Biology subjects

Bendia, A. G.

Publications and source records attributed to Bendia, A. G..

5 recordsLinked to original sources

bioRxiv2021

Deep-sea plastisphere: long-term colonization by plastic-associated bacterial and archaeal communities in the Southwest Atlantic Ocean

Marine plastic pollution is a global concern because of continuous release into the oceans over the last several decades. Although recent studies have made efforts to characterize the so-called plastisphere, or microbial community inhabiting plastic substrates, it is not clear whether the plastisphere is defined as a core community or as a random attachment of microbial cells. Likewise, little is known about the influence of the deep-sea environment on the plastisphere. In our experimental study, we evaluated the microbial colonization on polypropylene pellets and two types of plastic bags: regular high density polyethylene (HDPE) and HDPE with the oxo-biodegradable additive BDA. Gravel was used as control. Samples were deployed at three sites at 3,300 m depth in the Southwest Atlantic Ocean and left for microbial colonization for 719 days. For microbial communities analysis, DNA was extracted from the biofilm on plastic and gravel substrates, and then the 16S rRNA was sequenced through the Illumina Miseq platform. Cultivation was performed to isolate strains from the plastic and gravel substrates. Substrate type strongly influenced the microbial composition and structure, while no difference between sites was detected. Although several taxa were shared among plastics, we observed some groups specific for each plastic substrate. These communities comprised taxa previously reported from both epipelagic zones and deep-sea benthic ecosystems. The core microbiome (microbial taxa shared by all plastic substrates) was exclusively composed by low abundance taxa, with some members well-described in the plastisphere and with known plastic-degradation capabilities. Additionally, we obtained bacterial strains that have been previously reported inhabiting plastic substrates and/or degrading hydrocarbon compounds, which corroborates our metabarcoding data and suggests the presence of microbial members potentially active and involved with degradation of these plastics in the deep sea.

microbiology↗

bioRxiv2020

BATHYARCHAEOTA OCCURRENCE IN SHALLOW MARINE METHANE-RICH SEDIMENTS (SACO DO MAMANGUA, RIO DE JANEIRO, BRAZIL)

Methane gas (CH4) reservoirs have previously been reported in tropical marine sediments of Saco do Mamangua ria (Rio de Janeiro, Brazil). It is known that a methane microbiome can be established in methane seeps sites; however, they are still poorly characterised. In this study, we aimed to investigate the spatial and vertical distribution of the bacterial and archaeal composition and the community structure in the sediments of Saco do Mamangua ria. For this purpose, we collected sediment samples through 100 cm long gravity corer at three different sites and performed community analysis based on 16S rRNA gene sequencing, quantification of the methyl coenzyme M reductase-encoding gene (mcrA) and geochemical analysis, including CH4 stable isotope. Our results revealed a biogenic trend for CH4 isotopic signature and a high proportion of archaeal sequences assigned as Bathyarchaeota, with a spatial distribution throughout the inner areas of the channel and the deepest strata. OTUs classified within Bathyarchaeota and Chloroflexi (Dehalococcoidia) showed positive correlation with methane concentrations, sediment depth and oxidation-reduction potential. Due to their prevalence in the microbial community, we also performed phylogenetic analysis to understand the closeness of our Bathyarchaeota OTUs with Bathyarchaeota subgroups, and the results demonstrated a close relationship particularly with Bathy-8 and Bathy-13, which possess genes for acetogenesis and methanogenesis. Although direct relations between microbial populations and the biogenic methane emissions in Saco do Mamangua cannot be assured, our results emphasize the importance of further investigations about the potential role of Bathyarchaeota in the carbon cycling in methane-rich tropical shallow ecosystems.

microbiology↗

bioRxiv2020

Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica

Active volcanoes in Antarctica, in contrast to the rest of the icy landscape, have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers (<0 {degrees}C) and active fumaroles (up to 100 {degrees}C). Steep gradients in temperature, salinity and geochemistry over very short distances have been reported for Deception Island, and have been shown to effect microbial community structure and diversity. However, little is known regarding how these gradients affect ecosystem functioning, for example due to inhibition of key metabolic enzymes or pathways. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore how microbial functional diversity is shaped by extreme geochemical, salinity and temperature gradients in fumarole and glacier sediments. We observed that microbial communities from a 98 {degrees}C fumarole harbor specific hyperthermophilic molecular strategies, as well as reductive and autotrophic pathways, while those from <80 {degrees}C fumaroles possess more diverse metabolic and survival strategies capable of responding to fluctuating redox and temperature conditions. In contrast, glacier communities showed less diverse metabolic potentials, comprising mainly heterotrophic and carbon pathways. Through the reconstruction of genomes, we were able to clarify putative novel lifestyles of underrepresented taxonomic groups, especially those related to Nanoarchaeota and thermophilic ammonia-oxidizing archaeal lineages. Our results enhance understanding of the metabolic and survival capabilities of different extremophilic lineages of Bacteria and Archaea.

microbiology↗

bioRxiv2020

Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars

Although several studies have explored microbial communities in different terrestrial subsurface ecosystems, little is known about the diversity of their metabolic processes and survival strategies. The advance of bioinformatic tools is allowing the description of novel and not-yet cultivated microbial lineages in different ecosystems, due to the genome reconstruction approach from metagenomic data. The recovery of genomes has the potential of revealing novel lifestyles, metabolic processes and ecological roles of microorganisms, mainly in ecosystems that are largely unknown, and in which cultivation could be not viable. In this study, through shotgun metagenomic data, it was possible to reconstruct several genomes of cultivated and not-yet cultivated prokaryotic lineages from a quartzite cave, located in Minas Gerais state, Brazil, which showed to possess a high diversity of genes involved with different biogeochemical cycles, including reductive and oxidative pathways related to carbon, sulfur, nitrogen and iron. Tree genomes were selected, assigned as Truepera sp., Ca. Methylomirabilis sp. and Ca. Koribacter sp. based on their lifestyles (radiation resistance, anaerobic methane oxidation and potential iron oxidation) for pangenomic analysis, which exhibited genes involved with different DNA repair strategies, starvation and stress response. Since these groups have few reference genomes deposited in databases, our study adds important genomic information about these lineages. The combination of techniques applied in this study allowed us to unveil the potential relationships between microbial genomes and their ecological processes with the cave mineralogy, as well as to discuss their implications for the search for extant lifeforms outside our planet, in silica- and iron-rich environments, especially on Mars.

microbiology↗

bioRxiv2020

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial community based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. We observed differences of microbial structure according to the sampling location and depth, suggesting an influence of water circulation and availability of particulate organic matter. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Nitrosopumilus within Thaumarchaeota group were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i. e. Ca. Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

microbiology↗