scholarly journals Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent

2020 ◽  
Author(s):  
Sushmita Patwardhan ◽  
Francesco Smedile ◽  
Donato Giovannelli ◽  
Costantino Vetriani
Keyword(s):  
Shallow Water ◽  
Sulfide Oxidation ◽  
Taxonomic Composition ◽  
Nitrate Respiration ◽  
Metabolic Potential ◽  
Microbial Biofilms ◽  
Main Carbon Source ◽  
Two Stages ◽  
Active Venting ◽  
Water Gas

AbstractTor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2, H2S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO2 the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.

scholarly journals Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent

2021 ◽  
Vol 12 ◽  
Author(s):  
Sushmita Patwardhan ◽  
Francesco Smedile ◽  
Donato Giovannelli ◽  
Costantino Vetriani
Keyword(s):  
Shallow Water ◽  
Sulfide Oxidation ◽  
Taxonomic Composition ◽  
Nitrate Respiration ◽  
Metabolic Potential ◽  
Microbial Biofilms ◽  
Main Carbon Source ◽  
Two Stages ◽  
Active Venting ◽  
Water Gas

Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2 and H2S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO2 the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.

scholarly journals Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments

2020 ◽  
Author(s):  
Xiyang Dong ◽  
Jayne E. Rattray ◽  
D. Calvin Campbell ◽  
Jamie Webb ◽  
Anirban Chakraborty ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrogen Oxidation ◽  
Sulfide Oxidation ◽  
Cold Seep ◽  
Reductive Dehalogenation ◽  
Cold Seeps ◽  
Community Members ◽  
Metabolic Potential ◽  
Near Surface ◽  
Fumarate Addition

AbstractAt marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. In this work, we combined geochemical, metagenomic and metabolomic measurements in distinct sediment redox regimes to profile microbial activities within the uppermost 350 cm of a newly discovered cold seep in the NW Atlantic deep sea (2.3 km water depth). Depth-resolved metagenomic profiling revealed compositional and functional differentiation between near-surface sediments (dominated by Proteobacteria) and deeper subsurface layers (dominated by Atribacteria, Chloroflexi, Euryarchaeota and Lokiarchaeota). Metabolic capabilities of community members were inferred from 376 metagenome-assembled genomes spanning 46 phyla (including five novel candidate phyla). In deeper sulfate-reducing and methanogenic sediments, various community members are capable of anaerobically oxidizing short-chain alkanes (alkyl-CoM reductase pathway), longer-chain alkanes (fumarate addition pathway), and aromatic hydrocarbons (fumarate addition and subsequent benzoyl-CoA pathways). Geochemical profiling demonstrated that hydrocarbon substrates are abundant in this location, thermogenic in origin, and subject to biodegradation. The detection of alkyl-/arylalkylsuccinate metabolites, together with carbon isotopic signatures of ethane, propane and carbon dioxide, support that microorganisms are actively degrading hydrocarbons in these sediments. Hydrocarbon oxidation pathways operate alongside other deep seabed metabolisms such as sulfide oxidation, hydrogen oxidation, carbon fixation, fermentation and reductive dehalogenation. Upward migrated thermogenic hydrocarbons thus sustain diverse microbial communities with activities that affect subseafloor biogeochemical processes across the redox spectrum in deep sea cold seeps.

scholarly journals Middle Eocene Rhodoliths from Tropical and Mid-Latitude Regions

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 117 ◽  
Author(s):  
Julio Aguirre ◽  
Juan C. Braga ◽  
Victoriano Pujalte ◽  
Xabier Orue-Etxebarria ◽  
Edward Salazar-Ortiz ◽  
...  
Keyword(s):  
Shallow Water ◽  
Middle Eocene ◽  
Taxonomic Composition ◽  
Coralline Algae ◽  
Fold Belt ◽  
Carbonate Platforms ◽  
Benthic Foraminifers ◽  
Tropical Areas ◽  
The Impact ◽  
Water Carbonate

