scholarly journals Unraveling the Metabolic Potential of Asgardarchaeota in a Sediment from the Mediterranean Hydrocarbon-Contaminated Water Basin Mar Piccolo (Taranto, Italy)

2021 ◽  
Vol 9 (4) ◽  
pp. 859
Author(s):  
Andrea Firrincieli ◽  
Andrea Negroni ◽  
Giulio Zanaroli ◽  
Martina Cappelletti
Keyword(s):  
Archaeal Community ◽  
Hydrocarbon Biodegradation ◽  
Natural Ecosystems ◽  
Central Mediterranean ◽  
Metabolic Potential ◽  
Metabolic Role ◽  
Sequencing Studies ◽  
Terrestrial Environments ◽  
Metagenome Sequencing ◽  
Aliphatic And Aromatic Hydrocarbons

Increasing number of metagenome sequencing studies have proposed a central metabolic role of still understudied Archaeal members in natural and artificial ecosystems. However, their role in hydrocarbon cycling, particularly in the anaerobic biodegradation of aliphatic and aromatic hydrocarbons, is still mostly unknown in both marine and terrestrial environments. In this work, we focused our study on the metagenomic characterization of the archaeal community inhabiting the Mar Piccolo (Taranto, Italy, central Mediterranean) sediments heavily contaminated by petroleum hydrocarbons and polychlorinated biphenyls (PCB). Among metagenomic bins reconstructed from Mar Piccolo microbial community, we have identified members of the Asgardarchaeota superphylum that has been recently proposed to play a central role in hydrocarbon cycling in natural ecosystems under anoxic conditions. In particular, we found members affiliated with Thorarchaeota, Heimdallarchaeota, and Lokiarchaeota phyla and analyzed their genomic potential involved in central metabolism and hydrocarbon biodegradation. Metabolic prediction based on metagenomic analysis identified the malonyl-CoA and benzoyl-CoA routes as the pathways involved in aliphatic and aromatic biodegradation in these Asgardarchaeota members. This is the first study to give insight into the archaeal community functionality and connection to hydrocarbon degradation in marine sediment historically contaminated by hydrocarbons.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2139
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Yunjuan Peng ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n = 76), Denmark (n = 100), and France (n = 100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (p < 0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray–Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32, 11.67, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

scholarly journals Assessment of the Spatial Dynamics and Interactions among Multiple Ecosystem Services to Promote Effective Policy Making across Mediterranean Island Landscapes

2018 ◽  
Vol 10 (9) ◽  
pp. 3285 ◽  
Author(s):  
Roxanne Lorilla ◽  
Konstantinos Poirazidis ◽  
Stamatis Kalogirou ◽  
Vassilis Detsis ◽  
Aristotelis Martinis
Keyword(s):  
Ecosystem Services ◽  
Spatial Dynamics ◽  
Well Being ◽  
Temporal Variations ◽  
Spatial And Temporal Variation ◽  
Natural Ecosystems ◽  
Economic Resilience ◽  
Central Mediterranean ◽  
Ionian Islands ◽  
Trade Offs

To manage multiple ecosystem services (ES) effectively, it is essential to understand how the dynamics of ES maintain healthy ecosystems to avoid potential negative impacts on human well-being in the context of sustainable development. In particular, the Ionian Islands in the central Mediterranean are characterized by high natural, ecological, and recreational value; however, the intensification of human activities over time has resulted in the loss of natural ecosystems, which might have negatively impacted ES. Here, we aimed to assess and understand the spatiotemporal dynamics of ES supply and how these components interact across the Ionian Islands to optimize future ES provision and mitigate current trade-offs. We quantified multiple ecosystem services and analyzed their interactions at a temporal scale across the four prefectures of the Ionian Islands. Seven ES were quantified covering all three ES sections (provisioning, regulating and maintenance, and cultural) of the Common International Classification of Ecosystem Services (CICES). ES interactions were investigated by analyzing ES relationships, identifying ES bundles (sets of ES that repeatedly occur together across space and time), and specifying ES occurrence within bundles. The three ES groups exhibited similar patterns on some islands, but differed on islands with areas of high recreation in parallel to low provisioning and regulating ES. Temporal variations showed both stability and changes to the supply of ES, as well as in the interactions among them. Different patterns among the islands were caused by the degree of mixing between natural vegetation and olive orchards. This study identified seven ES bundles that had distinct compositions and magnitudes, with both unique and common bundles being found among the islands. The olive grove bundle delivered the most ES, while the non-vegetated bundle delivered negligible amounts of ES. Spatial and temporal variation in ES appear to be determined by agriculture, land abandonment, and increasing tourism, as well as the occurrence of fires. Knowledge about the spatial dynamics and interactions among ES could provide information for stakeholders and decision-making processes to develop appropriate sustainable management of the ecosystems on the Ionian Islands to secure ecological, social, and economic resilience.

scholarly journals Metagenomic analysis reveals rapid development of soil biota on fresh volcanic ash

