Metabolic reconstruction for Microcoleus vaginatus

2017 ◽  
Author(s):  
Anonymous
Keyword(s):  
Metabolic Reconstruction ◽  
Microcoleus Vaginatus

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 Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

2021 ◽  
Vol 9 (6) ◽  
pp. 1290
Author(s):  
Natalia Alvarez-Santullano ◽  
Pamela Villegas ◽  
Mario Sepúlveda Mardones ◽  
Roberto E. Durán ◽  
Raúl Donoso ◽  
...  
Keyword(s):  
Fatty Acids ◽  
De Novo ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Fine Tuning ◽  
Metabolic Reconstruction ◽  
Phylogenetic Groups ◽  
Outlier Group ◽  
Pha Genes ◽  
High Level

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner–Doudoroff (ED), pentose-phosphate (PP), and lower Embden–Meyerhoff–Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

scholarly journals Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

2021 ◽  
Vol 9 (4) ◽  
pp. 757
Author(s):  
Qing-Mei Li ◽  
Ying-Li Zhou ◽  
Zhan-Fei Wei ◽  
Yong Wang
Keyword(s):  
Comparative Genomics ◽  
Deep Sea ◽  
Binding Protein ◽  
Glycerol Metabolism ◽  
Metabolic Reconstruction ◽  
Type Ii Secretion ◽  
Phylogenetic Groups ◽  
Genes Encoding ◽  
Epipelagic Zone ◽  
Chitin Binding Protein

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

scholarly journals Genome reduction in an abundant and ubiquitous soil bacterial lineage

2016 ◽  
Author(s):  
Tess E Brewer ◽  
Kim M Handley ◽  
Paul Carini ◽  
Jack A Gibert ◽  
Noah Fierer
Keyword(s):  
Soil Bacteria ◽  
Large Population ◽  
Metabolic Reconstruction ◽  
Soil Environment ◽  
Genomic Databases ◽  
Bacterial Phylotypes ◽  
Bacterial Lineage ◽  
Metabolic Versatility ◽  
Soil Metagenome ◽  
Soil Bacterial

AbstractAlthough bacteria within theVerrucomicrobiaphylum are pervasive in soils around the world, they are underrepresented in both isolate collections and genomic databases. Here we describe a single verrucomicrobial phylotype within the classSpartobacteriathat is not closely related to any previously described taxa. We examined >1000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant phylotype. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘CandidatusUdaeobacter copiosus’. TheCa. U. copiosus genome is unusually small for soil bacteria, estimated to be only 2.81 Mbp compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests thatCa. U. copiosus is an aerobic chemoorganoheterotroph with numerous amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic ofCa. U. copiosus suggests that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil,Ca. U. copiosus appears to have identified an alternate strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

scholarly journals A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

2009 ◽  
Vol 5 (2) ◽  
pp. e1000285 ◽  
Author(s):  
Patrick F. Suthers ◽  
Madhukar S. Dasika ◽  
Vinay Satish Kumar ◽  
Gennady Denisov ◽  
John I. Glass ◽  
...  
Keyword(s):  
Mycoplasma Genitalium ◽  
Metabolic Reconstruction ◽  
A Genome ◽  
Genome Scale

scholarly journals Frontiers in metabolic reconstruction and modeling of plant genomes

2012 ◽  
Vol 63 (6) ◽  
pp. 2247-2258 ◽  
Author(s):  
S. M. D. Seaver ◽  
C. S. Henry ◽  
A. D. Hanson
Keyword(s):  
Metabolic Reconstruction ◽  
Plant Genomes

Comparative physiological responses of Microcoleus vaginatus and Bryum argenteum to enhanced UV-B radiation under field conditions

2019 ◽  
Vol 46 (3) ◽  
pp. 262
Author(s):  
Rong Hui ◽  
Rongliang Jia ◽  
Yang Zhao ◽  
Guang Song ◽  
Yanhong Gao
Keyword(s):  
Physiological Responses ◽  
Soluble Sugars ◽  
Western China ◽  
Desert Ecosystems ◽  
Bryum Argenteum ◽  
Microcoleus Vaginatus ◽  
Physiological Properties ◽  
Short Period ◽  
And Function ◽  
North Western

UV-B radiation is an important environmental factor affecting the composition and function of biological soil crusts (BSCs). The aim of this study was to compare the effects of enhanced UV-B radiation on BSCs from Tengger Desert, north-western China, which are dominated by the cyanobacterium Microcoleus vaginatus Gom. and moss Bryum argenteum Hedw. The BSCs were exposed to four UV-B supplemental treatments, including 2.75 (control), 3.08, 3.25, and 3.41Wm–2, for 40 days under field condition. In both the studied organisms, UV-B radiation significantly affected the physiological properties (total flavonoids, soluble proteins, soluble sugars, and proline contents). While marginally enhanced UV-B radiation for a short period favoured the growth of M. vaginatus and B. argenteum, excessively high and prolonged UV-B radiation suppressed the physiological properties of the two organisms. Moreover, response index revealed that UV-B radiation had more detrimental effects on B. argenteum, suggesting that B. argenteum is more sensitive to UV-B radiation than M. vaginatus. The findings of this study could help to predict and evaluate the possible changes in the structure and function of desert ecosystems, based on the variation in physiological responses of M. vaginatus and B. argenteum to enhanced UV-B radiation.

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