Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.

The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.

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

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.

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

Description of a Gram-negative, motile, circular-shaped bacterial strain, designated A511T 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 A511T (= CBAS 712T = CAIM 1939T) 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.

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

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.

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

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.

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

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%.

Halomonas coralii sp. nov. Isolated from Mussismilia braziliensis.

We report here the novel species Halomonas coralii. The nearly complete genome of strain 362.1T 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.

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

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-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L-1). 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.

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

On November 5th, 2015, the Fundão dam rupture released >50 million m3 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.

Genome Sequences of Vibrio maerlii sp. nov. and Vibrio rhodolitus sp. nov., Isolated from Rhodoliths.

We report here the genome sequences of the novel isolates G62T and G98T from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62T and 4.5 Mbp (4,085 CDS) for G98T. Genomic taxonomy places these new genomes into 2 new species.

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

Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67ET and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47T and Alteromonas macleodii ATCC 27126T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67ET 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 27126T and A. marina SW-47T. The DNA G + C contents of PEL67ET and PEL68C were 44.5%. The phenotypic features that differentiate PEL67ET 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 ß-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67ET (= CBAS 610T = CAIM 1925T).

Quantitative Detection of Active Vibrios Associated with White Plague Disease in Mussismilia braziliensis Corals.

Over recent decades several coral diseases have been reported as a significant threat to coral reef ecosystems causing the decline of corals cover and diversity around the world. The development of techniques that improve the ability to detect and quantify microbial agents involved in coral disease will aid in the elucidation of disease cause, facilitating coral disease detection and diagnosis, identification and pathogen monitoring, pathogen sources, vectors, and reservoirs. The genus Vibrio is known to harbor pathogenic strains to marine organisms. One of the best-characterized coral pathogens is Vibrio coralliilyticus, an aetilogic agent of White Plague Disease (WPD). We used Mussismilia coral tissue (healthy and diseased specimens) to develop a rapid reproducible detection system for vibrios based on RT-QPCR and SYBR chemistry. We were able to detect total vibrios in expressed RNA targeting the 16S rRNA gene at 5.23 × 106 copies/µg RNA and V. coralliilyticus targeting the pyrH gene at 5.10 × 103 copies/µg RNA in coral tissue. Detection of V. coralliilyticus in diseased and in healthy samples suggests that WPD in the Abrolhos Bank may be caused by a consortium of microorganism and not only a single pathogen. We developed a more practical and economic system compared with probe uses for the real-time detection and quantification of vibrios from coral tissues by using the 16S rRNA and pyrH gene. This qPCR assay is a reliable tool for the monitoring of coral pathogens, and can be useful to prevent, control, or reduce impacts in this ecosystem.

Aura-biomes are present in the water layer above coral reef benthic macro-organisms.

As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific "aura-biome". The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.

Draft Genome Sequence of Pseudoalteromonas sp. Strain PAB 2.2 Isolated from Abrolhos Bank (Brazil).

We present here the draft genome sequence of Pseudoalteromonas sp. strain PAB 2.2, isolated from water of Parcel de Abrolhos coral reef (17°57'32.7″; 38°30'20.3″), on Abrolhos Bank, at a depth of 12 m. The assembly consists of 4,434,635 bp and contains 40 contigs, with a G+C content of 41.60%.

Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensis.

Infectious diseases such as white plague syndrome (WPS) and black band disease (BBD) have caused massive coral loss worldwide. We performed a metaproteomic study on the Abrolhos coral Mussismilia braziliensis to define the types of proteins expressed in healthy corals compared to WPS- and BBD-affected corals. A total of 6363 MS/MS spectra were identified as 361 different proteins. Healthy corals had a set of proteins that may be considered markers of holobiont homoeostasis, including tubulin, histone, Rab family, ribosomal, peridinin-chlorophyll a-binding protein, F0F1-type ATP synthase, alpha-iG protein, calmodulin and ADP-ribosylation factor. Cnidaria proteins found in healthy M. braziliensis were associated with Cnidaria-Symbiodinium endosymbiosis and included chaperones (hsp70, hsp90 and calreticulin), structural and membrane modelling proteins (actin) and proteins with functions related to intracellular vesicular traffic (Rab7 and ADP-ribosylation factor 1) and signal transduction (14-3-3 protein and calmodulin). WPS resulted in a clear shift in the predominance of proteins, from those related to aerobic nitrogen-fixing bacteria (i.e. Rhizobiales, Sphingomonadales and Actinomycetales) in healthy corals to those produced by facultative/anaerobic sulphate-reducing bacteria (i.e. Enterobacteriales, Alteromonadales, Clostridiales and Bacteroidetes) in WPS corals. BBD corals developed a diverse community dominated by cyanobacteria and sulphur cycle bacteria. Hsp60, hsp90 and adenosylhomocysteinase proteins were produced mainly by cyanobacteria in BBD corals, which is consistent with elevated oxidative stress in hydrogen sulphide- and cyanotoxin-rich environments. This study demonstrates the usefulness of metaproteomics for gaining better comprehension of coral metabolic status in health and disease, especially in reef systems such as the Abrolhos that are suffering from the increase in global and local threatening events.

Multiple Symbiodinium Strains Are Hosted by the Brazilian Endemic Corals Mussismilia spp.

Corals of genus Mussismilia (Mussidae) are one of the oldest extant clades of scleractinians. These Neogene relicts are endemic to the Brazilian coast and represent the main reef-building corals in the Southwest Atlantic Ocean (SAO). The relatively low-diversity/high-endemism SAO coralline systems are under rapid decline from emerging diseases and other local and global stressors, but have not been severely affected by coral bleaching. Despite the biogeographic significance and importance for understanding coral resilience, there is scant information about the diversity of Symbiodinium in this ocean basin. In this study, we established the first culture collections of Symbiodinium from Mussismilia hosts, comprising 11 isolates, four of them obtained by fluorescent-activated cell sorting (FACS). We also analyzed Symbiodinium diversity directly from Mussismilia tissue samples (N = 16) and characterized taxonomically the cultures and tissue samples by sequencing the dominant ITS2 region. Symbiodinium strains A4, B19, and C3 were detected. Symbiodinium C3 was predominant in the larger SAO reef system (Abrolhos), while Symbiodinium B19 was found only in deep samples from the oceanic Trindade Island. Symbiodinium strains A4 and C3 isolates were recovered from the same Mussismilia braziliensis coral colony. In face of increasing threats, these results indicate that Symbiodinium community dynamics shall have an important contribution for the resilience of Mussismilia spp. corals.

Microbiota of the major South Atlantic reef building coral Mussismilia.

The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation.

Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis.

Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.

Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals.

Coral health is under threat throughout the world due to regional and global stressors. White plague disease (WP) is one of the most important threats affecting the major reef builder of the Abrolhos Bank in Brazil, the endemic coral Mussismilia braziliensis. We performed a metagenomic analysis of healthy and WP-affected M. braziliensis in order to determine the types of microbes associated with this coral species. We also optimized a protocol for DNA extraction from coral tissues. Our taxonomic analysis revealed Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinomycetes as the main groups in all healthy and WP-affected corals. Vibrionales, members of the Cytophaga-Flavobacterium-Bacteroides complex, Rickettsiales, and Neisseriales were more abundant in the WP-affected corals. Diseased corals also had more eukaryotic metagenomic sequences identified as Alveolata and Apicomplexa. Our results suggest that WP disease in M. braziliensis is caused by a polymicrobial consortium.