| 1. |
- Giongo, Adriana, et al.
(författare)
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Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams
- 2020
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Ingår i: Heliyon. - : Elsevier. - 2405-8440. ; 6:8, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m(3) of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities' structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.
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| 2. |
- 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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
- Proenca, Audrey Menegaz, et al.
(författare)
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Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates
- 2022
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Ingår i: Archives of Microbiology. - : Springer. - 0302-8933 .- 1432-072X. ; 204:4
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Tidskriftsartikel (refereegranskat)abstract
- Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.
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| 7. |
- Rocchetti, Giulia Albani, et al.
(författare)
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Selecting the best candidates for resurrecting extinct-in-the-wild plants from herbaria
- 2022
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Ingår i: Nature Plants. - : Springer Science and Business Media LLC. - 2055-0278. ; 8:12, s. 1385-1393
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Tidskriftsartikel (refereegranskat)abstract
- Resurrecting extinct species is a fascinating and challenging idea for scientists and the general public. Whereas some theoretical progress has been made for animals, the resurrection of extinct plants (de-extinction sensu lato) is a relatively recently discussed topic. In this context, the term ‘de-extinction’ is used sensu lato to refer to the resurrection of ‘extinct in the wild’ species from seeds or tissues preserved in herbaria, as we acknowledge the current impossibility of knowing a priori whether a herbarium seed is alive and can germinate. In plants, this could be achieved by germinating or in vitro tissue-culturing old diaspores such as seeds or spores available in herbarium specimens. This paper reports the first list of plant de-extinction candidates based on the actual availability of seeds in herbarium specimens of globally extinct plants. We reviewed globally extinct seed plants using online resources and additional literature on national red lists, resulting in a list of 361 extinct taxa. We then proposed a method of prioritizing candidates for seed-plant de-extinction from diaspores found in herbarium specimens and complemented this with a phylogenetic approach to identify species that may maximize evolutionarily distinct features. Finally, combining data on seed storage behaviour and longevity, as well as specimen age in the novel ‘best de-extinction candidate’ score (DEXSCO), we identified 556 herbarium specimens belonging to 161 extinct species with available seeds. We expect that this list of de-extinction candidates and the novel approach to rank them will boost research efforts towards the first-ever plant de-extinction.
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