Diversity of bacterial communities related to the nitrogen cycle in a coastal tropical bay.

A culture-independent molecular phylogenetic analysis was carried out to study for the first time the diversity of bacterial ammonia monooxygenase subunit A (amoA) and nitrogenase reductase subunit H (nifH) genes from Urca inlet at Guanabara Bay in Rio de Janeiro, Brazil. Most bacterial amoA and nifH sequences exhibited identities of less than 95% to those in the GenBank database revealing that novel ammonia-oxidizing bacteria and nitrogen-fixing microorganisms may exist in this tropical marine environment. The observation of a large number of clones related to uncultured bacteria also indicates the necessity to describe these microorganisms and to develop new cultivation methodologies.

Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6 tag pyrosequencing.

The bacterioplankton diversity of coastal waters along a latitudinal gradient between Puerto Rico and Argentina was analyzed using a total of 134,197 high-quality sequences from the V6 hypervariable region of the small-subunit ribosomal RNA gene (16S rRNA) (mean length of 60 nt). Most of the OTUs were identified into Proteobacteria, Bacteriodetes, Cyanobacteria, and Actinobacteria, corresponding to approx. 80% of the total number of sequences. The number of OTUs corresponding to species varied between 937 and 1946 in the seven locations. Proteobacteria appeared at high frequency in the seven locations. An enrichment of Cyanobacteria was observed in Puerto Rico, whereas an enrichment of Bacteroidetes was detected in the Argentinian shelf and Uruguayan coastal lagoons. The highest number of sequences of Actinobacteria and Acidobacteria were obtained in the Amazon estuary mouth. The rarefaction curves and Good coverage estimator for species diversity suggested a significant coverage, with values ranging between 92 and 97% for Good coverage. Conserved taxa corresponded to aprox. 52% of all sequences. This study suggests that human-contaminated environments may influence bacterioplankton diversity.

Relationships between fecal indicators and pathogenic microorganisms in a tropical lagoon in Rio de Janeiro, Brazil.

Rodrigo de Freitas Lagoon is an urban ecosystem undergoing accelerated degradation, therefore selected as a model for microbiological quality studies of tropical lagoons. The aim of this study was to evaluate the abundance and the spatial distribution of fecal pollution indicators and pathogenic microorganisms in the lagoon. The relationships between microbial groups and abiotic measurements were also determined to evaluate the influence of environmental conditions on bacterial distribution and to identify the capability of coliforms and Enterococcus to predict the occurrence of Vibrio, Staphylococcus aureus, and Salmonella. Surface water samples were collected monthly, from December 1999 to October 2000. Analyses were performed by traditional culture techniques. A uniform spatial distribution was observed for all bacterial groups. The fecal pollution indicators occurred in low abundances while potentially pathogenic microorganisms were consistently found. Therefore, our study supported the use of counts of coliforms and Enterococcus to indicate only recent fecal contamination.

Archaeal and bacterial communities of heavy metal contaminated acidic waters from zinc mine residues in Sepetiba Bay.

Mining of metallic sulfide ore produces acidic water with high metal concentrations that have harmful consequences for aquatic life. To understand the composition and structure of microbial communities in acid mine drainage (AMD) waters associated with Zn mine tailings, molecular diversity of 16S genes was examined using a PCR, cloning, and sequencing approach. A total of 78 operational taxonomic units (OTUs) were obtained from samples collected at five different sites in and around mining residues in Sepetiba Bay, Brazil. We analyzed metal concentration, physical, chemical, and microbiological parameters related to prokaryotic diversity in low metal impacted compared to highly polluted environments with Zn at level of gram per liter and Cd-Pb at level of microgram per liter. Application of molecular methods for community structure analyses showed that Archaea and Bacteria groups present a phylogenetic relationship with uncultured environmental organisms. Phylogenetic analysis revealed that bacteria present at the five sites fell into seven known divisions, alpha-Proteobacteria (13.4%), beta-Proteobacteria (16.3%), gamma-Proteobacteria (4.3%), Sphingobacteriales (4.3%), Actinobacteria (3.2%) Acidobacteria (2.1%), Cyanobacteria (11.9%), and unclassified bacteria (44.5%). Almost all archaeal clones were related to uncultivated Crenarchaeota species, which were shared between high impacted and low impacted waters. Rarefaction curves showed that bacterial groups are more diverse than archaeal groups while the overall prokaryotic biodiversity is lower in high metal impacted environments than in less polluted habitats. Knowledge of this microbial community structure will help in understanding prokaryotic diversity, biogeography, and the role of microorganisms in zinc smelting AMD generation and perhaps it may be exploited for environmental remediation procedures in this area.

Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro.

This study is the first to apply a comparative analysis of environmental chemistry, microbiological parameters and bacterioplankton 16S rRNA clone libraries from different areas of a 50 km transect along a trophic gradient in the tropical Guanabara Bay ecosystem. Higher bacterial diversity was found in the coastal area, whereas lower richness was observed in the more polluted inner bay water. The significance of differences between clone libraries was examined with LIBSHUFF statistics. Paired reciprocal comparisons indicated that each of the libraries differs significantly from the others, and this is in agreement with direct interpretation of the phylogenetic tree. Furthermore, correspondence analyses showed that some taxa are related to specific abiotic, trophic and microbiological parameters in Guanabara Bay estuarine system.

Archaeal communities in a tropical estuarine ecosystem: Guanabara Bay, Brazil.

Guanabara Bay is an eutrophic estuarine system located in a humid tropical region surrounded by the second largest metropolitan area of Brazil. This study explores the contrasting environmental chemistry and microbiological parameters that influence the archaeaplankton diversity in a pollution gradient in Guanabara Bay ecosystem. The environments sampled ranged from completely anoxic waters in a polluted inner channel to the adjacent, relatively pristine, coastal Atlantic Ocean. Partial archaeal 16S rDNA sequences in water samples were retrieved by polymerase chain reaction (PCR) and analyzed using denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Sequences were subjected to phylogenetic and diversity analyses. Community structure of the free-living archaeal assemblages was different from that of the particle-attached archaea according to DGGE. Gene libraries revealed that phylotype identification was consistent with environmental setting. Archaeal phylotypes found in polluted anoxic waters and in more pristine waters were closely related to organisms that have previously been found in these environments. However, inner bay archaea were related to organisms found in oil, industrial wastes, and sewage, implying that water pollution controls archaea communities in this system. The detection of a substantial number of uncultured phylotypes suggests that Guanabara Bay harbors a pool of novel archaeaplankton taxa.

Distribution of HNA and LNA bacterial groups in the Southwest Atlantic Ocean

Bacterioplankton was studied in a large area of Southwest Atlantic Ocean between 13 and 25°S and 28 and 42°W. Samples were collected in 108 stations at 20 m depth. Bacteria were enumerated by flow cytometry after nucleic acid staining with syto13 and two subgroups were differentiated: low nucleic acid content (LNA) and high nucleic acid content (HNA) bacteria. Total bacterial numbers varied from 0.37 to 5.53 10(5) cells mL-1. HNA cells represented 15 to 70 percent of the total number while LNA cells represented 30 to 85 percent. Heterotrophic bacterial production was determined by incorporation of tritiated leucine and ranged from 2.7 to 171.07 ng C L-1 h-1. No significant correlation was found between abundance and production. Nevertheless with support of multivariate analysis between bacterial abundance, bacterial production, chlorophyll a and other oceanographic data the distribution of the groups in two different oceanic provinces could be explained by nutrient availability. HNA bacteria accounted for the high percentage of cells found in the area north of 19°S, linked to higher temperature waters and riverine nutrients inputs. LNA bacteria were the dominant cells south of this latitude and were correlated to the higher values of nitrate found for the same area.

Um estudo do bacterioplâncton foi realizado numa área extensa do Oceano Atlântico Sudoeste entre 13 e 25°S e 28 e 42°W. As amostras foram coletadas em 108 estações oceanográficas a 20 m de profundidade. A abundância bacteriana foi determinada por citometria de fluxo após coloração dos ácidos nucléicos com Syto13. Dois grupos de bactérias foram enumerados e distinguidos: bactérias com alto conteúdo de ácidos nucleicos (HNA) e bactérias com baixo conteúdo de ácidos nucleicos (LNA). O número de bactérias variou de 0,37 a 5,53 10(5) células mL-1. As células HNA representaram de 15 a 70 por cento da abundância total enquanto as células LNA representaram de 30 a 85 por cento. A produção bacteriana foi determinada por incorporação de leucina tritiada e variou de 2,7 a 171,07 ng C L-1 h-1. A correlação entre abundância e produção bacterianas não foi significativa. Entretanto uma análise multivariada realizada entre abundância, produção, clorofila a e outros dados oceanográficos revelou que a distribuição dos dois grupos em diferentes províncias oceânicas pode ser atribuída a disponibilidade de nutrientes. As bactérias HNA foram responsáveis pelo maior percentual de células na área ao norte de 19°S e estiveram relacionadas às águas quentes e aos nutrientes de origem pluvial. As bactérias LNA foram dominantes ao sul dessa latitude e estiveram relacionadas à disponibilidade de nitrato cujos valores foram mais altos nessa região.

