scholarly journals Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition

2017 ◽  
Author(s):  
Valerie Hubalek ◽  
Moritz Buck ◽  
BoonFei Tan ◽  
Julia Foght ◽  
Annelie Wendeberg ◽  
...  
Keyword(s):  
Anaerobic Degradation ◽  
Oil Reservoirs ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Anaerobic Conditions ◽  
Central Importance ◽  
Fermentation Products ◽  
Methanogenic Condition ◽  
Metabolic Interactions ◽  
Multiple Interactions

AbstractSyntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance1. Using micro-manipulation combined with shotgun metagenomic approaches, we disentangled the genomes of complex consortia inside a short chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes of this study, encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H2 metabolism. Instead, inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature in the consortia. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H2-producing and syntrophic alkane degrader–methanogen partnership2. Our study uncovers the complexity of ‘interactomes’ within microbial consortia mediating hydrocarbon transformation under anaerobic conditions.

scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

scholarly journals Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

2020 ◽  
Author(s):  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Stephen R. Lindemann
Keyword(s):  
Microbial Diversity ◽  
Structural Complexity ◽  
Structure And Function ◽  
Microbial Consortia ◽  
Carbohydrate Structure ◽  
High Dilution ◽  
Chemical Complexity ◽  
Metabolic Interactions ◽  
And Function

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

scholarly journals Effects of detritus chemical composition on the anaerobic mineralization of Salvinia auriculata and Utricularia breviscapa

2015 ◽  
Vol 27 (2) ◽  
pp. 202-212
Author(s):  
Marcela Bianchessi da Cunha Santino ◽  
Irineu Bianchini Júnior
Keyword(s):  
Organic Carbon ◽  
Anaerobic Degradation ◽  
Aquatic Macrophytes ◽  
Life Forms ◽  
Mass Balances ◽  
Anaerobic Conditions ◽  
Gas Formation ◽  
Set Up ◽  
Loss Experiment ◽  
Carbon Particulate

Aim: This study was conducted to evaluate the effect of the detritus composition on the anaerobic mineralization of two species of aquatic macrophytes with different life forms (submerged and free floating). The hypothesis that guided this study was that the carbon concentration derived from detritus hydrosoluble fraction can act as a facilitating factor on its degradation.Material and MethodsIncubations containing detritus and water sample from the Óleo Lagoon (21° 33’ to 21° 37’ S and 47° to 47° 45’ to 51’ W) for each specie (Salvinia auriculata and Utricularia breviscapa) were set-up with: (i) integral detritus (sample of dried plant), (ii) lignocellulosic matrix (particulate organic matter (POM) remaining from leachate extraction) and (iii) leachate. The incubations were kept in the dark under anaerobic conditions. Daily rates of gas formation were evaluated and after 138 days, the incubations were fractioned in dissolved and particulate fractions and the mass balances were performed. A mass loss experiment (180 days) was performed for assessment of the dissolved organic carbon, particulate organic carbon and mineralized carbon variations.ResultsRegardless of the type of detritus (S. auriculata and U. breviscapa), C-mineralization was faster and higher in the DOC incubations (ca. 85%). For U. breviscapa the POM mineralization was slower than the corresponding integral detritus and S. auriculata mineralization was slower than U. breviscapa.ConclusionsThe composition of the detritus (i.e. macrophyte type, presence and proportion of leachate) interfered synergistically in anaerobic degradation of these plants. The leachate tends to act as a facilitator, supporting the growth of microorganisms and intensifying mineralization.

scholarly journals Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of Escherichia coli

2010 ◽  
Vol 76 (8) ◽  
pp. 2397-2401 ◽  
Author(s):  
Xueli Zhang ◽  
K. T. Shanmugam ◽  
Lonnie O. Ingram
Keyword(s):  
Escherichia Coli ◽  
Electron Acceptors ◽  
Carbon Flow ◽  
Glycerol Dehydrogenase ◽  
Glycerol Metabolism ◽  
Wild Type ◽  
Anaerobic Conditions ◽  
Mineral Salts ◽  
Succinate Production ◽  
Fermentation Products