During the greenhouse conditions prevailing in the early–middle Eocene, larger benthic foraminifers (LBF) spread out on carbonate platforms worldwide while rhodolith beds were scarcely represented. This reduction in rhodolith beds coincided with a relative decrease in coralline algal diversity and with a drastic decline of coral reef abundance. Middle Eocene rhodoliths from two tropical (San Jacinto Fold Belt in northern Colombia and Bahoruco Peninsula in the Dominican Republic) and two mid-latitude (Salinas Menores Ravine and Sierra del Zacatín in Southern Spain) localities were studied. Rhodolith rudstones in the tropical areas accumulated on relatively deep (several tens of meters) platform environments and were also redeposited in deeper settings downslope. In Salinas Menores, rhodoliths are dispersed in planktic foraminifer-rich marls. Miliolids are common in the infilling of constructional voids in these rhodoliths, indicating that they originally grew in shallow-water inner-shelf settings and afterwards they were transported to deeper environments. In Sierra del Zacatín, rhodoliths are scarce and coralline algae mainly occur as crusts attached to and intergrowing with corals. Here, LBF dominated shallow-water carbonate platforms. In terms of taxonomic composition, coralline algae of the order Hapalidiales are the most abundant in the study areas, followed by Sporolithales. The order Corallinales is poorly represented except in Salinas Menores, where it is relatively abundant and diverse. The impact of high temperatures due to high levels of atmospheric CO2 during the Eocene and widespread oligotrophic conditions, which favored formation of LBF-rich lithofacies, might account for the low abundance of rhodolith beds at mid and high latitudes. In contrast, the more productive equatorial regions would have favored the formation of rhodolith beds.

Study on a New Cement for Deepwater Well Cementing

2012 ◽  
Vol 174-177 ◽  
pp. 1321-1325 ◽  
Author(s):  
Cheng Wen Wang ◽  
Zhi Gang Peng ◽  
Rui He Wang
Keyword(s):  
Low Temperature ◽  
Shallow Water ◽  
Gas Flow ◽  
Low Density ◽  
Test Results ◽  
Migration Control ◽  
Calcium Sulphoaluminate ◽  
Early Strength ◽  
Water Gas

In view of the new concerns in deepwater cementing, such as low temperature, shallow water/gas flow and so on, that can not be efficiently solved with conventional cement systems, a new SP-D cement with calcium sulphoaluminate and silicate was developed to adapt to deepwater low-temperature cementing. Test results show that the SP-D cement possesses high early-strength under low-temperature, favorable compatibility with conventional accelerators and retarders, and can be used to prepare the low density cement slurries combining with microsphere. The research offers a new SP-D cement for deepwater cementing with favorable high early-strength, improved migration control ability and minute expansion of set cement, and also shows prospective solution for the confronted problems in deepwater cementing.

scholarly journals Interplay between the human gut microbiome and host metabolism

2019 ◽  
Author(s):  
Alessia Visconti ◽  
Caroline I. Le Roy ◽  
Fabio Rosa ◽  
Niccolo Rossi ◽  
Tiphaine C. Martin ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Taxonomic Composition ◽  
Metagenomic Sequencing ◽  
Human Gut ◽  
Metabolic Potential ◽  
Microbial Ecosystem ◽  
Microbiome Composition ◽  
Shotgun Metagenomic Sequencing ◽  
Key Species

AbstractThe human gut is inhabited by a complex and metabolically active microbial ecosystem regulating host health. While many studies have focused on the effect of individual microbial taxa, the metabolic potential of the entire gut microbial ecosystem has been largely under-explored. We characterised the gut microbiome of 1,004 twins via whole shotgun metagenomic sequencing (average 39M reads per sample). We observed greater similarity, across unrelated individuals, for functional metabolic pathways (82%) than for taxonomic composition (43%). We conducted a microbiota-wide association study linking both taxonomic information and microbial metabolic pathways with 673 blood and 713 faecal metabolites (Metabolon, Inc.). Metabolic pathways associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species-level results identified less than 3,000 associations, suggesting that coordinated action of multiple taxa is required to affect the metabolome. Finally, we estimated that the microbiome mediated a crosstalk between 71% of faecal and 15% of blood metabolites, highlighting six key species (unclassified Subdoligranulum spp., Faecalibacterium prausnitzii, Roseburia inulinivorans, Methanobrevibacter smithii, Eubacterium rectale, and Akkermansia muciniphila). Because of the large inter-person variability in microbiome composition, our results underline the importance of studying gut microbial metabolic pathways rather than focusing purely on taxonomy to find therapeutic and diagnostic targets.

