Publications by authors named "Fabiano L Thompson"

162 Publications

Genome sequence of Vibrio fluvialis 362.3 isolated from coral Mussismilia braziliensis reveals genes related to marine environment adaptation.

Arch Microbiol 2021 Apr 7. Epub 2021 Apr 7.

Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

Vibrio fluvialis is a halophilic bacterium frequently found in estuarine and coastal waters environments. The strain 362.3 was isolated from Mussismilia braziliensis coral of Abrolhos Bank. In this study, to gain insights into the marine adaptation in V. fluvialis, we sequenced the genome of 362.3 strain, which comprised 4,607,294 bp with a G + C content of 50.2%. In silico analysis showed that V. fluvialis 362.2 encodes genes related to chitin catabolic pathway, iron metabolism, osmotic stress and membrane transport.
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http://dx.doi.org/10.1007/s00203-021-02279-6DOI Listing
April 2021

Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef.

Sci Total Environ 2021 Mar 7;760:143411. Epub 2020 Nov 7.

Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address:

The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δC) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m day. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143411DOI Listing
March 2021

Vibrio tetraodonis sp. nov.: genomic insights on the secondary metabolites repertoire.

Arch Microbiol 2021 Jan 25;203(1):399-404. Epub 2020 Aug 25.

Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.

Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A511 obtained from the skin of the pufferfish Sphoeroides spengleri (Family Tetraodontidae), collected in Arraial do Cabo, Brazil. Optimum growth occurs at 20-28 °C in the presence of 3% NaCl. The genome sequence of the novel isolate consisted of 4.36 Mb, 3,976 coding genes and G + C content of 42.5%. Genomic taxonomy analyses based on average amino acid (AAI), genome-to-genome-distance (GGDH) and phylogenetic reconstruction placed A511 (= CBAS 712 = CAIM 1939) into a new species of the genus Vibrio (Vibrio tetraodonis sp. nov.). The genome of the novel species contains eight genes clusters (~ 183.9 Kbp in total) coding for different types of bioactive compounds that hint to several possible ecological roles in the pufferfish host.
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http://dx.doi.org/10.1007/s00203-020-02019-2DOI Listing
January 2021

A new genomic taxonomy system for the Synechococcus collective.

Environ Microbiol 2020 11 23;22(11):4557-4570. Epub 2020 Aug 23.

Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.
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http://dx.doi.org/10.1111/1462-2920.15173DOI Listing
November 2020

New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay.

Mar Genomics 2020 Dec 17;54:100789. Epub 2020 Jun 17.

Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil. Electronic address:

The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0-4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.
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http://dx.doi.org/10.1016/j.margen.2020.100789DOI Listing
December 2020

Oil leakage induces changes in microbiomes of deep-sea sediments of Campos Basin (Brazil).

Sci Total Environ 2020 Oct 21;740:139556. Epub 2020 May 21.

Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address:

The Campos Basin (100,000 km) is located on the continental shelf of southeastern Brazil. Despite the significant oil and gas industrial activities underway in the Campos Basin, scarce information is available regarding the hydrocarbon contents and microbial communities in the deep-sea sediments. To gain new insights on these aspects, we first obtained deep-sea sediment samples with different degrees of oil exposure. We obtained samples from a seabed fissure (N = 28), surroundings (250 m to 500 m from the fissure; N = 24), and a control area (N = 4). We used shotgun metagenomics to characterize the taxonomic and metabolic diversity and analyzed biogeochemical parameters (metal and oil concentration) of all samples. The high levels of unresolved complex mixture of hydrocarbons in the fissure indicate a potentially recent petrogenic contribution in these sediments. The fissure area was found to have a higher abundance of hydrocarbonoclastic bacterial genera and hydrocarbon degradation genes. These bacteria may be used as biosensors of sediment contamination. The effects of oil contamination, mainly around the fissure, are less clear at 250 m and 500 m, suggesting that the surroundings may not have been heavily affected by the oil leakage. Our study demonstrates that metagenomics can disclose biosensors for environmental monitoring.
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http://dx.doi.org/10.1016/j.scitotenv.2020.139556DOI Listing
October 2020

Rapid screening of marine bacterial symbionts using MALDI-TOF MS.

