Anderson S. Cabral

Structuring of bacterioplankton diversity in a large tropical bay.

Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).

Killer yeasts inhibit the growth of the phytopathogen Moniliophthora perniciosa, the causal agent of Witches' Broom disease

Fruit and soil yeasts isolated from the Amazon, Atlantic Rainforests and an organic farm were screened for killer activity against yeasts. Killer yeasts were then tested against the phytopathogen Moniliophthora perniciosa (syn. Crinipellis perniciosa) and a Dipodascus capitatus strain and a Candida sp strain inhibited its growth.

Candida middelhoveniana sp. nov., a new yeast species found on the rhizoplane of organically cultivated sugarcane.

A novel yeast species within the Metschnikowiaceae is described based on a strain from the sugarcane (Saccharum sp.) rhizoplane of an organically managed farm in Rio de Janeiro, Brazil. The D1/D2 domain of the large subunit ribosomal RNA gene sequence analysis showed that the closest related species were Candida tsuchiyae with 86.2% and Candida thailandica with 86.7% of sequence identity. All three are anamorphs in the Clavisporaopuntiae clade. The name Candida middelhoveniana sp. nov. is proposed to accommodate this highly divergent organism with the type strain Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (IMUFRJ) 51965T (=Centraalbureau voor Schimmelcultures (CBS) 12306T, Universidade Federal de Minas Gerais (UFMG)-70T, DBVPG 8031T) and the GenBank/EMBL/DDBJ accession number for the D1/D2 domain LSU rDNA sequence is FN428871. The Mycobank deposit number is MB 519801.

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica)

Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 104–105) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome.

The Caatinga is a semi-arid biome in northeast Brazil. The Paraguaçú River is located in the Caatinga biome, and part of its course is protected by the National Park of Chapada Diamantina (PNCD). In this study we evaluated the effect of PNCD protection on the water quality and microbial community diversity of this river by analyzing water samples obtained from points located inside and outside the PNCD in both wet and dry seasons. Results of water quality analysis showed higher levels of silicate, ammonia, particulate organic carbon, and nitrite in samples from the unprotected area compared with those from protected areas. Pyrosequencing of the 16S rRNA genes revealed that Burkholderiales was abundant in samples from all three sites during both seasons and was represented primarily by the genus Polynucleobacter and members of the Comamonadaceae family (e.g., genus Limnohabitans). During the dry season, the unprotected area showed a higher abundance of Flavobacterium sp. and Arthrobacter sp., which are frequently associated with the presence and/or degradation of arsenic and pesticide compounds. In addition, genes that appear to be related to agricultural impacts on the environment, as well as those involved in arsenic and cadmium resistance, copper homeostasis, and propanediol utilization, were detected in the unprotected areas by metagenomic sequencing. Although PNCD protection improves water quality, agricultural activities around the park may affect water quality within the park and may account for the presence of bacteria capable of pesticide degradation and assimilation, evidencing possible anthropogenic impacts on the Caatinga.

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle

Corals display circadian physiological cycles, changing from autotrophy during the day to heterotrophy during the night. Such physiological transition offers distinct environments to the microbial community associated with corals: an oxygen-rich environment during daylight hours and an oxygen-depleted environment during the night. Most studies of coral reef microbes have been performed on samples taken during the day, representing a bias in the understanding of the composition and function of these communities. We hypothesized that coral circadian physiology alters the composition and function of microbial communities in reef boundary layers. Here, we analyzed microbial communities associated with the momentum boundary layer (MBL) of the Brazilian endemic reef coral Mussismilia braziliensis during a diurnal cycle, and compared them to the water column. We determined microbial abundance and nutrient concentration in samples taken within a few centimeters of the corals surface every 6 h for 48 h, and sequenced microbial metagenomes from a subset of the samples. We found that dominant taxa and functions in the coral MBL community were stable over the time scale of our sampling, with no significant shifts between night and day samples. Interestingly, the two water column metagenomes sampled 1 m above the corals were also very similar to the MBL metagenomes. When all samples were analyzed together, nutrient concentration significantly explained 40% of the taxonomic dissimilarity among dominant genera in the community. Functional profiles were highly homogenous and not significantly predicted by any environmental variables measured. Our data indicated that water flow may overrule the effects of coral physiology in the MBL bacterial community, at the scale of centimeters, and suggested that sampling resolution at the scale of millimeters may be necessary to address diurnal variation in community composition.

Virioplankton Assemblage Structure in the Lower River and Ocean Continuum of the Amazon