scholarly journals Anaerobic Biofilm Enriched With an Ammonia Tolerant Methanogenic Consortium to Improve Wastewater Treatment in The Fishing Industry

2021 ◽  
Author(s):  
Manuel Alarcon ◽  
Nathaly Ruiz-Tagle ◽  
Fidelina Gonzalez ◽  
Paz Jopia-Contreras ◽  
Estrella Aspé ◽  
...  
Keyword(s):  
Methane Production ◽  
Inhibitory Effect ◽  
Taxonomic Composition ◽  
Industrial Wastes ◽  
Microbial Consortia ◽  
Fish Processing ◽  
Methanogenic Activity ◽  
Microbial Biofilms ◽  
High Concentrations ◽  
Production Of Ammonia

Abstract The digestion efficiency of liquid industrial wastes increases when using bioreactors colonized by microbial biofilms. High concentrations of proteins derived from the fish processing industry lead to the production of ammonia, which inhibits methane production. Two bioreactors were constructed to compare methanogenic activity: one enriched with mMPA consortia (control bioreactor), and the second with NH3 tolerant consortia (treatment bioreactor). Ammonia tolerant activity was assessed by applying an ammonia shock (755 mg NH3/L). Methane production, consumption of total organic carbon (TOC) and the taxonomic composition of bacteria and archaea was evaluated using 16S rDNA in the acclimatization, ammonia shock, and recovery phases. The ammonia shock significantly affected both methane production and the consumption of TOC in the control reactor (p<0.05) and taxonomical composition of the microbial consortia (OTU). These values remained constant in the treatment reactor. The analysis of biofilm composition showed a predominance of Methanosarcinaceae (Methanomethylovorans sp., and probably two different species of Methanosarcina sp.) in bioreactors. These results demonstrate that using acclimated biofilms enriched with ammonia tolerant methanogens control the inhibitory effect of ammonia on methanogenesis.

Clearer than mud? Using environmental DNA to track historical shifts in lake communities.

2021 ◽  
Author(s):  
John Pearman ◽  
Laura Biessy ◽  
Georgia Thomson-Laing ◽  
Lizette Reyes ◽  
Claire Shepherd ◽  
...  
Keyword(s):  
New Zealand ◽  
Microbial Communities ◽  
Environmental History ◽  
Environmental Changes ◽  
Environmental Dna ◽  
Taxonomic Composition ◽  
Molecular Methods ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Dna And Rna

&lt;p&gt;A continuous record of environmental history is stored in lake sediments providing an avenue to explore current and historical lake communities. Traditionally paleolimnological methods have focussed on macroscopic indicators (e.g. pollen, chronomids, diatoms) to investigate environmental changes but the application of environmental DNA techniques has enabled the investigation of microbial communities and other soft bodied organisms through time. The &amp;#8216;Our lakes&amp;#8217; health; past, present, future (Lakes380)&amp;#8217; project aims to combined traditional and molecular methods to explore shifts in biological communities over the last 1,000 years (pre-human arrival in New Zealand). Sediments cores have been collected from a wide diversity of lakes across New Zealand and 16S rRNA gene metabarcoding approaches of both DNA and RNA applied to reveal how microbial community changes across time and especially in response to the arrival of humans and associated changes to the landscape and lake environments. We further investigate the changes in inferred metabolic potential of the microbial communities as the taxonomic composition of the lake differs over time. Finally, we combine these novel molecular methods with hyperspectral scanning and pollen data to increase the knowledge of changes in lake communities and identifying the timing of changes in lake health. The combination of methodologies provides a greater understanding of the environmental history of lake systems and will help to inform management decisions relating to the restoration and protection of lake health.&lt;/p&gt;

scholarly journals Critical control in transcritical shallow-water flow over two obstacles

