scholarly journals Metagenomic analysis reveals large potential for carbon, nitrogen and sulfur cycling in coastal methanic sediments of the Bothnian Sea

2019 ◽  
Author(s):  
Olivia Rasigraf ◽  
Niels A.G.M. van Helmond ◽  
Jeroen Frank ◽  
Wytze K. Lenstra ◽  
Matthias Egger ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Archaeal Community ◽  
Iron Sulfate ◽  
Sediment Layer ◽  
Organic Substrates ◽  
Metagenomic Sequencing ◽  
Reactive Iron ◽  
Microbial Network ◽  
Bothnian Sea

AbstractThe Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane and ammonium in the sediments potentially enabling an intricate microbial network. Therefore, we analyzed and compared biogeochemical and microbial profiles at one offshore and two near coastal sites in the Bothnian Sea. 16S rRNA amplicon sequence analysis revealed stratification of both bacterial and archaeal taxa in accordance with the geochemical gradients of iron, sulfate and methane. The communities at the two near coastal sites were more similar to each other than that at the offshore site located at a greater water depth. To obtain insights into the metabolic networks within the iron-rich methanic sediment layer located below the sulfate-methane transition zone (SMTZ), we performed metagenomic sequencing of sediment-derived DNA. Genome bins retrieved from the most abundant bacterial and archaeal community members revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. Nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene-centric fermentative metabolism analysis indicated the central role of acetate, formate, alcohols and hydrogen in the analyzed anaerobic sediment. Methanogenic/-trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae and ANME-2 archaea. Thorarchaeota and Bathyarchaeota encoded pathways for acetogenesis. Our results indicate flexible metabolic capabilities of core community bacterial and archaeal taxa, which can adapt to changing redox conditions, and with a spatial distribution in Bothnian Sea sediments that is likely governed by the quality of available organic substrates.

scholarly journals Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0240953
Author(s):  
Christian Schulz ◽  
Eivind Almaas
Keyword(s):  
Phylogenetic Trees ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Significant Heterogeneity ◽  
Metabolic Reaction ◽  
High Quality ◽  
Conserved Genes ◽  
Genome Scale

Approaches for systematizing information of relatedness between organisms is important in biology. Phylogenetic analyses based on sets of highly conserved genes are currently the basis for the Tree of Life. Genome-scale metabolic reconstructions contain high-quality information regarding the metabolic capability of an organism and are typically restricted to metabolically active enzyme-encoding genes. While there are many tools available to generate draft reconstructions, expert-level knowledge is still required to generate and manually curate high-quality genome-scale metabolic models and to fill gaps in their reaction networks. Here, we use the tool AutoKEGGRec to construct 975 genome-scale metabolic draft reconstructions encoded in the KEGG database without further curation. The organisms are selected across all three domains, and their metabolic networks serve as basis for generating phylogenetic trees. We find that using all reactions encoded, these metabolism-based comparisons give rise to a phylogenetic tree with close similarity to the Tree of Life. While this tree is quite robust to reasonable levels of noise in the metabolic reaction content of an organism, we find a significant heterogeneity in how much noise an organism may tolerate before it is incorrectly placed in the tree. Furthermore, by using the protein sequences for particular metabolic functions and pathway sets, such as central carbon-, nitrogen-, and sulfur-metabolism, as basis for the organism comparisons, we generate highly specific phylogenetic trees. We believe the generation of phylogenetic trees based on metabolic reaction content, in particular when focused on specific functions and pathways, could aid the identification of functionally important metabolic enzymes and be of value for genome-scale metabolic modellers and enzyme-engineers.

scholarly journals Organic sediment formed during inundation of a degraded fen grassland emits large fluxes of CH<sub>4</sub> and CO<sub>2</sub>

2011 ◽  
Vol 8 (6) ◽  
pp. 1539-1550 ◽  
Author(s):  
M. Hahn-Schöfl ◽  
D. Zak ◽  
M. Minke ◽  
J. Gelbrecht ◽  
J. Augustin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Plant Litter ◽  
Electron Acceptors ◽  
Sediment Layer ◽  
Organic Substrates ◽  
Peat Layer ◽  
Ch4 Production ◽  
Fresh Plant ◽  
Fresh Organic Matter ◽  
Organic Sediment