The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume. ABSTRACT The Amazon River watershed and its associated plume comprise a vast continental and oceanic area. The microbial activities along this continuum contribute substantially to global carbon and nutrient cycling, and yet there is a dearth of information on the diversity, abundance, and possible roles of viruses in this globally important river. The aim of this study was to elucidate the diversity and structure of virus assemblages of the Amazon River-ocean continuum. Environmental viral DNA sequences were obtained for 12 locations along the river’s lower reach (n = 5) and plume (n = 7). Sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes. Despite the spatial connectivity mediated by the river, virome analyses and physical-chemical water parameters clearly distinguished river and plume ecosystems. Bacteriophages were ubiquitous in the continuum and were more abundant in the transition region. Eukaryotic viruses occurred mostly in the river, while the plume had more viruses of autotrophic organisms (Prochlorococcus, Synechococcus) and heterotrophic bacteria (Pelagibacter). The viral families Microviridae and Myoviridae were the most abundant and occurred throughout the continuum. The major functions of the genes in the continuum involved viral structures and life cycles, and viruses from plume locations and Tapajós River showed the highest levels of functional diversity. The distribution patterns of the viral assemblages were defined not only by the occurrence of possible hosts but also by water physical and chemical parameters, especially salinity. The findings presented here help to improve understanding of the possible roles of viruses in the organic matter cycle along the river-ocean continuum. IMPORTANCE The Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazon are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the river and ocean in order to elucidate their possible roles. DNA sequence assembly yielded 29,358 scaffolds, encoding 82,546 viral proteins, with 15 new complete viral genomes from the 12 river and ocean locations. Viral diversity was clearly distinguished by river and ocean. Bacteriophages were the most abundant and occurred throughout the continuum. Viruses that infect eukaryotes were more abundant in the river, whereas phages appeared to have strong control over the host prokaryotic populations in the plume.

Virioplankton dynamics are related to eutrophication levels in a tropical urbanized bay

Virioplankton are an important and abundant biological component of marine and freshwater ecosystems. Often overlooked, aquatic viruses play an important role in biogeochemical cycles on a global scale, infecting both autotrophic and heterotrophic microbes. Viral diversity, abundance, and viral interactions at different trophic levels in aqueous environments are not well understood. Tropical ecosystems are less frequently studied than temperate ecosystems, but could provide new insights into how physical and chemical variability can shape or force microbial community changes. In this study, we found high viral abundance values in Guanabara Bay relative to other estuaries around the world. Viral abundance was positively correlated with bacterioplankton abundance and chlorophyll a concentrations. Moreover, prokaryotic and viral abundance were positively correlated with eutrophication, especially in surface waters. These results provide novel baseline data on the quantitative distribution of aquatic viruses in tropical estuaries. They also provide new information on a complex and dynamic relationship in which environmental factors influence the abundance of bacterial hosts and consequently their viruses. Guanabara Bay is characterized by spatial and seasonal variations, and the eutrophication process is the most important factor explaining the structuring of virioplankton abundance and distribution in this tropical urbanized bay.

Vertical distribution of mesozooplankton and ichthyoplankton communities in the South-western Atlantic Ocean (23°14′1″S 40°42′19″W)

ana c. t. bonecker, cristina de o. dias, marcia s. de castro, pedro f. de carvalho, adriana v. araujo, rodolfo paranhos, anderson s. cabral and sergio l. c. bonecker Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Zoologia, Av. Carlos Chagas Filho, 373 – Prédio do CCS, Bloco A, Sala A0-084, Ilha do Fundão – 21.941-902, Rio de Janeiro, RJ, Brasil, Universidade Federal do Rio de Janeiro, Laboratório de Hidrobiologia, Departamento de Biologia Marinha, Instituto de Biologia, Av. Carlos Chagas Filho, 373 – Prédio do CCS, Bloco A, Cidade Universitária, Ilha do Fundão – 21.941-902, Rio de Janeiro, Brasil

VIRIOPLÂNCTON E BACTERIOPLÂNCTON: DESCRITORES ESPACIAIS E TEMPORAIS

RESUMO A estrutura e consequente funcao da cadeia alimentar das aguas oceânicas profundas e assunto de crescente interesse em oceanografia. Os perfis verticais (1-2.300 m) do bacterioplâncton e virioplâncton no Oceano Atlântico Sudoeste obtidos no ano de 2009 foram analisados e descritos nesse estudo. O numero de virus, bacterias totais, HNA e LNA foi determinado por meio de citometria em fluxo. Normalmente, as bacterias com baixo teor de acidos nucleicos (LNA) dominaram a camada eufotica, correspondendo a mais de 80-90% da abundância bacteriana total. O numero total de bacterias diminuiu cerca de uma ordem de grandeza com o aumento da profundidade. Apesar disso, a proporcao de bacterias com alto teor de acidos nucleicos (HNA) aumentou ao longo do perfil vertical. Nas maiores profundidades, as celulas HNA tenderam a dominar a abundância de bacterias heterotroficas, representando cerca de 80-90% do numero total. Nas maiores profundidades, as condicoes ambientais sao mais favoraveis as bacterias do que aos seus competidores e predadores, uma vez que existe uma grande disponibilidade de nutrientes, algumas fontes de carbono que podem ser rapidamente captadas, e uma menor pressao de predacao. A interacao dos fatores mencionados anteriormente gera melhores condicoes para o desenvolvimento de determinadas populacoes bacterianas, favorecendo o crescimento e a dominância de celulas HNA ao inves de LNA. As celulas HNA, mais numerosas nas aguas profundas, sao reconhecidas como mais versateis e, portanto, responsaveis por uma parcela significativa do metabolismo batipelagico. Tais celulas sao de grande importância na alca microbiana da camada afotica, e seu estudo contribui para o maior entendimento da ecologia microbiana em aguas profundas. Nao observamos variacao sazonal para o bacterioplâncton, entretanto o virioplâncton foi significativamente mais abundante no verao, mostrando que a comunidade microbiana foi controlada pela infeccao viral.