sulfur oxidation gene expression increased with thiosulfate compared to controls. Moreover, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation. These findings imply that this bacterium could use their lithotrophic potential to gain additional energy from sulfur oxidation for both improving their growth and survival. This thesis concludes that analyses in model organisms under defined growth conditions gives invaluable knowledge about the regulatory networks and physiological strategies that ensure the growth and survival of heterotrophic bacteria. This is critically important for interpreting bacterial responses to dynamic environmental changes. Moreover, these analyses are crucial for understanding genetic and proteomic responses in microbial communities or uncultivated organisms in terms of defining ecological niches of planktonic bacteria

The purpose of this paper is to present a comparative study of marine bacteria, molds and actinomycetes in regard to their ability to degrade certain pure and mixed complex compounds possibly occurring in the lagoon waste traps of the Texas Gulf Coast. This comparison was made using a differential oxygen uptake as the index of specific compound utilization.

A poluição, alteração física do habitat e a introdução de espécies invasoras via água de lastro, representam os maiores impactos antropogênicos para os ambientes costeiros. Foram pesquisadas em amostras da região costeira de S. Paulo, regiões portuárias brasileiras e de tanques de lastro de navios, bactérias das espécies Vibrio cholerae (Vc), V. parahaemolyticus (Vp) e V. vulnificus (Vv) que são as que têm maior implicação na saúde pública. As amostras foram avaliadas levando-se em conta parâmetros físico-químicos e microbiológicos e suas relações com a presença de Vc, Vp e Vv. As relações clonais foram verificadas através das técnicas de ERIC, BOX e REP-PCR. Foram identificadas 90 cepas de Vp e 11 de Vc. Foram observadas correlações entre alguns parâmetros microbiológicos e a presença de vibrios. A análise clonal permitiu verificar a alta diversidade das cepas. Concluiu-se que Vc e Vp são autóctones do ambiente costeiro brasileiro e podem ser tornar reservatórios para determinados fatores associados à virulência, gerando cepas com potencial epidêmico. / Pollution, physical alteration of habitat and the introduction of alien species through ballast water constitute the biggest anthropogenic impacts on coastal environments. We examined samples taken from the coastal region of S. Paulo state, Brazilian ports and ship ballast tanks, for bacteria of the species Vibrio cholerae (Vc), V. parahaemolyticus (Vp) and V. vulnificus (Vv) which have the most significant implication for public health. The samples were evaluated for microbiological and physical-chemical parameters as well as the presence of Vc, Vp and Vv. Clonal relationships of bacterial isolates were determined through ERIC, BOX and REP-PCR. A total of 90 strains of Vp and 11 of Vc were identified. Correlations between some microbiological parameters and the presence of vibrios were observed. The clonal analysis revealed extensive strain diversity. We concluded that Vc and Vp are autochthonous bacteria of the Brazilian coastal environment that can become reservoirs for factors associated with virulence, and are capable of generating strains with epidemic potential.

A ressurgência da massa de Água Central do Altântico Sul (ACAS) é o principal processo oceanográfico de disponibilização de nutrientes na zona eufótica da plataforma continental sudeste do Brasil (PCSE). Isto gera um acréscimo na população de organismos autotróficos e consequente de heterotróficos que produzem e oxidam a matéria orgânica gerada. O que possibilita um aumento no fluxo de carbono e consequentemente a manutenção dos recursos pesqueiros na região durante o verão. A abundância de micro-organismos autotróficos e heterotróficos planctônicos e a relação destes com as massas de água da PCSE foram avaliadas no verão de 2013. Para o tal, os micro-organismos autotróficos, menores que 20 µm foram quantificados por citometria de fluxo. Foram realizadas análises de abundância do gene 16S de bactérias, archaeas e do clado Sar11 e a expressão dos genes rubisco e proteorodpsina por meio de PCR em tempo real. O valor médio obtido de micro-organismos autrotróficos, Prochlorococcus spp. e Synechococcus spp. foi de 15.151 e de 8.313 células.ml-1, respectivamente. E de bactérias heterotróficas de 7.4x105 células.ml-1. Em relação aos domínios, a distribuição de Bacteria ocorreu na superfície e de Archaea no fundo da região oceânica. Os resultados indicam que a distribuição dos micro-organismos ocorreu conforme as características físicas e a disponibilidade de nutrientes das massas de água. Bactérias heterotróficas foram abundantes em regiões costeiras provavelmente devido a maior disponibilidade de matéria orgânica, o que corrobora com o resultado encontrado de maior biomassa de carbono em região costeira. / The resurgence of South Atlantic Central Waters (ACAS) is the main oceanographic process that involves availability of nutrients in the photic zone of the southeast continental shelf in Brazil. This causes an increase in the population of autotrophs and heterotrophic organisms (that produce and oxidizes the organic matter). The carbon flux increase and consequently the maintenance of fish resource in the region during the 2013 summer. The abundance of autotrophic and heterotrophic planktonic microorganisms was evaluated and also was studied their relation with the masses of water of the continental shelf. Thus, autotrophic microorganisms, smaller than 20 microns were quantified by flow cytometry. Using real time PCR were analysed 16S abundance of bacteria, archaea and SAR11 clade and the expression of the rubisco and proteorhodopsin gene. Autotrophic microorganisms, Prochlorococcus spp. and Synechococcus spp. had a mean value of 15.151 and 8.313 cell.ml-1, respectively. Heterotrophic bacteria had a mean value of 7.4x105 cell.ml-1. In relation to the domains, the distribution of bacteria occurred in the surface and the Archaea in the deep of the ocean region. The results indicate that the distribution of micro-organisms occur as the physical characteristics and the availability of nutrients of water masses. Heterotrophic bacteria were abundant in coastal areas probably due to increased of organic matter, which corroborates the result of higher biomass carbon in coastal region.