| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Braga, R., et al.
(författare)
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Modelling methane hydrate stability changes and gas release due to seasonal oscillations in bottom water temperatures on the Rio Grande cone, offshore southern Brazil
- 2020
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Ingår i: Marine and Petroleum Geology. - : Elsevier. - 0264-8172 .- 1873-4073. ; 112, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- The stability of methane hydrates on continental margins worldwide is sensitive to changes in temperature and pressure conditions. It has been shown how gradual increases in bottom water temperatures due to ocean warming over post-glacial timescales can destabilize shallow oceanic hydrate deposits, causing their dissociation and gas release into the ocean. However, bottom water temperatures (BWT) may also vary significantly over much shorter timescales, including due to seasonal temperature oscillations of the ocean bottom currents. In this study, we investigate how a shallow methane hydrate deposit responds to seasonal BWT oscillations with an amplitude of up to 1.5 °C. We use the TOUGH + HYDRATE code to model changes in the methane hydrate stability zone (MHSZ) using data from the Rio Grande Cone, in the South Atlantic Ocean off the Brazilian coast. In all the cases studied, BWT oscillations resulted in significant gaseous methane fluxes into the ocean for up to 10 years, followed by a short period of small fluxes of gaseous methane into the ocean, until they stopped completely. On the other hand, aqueous methane was released into the ocean during the 100 years simulated, for all the cases studied. During the temperature oscillations, the MHSZ recedes continuously both horizontally and, in a smaller scale, vertically, until a permanent and a seasonal region in MHSZ are defined. Sensitivity tests were carried out for parameters of porosity, thermal conductivity and initial hydrate saturation, which were shown to play an important role on the volume of methane released into the ocean and on the time interval in which such release occurs. Overall, the results indicate that in a system with no gas recharge from the bottom, seasonal temperature oscillations alone cannot account for long-term gas release into the ocean.
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| 3. |
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| 4. |
- Giongo, Adriana, et al.
(författare)
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Discovery of a chemosynthesis-based community in the western South Atlantic Ocean
- 2016
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Ingår i: Deep Sea Research Part I. - : Elsevier. - 0967-0637 .- 1879-0119. ; 112, s. 45-56
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Tidskriftsartikel (refereegranskat)abstract
- Chemosynthetic communities have been described from a variety of deep-sea environments across the world's oceans. They constitute very interesting biological systems in terms of their ecology, evolution and biogeography, and also given their potential as indicators of the presence and abundance of consistent hydrocarbon-based nutritional sources. Up to now such peculiar biotic assemblages have not been reported for the western South Atlantic Ocean, leaving this large region undocumented with respect to the presence, composition and history of such communities. Here we report on the presence of a chemosynthetic community off the coast of southern Brazil, in an area where high-levels of methane and the presence of gas hydrates have been detected. We performed metagenomic analyses of the microbial community present at this site, and also employed molecular approaches to identify components of its benthic fauna. We conducted phylogenetic analyses comparing the components of this assemblage to those found elsewhere in the world, which allowed a historical assessment of the structure and dynamics of these systems. Our results revealed that the microbial community at this site is quite diverse, and contains many components that are very closely related to lineages previously sampled in ecologically similar environments across the globe. Anaerobic methanotrophic (ANME) archaeal groups were found to be very abundant at this site, suggesting that methane is indeed an important source of nutrition for this community. In addition, we document the presence at this site of a vestimentiferan siboglinid polychaete and the bivalve Acharax sp., both of which are typical components of deep-sea chemosynthetic communities. The remarkable similarity in biotic composition between this area and other deep-sea communities across the world supports the interpretation that these assemblages are historically connected across the global oceans, undergoing colonization from distant sites and influenced by local ecological features that select a stereotyped suite of specifically adapted organisms. (C) 2015 Elsevier Ltd. All rights reserved.
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| 5. |
- Giongo, Adriana, et al.
