scholarly journals Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

2020 ◽  
Vol 8 (11) ◽  
pp. 1719
Author(s):  
Gi-Yong Jung ◽  
Sung-Keun Rhee ◽  
Young-Soo Han ◽  
So-Jeong Kim
Keyword(s):  
Methane Oxidation ◽  
Carbon Sources ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Phylogenomic Analysis ◽  
Atmospheric Methane ◽  
Methane Oxidizing Bacteria ◽  
Metabolic Versatility ◽  
Physiological Properties ◽  
Ph Range

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

scholarly journals USC γ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves

2021 ◽  
Author(s):  
Xiao-Yu Cheng ◽  
Xiao-Yan Liu ◽  
Hong-Mei Wang ◽  
Chun-Tian Su ◽  
Rui Zhao ◽  
...  
Keyword(s):  
Methane Oxidation ◽  
Community Composition ◽  
Atmospheric Methane ◽  
Ecological Significance ◽  
Community Interactions ◽  
Karst Caves ◽  
Methane Oxidizing Bacteria ◽  
Methane Sink

Karst caves have recently been demonstrated to be a potential atmospheric methane sink, presumably due to consumption by methane-oxidizing bacteria. However, the sparse knowledge about the diversity, distribution, and community interactions of methanotrophs requires us to seek further understanding of the ecological significance of methane oxidation in these ecosystems.

scholarly journals Facultative methanotrophs – diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Microbiology ◽  
2020 ◽  
Vol 166 (10) ◽  
pp. 894-908
Author(s):  
Muhammad Farhan Ul Haque ◽  
Hui-Juan Xu ◽  
J. Colin Murrell ◽  
Andrew Crombie
Keyword(s):  
Molecular Ecology ◽  
Significant Proportion ◽  
Vital Role ◽  
Short Chain ◽  
Atmospheric Methane ◽  
Biotechnological Potential ◽  
Content Type ◽  
Methane Oxidizing Bacteria ◽  
Metabolic Versatility ◽  
Carbon Compounds

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

scholarly journals ­Genomic data mining of the marine actinobacteriaStreptomycessp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2912 ◽  
Author(s):  
Agustina Undabarrena ◽  
Juan A. Ugalde ◽  
Michael Seeger ◽  
Beatriz Cámara
Keyword(s):  
Oxidative Stress ◽  
Culture Media ◽  
Genome Mining ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Morphological Characterization ◽  
Metal Resistance ◽  
Biological Traits ◽  
Strong Response ◽  
Metabolic Versatility

Streptomycessp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureusandL. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search inStreptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derivedStreptomycessp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described forStreptomyces. In addition,Streptomycessp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strainStreptomyces violaceoruberA3(2). Moreover,Streptomycessp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility ofStreptomycessp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

scholarly journals Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yuan Lin ◽  
Liye Wang ◽  
Ke Xu ◽  
Kan Li ◽  
Hongqiang Ren
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Phosphorus Removal ◽  
Heavy Metal Resistance ◽  
Resistance Mechanisms ◽  
Metal Resistance ◽  
Energy Utilization ◽  
Nitrogen And Phosphorus ◽  
Denitrifying Phosphorus Removal ◽  
Metabolic Versatility

Abstract Background Denitrifying phosphorus removal sludge (DPRS) is widely adopted for nitrogen and phosphorus removal in wastewater treatment but faces threats from heavy metals. However, a lack of understanding of the taxon-specific heavy metal-resistance mechanisms hinders the targeted optimization of DPRS’s robustness in nutrient removal. Results We obtained 403 high- or medium-quality metagenome-assembled genomes from DPRS treated by elevating cadmium, nickel, and chromium pressure. Then, the proteomic responses of individual taxa under heavy metal pressures were characterized, with an emphasis on functions involving heavy metal resistance and maintenance of nutrient metabolism. When oxygen availability was constrained by high-concentration heavy metals, comammox Nitrospira overproduced highly oxygen-affinitive hemoglobin and electron-transporting cytochrome c-like proteins, underpinning its ability to enhance oxygen acquisition and utilization. In contrast, Nitrosomonas overexpressed ammonia monooxygenase and nitrite reductase to facilitate the partial nitrification and denitrification process for maintaining nitrogen removal. Comparisons between phosphorus-accumulating organisms (PAOs) demonstrated different heavy metal-resistance mechanisms adopted by Dechloromonas and Candidatus Accumulibacter, despite their high genomic similarities. In particular, Dechloromonas outcompeted the canonical PAO Candidatus Accumulibacter in synthesizing polyphosphate, a potential public good for heavy metal detoxification. The superiority of Dechloromonas in energy utilization, radical elimination, and damaged cell component repair also contributed to its dominance under heavy metal pressures. Moreover, the enrichment analysis revealed that functions involved in extracellular polymeric substance formation, siderophore activity, and heavy metal efflux were significantly overexpressed due to the related activities of specific taxa. Conclusions Our study demonstrates that heavy metal-resistance mechanisms within a multipartite community are highly heterogeneous between different taxa. These findings provide a fundamental understanding of how the heterogeneity of individual microorganisms contributes to the metabolic versatility and robustness of microbiomes inhabiting dynamic environments, which is vital for manipulating the adaptation of microbial assemblages under adverse environmental stimuli.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

scholarly journals Heavy Metal Tolerance Trend in Extended-Spectrum β-Lactamase Encoding Strains Recovered from Food Samples