Abstract. Peatland restoration by inundation of drained areas can alter local greenhouse gas emissions as CO2 and CH4. Factors that can influence these emissions include the quality and amount of substrates available for anaerobic degradation processes and the sources and availability of electron acceptors. In order to learn about possible sources of high CO2 and CH4. emissions from a rewetted degraded fen grassland, we performed incubation experiments that tested the effects of fresh plant litter in the flooded peats on pore water chemistry and CO2 and CH4. production and emission. The position in the soil profile of the pre-existing drained peat substrate affected initial rates of anaerobic CO2 production subsequent to flooding, with the uppermost peat layer producing the greatest specific rates of CO2 evolution. CH4 production rates depended on the availability of electron acceptors and was significant only when sulfate concentrations were reduced in the pore waters. Very high specific rates of both CO2 (maximum of 412 mg C d−1 kg−1 C) and CH4 production (788 mg C d−1 kg−1 C) were observed in a new sediment layer that accumulated over the 2.5 years since the site was flooded. This new sediment layer was characterized by overall low C content, but represented a mixture of sand and relatively easily decomposable plant litter from reed canary grass killed by flooding. Samples that excluded this new sediment layer but included intact roots remaining from flooded grasses had specific rates of CO2 (max. 28 mg C d−1 kg−1 C) and CH4 (max. 34 mg C d−1 kg−1 C) production that were 10–20 times lower than for the new sediment layer and were comparable to those of a newly flooded upper peat layer. Lowest rates of anaerobic CO2 and CH4 production (range of 4–8 mg C d−1 kg−1 C and <1 mg C d−1 kg−1 C) were observed when all fresh organic matter sources (plant litter and roots) were excluded. In conclusion, the presence of fresh organic substrates such as plant and root litter originating from plants killed by inundation has a high potential for CH4 production, whereas peat without any fresh plant-derived material is relatively inert. Significant anaerobic CO2 and CH4 production in peat only occurs when some labile organic matter is available, e.g. from remaining roots or root exudates.

scholarly journals The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella

2021 ◽  
Vol 17 (8) ◽  
pp. e1009326
Author(s):  
Héloise Rytter ◽  
Anne Jamet ◽  
Jason Ziveri ◽  
Elodie Ramond ◽  
Mathieu Coureuil ◽  
...  
Keyword(s):  
Pentose Phosphate Pathway ◽  
Metabolic Pathways ◽  
Pathogenic Bacteria ◽  
Metabolic Networks ◽  
Tricarboxylic Acid Cycle ◽  
Sulfur Metabolism ◽  
Time Lapse ◽  
Pentose Phosphate ◽  
Francisella Novicida

Metabolic pathways are now considered as intrinsic virulence attributes of pathogenic bacteria and thus represent potential targets for antibacterial strategies. Here we focused on the role of the pentose phosphate pathway (PPP) and its connections with other metabolic pathways in the pathophysiology of Francisella novicida. The involvement of the PPP in the intracellular life cycle of Francisella was first demonstrated by studying PPP inactivating mutants. Indeed, we observed that inactivation of the tktA, rpiA or rpe genes severely impaired intramacrophage multiplication during the first 24 hours. However, time-lapse video microscopy demonstrated that rpiA and rpe mutants were able to resume late intracellular multiplication. To better understand the links between PPP and other metabolic networks in the bacterium, we also performed an extensive proteo-metabolomic analysis of these mutants. We show that the PPP constitutes a major bacterial metabolic hub with multiple connections to glycolysis, the tricarboxylic acid cycle and other pathways, such as fatty acid degradation and sulfur metabolism. Altogether our study highlights how PPP plays a key role in the pathogenesis and growth of Francisella in its intracellular niche.

scholarly journals Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1261
Author(s):  
Dong Liu ◽  
Parag Bhople ◽  
Katharina Maria Keiblinger ◽  
Baorong Wang ◽  
Shaoshan An ◽  
...  
Keyword(s):  
Loess Plateau ◽  
Microbial Biomass Carbon ◽  
Network Connectivity ◽  
Metagenomic Sequencing ◽  
The Loess Plateau ◽  
Chinese Loess ◽  
Mediated Effects ◽  
Microbial Network ◽  
Barren Soil ◽  
Plant Restoration