(författare)
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Distinct deep subsurface microbial communities in two sandstone units separated by a mudstone layer
- 2020
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Ingår i: Geosciences Journal. - : Springer. - 1226-4806 .- 1598-7477. ; 24, s. 267-274
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Tidskriftsartikel (refereegranskat)abstract
- Deep subsurface microbial communities are more abundant in coarse-grained sedimentary rocks such as sandstones than in fine-grained mudstones. The low porosity and low permeability of mudstones are believed to restrict microbial life. Then, it is expected that distinct, isolated microbial communities may form in sandstones separated by mudstones. In this context, the connectivity between microbial communities in different sandstone units can be investigated to infer evolutionary patterns of diversification in space-time, which may potentially contribute with relevant data for analyses of hydraulic connectivity and stratigraphic correlation. In this work, we used high throughput DNA sequencing of a ribosomal 16S gene fragment to characterize the prokaryotic communities found in Permian sandstone samples of the same core that are separated by one mudstone interval, in the Charqueadas coal field, Parana Basin (Southern Brazil). Our samples were collected at ∌300 m deep, in porous sandstones separated by a thick mudstone package. Differences in the bacterial community structure between samples were observed for the classified OTUs, from phylum to genus. Molecular biology might be further applied as a possible tool to help to understand the spatial and temporal distribution of depositional facies, and the efficiency of low permeability rocks to compartmentalize reservoirs. Ongoing studies aim to extend the present investigation into further analyses regarding lateral changes in microbial communities present in the same sandstone units.
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| 6. |
- Ketzer, João Marcelo, et al.
(författare)
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Gas hydrate dissociation linked to contemporary ocean warming in the southern hemisphere
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- Ocean warming related to climate change has been proposed to cause the dissociation of gas hydrate deposits and methane leakage on the seafloor. This process occurs in places where the edge of the gas hydrate stability zone in sediments meets the overlying warmer oceans in upper slope settings. Here we present new evidence based on the analysis of a large multi-disciplinary and multi-scale dataset from such a location in the western South Atlantic, which records massive gas release to the ocean. The results provide a unique opportunity to examine ocean-hydrate interactions over millennial and decadal scales, and the first evidence from the southern hemisphere for the effects of contemporary ocean warming on gas hydrate stability. Widespread hydrate dissociation results in a highly focused advective methane flux that is not fully accessible to anaerobic oxidation, challenging the assumption that it is mostly consumed by sulfate reduction before reaching the seafloor.
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| 7. |
- Ketzer, João Marcelo, et al.
(författare)
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Gas Hydrate Systems on the Brazilian Continental Margin
- 2022
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Ingår i: World Atlas of Submarine Gas Hydrates in Continental Margins. - Cham : Springer. - 9783030811853 - 9783030811860 ; , s. 343-352
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Bokkapitel (refereegranskat)abstract
- The existence of gas hydrate systems along Brazil’s vast continental margin has been known since the 1980s, based on observations of bottom simulating reflectors (BSRs) in two large shelf-slope depocenters: (1) the Amazon deep-sea fan in the Foz do Amazonas Basin and (2) Rio Grande Cone in Pelotas Basin. These depocenters are both undergoing gravitational collapse above deep detachment surfaces, resulting in upslope extensional and downslope compressional domains. The BSR is discontinuous across the Amazon deep-sea fan, mainly observed at water depths of 600–2800 m and at anticlines within an upper slope thrust-fold belt related to the compressional domain of the fan. Conversely, a fairly continuous BSR extends across Rio Grande Cone at water depths of 520–3500 m, within both extensional and compressional domains. Interestingly, the well-defined BSR that spans Rio Grande Cone rises to meet the seafloor at water depths of 515–520 m, forming an unusual ‘BSR outcrop’. This phenomenon has been observed previously in only a few locations worldwide. Gas hydrates have been recovered within piston cores taken from seafloor seeps in both depocenters, and analyses reveal that gas is dominated by methane of microbial origin.
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| 8. |
- Ketzer, João Marcelo, et al.