2021 ◽  
Vol 18 (9) ◽  
pp. 4718
Author(s):  
Kashaf Junaid ◽  
Hasan Ejaz ◽  
Iram Asim ◽  
Sonia Younas ◽  
Humaira Yasmeen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Metal Tolerance ◽  
Heavy Metal Tolerance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Food Samples ◽  
Esbl Production ◽  
Extended Spectrum ◽  
Retail Food ◽  
Esbl Producers

This study evaluates bacteriological profiles in ready-to-eat (RTE) foods and assesses antibiotic resistance, extended-spectrum β-lactamase (ESBL) production by gram-negative bacteria, and heavy metal tolerance. In total, 436 retail food samples were collected and cultured. The isolates were screened for ESBL production and molecular detection of ESBL-encoding genes. Furthermore, all isolates were evaluated for heavy metal tolerance. From 352 culture-positive samples, 406 g-negative bacteria were identified. Raw food samples were more often contaminated than refined food (84.71% vs. 76.32%). The predominant isolates were Klebsiella pneumoniae (n = 76), Enterobacter cloacae (n = 58), and Escherichia coli (n = 56). Overall, the percentage of ESBL producers was higher in raw food samples, although higher occurrences of ESBL-producing E. coli (p = 0.01) and Pseudomonas aeruginosa (p = 0.02) were observed in processed food samples. However, the prevalence of ESBL-producing Citrobacter freundii in raw food samples was high (p = 0.03). Among the isolates, 55% were blaCTX-M, 26% were blaSHV, and 19% were blaTEM. Notably, heavy metal resistance was highly prevalent in ESBL producers. These findings demonstrate that retail food samples are exposed to contaminants including antibiotics and heavy metals, endangering consumers.

scholarly journals Unexpected metabolic versatility among type II methanotrophs in the Alphaproteobacteria

2020 ◽  
Vol 401 (12) ◽  
pp. 1469-1477
Author(s):  
Anna Hakobyan ◽  
Werner Liesack
Keyword(s):  
Global Climate Change ◽  
Global Climate ◽  
Type Ii ◽  
Mixotrophic Growth ◽  
Methane Cycle ◽  
Oxidation Activity ◽  
Methane Oxidizing Bacteria ◽  
Metabolic Versatility ◽  
Carbon Compounds ◽  
Growth Requirement

AbstractAerobic methane-oxidizing bacteria, or methanotrophs, play a crucial role in the global methane cycle. Their methane oxidation activity in various environmental settings has a great mitigation effect on global climate change. Alphaproteobacterial methanotrophs were among the first to be taxonomically characterized, nowadays unified in the Methylocystaceae and Beijerinckiaceae families. Originally thought to have an obligate growth requirement for methane and related one-carbon compounds as a source of carbon and energy, it was later shown that various alphaproteobacterial methanotrophs are facultative, able to grow on multi-carbon compounds such as acetate. Most recently, we expanded our knowledge of the metabolic versatility of alphaproteobacterial methanotrophs. We showed that Methylocystis sp. strain SC2 has the capacity for mixotrophic growth on H2 and CH4. This mini-review will summarize the change in perception from the long-held paradigm of obligate methanotrophy to today’s recognition of alphaproteobacterial methanotrophs as having both facultative and mixotrophic capabilities.

scholarly journals Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus

2021 ◽  
Vol 9 (3) ◽  
pp. 499
Author(s):  
Majid Rasool Kamli ◽  
Nada A. Y. Alzahrani ◽  
Nahid H. Hajrah ◽  
Jamal S. M. Sabir ◽  
Adeel Malik
Keyword(s):  
Heavy Metal ◽  
Enzyme Activities ◽  
Heavy Metal Resistance ◽  
Industrial Applications ◽  
Metal Resistance ◽  
The Family ◽  
Antiviral Activities ◽  
Genome Level ◽  
Genome Analyses ◽  
Unique Species

Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications.

scholarly journals Retromobilization of heavy metal resistance genes in unpolluted and heavy metal polluted soil

1995 ◽  
Vol 18 (3) ◽  
pp. 191-203 ◽  
Author(s):  
Eva M. Top ◽  
Helene Rore ◽  
Jean-Marc Collard ◽  
Veerle Gellens ◽  
Galina Slobodkina ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Resistance Genes ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Polluted Soil
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