ABSTRACT The fermentative metabolism of Escherichia coli was reengineered to efficiently convert glycerol to succinate under anaerobic conditions without the use of foreign genes. Formate and ethanol were the dominant fermentation products from glycerol in wild-type Escherichia coli ATCC 8739, followed by succinate and acetate. Inactivation of pyruvate formate-lyase (pflB) in the wild-type strain eliminated the production of formate and ethanol and reduced the production of acetate. However, this deletion slowed growth and decreased cell yields due to either insufficient energy production or insufficient levels of electron acceptors. Reversing the direction of the gluconeogenic phosphoenolpyruvate carboxykinase reaction offered an approach to solve both problems, conserving energy as an additional ATP and increasing the pool of electron acceptors (fumarate and malate). Recruiting this enzyme through a promoter mutation (pck*) to increase expression also increased the rate of growth, cell yield, and succinate production. Presumably, the high NADH/NAD+ ratio served to establish the direction of carbon flow. Additional mutations were also beneficial. Glycerol dehydrogenase and the phosphotransferase-dependent dihydroxyacetone kinase are regarded as the primary route for glycerol metabolism under anaerobic conditions. However, this is not true for succinate production by engineered strains. Deletion of the ptsI gene or any other gene essential for the phosphotranferase system was found to increase succinate yield. Deletion of pflB in this background provided a further increase in the succinate yield. Together, these three core mutations (pck*, ptsI, and pflB) effectively redirected carbon flow from glycerol to succinate at 80% of the maximum theoretical yield during anaerobic fermentation in mineral salts medium.

scholarly journals A gap-filling algorithm for prediction of metabolic interactions in microbial communities

2021 ◽  
Vol 17 (11) ◽  
pp. e1009060
Author(s):  
Dafni Giannari ◽  
Cleo Hanchen Ho ◽  
Radhakrishnan Mahadevan
Keyword(s):  
Microbial Communities ◽  
Individual Species ◽  
Metabolic Reconstruction ◽  
Interspecies Interactions ◽  
Gap Filling ◽  
Bifidobacterium Adolescentis ◽  
Filling Method ◽  
Metabolic Interactions ◽  
Enzyme Functions ◽  
Genome Scale

The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.

scholarly journals Anaerobic Biodegradation of Wheat Straw Lignin: The Influence of Wet Explosion Pretreatment

Energies ◽  
2021 ◽  
Vol 14 (18) ◽  
pp. 5940
Author(s):  
Muhammad Usman Khan ◽  
Birgitte Kiaer Ahring
Keyword(s):  
Anaerobic Digestion ◽  
Wheat Straw ◽  
Anaerobic Degradation ◽  
Lignin Degradation ◽  
Anaerobic Conditions ◽  
Feed Material ◽  
Energy Product ◽  
Wet Explosion Pretreatment ◽  
Methane Potential ◽  
Wet Explosion

Large amounts of lignin residue is expected in the future when biorefineries for producing biofuels and bio-products will increase in numbers. It is, therefore, valuable to find solutions for using this resource for the sustained production of useful bioenergy or bio-products. Anaerobic digestion could potentially be an option for converting the biorefinery lignin into a valuable energy product. However, lignin is recalcitrant to biodegradation under anaerobic conditions unless the structure is modified. Wet oxidation followed by steam explosion (wet explosion) was previously found to make significant changes to the lignin structure allowing for biodegradation under anaerobic conditions. In this study, we examine the effect of wet explosion pretreatment for anaerobic digestion of wheat straw lignin under mesophilic (37 o C) conditions. Besides the biorefinery lignin produced from wheat straw, untreated lignin was further tested as feed material for anaerobic digestion. Our results showed that wet exploded lignin pretreated with 2% NaOH showed the highest lignin degradation (41.8%) as well as the highest methane potential of 157.3±9.9 ml/g VS. The untreated lignin with no pretreatment showed the lowest methane yield of 65.8±4.8 and only 3.5% of the lignin was degraded. Overall, increased severity of the pretreatment was found to enhance anaerobic degradation of lignin.