Arch Microbiol 2020 Oct 11;202(8):2329-2336. Epub 2020 Jun 11.

Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.
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http://dx.doi.org/10.1007/s00203-020-01917-9DOI Listing
October 2020

Remote sensing, isotopic composition and metagenomics analyses revealed Doce River ore plume reached the southern Abrolhos Bank Reefs.

Sci Total Environ 2019 Dec 29;697:134038. Epub 2019 Aug 29.

Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Instituto de Biologia, CCS, Laboratório de Microbiologia, Anexo ao Bloco A, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil. Electronic address:

On November 5th, 2015, the Fundão dam rupture released >50 million m of ore tailings into the Doce River, Minas Gerais State, Brazil. The huge volume of mud spread along the river and reached the sea, 17 days after the disaster, in Regência, Espírito Santo State (ES). In 2018, after three years of the disaster, the impacts of the ore tailings in the marine environment are still unclear. This study aims to investigate possible short-term impacts in marine biodiversity caused by the ore tailings' mud over the reef ecosystems that are closest to the disaster area: i.e. recently discovered reefs in the southern Abrolhos Bank. A remote sensing surveillance including winds, sea surface temperature, total suspended material and watercolor (MODIS Aqua data) indicated that the iron tailings plume reached the southern portion of Abrolhos Bank on June 16th, 2016. Subsequently, to obtain further evidence of the presence of the tailings in the coral reefs, water samples were collected in a gradient spanning from the river estuary to the reefs in southern Abrolhos Bank, we also analyzed the isotopic and microbial composition of the samples, as well as the reef benthic composition. Despite no clues of negative impact on benthic (coral) communities, isotopic analysis confirmed the presence of the plume over the reefs area. This study serves as a baseline for future long-term impact assessments of the health of coral reefs in the Abrolhos Bank.
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http://dx.doi.org/10.1016/j.scitotenv.2019.134038DOI Listing
December 2019

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.

Microb Ecol 2020 Aug 14;80(2):249-265. Epub 2020 Feb 14.

Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081 (= CBAS 745) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081 exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
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http://dx.doi.org/10.1007/s00248-019-01480-xDOI Listing
August 2020

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume.

BMC Microbiol 2020 01 15;20(1):13. Epub 2020 Jan 15.

Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.

Background: Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume.

Results: The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25.

Conclusions: Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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http://dx.doi.org/10.1186/s12866-020-1698-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964070PMC
January 2020

New tetrodotoxin analogs in Brazilian pufferfishes tissues and microbiome.

Chemosphere 2020 Mar 30;242:125211. Epub 2019 Oct 30.

Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.

While tetrodotoxin (TTX) is commonly found in pufferfish tissues, it is unclear if bacterial symbionts isolated from pufferfish tissues can produce TTX. In this investigation, UPLC qTOF-MS/MS analysis of tissue extracts obtained from Sphoeroides spengleri and Canthigaster figuereidoi identified TTX in their composition, indicating their consumption is unsafe. UPLC qTOF-MS/MS analysis coupled with Molecular Networking indicated new TTX analogs (methyl-TTX, TTX-acetate, hydroxypropyl-TTX and glycerol-TTX). Bacterial extracts from sixteen strains revealed a compound with a [M+H] ion at m/z 320.1088, identical to TTX. However, TTX itself was not detected in these cultures by UPLC-MS/MS. Neurotoxicity of Vibrio A665 purified fraction 2 (with precursor [M+H] ion at m/z 320.1088) was significant in human neural stem cells (hNSCs), but the Na blockage activity was not confirmed by the veratridine/ouabain essays, indicating a possible difference in the mechanism of action between the bacterium A665 purified fraction 2 and TTX. Vibrios symbionts of pufferfish point out involving in the production of TTX precursors.
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http://dx.doi.org/10.1016/j.chemosphere.2019.125211DOI Listing
March 2020

Enterovibrio baiacu sp. nov.