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.

scholarly journals Boundary conditions for early life converge to an organo-sulfur metabolism

2018 ◽  
Author(s):  
Joshua E. Goldford ◽  
Hyman Hartman ◽  
Robert Marsland ◽  
Daniel Segrè
Keyword(s):  
Boundary Conditions ◽  
Early Life ◽  
Metabolic Networks ◽  
Sulfur Metabolism ◽  
Continuous Production ◽  
Carbon Sources ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Molecular Precursors ◽  
Combine Network

AbstractIt has been suggested that a deep memory of early life is hidden in the architecture of metabolic networks, whose reactions could have been catalyzed by small molecules or minerals prior to genetically encoded enzymes (1–6). A major challenge in unraveling these early steps is assessing the plausibility of a connected, thermodynamically consistent proto-metabolism under different geochemical conditions, which are still surrounded by high uncertainty. Here we combine network-based algorithms (9, 10) with physicochemical constraints on chemical reaction networks to systematically show how different combinations of parameters (temperature, pH, redox potential and availability of molecular precursors) could have affected the evolution of a proto-metabolism. Our analysis of possible trajectories indicates that a subset of boundary conditions converges to an organo-sulfur-based proto-metabolic network fueled by a thioester- and redox-driven variant of the reductive TCA cycle, capable of producing lipids and keto acids. Surprisingly, environmental sources of fixed nitrogen and low-potential electron donors seem not to be necessary for the earliest phases of biochemical evolution. We use one of these networks to build a steady-state dynamical metabolic model of a proto-cell, and find that different combinations of carbon sources and electron acceptors can support the continuous production of a minimal ancient “biomass” composed of putative early biopolymers and fatty acids.

scholarly journals Structure and function of the cytochrome P450 peroxygenase enzymes

2018 ◽  
Vol 46 (1) ◽  
pp. 183-196 ◽  
Author(s):  
Andrew W. Munro ◽  
Kirsty J. McLean ◽  
Job L. Grant ◽  
Thomas M. Makris
Keyword(s):  
Fatty Acids ◽  
Cytochromes P450 ◽  
Structural Data ◽  
Short Review ◽  
Biochemical Properties ◽  
Organic Substrates ◽  
Reactive Iron ◽  
Redox Partner ◽  
Wide Range ◽  
And Function

The cytochromes P450 (P450s or CYPs) constitute a large heme enzyme superfamily, members of which catalyze the oxidative transformation of a wide range of organic substrates, and whose functions are crucial to xenobiotic metabolism and steroid transformation in humans and other organisms. The P450 peroxygenases are a subgroup of the P450s that have evolved in microbes to catalyze the oxidative metabolism of fatty acids, using hydrogen peroxide as an oxidant rather than NAD(P)H-driven redox partner systems typical of the vast majority of other characterized P450 enzymes. Early members of the peroxygenase (CYP152) family were shown to catalyze hydroxylation at the α and β carbons of medium-to-long-chain fatty acids. However, more recent studies on other CYP152 family P450s revealed the ability to oxidatively decarboxylate fatty acids, generating terminal alkenes with potential applications as drop-in biofuels. Other research has revealed their capacity to decarboxylate and to desaturate hydroxylated fatty acids to form novel products. Structural data have revealed a common active site motif for the binding of the substrate carboxylate group in the peroxygenases, and mechanistic and transient kinetic analyses have demonstrated the formation of reactive iron-oxo species (compounds I and II) that are ultimately responsible for hydroxylation and decarboxylation of fatty acids, respectively. This short review will focus on the biochemical properties of the P450 peroxygenases and on their biotechnological applications with respect to production of volatile alkenes as biofuels, as well as other fine chemicals.