scholarly journals pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Zehra Esra Ilhan ◽  
Andrew K. Marcus ◽  
Dae-Wook Kang ◽  
Bruce E. Rittmann ◽  
Rosa Krajmalnik-Brown
Keyword(s):  
Fatty Acids ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Short Chain Fatty Acids ◽  
Human Gut ◽  
Fermentation Products ◽  
Metabolic Products ◽  
Metabolic Interactions

ABSTRACT The human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are unknown. Here, we show that, for in vitro conditions, pH was the strongest driver of microbial community structure and function and microbial and metabolic interactions among pH-sensitive fermentative species. The balance between bicarbonate alkalinity and formation of fatty acids by fermentation determined the pH, which controlled microbial community structure. Our results underscore the influence of pH balance on microbial function in diverse microbial ecosystems such as the human gut. pH and fermentable substrates impose selective pressures on gut microbial communities and their metabolisms. We evaluated the relative contributions of pH, alkalinity, and substrate on microbial community structure, metabolism, and functional interactions using triplicate batch cultures started from fecal slurry and incubated with an initial pH of 6.0, 6.5, or 6.9 and 10 mM glucose, fructose, or cellobiose as the carbon substrate. We analyzed 16S rRNA gene sequences and fermentation products. Microbial diversity was driven by both pH and substrate type. Due to insufficient alkalinity, a drop in pH from 6.0 to ~4.5 clustered pH 6.0 cultures together and distant from pH 6.5 and 6.9 cultures, which experienced only small pH drops. Cellobiose yielded more acidity than alkalinity due to the amount of fermentable carbon, which moved cellobiose pH 6.5 cultures away from other pH 6.5 cultures. The impact of pH on microbial community structure was reflected by fermentative metabolism. Lactate accumulation occurred in pH 6.0 cultures, whereas propionate and acetate accumulations were observed in pH 6.5 and 6.9 cultures and independently from the type of substrate provided. Finally, pH had an impact on the interactions between lactate-producing and -consuming communities. Lactate-producing Streptococcus dominated pH 6.0 cultures, and acetate- and propionate-producing Veillonella, Bacteroides, and Escherichia dominated the cultures started at pH 6.5 and 6.9. Acid inhibition on lactate-consuming species led to lactate accumulation. Our results provide insights into pH-derived changes in fermenting microbiota and metabolisms in the human gut. IMPORTANCE The human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are unknown. Here, we show that, for in vitro conditions, pH was the strongest driver of microbial community structure and function and microbial and metabolic interactions among pH-sensitive fermentative species. The balance between bicarbonate alkalinity and formation of fatty acids by fermentation determined the pH, which controlled microbial community structure. Our results underscore the influence of pH balance on microbial function in diverse microbial ecosystems such as the human gut.

Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2090-2096 ◽  
Author(s):  
Benoît Pugin ◽  
Jenny M. Blamey ◽  
Bonnie K. Baxter ◽  
Juergen Wiegel
Keyword(s):  
Type Species ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Rrna Gene ◽  
Anaerobic Conditions ◽  
Fermentation Products ◽  
Aerobic Conditions ◽  
Content Type ◽  
Link Type

