Life at the Dallol geothermal area, Ethiopia- a Planetary Field Analog on Earth

2020 ◽  
Author(s):  
Cristina Escudero ◽  
Jose M. Martínez ◽  
Nuria Rodríguez ◽  
Ricardo Amils ◽  
Felipe Gómez
Keyword(s):  
Hydrothermal System ◽  
Extreme Environment ◽  
Lower Percentage ◽  
Geothermal Area ◽  
Reduced Sulfur Compounds ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Hydrothermal Springs ◽  
Lipid Biomarker ◽  
In Situ Hybridizations

<p><strong>Introduction</strong></p><p>Dallol volcano area, proposed as a Mars analog, is considered one of the most extreme environment on Earth. It is located in the Danakil depression, a tectonically and volcanically active region in Ethiopia. The hydrothermal springs that compose the system discharge hyperacidic hot Fe-rich brines, which results in halite deposition when they contact with the atmosphere. As a result, Dallol geothermal area shows extremely high temperature (90-108°C in the springs), pH from -1.7 to 4, and supersaturated salt deposits [1-3].</p><p>Still, <em>life finds a way</em>. Despite these extreme features, microorganisms inhabiting Dallol geothermal region, as members of the class Nanohaloarchaea, have been described [3,4]. The analysis of the biodiversity that are surviving and thriving in such polyextreme system, as well as the study of their metabolic potential, could be fundamental to establish the habitability conditions to search for life on other planets.</p><p><strong>Methods</strong></p><p>We applied Shotgun metagenomics and Fluorescence in situ Hybridizations (FISH) methods to analyze the biodiversity and metabolic potential of Dallol geothermal area microbiome.</p><p><strong>Results</strong></p><p>Our results show the presence of both bacteria and archaea in the Dallol geothermal area, being Bacteria the most abundant domain in this environment. The detected microorganisms are mostly halophiles. However, there is a lower percentage of microorganisms described in extremely hot or acidic environments. FISH experiments corroborated that both bacteria and archaea are alive and active in the system.</p><p>Metagenomics analysis shows a predominance of metabolisms based on photosynthesis, heterotrophy and fermentation. In addition, metabolisms that use hydrogen and reduced sulfur compounds as an energy source stand out.</p><p>Additionally, genes related to the response to oxidative stress, heat shock, osmotic stress and detoxification have been detected, which could be involved in the adaptation of these microorganisms to the extreme conditions of the Dallol volcano area.</p><p><strong>References</strong></p><p>[1] Cavalazzi, B., et al. (2019). The Dallol geothermal area, Northern Afar (Ethiopia)—An exceptional planetary field analog on Earth. Astrobiology, 19(4), 553-578.</p><p>[2] Kotopoulou, E., et al. (2018). A polyextreme hydrothermal system controlled by iron: the case of Dallol at the Afar Triangle. ACS Earth and Space Chemistry, 3(1), 90-99.</p><p>[3] Carrizo, D., et al. (2019). Lipid Biomarker and Carbon Stable Isotope Survey on the Dallol Hydrothermal System in Ethiopia. Astrobiology, 19(12), 1474-1489.</p><p>[4] Gómez, F., et al. (2019). Ultra-small microorganisms in the polyextreme conditions of the Dallol volcano, Northern Afar, Ethiopia. Scientific reports, 9(1), 1-9.</p>

scholarly journals Mercury methylation trait dispersed across diverse anaerobic microbial guilds in a eutrophic sulfate-enriched lake

2020 ◽  
Author(s):  
Benjamin D. Peterson ◽  
Elizabeth A. McDaniel ◽  
Anna G. Schmidt ◽  
Ryan F. Lepak ◽  
Patricia Q. Tran ◽  
...  
Keyword(s):  
Water Quality ◽  
Biogeochemical Cycles ◽  
Quality Parameters ◽  
Mercury Methylation ◽  
Natural Ecosystems ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Sulfate Reducing ◽  
Polysaccharide Degradation ◽  
Glucoside Hydrolases