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hokyung Song ◽  
Dorsaf Kerfahi ◽  
Koichi Takahashi ◽  
Sophie L. Nixon ◽  
Binu M. Tripathi ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Volcanic Ash ◽  
Rapid Development ◽  
Soil Biota ◽  
Rrna Gene ◽  
Natural Ecosystems ◽  
Soil Community ◽  
Range Of Functions ◽  
Similar Range ◽  
Metagenome Sequencing

AbstractLittle is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates across Japan and compared over 3 years, against the developed soils of surrounding natural ecosystems. DNA was extracted from mesocosms and community composition assessed using 16S rRNA gene sequences. Metagenome sequences were obtained using shotgun metagenome sequencing. While at 12 months there was insufficient DNA for sequencing, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functional genes to the developed soils, with a similar range of functions. In a surprising contrast with our hypotheses, we found that the developing ash-soil community already showed a similar gene function diversity, phylum diversity and overall relative abundances of kingdoms of life when compared to developed forest soils. The ash mesocosms also did not show any increased relative abundance of genes associated with autotrophy (rbc, coxL), nor increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources (nifH). Although gene identities and taxonomic affinities in the developing ash-soils are to some extent distinct from the natural vegetation soils, it is surprising that so many of the key components of a soil community develop already by the 24-month stage. In this system, however, rapid development may be facilitated by the relatively moderate pH of the Sakurajima ash, proximity of our mesocosms to propagule sources, and the rapid establishment of a productive bryophyte and lichen layer on the surface. Ash from other volcanoes richer in acids or more distant from propagule sources could show a different pattern and slower soil biota development.

scholarly journals Diversity and origins of anaerobic metabolism in mitochondria and related organelles

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140326 ◽  
Author(s):  
Courtney W. Stairs ◽  
Michelle M. Leger ◽  
Andrew J. Roger
Keyword(s):  
Metabolic Pathways ◽  
Anaerobic Metabolism ◽  
Low Oxygen ◽  
Metabolic Potential ◽  
Free Living ◽  
Eukaryotic Diversity ◽  
The Past ◽  
Microbial Eukaryotes ◽  
Sequencing Studies ◽  
Diversity Of Life

Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes (protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.

Effect of Dispersants on Oil Biodegradation Under Simulated Marine Conditions

1999 ◽  
Vol 1999 (1) ◽  
pp. 169-176 ◽  
Author(s):  
Richard P. J. Swannell ◽  
Fabien Daniel
Keyword(s):  
Crude Oil ◽  
Cluster Formation ◽  
Hydrocarbon Biodegradation ◽  
Dispersed Oil ◽  
Oil Biodegradation ◽  
Size Number ◽  
Degrading Bacteria ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
Micro Organisms ◽  
Neutrally Buoyant

ABSTRACT A study was undertaken on the dispersion, microbial colonisation and biodegradation of chemically-dispersed weathered Forties crude oil under simulated marine conditions in laboratory microcosms. The measurements of droplet size, number and microbial colonisation were made using new techniques developed by the project team. Rapid growth of indigenous micro-organisms capable of degrading both crude oil and dispersants was observed in the presence of chemically-dispersed oil. These organisms colonised the dispersed oil and biodegraded the aliphatic and aromatic hydrocarbons. These processes was stimulated by the addition of inorganic nutrients. Some colonised droplets agglomerated into neutrally-buoyant “clusters” (100 µm- 2 mm diameter) consisting of oil, bacteria, protozoa, and nematodes. After substantial hydrocarbon biodegradation these clusters sank to the bottom of the microcosms. No biodegradation or cluster formation was noted in “killed” controls in which biological activity had been inhibited. Different dispersants promoted microbial growth to differing extents. These results suggest that the addition of dispersants can increase the rate of oil biodegradation under natural conditions by promoting the growth of indigenous hydrocarbon-degrading bacteria, as well as increasing the surface area of oil available for microbial colonisation.

scholarly journals CANT-HYD: A curated database of phylogeny-derived Hidden Markov Models for annotation of marker genes involved in hydrocarbon degradation

2021 ◽  
Author(s):  
Varada Khot ◽  
Jackie Zorz ◽  
Daniel A Gittins ◽  
Anirban Chakraborty ◽  
Emma Bell ◽  
...  
Keyword(s):  
Markov Models ◽  
Hydrocarbon Degradation ◽  
Marker Genes ◽  
Degradation Pathways ◽  
Metabolic Potential ◽  
Accurate Identification ◽  
Isolation And Characterization ◽  
Anaerobic Hydrocarbon Degradation ◽  
Aliphatic And Aromatic Hydrocarbons

Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Furthermore, sequence homology between hydrocarbon degradation genes and genes with other functions often results in misannotation. A tool that systematically identifies hydrocarbon metabolic potential is therefore needed. We present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database containing HMMs of 37 marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we show that hydrocarbon metabolic potential is widespread in the tree of life and identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate scalability by analyzing large metagenomic datasets for the prediction of hydrocarbon utilization in diverse environments. To the best of our knowledge, CANT-HYD is the first comprehensive tool for robust and accurate identification of marker genes associated with aerobic and anaerobic hydrocarbon degradation.