Novel strains of facultatively aerobic, moderately alkaliphilic and facultatively halophilic bacteria were isolated from a sediment sample taken from the Southern Arm of Great Salt Lake, Utah. Cells of strain JW/BP-GSL-QDT (and related strains JW/BP-GSL-RA and JW/BP-GSL-WB) were rod-shaped, spore-forming, motile bacteria with variable Gram-staining. Strain JW/BP-GSL-QDT grew under aerobic conditions between 14.5 and 47 °C (optimum 39 °C), in the pH37 °C range 6.5–10.3 (optimum pH37 °C 8.0), and between 0.1 and 4.5 M Na+ (optimum 0.9 M Na+). No growth was observed in the absence of supplemented Na+. Strain JW/BP-GSL-QDT utilized l-arabinose, d-fructose, d-galactose, d-glucose, inulin, lactose, maltose, mannitol, d-mannose, pyruvate, d-ribose, d-sorbitol, starch, trehalose, xylitol and d-xylose under both aerobic and anaerobic conditions, and used ethanol and methanol only under aerobic conditions. Strains JW/BP-GSL-WB and JW/BP-GSL-RA had the same profiles except that methanol was not used aerobically. During growth on glucose, the major organic compounds formed under aerobic conditions were acetate and lactate, and under anaerobic conditions, the fermentation products were formate, acetate, lactate and ethanol. Oxidase and catalase activities were not detected and cytochrome was absent. No respiratory quinones were detected. The main cellular fatty acids were iso-C15 : 0 (39.1 %) and anteiso-C15 : 0 (36.3 %). Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. Additionally, a small amount of an unknown glycolipid was detected. The DNA G+C content of strain JW/BP-GSL-QDT was 35.4 mol% (determined by HPLC). For strain JW/BP-GSL-QDT the highest degree of 16S rRNA gene sequence similarity was found with Amphibacillus jilinensis (98.6 %), Amphibacillus sediminis (96.7 %) and Amphibacillus tropicus (95.6 %). The level of DNA–DNA relatedness between strain JW/BP-GSL-QDT and A. jilinensis Y1T was 58 %. On the basis of physiological, chemotaxonomic and phylogenetic data, strain JW/BP-GSL-QDT represents a novel species of the genus Amphibacillus , for which the name Amphibacillus cookii sp. nov. is proposed. The type strain is JW/BP-GSL-QDT ( = ATCC BAA-2118T = DSM 23721T).

scholarly journals Glucose, l-Malic Acid and pH Effect on Fermentation Products in Biological Deacidification

2009 ◽  
Vol 27 (Special Issue 1) ◽  
pp. S319-S322 ◽  
Author(s):  
A. Kunicka-Styczyńska
Keyword(s):  
Malic Acid ◽  
Ph Effect ◽  
Hplc Method ◽  
Optimal Parameters ◽  
Wine Yeasts ◽  
Anaerobic Conditions ◽  
Fermentation Products ◽  
Yeast Strains ◽  
Industrial Strains ◽  
Selection Of

Industrial wine yeasts <I>Saccharomyces cerevisiae</I> Syrena, an interspecies hybrid (<I>S. cerevisiae × S. bayanus</I>) HW2-3 and <I>Schizosaccharomyces pombe</I> met 3–15 h<sup>+>/sup> were examined to determine changes in fermentation profiles in different environmental conditions in YG medium with different concentrations of glucose (2, 6, 40 or 100 g/l), L-malic acid (4, 7 or 11 g/l) and at pH 3.0, 3.5 and 5.0. The results were obtained by HPLC method (organic acids, acetaldehyde, glycerol, diacetyl) and enzymatically (L-malic acid, ethanol). In anaerobic conditions (100 g/l glucose), the optimal parameters for L-malic acid decomposition for <I>S. cerevisiae</I> Syrena and the hybrid HW2-3 were 11 g/l L-malic acid and pH 3.0 and 3.5, respectively. <I>S. pombe</I> expressed the highest demalication activity at 40 and 100 g/l glucose, 7 g/l L-malic acid and pH 3.0. The fermentation profiles of selected metabolites of yeast were unique for specific industrial strains. These profiles may help in the proper selection of yeast strains to fermentation and make it possible to predict the organoleptic changes in the course of fruit must fermentation.

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