AbstractMercury (Hg) methylation is a microbially mediated process that converts inorganic Hg into the bioaccumulative neurotoxin methylmercury (MeHg). Exploring the diversity and metabolic potential of the dominant Hg-methylating microorganisms can provide insights into how biogeochemical cycles and water quality parameters underlie MeHg production. However, our understanding of the ecophysiology of methylators in natural ecosystems is still limited. Here, we used shotgun metagenomics paired with biogeochemical data to identify likely hotspots for MeHg production in a lake with elevated sulfate levels and characterize the microbial methylators and the flanking microbial community. Identified putative methylators were dominated by hgcA sequences divergent from those in canonical, experimentally confirmed methylators. Using genome-resolved metagenomics, these sequences were identified within genomes associated with Bacteroidetes and the recently described phylum Kiritimatiellaeota. Over half of the hgcA abundance comes from genomes corresponding to obligately fermentative organisms, many of which have a large number of glucoside hydrolases for polysaccharide degradation. Sulfate-reducing genomes encoding hgcA were also identified, but only accounted for 22% of the abundance of hgcA+ genomes. This work highlights the diverse dispersal of the methylation trait across the microbial anoxic food web.

scholarly journals Ecophysiology of the cosmopolitan OM252 bacterioplankton (Gammaproteobacteria)

2021 ◽  
Author(s):  
Emily R. Savoie ◽  
V. Celeste Lanclos ◽  
Michael W. Henson ◽  
Chuankai Cheng ◽  
Eric W. Getz ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Sequence Data ◽  
Carbon Sources ◽  
Growth Dynamics ◽  
Distinct Species ◽  
Reduced Sulfur Compounds ◽  
Metabolic Potential ◽  
Phenotypic Data ◽  
Representative Strain ◽  
Marine Microbial Communities

AbstractAmong the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus (Candidatus Halomarinus), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors, with subclade I genomes encoding the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance but a mesophilic temperature range for growth, with a maximum of 0.36 doublings/hr at 35°C. Cells were curved rod/spirillum-shaped, ~1.5 × 0.2 μm. Growth on thiosulfate as the sole electron donor under autotrophic conditions was roughly one third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some Ca. Halomarinus organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur.ImportanceMarine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic datasets, we examined the diversity within the OM252 clade, the distribution of these taxa in the world’s oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point towards the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly “heterotrophic” taxa.

scholarly journals Influence of taxonomic and functional content of microbial communities on the quality of fermented cocoa pulp-bean mass

2021 ◽  
Author(s):  
Jatziri Mota-Gutierrez ◽  
Ilario Ferrocino ◽  
Manuela Giordano ◽  
Mirna Leonor Suarez-Quiroz ◽  
Oscar Gonzalez-Ríos ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbiological Quality ◽  
Chemical Properties ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Fermentation Time ◽  
Physico Chemical ◽  
The Difference ◽  
The Impact

The microbial metabolism drives the changes in the physico-chemical properties and consequently the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function and metabolic potential of microbial communities’ present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physico-chemical, microbiological, quality and sensory analysis to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavours. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri and Acetobacter pasteurianus were the most prevalent. The fermentation time and roasting are the most important determinants of cocoa quality while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is an urgent need for developing fermentation protocols according to regions, countries and cocoa varieties to guarantee safety and desirable flavour development. Importance. Monitoring the composition, structure, functionalities and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.

scholarly journals Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
L. V. Alteio ◽  
F. Schulz ◽  
R. Seshadri ◽  
N. Varghese ◽  
W. Rodriguez-Reillo ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Single Cell ◽  
Forest Soil ◽  
Carbon Metabolism ◽  
Cell Sorting ◽  
Phylogenetic Diversity ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Rare Biosphere ◽  
Depth Analysis

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes. Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

scholarly journals Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

2016 ◽  
Vol 82 (17) ◽  
pp. 5186-5196 ◽  
Author(s):  
Federico M. Ibarbalz ◽  
Esteban Orellana ◽  
Eva L. M. Figuerola ◽  
Leonardo Erijman
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
Activated Sludge ◽  
Functional Categories ◽  
Community Structures ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Wastewater Treatment Systems ◽  
Influent Wastewater ◽  
Gc Contents

ABSTRACTThis study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols.IMPORTANCEThis work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.

scholarly journals Metagenomic insights into the metabolism and ecologic functions of the widespread DPANN archaea from deep-sea hydrothermal vents

2020 ◽  
Author(s):  
Ruining Cai ◽  
Jing Zhang ◽  
Rui Liu ◽  
Chaomin Sun
Keyword(s):  
Genome Size ◽  
Deep Sea ◽  
Hydrothermal System ◽  
Hydrothermal Vents ◽  
De Novo ◽  
Extreme Environment ◽  
Acid Synthesis ◽  
Amino Acid Synthesis ◽  
Ecological Roles ◽  
Hydrothermal Environment