2015 ◽  
Vol 780 ◽  
pp. 480-502 ◽  
Author(s):  
Roger H. J. Grimshaw ◽  
Montri Maleewong
Keyword(s):  
Shallow Water ◽  
Weakly Nonlinear ◽  
Hydraulic Flow ◽  
Second Stage ◽  
Model Flow ◽  
Nonlinear Simulations ◽  
Flow Over Topography ◽  
Closure Conditions ◽  
Two Stages ◽  
Volume Method

The nonlinear shallow-water equations are often used to model flow over topography. In this paper we use these equations both analytically and numerically to study flow over two widely separated localised obstacles, and compare the outcome with the corresponding flow over a single localised obstacle. Initially we assume uniform flow with constant water depth, which is then perturbed by the obstacles. The upstream flow can be characterised as subcritical, supercritical and transcritical, respectively. We review the well-known theory for flow over a single localised obstacle, where in the transcritical regime the flow is characterised by a local hydraulic flow over the obstacle, contained between an elevation shock propagating upstream and a depression shock propagating downstream. Classical shock closure conditions are used to determine these shocks. Then we show that the same approach can be used to describe the flow over two widely spaced localised obstacles. The flow development can be characterised by two stages. The first stage is the generation of upstream elevation shock and downstream depression shock from each obstacle alone, isolated from the other obstacle. The second stage is the interaction of two shocks between the two obstacles, followed by an adjustment to a hydraulic flow over both obstacles, with criticality being controlled by the higher of the two obstacles, and by the second obstacle when they have equal heights. This hydraulic flow is terminated by an elevation shock propagating upstream of the first obstacle and a depression shock propagating downstream of the second obstacle. A weakly nonlinear model for sufficiently small obstacles is developed to describe this second stage. The theoretical results are compared with fully nonlinear simulations obtained using a well-balanced finite-volume method. The analytical results agree quite well with the nonlinear simulations for sufficiently small obstacles.

scholarly journals Review: Formation and Metabolic Function of Coral Rubble Biofilms in the Reef Ecosystem

2021 ◽  
Vol 32 ◽  
pp. 46-56
Author(s):  
Andres Sanchez-Quinto ◽  
Luisa Falcon
Keyword(s):  
Nitrogen Fixation ◽  
Coral Reefs ◽  
Sulfate Reduction ◽  
Sulfide Oxidation ◽  
Taxonomic Composition ◽  
Coralline Algae ◽  
Metabolic Processes ◽  
Coral Rubble ◽  
Functional Roles ◽  
Healthy Coral

When coral dies, their calcareous skeletons constitute coral rubble in conjunction with the cementing activity of coralline algae and bacteria, creating a secondary reef structure which takes from years to decades to form. Healthy coral reefs differ from coral—rubble dominated reefs in microbial taxonomic composition and metabolic functional roles. The metabolisms of healthy reefs are dominated by autotrophic pathways, where carbon and nitrogen fixation dominate, while the metabolism of rubble—dominated reefs predominate in degradation of organic matter. Nitrogen fixation is 3 orders of magnitude lower in rubble—dominated reefs than in healthy reefs. Coral—rubble harbors a vast diversity of microbes that can precipitate carbonate through coupling several metabolic processes including photosynthesis, ureolysis, ammonification, denitrification, sulfate reduction, methane oxidation, and anaerobic sulfide oxidation. All these metabolic processes were found in rubble microbial communities, but ammonification and sulfate reduction were most prevalent. Anthropogenic and non—anthropogenic perturbations of healthy coral reefs in the past decades have led to the prevalence of rubble—dominated reefs in areas of the Caribbean where the ecological and functional shifts of the community still need further study.

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