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BackgroundUpwelling systems are characterised by an intense primary biomass production in the surface (warmest) water after the outcrop of the bottom (coldest) water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region.Methodology/Principal FindingsWe carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity) and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I.Conclusions/SignificanceThe variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial diversity in areas close to anthropogenic activity; functional roles and geochemical processes; phylogeny of the uncharacterised diversity; and seasonal variations of the microbial assemblages.

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The majority of oil from oceanic oil spills converges on coastal ecosystems such as mangrove forests. A major challenge to mangrove bioremediation is defining the mangrove's pollution levels and measuring its recuperation from pollution. Bioindicators can provide a welcome tool for defining such recovery. To determine if the microbial profiles reflected variation in the pollutants, samples from different locations within a single mangrove with a history of exposure to oil were chemically characterised, and the microbial populations were evaluated by a comprehensive range of conventional and molecular methods. Multivariate ordination of denaturing gradient gel electrophoresis (DGGE) microbial community fingerprints revealed a pronounced separation between the sediment and rhizosphere samples for all analysed bacterial communities (Bacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria and Pseudomonas). A Mantel test revealed significant relationships between the sediment chemical fertility and oil-derived pollutants, most of the bacterial community fingerprints from sediment samples, and the counts by different cultivation strategies. The level of total petroleum hydrocarbons was significantly associated with the Bacteria and Betaproteobacteria fingerprints, whereas anthracene and the total level of polycyclic aromatic hydrocarbons were associated with the Actinobacteria. These results show that microbial communities from the studied mangrove reflect the spatial variation of the chemicals in the sediment, demonstrating the specific influences of oil-derived pollutants.

Volume 75, no. 10, p. 3331-3343, 2009. The tentative affiliation of 20 16S rRNA gene sequences into bacterial phyla was not registered correctly as shown in Fig. 4b. This was because affiliations assigned by the RDP Classifier tool with low confidence thresholds (i.e., below 50%) were inadvertently regarded as stringent. Previously recorded as Aquificae (2), Bacteroidetes (1), Deferribacteres (3), Dictyoglomi (2), Firmicutes (7), and Proteobacteria (5), 12 of these sequences actually belong to one bacterial lineage of uncertain affiliation as described by Kamke et al. (ISME J. 4:498-508, 2010). The remaining 8 sequences are firmly affiliated with the Chloroflexi (4), Acidobacteria (2), and Proteobacteria (2) phyla. In addition, one clone sequence has been removed from the analyzed data set because of vector contamination. As a consequence, the following modifications to the article are needed.

Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using "direct" and "indirect" approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups-Pseudomonas and Actinobacteria-revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma-and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of spongeassociated microbiota performed with other sponge species.

The ascomycetous yeast communities associated with 3 bivalve mollusk, and 4 crab species were studied in the mangrove at Coroa Grande on Sepetiba Bay in Rio de Janeiro, Brazil. These were made up mostly of diverse but sparse and apparently allochtonous yeast populations. The striking exception was a prevalent population of the species Kluyveromyces aestuarii, which predominated the yeast communities of 2 detritus feeding crabs, Sesarma rectum and Uca spp., and the shipworm Neoteredo reynei. However, K. aestuarii was absent from the omnivorous crabs Aratus pisonii and Goniopsis cruentata, and the clam Anomalocardia brasiliana, and was rare in the clam Tagelus plebeius from mostly submerged more sandy sediments. Pichia membranaefaciens, Candida valida-like, Candida krusei, Candida sorbosa, Candida colliculosa-like, Candida famata-like, Kloeckera spp., Candida guilliermondii, Candida albicans, Candida silvae, Geotrichum spp., Rhodotorula spp., Cryptococcus spp., and the methylotrophic yeast Candida boidinii were frequently isolated. The 322 ascomycetous yeast cultures representing 252 isolates from crabs and mollusks were classified as 40 species that fit standard descriptions, and 44 putative new species. The ascomycetous yeast communities of the mangrove ecosystem include many new biotypes that require better taxonomic definition.

Yeasts and coliform bacteria were isolated from water that accumulated in the central cups and adjacent leaf axilae of two bromeliads, Neoregelia cruenta of a coastal sand dune and Quesnelia quesneliana of a mangrove ecosystem near the city of Rio de Janeiro, Brazil. The mean total coliform counts were above 10,000 per 100 mL for waters of both plants, but the mean fecal coliform counts were only 74 per 100 mL for Q. quesneliana and mostly undetected in water from N. cruenta. Of 90 fecal coliform isolates, 51 were typical of Escherichia coli in colony morphology and indol, methyl red, Volges-Proskauer, and citrate (IMViC) tests. Seven representatives of the typical E. coli cultures were identified as this species, but the identifications of nine other coliform bacteria were mostly dubious. The yeast community of N. cruenta was typical of plant surfaces with basidiomycetous yeasts anamorphs, and the black yeast Aureobasidium pullulans was prevalent. Quesnelia quesneliana had a substantial proportion of ascomycetous yeasts and their anamorphs, including a probable new biotype of Saccharomyces unisporus. Our results suggested that the microbial communities in bromeliad waters are typically autochtonous and not contaminants.