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 Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils

Archaea ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Aline Belmok ◽  
Thiago Rodrigues-Oliveira ◽  
Fabyano A. C. Lopes ◽  
Heloisa S. Miranda ◽  
Ricardo H. Krüger ◽  
...  
Keyword(s):  
16S Rrna ◽  
Vegetation Structure ◽  
Archaeal Community ◽  
Fire Frequency ◽  
Sensu Stricto ◽  
Burned Area ◽  
Long Term Effects ◽  
Terrestrial Environments ◽  
Archaeal Communities

The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerradosensu strictosoils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA andamoAgenes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1cThaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higheramoAdiversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.

scholarly journals The Diversity, Composition, and Metabolic Pathways of Archaea in Pigs

2021 ◽  
Author(s):  
Feilong Deng ◽  
Yushan Li ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
Samantha Howe ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Antibiotic Resistance Genes ◽  
Alpha Diversity ◽  
Distance Matrix ◽  
Archaeal Community ◽  
Gene Families ◽  
Shannon Index ◽  
Metabolic Potential ◽  
Substantial Progress ◽  
Archaeal Communities

Archaea are an essential class of gut microorganisms in humans and animals. Despite the substantial progress in gut microbiome research in the last decade, most studies have focused on bacteria, and little is known about archaea in mammals. In this study, we investigated the composition, diversity, and functional potential of gut archaeal communities in pigs by re-analyzing a published metagenomic dataset including a total of 276 fecal samples from three countries: China (n=76), Denmark (n=100), and France (n=100). For alpha diversity (Shannon Index) of the archaeal communities, Chinese pigs were less diverse than Danish and French pigs (P&lt;0.001). Consistently, Chinese pigs also possessed different archaeal community structures from the other two groups based on the Bray-Curtis distance matrix. Methanobrevibacter was the most dominant archaeal genus in Chinese pigs (44.94%) and French pigs (15.41%), while Candidatus Methanomethylophilus was the most predominant in Danish pigs (15.71%). At the species level, the relative abundance of Candidatus Methanomethylophilus alvus, Natrialbaceae archaeon XQ INN 246, and Methanobrevibacter gottschalkii were greatest in Danish, French, and Chinese pigs with a relative abundance of 14.32%, 11.67%, and 16.28%, respectively. In terms of metabolic potential, the top three pathways in the archaeal communities included the MetaCyc pathway related to the biosynthesis of L-valine, L-isoleucine, and isobutanol. Interestingly, the pathway related to hydrogen consumption (METHANOGENESIS-PWY) was only observed in archaeal reads, while the pathways participating in hydrogen production (FERMENTATION-PWY and PWY4LZ-257) were only detected in bacterial reads. Archaeal communities also possessed CAZyme gene families, with the top five being: AA3, GH43, GT2, AA6, and CE9. In terms of antibiotic resistance genes (ARGs), the class of multidrug resistance was the most abundant ARG, accounting for 87.41% of archaeal ARG hits. Our study reveals the diverse composition and metabolic functions of archaea in pigs, suggesting that archaea might play important roles in swine nutrition and metabolism.

scholarly journals Qualitative microbiome profiling along a wastewater system in Kampala, Uganda

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pierre H. H. Schneeberger ◽  
Samuel Fuhrimann ◽  
Sören L. Becker ◽  
Joël F. Pothier ◽  
Brion Duffy ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Capital City ◽  
Human Pathogens ◽  
Sequencing Data ◽  
Natural Ecosystems ◽  
Gastrointestinal Infections ◽  
Freshwater Bodies ◽  
Microbial Analysis ◽  
Treatment Facilities ◽  
Metagenome Sequencing

AbstractKampala, the capital city of Uganda, is rapidly expanding without adequate wastewater treatment facilities to accommodate the current estimated population of 1.68 million people. Hence, freshwater bodies and natural ecosystems around the city are heavily polluted with organic and inorganic contaminants. Yet, there is a paucity of data on pathogenic microorganisms, which potentially threatens health of local communities. We performed a qualitative microbial analysis using a whole metagenome sequencing approach encompassing over 150 gigabases of sequencing data to characterize the Nakivubo wastewater system, which includes a wastewater channel and surrounding wetlands. We found that microbial diversity is heterogeneous throughout the system and that three community state types could be differentiated. We showed the presence of various waterborne agents of gastrointestinal infections in humans, which were associated with leakage occurring around two locations along the wastewater channel. Our data indicate that the microbial decontamination capacity of the local wastewater treatment facility was insufficient at the time of sampling, and that several areas of the wetlands were contaminated with human pathogens, indicating that parts of the wetlands are potentially unsafe for urban agriculture.

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