Heterotrophic bacteria abundances in Rodrigo de Freitas Lagoon (Rio de Janeiro, Brazil)

The Rodrigo de Freitas Lagoon (RJ, Brazil) is an important coastal ecosystem that has been submitted to an accelerated degradation process. The aim of this work was to determine the abundance and the spatial distribution of total heterotrophic (by flow cytometry) and cultivated bacteria ("pour plate" method on R2A agar). Another objective was to evaluate the lagoon's influence on water quality of Ipanema and Leblon beaches. Physical and chemical data were acquired too. Sub-superficial water samples were taken monthly, from December 1999 to October 2000. On lagoon, the cultivated bacteria abundance varied from 6.9x10(5) to 5.0x10(7) CFU.100 mL-1. On Ipanema and Leblon beaches, this parameter yielded 1.4x10(5) and 2.8x10(6) CFU.100 mL-1, respectively. Total bacterial abundance varied from 2.9x10(7) to 3.2x10(7) cells.mL-1 on lagoon. On Ipanema and Leblon, this parameter yielded 8.7x10(6) and 1.1x10(7) cells.mL-1, respectively. Two sub-groups were determined with dominance of HNA cells. Samples were added latter to better understand the bacteria present on these environments. Bacterial abundance were analyzed only by flow cytometry and the results varied from 8.3x10(6) to 2.5x10(7) cells.mL-1 on lagoon. On the beach, this parameter yielded 6.9x10(6) cells. mL-1. Two bacterial sub-groups were also observed, with dominance of HNA on lagoon and LNA on the beach. The results showed that the Rodrigo de Freitas Lagoon is an eutrophic ecosystem where the bacterial populations and the physical and chemical parameters do not differ spatially. The data also confirmed that the outflow of the lagoon's polluted waters affect the sanitary conditions of Ipanema and Leblon beaches.

A Lagoa Rodrigo de Freitas (RJ, Brasil) é um importante ecossistema que vêm sendo submetido a um acelerado processo de degradação. O objetivo desse estudo foi determinar a abundância e a distribuição espacial das bactérias heterotróficas totais (citometria em fluxo) e cultivadas ("pour plate" em ágar R2A). Outro objetivo foi avaliar a influência da lagoa na qualidade das águas de Ipanema e do Leblon. Dados físico-químicos também foram adquiridos. Amostras de água sub-superficiais foram coletadas mensalmente, de dezembro de 1999 a outubro de 2000. Na lagoa, a abundância de bactérias cultivadas variou de 6,9x10(5) a 5,0x10(7) UFC.100 mL-1. Em Ipanema e no Leblon, esse parâmetro atingiu 1,4x10(5) e 2,8x10(6) UFC.100 mL-1, respectivamente. A abundância bacteriana total variou de 2,9x10(7) a 3,2x10(7) células.mL-1 na lagoa. Em Ipanema e no Leblon, este parâmetro alcançou, respectivamente, 8,7x10(6) a 1,1x10(7) células.mL-1. Dois sub-grupos bacterianos foram observados nas estações, com predomínio de células HNA. Amostras foram posteriormente coletadas visando um maior entendimento sobre as bactérias presentes nesses ambientes. A abundância bacteriana foi analisada apenas por citometria em fluxo e os resultados oscilaram entre 8,3x10(6) e 2,5x10(7) células.mL-1 na lagoa. Na praia, esse parâmetro atingiu 6,9x10(6) células.mL-1. Dois sub-grupos bacterianos também foram observados, com predomínio de células HNA na lagoa e LNA na praia adjacente. Os resultados indicaram que a lagoa é um ecossistema eutrofizado, onde as bactérias e os parâmetros físico-químicos distribuem-se de modo uniforme. Os dados ainda indicaram que as águas poluídas da lagoa afetam a qualidade das praias de Ipanema e do Leblon.