Diagenesis and pyritization of crinoid ossicles

1987 ◽  
Vol 24 (12) ◽  
pp. 2486-2498 ◽  
Author(s):  
Uwe Brand ◽  
Joan O. Morrison
Keyword(s):  
Organic Matter ◽  
Organic Matter Content ◽  
Water Source ◽  
Selective Dissolution ◽  
Matter Content ◽  
Sediment Layer ◽  
Reactive Iron ◽  
Diagenetic Alteration ◽  
Diagenetic Fluids ◽  
Organic Tissue

Diagenetic alteration of original high-Mg calcite crinoid skeletal material was achieved by reaction of the calcium carbonate with isotopically light meteoric water. The light δ18O values (−10.57 ± 0.74‰, PDB) are a reflection of the water source, whereas the δ13C values (−3.49 ± 2.63‰, PDB) are a consequence of the high reactive-organic-matter content in the sediments of the Brush Creek at Sewickley, Pennsylvania. High Fe (22 970 ± 30 440 ppm) and Mn (3760 ± 1450 ppm) contents suggest further that the diagenetic fluids were reducing waters that reacted with the crinoid ossicles in the shallow-burial marine and meteoric environments.Four different types of pyrite are found within crinoid ossicles. Framboidal pyrite, aggregate pyrite, and nanopyrite are generally found in the pores of the stereom. Micropyrite, which is present in the form of octahedral, dodecahedral, and pyritohedral crystals, and nanopyrite and aggregate pyrite replace the calcitic stereom. The degree of pyritization and the pore filling increase toward the outer periphery of the crinoid ossicles. Pyrite formation of the crinoid ossicles took place in two stages. In stage I, upon death, the crinoids disarticulated and were quickly buried. In this shallow sediment layer (1–10 cm) the pore water was both undersaturated with respect to calcite and oxidizing. This brought about oxidation of the organic tissue in the stroma of the crinoids and selective dissolution of the high-Mg calcite skeletons. With further burial in stage II, in the presence of reactive organic matter local iron was solubilized, marine sulphate was reduced to sulphide, and isotopically light carbon was produced by bacterial action. Reactive iron combined with sulphur to form framboidal and nanopyrite in the pores of the stereoms. With further burial the micropyrite formed in the crinoid ossicles. Termination of the pyritization process came about with depletion of the iron and (or) sulphur, and this process proceeded very rapidly under shallow-burial conditions while the crinoids resided in the microbial sulphate-reduction zone of the marine–phreatic environment.Fossils are preserved in different stages, with brachiopod valves preserved in their original low-Mg calcite mineralogy, whereas molluscs and crinoids show the complete trend from preserved aragonite and high-Mg calcite, respectively, to diagenetic low-Mg calcite. The preservation potential of fossils is closely linked to the thermodynamic stability of the skeletal carbonate in the presence of diagenetic fluids. Carbon/sulphur ratios support the assertion that Brush Creek sediments were deposited in normal marine waters and favour generally oxic redox conditions for Pennsylvanian seawater.

scholarly journals Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China

2021 ◽  
Vol 12 (11) ◽  
Author(s):  
Xi Wang ◽  
Yujie Ning ◽  
Cheng Li ◽  
Yi Gong ◽  
Ruitian Huang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
Metabolic Networks ◽  
Unsaturated Fatty Acids ◽  
Abundant Species ◽  
Metagenomic Sequencing ◽  
Serum Samples ◽  
Genetic And Environmental Factors ◽  
Specific Species ◽  
Beck Disease

AbstractKashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.

scholarly journals Correlation Between Salivary Microbiology and H2S Concentration of Oral Cavity

2021 ◽  
Author(s):  
Jiarui Jiang ◽  
Yufeng Huang ◽  
Na Luo ◽  
Qili Mi ◽  
Xuemei Li ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Oral Cavity ◽  
Sulfur Metabolism ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Oral Diseases ◽  
Oral Malodor ◽  
High Group ◽  
Oral Microbes ◽  
Oral Microorganisms