Curr Microbiol 2020 Jan 16;77(1):154-157. Epub 2019 Oct 16.

Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Avenida Carlos Chagas Fo, s/n, Bloco A, Ilha Do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.

We report here the novel species to encompass the isolate A649 (=CBAS 716 = CBRVS P1061) obtained from viscera of the healthy pufferfish Sphoeroides spengleri (Family Tetraodontidae). Genomic taxonomy analysis demonstrates that the novel strain A649 had < 95% average amino acid identity/average nucleotide identity (AAI/ANI) and < 70% similarity of genome-to-genome distance (GGDH) towards its closest neighbors which places A649 into a new Enterovibrio species (Enterovibrio baiacu sp nov.). In silico phenotyping disclosed several features that may be used to differentiate related Enterovibrio species. The nearly complete genome assembly of strain A649 consisted of 5.4 Mbp and 4826 coding genes.
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http://dx.doi.org/10.1007/s00284-019-01785-7DOI Listing
January 2020

Genome sequence of Shewanella corallii strain A687 isolated from pufferfish (Sphoeroides spengleri).

Genet Mol Biol 2020 17;43(1):e20180314. Epub 2020 Feb 17.

Universidade Federal do Rio de Janeiro, Institute of Biology and SAGE-COPPE, Rio de Janeiro, RJ, Brazil.

We present here the genome sequence of Shewanella corallii strain A687 isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae). The assembly consists of 5,215,037 bp and contains 284 contigs, with a G+C content of 50.3%.
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http://dx.doi.org/10.1590/1678-4685-GMB-2018-0314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197997PMC
February 2020

" Colwellia aromaticivorans" sp. nov., " Halocyntiibacter alkanivorans" sp. nov., and " Ulvibacter alkanivorans" sp. nov. Genome Sequences.

Microbiol Resour Announc 2019 Apr 11;8(15). Epub 2019 Apr 11.

Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil

Unplanned oil spills during offshore production are a serious problem for the industry and the marine environment. Here, we present the genome sequence analysis of three novel hydrocarbon-degrading bacteria, namely, " Colwellia aromaticivorans" sp. nov., " Halocyntiibacter alkanivorans" sp. nov., and " Ulvibacter alkanivorans" sp. nov.
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http://dx.doi.org/10.1128/MRA.00086-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460022PMC
April 2019

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim.

Curr Microbiol 2019 Jun 5;76(6):687-697. Epub 2019 Apr 5.

Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.

Although some previous studies have described the microbial diversity of termite in Brazil, the lack of studies about this subject is still evident. In the present study, we described by whole genome sequencing, the gut microbiota of seven species of termites (Termitidae) with different feeding habits from four Brazilian locations. For the litter species, the most abundant bacterial phylum was Firmicutes, where Cornitermes cumulans and Syntermes dirus (Syntermitinae) were identified. For the humus species, the most abundant bacterial phylum was Proteobacteria where three species were studied: Cyrilliotermes strictinasus (Syntermitinae), Grigiotermes bequaerti (Apicotermitinae), and Orthognathotermes mirim (Termitinae). For the wood termites, Firmicutes and Spirochaetes were the most abundant phyla, respectively, where two species were identified: Nasutitermes aquilinus and Nasutitermes jaraguae (Nasutitermitinae). The gut microbiota of all four examined subfamilies shared a conserved functional and carbohydrate-active enzyme profile and specialized in cellulose and chitin degradation. Taken together, these results provide insight into the partnerships between termite and microbes that permit the use of refractory energy sources.
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http://dx.doi.org/10.1007/s00284-019-01662-3DOI Listing
June 2019

Halomonas coralii sp. nov. Isolated from Mussismilia braziliensis.

Curr Microbiol 2019 Jun 4;76(6):678-680. Epub 2019 Apr 4.

Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

We report here the novel species Halomonas coralii. The nearly complete genome of strain 362.1 consisted of 4.4 Mbp (3989 CDS; 66.3% GC). Genomic taxonomy analysis demonstrates that the novel strain has < 83% AAI and < 29% GGDH towards its closest neighbors.
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http://dx.doi.org/10.1007/s00284-019-01674-zDOI Listing
June 2019

Metagenomics sheds light on the metabolic repertoire of oil-biodegrading microbes of the South Atlantic Ocean.