ABSTRACTDue to the particularity of metabolism and the importance of ecological roles, the archaea living in deep-sea hydrothermal system always attract great attention. Included, the DPANN superphylum archaea, which are massive radiation of organisms, distribute widely in hydrothermal environment, but their metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes comprised in 43 reconstructed genomes from deep-sea hydrothermal sediments, presenting high abundance in the archaea kingdom. Phylogenetic analysis shows 6 phyla comprising Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota and a new candidate phylum designated DPANN-HV-2 are included in the 20 DPANN archaeal members, indicating their wide diversity in this extreme environment. Metabolic analysis presents their metabolic deficiencies because of their reduced genome size, such as gluconeogenesis, de novo nucleotide and amino acid synthesis. However, they possess alternative and economical strategies to fill this gap. Furthermore, they were detected to have multiple capacities of assimilating carbon dioxide, nitrogen and sulfur compounds, suggesting their potentially important ecologic roles in the hydrothermal system.IMPORTANCEDPANN archaea show high distribution in the hydrothermal system. However, they possess small genome size and some incomplete biological process. Exploring their metabolism is helpful to know how such small lives adapt to this special environment and what ecological roles they play. It was ever rarely noticed and reported. Therefore, in this study, we provide some genomic information about that and find their various abilities and potential ecological roles. Understanding their lifestyles is helpful for further cultivating, exploring deep-sea dark matters and revealing microbial biogeochemical cycles in this extreme environment.

scholarly journals A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaochen Yin ◽  
Tomer Altman ◽  
Erica Rutherford ◽  
Kiana A. West ◽  
Yonggan Wu ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Diagnosis ◽  
Therapeutic Drug ◽  
Resonance Spectroscopy ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Human Gut ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Prediction Approach

Metabolomic analyses of human gut microbiome samples can unveil the metabolic potential of host tissues and the numerous microorganisms they support, concurrently. As such, metabolomic information bears immense potential to improve disease diagnosis and therapeutic drug discovery. Unfortunately, as cohort sizes increase, comprehensive metabolomic profiling becomes costly and logistically difficult to perform at a large scale. To address these difficulties, we tested the feasibility of predicting the metabolites of a microbial community based solely on microbiome sequencing data. Paired microbiome sequencing (16S rRNA gene amplicons, shotgun metagenomics, and metatranscriptomics) and metabolome (mass spectrometry and nuclear magnetic resonance spectroscopy) datasets were collected from six independent studies spanning multiple diseases. We used these datasets to evaluate two reference-based gene-to-metabolite prediction pipelines and a machine-learning (ML) based metabolic profile prediction approach. With the pre-trained model on over 900 microbiome-metabolome paired samples, the ML approach yielded the most accurate predictions (i.e., highest F1 scores) of metabolite occurrences in the human gut and outperformed reference-based pipelines in predicting differential metabolites between case and control subjects. Our findings demonstrate the possibility of predicting metabolites from microbiome sequencing data, while highlighting certain limitations in detecting differential metabolites, and provide a framework to evaluate metabolite prediction pipelines, which will ultimately facilitate future investigations on microbial metabolites and human health.

scholarly journals Lipid Biomarker and Carbon Stable Isotope Survey on the Dallol Hydrothermal System in Ethiopia

Astrobiology ◽  
2019 ◽  
Vol 19 (12) ◽  
pp. 1474-1489 ◽  
Author(s):  
Daniel Carrizo ◽  
Laura Sánchez-García ◽  
Nuria Rodriguez ◽  
Felipe Gómez
Keyword(s):  
Stable Isotope ◽  
Hydrothermal System ◽  
Carbon Stable Isotope ◽  
Lipid Biomarker

scholarly journals Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Christian Milani ◽  
Giulia Alessandri ◽  
Leonardo Mancabelli ◽  
Marta Mangifesta ◽  
Gabriele Andrea Lugli ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Host Species ◽  
Taxonomic Composition ◽  
Tree Of Life ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Fecal Samples ◽  
Functional Features ◽  
Host Physiology ◽  
The Impact

ABSTRACT In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host’s diet. IMPORTANCE Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.

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