(författare)
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Gas Seeps at the Edge of the Gas Hydrate Stability Zone on Brazil’s Continental Margin
- 2019
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Ingår i: Geosciences. - : MDPI. - 2076-3263. ; 9:5, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Gas hydrate provinces occur in two sedimentary basins along Brazil’s continental margin: (1) The Rio Grande Cone in the southeast, and (2) the Amazon deep-sea fan in the equatorial region. The occurrence of gas hydrates in these depocenters was first detected geophysically and has recently been proven by seafloor sampling of gas vents, detected as water column acoustic anomalies rising from seafloor depressions (pockmarks) and/or mounds, many associated with seafloor faults formed by the gravitational collapse of both depocenters. The gas vents include typical features of cold seep systems, including shallow sulphate reduction depths (<4 m), authigenic carbonate pavements, and chemosynthetic ecosystems. In both areas, gas sampled in hydrate and in sediments is dominantly formed by biogenic methane. Calculation of the methane hydrate stability zone for water temperatures in the two areas shows that gas vents occur along its feather edge (water depths between 510 and 760 m in the Rio Grande Cone and between 500 and 670 m in the Amazon deep-sea fan), but also in deeper waters within the stability zone. Gas venting along the feather edge of the stability zone could reflect gas hydrate dissociation and release to the oceans, as inferred on other continental margins, or upward fluid flow through the stability zone facilitated by tectonic structures recording the gravitational collapse of both depocenters. The potential quantity of venting gas on the Brazilian margin under different scenarios of natural or anthropogenic change requires further investigation. The studied areas provide natural laboratories where these critical processes can be analyzed and quantified.
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| 9. |
- Medina-Silva, Renata, et al.
(författare)
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Microbial diversity from chlorophyll maximum, oxygen minimum and bottom zones in the southwestern Atlantic Ocean
- 2018
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Ingår i: Journal of Marine Systems. - : Elsevier. - 0924-7963 .- 1879-1573. ; 178, s. 52-61
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Tidskriftsartikel (refereegranskat)abstract
- Conspicuous physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deeper zones as well as moving deeper water masses up towards shallower depths. Water samples within a 50-km radius in a pockmark location of the southwestern Atlantic Ocean were collected and the prokaryotic communities from different water depths - chlorophyll maximum, oxygen minimum and deep-sea bottom (down to 1355 m) - were described. At phylum level, Proteobacteria were the most frequent in all water depths, Cyanobacteria were statistically more frequent in chlorophyll maximum zone, while Thaumarchaeota were significantly more abundant in both oxygen minimum and bottom waters. The most frequent microorganism in the chlorophyll maximum and oxygen minimum zones was a Pelagibacteraceae operational taxonomic unit (OTU). At the bottom, the most abundant genus was the archaeon Nitrosopurnilus. Beta diversity analysis of the 16S rRNA gene sequencing data uncovered in this study shows high spatial hetero-geneity among water zones communities. Our data brings important contribution for the characterisation of oceanic microbial diversity, as it consists of the first description of prokaryotic communities occurring in different oceanic water zones in the southwestern Atlantic Ocean.
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| 10. |
- Medina-Silva, Renata, et al.
(författare)
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Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water
- 2017
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Ingår i: Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 111:4, s. 533-550
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Tidskriftsartikel (refereegranskat)abstract
- As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the ‘Vestimentifera’ clade containing specialists that depend on microbial chemosynthetic endosymbionts for nutrition. Little information exists concerning the microbiota of the external portion of the vestimentiferan trunk wall. We employed 16S rDNA-based metabarcoding to describe the external microbiota of the chitin tubes from the vestimentiferan Escarpia collected from a chemosynthetic community in a cold seep area at the southwestern Atlantic Ocean. The most abundant operational taxonomic unit (OTU) belonged to the family Pirellulaceae (phylum Planctomycetes), and the second most abundant OTU belonged to the order Methylococcales (phylum Proteobacteria), composing an average of 21.1 and 15.4% of the total reads on tubes, respectively. These frequencies contrasted with those from the surrounding environment (sediment and water), where they represent no more than 0.1% of the total reads each. Moreover, some taxa with lower abundances were detected only in Escarpia tube walls. These data constitute on the first report of an epibiont microbial community found in close association with external surface of a cold-seep metazoan, Escarpia sp., from a chemosynthetic community in the southwestern Atlantic Ocean.
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