Environ Pollut 2019 Jun 6;249:295-304. Epub 2019 Mar 6.

Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address:

Unplanned oil spills during offshore oil production are a serious problem for the industry and the marine environment. Here we assess the biodegradation potential of marine microorganisms from three water depths in the Campos Basin (South Atlantic Ocean): (i) 5 m (surface), (ii) ∼80 m (chlorophyll maximum layer), and (iii) ∼1200 m (near the bottom). After incubating seawater samples with or without crude oil for 52 days, we used metagenomics and classic microbiology techniques to analyze microbial abundance and diversity, and measured physical-chemical parameters to better understand biodegradation processes. We observed increased microbial abundance and concomitant decreases in dissolved oxygen and hydrocarbon concentrations, indicating oil biodegradation in the three water depths treatments within approximately 27 days. An increase in metagenomic sequences of oil-degrading archaea, fungi, and bacteria (Alcanivorax, Alteromonas, Colwellia, Marinobacter, and Pseudomonas) accompanied by a significant increase in metagenomic sequences involved in the degradation of aromatic compounds indicate that crude oil promotes the growth of microorganisms with oil degradation potential. The abundance of genes involved in biodegrading benzene, toluene, ethylbenzene, xylene, alkanes, and poly-aromatic hydrocarbons peaked approximately 3 days after oil addition. All 12 novel metagenome-assembled genomes contained genes involved in hydrocarbon degradation, indicating the oil-degrading potential of planktonic microbes in the Campos Basin.
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http://dx.doi.org/10.1016/j.envpol.2019.03.007DOI Listing
June 2019

Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.

Sci Total Environ 2019 Mar 9;654:1209-1217. Epub 2018 Nov 9.

Núcleo Professor Rogerio Valle de Produção Sustentável-SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Instituto de Biologia, CCS, Laboratório de Microbiologia, Anexo ao Bloco A, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil. Electronic address:

To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.
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http://dx.doi.org/10.1016/j.scitotenv.2018.11.112DOI Listing
March 2019

Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection.

Sci Rep 2019 02 26;9(1):2760. Epub 2019 Feb 26.

Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA.

Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980's. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.
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http://dx.doi.org/10.1038/s41598-019-39406-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391440PMC
February 2019

Genome Sequences of sp. nov. and sp. nov., Isolated from Rhodoliths.

Microbiol Resour Announc 2018 Nov 15;7(19). Epub 2018 Nov 15.

Institute of Biologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

We report here the genome sequences of the novel isolates G62 and G98 from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62 and 4.5 Mbp (4,085 CDS) for G98. Genomic taxonomy places these new genomes into 2 new species.
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http://dx.doi.org/10.1128/MRA.01039-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256479PMC
November 2018

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.

Front Microbiol 2018 4;9:2203. Epub 2018 Oct 4.

Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 10 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.
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http://dx.doi.org/10.3389/fmicb.2018.02203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180206PMC
October 2018

Environmental conditions affect activity and associated microorganisms of marine sponges.

Mar Environ Res 2018 Nov 20;142:59-68. Epub 2018 Sep 20.

Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123. PO Box 34, Muscat, Oman; Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud 123. PO Box 50, Muscat, Oman. Electronic address:

Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.
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http://dx.doi.org/10.1016/j.marenvres.2018.09.020DOI Listing
November 2018

Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.

BMC Genomics 2018 Sep 24;19(1):701. Epub 2018 Sep 24.

Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-599, Brazil.

Background: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.

Results: Under high pCO conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO.

Conclusions: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO, providing a more comprehensive approach to OA studies by assessing the host holobiont.
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http://dx.doi.org/10.1186/s12864-018-5064-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154897PMC
September 2018

Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses.

Trends Microbiol 2018 11 21;26(11):955-965. Epub 2018 Jun 21.

Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. Electronic address:

Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
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http://dx.doi.org/10.1016/j.tim.2018.05.015DOI Listing
November 2018

Draft Genome Sequence of Muricauda sp. Strain K001 Isolated from a Marine Cyanobacterial Culture.

Genome Announc 2018 May 31;6(22). Epub 2018 May 31.

Department of Cellular Biology, Biological Sciences Institute, University of Brasília, Brasília, Brazil

We report the whole-genome sequence of sp. strain K001 isolated from a marine cyanobacterial culture. This genome sequence will improve our understanding of the influence of heterotrophic bacteria on the physiology of cyanobacteria and may contribute to the development of new natural products.
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http://dx.doi.org/10.1128/genomeA.00451-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5981047PMC
May 2018

An observational clinical case of Zika virus-associated neurological disease is associated with primary IgG response and enhanced TNF levels.

J Gen Virol 2018 07;99(7):913-916

Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.

Descriptive clinical data help to reveal factors that may provoke Zika virus (ZIKV) neuropathology. The case of a 24-year-old female with a ZIKV-associated severe acute neurological disorder was studied. The levels of ZIKV in the cerebrospinal fluid (CSF) were 50 times higher than the levels in other compartments. An acute anti-flavivirus IgG, together with enhanced TNF-alpha levels, may have contributed to ZIKV invasion in the CSF, whereas the unbiased genome sequencing [obtained by next-generation sequencing (NGS)] of the CSF revealed that no virus mutations were associated with the anatomic compartments (CSF, serum, saliva and urine).
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http://dx.doi.org/10.1099/jgv.0.001080DOI Listing
July 2018

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.

Microb Ecol 2018 Oct 15;76(3):825-838. Epub 2018 Mar 15.

Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Caixa Postal 780 - CEP13560-970, São Carlos, SP, CEP 13566-590, Brazil.

Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.
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http://dx.doi.org/10.1007/s00248-018-1172-6DOI Listing
October 2018

Occurrence of Harmful Cyanobacteria in Drinking Water from a Severely Drought-Impacted Semi-arid Region.

Front Microbiol 2018 28;9:176. Epub 2018 Feb 28.

Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.

Harmful cyanobacterial blooms have become increasingly common in freshwater ecosystems in recent decades, mainly due to eutrophication and climate change. Water becomes unreliable for human consumption. Here, we report a comprehensive study carried out to investigate the water quality of several Campina Grande reservoirs. Our approach included metagenomics, microbial abundance quantification, ELISA test for three cyanotoxins (microcystin, nodularins, and cylindrospermopsin), and ecotoxicological tests with zebrafish embryos. Cytometry analysis showed high cyanobacterial abundance, while metagenomics identified an average of 10.6% of cyanobacterial sequences, and demonstrated the presence of , , and toxin coding genes in all ponds. Zebrafish embryos reared with pond water had high mortality and diverse malformations. Among the ponds analyzed, Araçagi showed the highest lethality (an average of 62.9 ± 0.8%), followed by Boqueirão (lethality average of 62.5 ± 0.8%). Here, we demonstrate that water from ponds undergoing extremely drought conditions have an abundance of potentially harmful cyanobacteria and their toxins. Our findings are consistent with a scenario in which polluted drinking water poses a great risk to human health.
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http://dx.doi.org/10.3389/fmicb.2018.00176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5835534PMC
February 2018

Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.

Front Microbiol 2018 19;9:227. Epub 2018 Feb 19.

Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France.

The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, , which is also pathogenic to fish. Here we report the first assembly of the complete genome of CECT4600, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.
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http://dx.doi.org/10.3389/fmicb.2018.00227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5825899PMC
February 2018

Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil.

Antonie Van Leeuwenhoek 2018 Jul 18;111(7):1131-1138. Epub 2018 Jan 18.

Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.

Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67E and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47 and Alteromonas macleodii ATCC 27126. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67E and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126 and A. marina SW-47. The DNA G + C contents of PEL67E and PEL68C were 44.5%. The phenotypic features that differentiate PEL67E and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67E (= CBAS 610 = CAIM 1925).
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http://dx.doi.org/10.1007/s10482-018-1016-xDOI Listing
July 2018