Abstract Background: Halitosis is caused by metabolites produced by oral microorganisms. Hydrogen sulfide is the most important compound that leads to the oral malodor, and is thought to be closely correlated with the activity of oral microorganism. Therefore, it is important to clarify the correlation between oral microbes and metabolites. Methods: Based on the 16S rRNA gene amplicon and shotgun metagenomic sequencing of oral microorganism, and oral malodor test, this study attempted to explain the contribution of oral microorganisms to the hydrogen sulfide of oral malodor. Results: The data shows that microbial taxa consisted in the H2S low and high groups are different, and most of the enriched taxa in the H2S high group are genus that correlated with H2S concentration. The two species Fusobaeterium periodonticum and Prevotella nanceiensis are significant different in both coverage breadth and depth and LPS biosynthesis contributions in two groups. According to KEGG metabolism pathways detected by HUMAnN2, subjects of the H2S high group may have a high risk to bacterial infection, since the LPS biosynthesis is enrichment. The contribution of F. periodonticum to sulfur metabolism between two groups is significantly different, and the relative abundance of F. periodonticum is higher in the H2S high group as well. Conclusions: The H2S content, is significantly associated with the composition and abundance of microorganisms in the oral cavity. The increase of microbial abundance and metabolism of some sulfide products are the main causes of halitosis. The most of the enriched microorganisms enriched in people with high H2S are associated with oral diseases such as caries and periodontal diseases, indicating that the diseases associated with oral microbes are not independent of each other and have some associations between some oral diseases.

Genomic variation of microbial populations on a continuous 10,000-year sediment sequence from Lake Cadagno (Piora Valley, Switzerland)

2021 ◽  
Author(s):  
Paula Catalina Rodriguez Ramirez ◽  
Jasmine Berg ◽  
Longhui Deng ◽  
Hendrik Vogel ◽  
Mark A. Lever ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sulfate Reduction ◽  
Microbial Populations ◽  
Gene Copy ◽  
Sulfur Cycling ◽  
Rrna Gene ◽  
Sediment Layer ◽  
Metagenomic Sequencing ◽  
Sulfate Reducing

&lt;p&gt;Lake Cadagno is a meromictic Alpine lake located in the Piora Valley, Switzerland. In 2019, a 10,000-year (10 m)sediment sequence was collected and found to contain three main lithological units: glacial sediment deposited under oxic conditions; a Mn-rich and organic-matter-rich sediment layer deposited during the transition from an oxic late-glacial lake to the onset of anoxia, and dark, sulfidic sediments deposited during the period of euxinia to the present. This study investigates the relationships between the physical-chemical properties and microorganisms of the sediment sequenceusing genome-resolved and targeted metagenomics.&amp;#160; &amp;#160;&lt;/p&gt;&lt;p&gt;Results show that 16S rRNA gene abundance peaks in upper 1-32 cm of the sediment core (10&lt;sup&gt;8&lt;/sup&gt; copies per gram of sediment) and decreases with depth. The abundance of a marker gene for sulfate reduction, dsrB, is positively correlated to 16S rRNA gene copy numbers, decreasing with depth from approximately 10&lt;sup&gt;8&lt;/sup&gt; copies per gram of sediment in the top 30 cm to 10&lt;sup&gt;4&lt;/sup&gt; gene copies per gram of sediment at 900 cm below the sediment depth.&amp;#160; These results suggest that sulfate-reducing microbial communities in surface sediments harvest the bioavailable oxidized sulfur inorganic species. In contrast, the presence of sulfate-reducing genes in sediments with sulfate concentrations below detection may indicate the engagement of microbial populations in sulfur cycling using alternative metabolic strategies (e.g. secondary fermentation).&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Moreover, a clear differentiation between surface and deep sediment communities is observed. Sequencing of dsrB amplicons show a decrease in dsrB sequence richness with depth and sediment age. A clear transition from a surface section dominated (&gt;80% relative abundance) by Deltaproteobacteria-related dsrB sequences from well-studied groups, to a deeper section below 40 cm dominated by a group of unclassified dsrB sequences most likely related to Firmicutes or Chloroflexi is also observed. The identity of these unclassified dsrB sequences will be determined by genome-resolved metagenomic sequencing (currently in progress). Furthermore, these analyses will give information on the presence of complete sulfate-reduction pathways and/or genes related to sulfur cycling in these microbial groups. By reconstructing the genomes of sulfate reducers and other microbial populations throughout the core, we will investigate whether there are genomic changes associated with the main geochemical trends. This work will enable us to assess the influence of a changing lake with the evolution of sediment-dwelling prokaryotic populations over thousands of years.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

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