Comparative Genomics Begins to Unravel the Ecophysiology of Bioleaching

2009 ◽  
Vol 71-73 ◽  
pp. 143-150 ◽  
Author(s):  
David S. Holmes ◽  
Juan Pablo Cárdenas ◽  
Jorge H. Valdés ◽  
Raquel Quatrini ◽  
M. Esparza ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Iron Uptake ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Biological Processes ◽  
Metabolic Potential ◽  
Polysaccharide Biosynthesis ◽  
Usable Knowledge ◽  
Spatial And Temporal Changes ◽  
Acidic Environments

The metabolic potential of 16 bioleaching microorganisms (Eubacteria and Archaea) has been investigated, allowing the prediction of potential inter- and intra-species physiological interactions (ecophysiology) during spatial and temporal changes that are known to occur within industrial bioleaching heaps. Genome analysis has allowed preliminary models to be built for genes and pathways involved in key processes such as nitrogen and carbon cycling, sulfur and iron uptake and homeostasis, extra-cellular polysaccharide biosynthesis, heavy metal resistance and energy metabolism. This paper will focus on the diverse ways that microorganisms obtain carbon from their environment with a particular emphasis on elucidating how these processes might be expected to vary over space and time during the lifetime of a bioleaching operation. It is anticipated that this knowledge will improve our understanding of fundamental biological processes in extremely acidic environments and it is hoped that it will capture usable knowledge that can be applied to bioleaching. Comparative genomics between two strains of Acidthiobacillus ferrooxidans highlights the importance of lateral gene transfer in increasing genetic and metabolic potential and suggests that classical molecular DNA techniques, such as rDNA typing, significantly underestimate the microbial diversity of bioleaching heaps.

scholarly journals Genomic Potential of Marinobacter aquaeolei, a Biogeochemical “Opportunitroph”

2011 ◽  
Vol 77 (8) ◽  
pp. 2763-2771 ◽  
Author(s):  
Esther Singer ◽  
Eric A. Webb ◽  
William C. Nelson ◽  
John F. Heidelberg ◽  
Natalia Ivanova ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Genome Structure ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Polluted Water ◽  
Metabolic Potential ◽  
Genetic Characteristics ◽  
Content Type ◽  
Marinobacter Aquaeolei ◽  
The Many

ABSTRACTThe genus ofMarinobacteris one of the most ubiquitous in the global oceans and assumed to significantly impact various biogeochemical cycles. The genome structure and content ofMarinobacter aquaeoleiVT8 was analyzed and compared with those from other organisms with diverse adaptive strategies. Here, we report the many “opportunitrophic” genetic characteristics and strategies thatM. aquaeoleihas adopted to promote survival under various environmental conditions. Genome analysis revealed its metabolic potential to utilize oxygen and nitrate as terminal electron acceptors, iron as an electron donor, and urea, phosphonate, and various hydrocarbons as alternative N, P, and C sources, respectively. Miscellaneous sensory and defense mechanisms, apparently acquired via horizontal gene transfer, are involved in the perception of environmental fluctuations and antibiotic, phage, toxin, and heavy metal resistance, enabling survival under adverse conditions, such as oil-polluted water. Multiple putative integrases, transposases, and plasmids appear to have introduced additional metabolic potential, such as phosphonate degradation. The genomic potential ofM. aquaeoleiand its similarity to other opportunitrophs are consistent with its cosmopolitan occurrence in diverse environments and highly variable lifestyles.

scholarly journals Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

2021 ◽  
Vol 9 (7) ◽  
pp. 1402
Author(s):  
Sania Arif ◽  
Corinna Willenberg ◽  
Annika Dreyer ◽  
Heiko Nacke ◽  
Michael Hoppert
Keyword(s):  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
Heavy Metal Resistance ◽  
18S Rrna Gene ◽  
Metal Resistance ◽  
Geothermal Field ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Eukaryotic Diversity

The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment.

scholarly journals Analysis and Comparative Genomics of the SXT/R391 Family ICE, pMERPH

2019 ◽  
Author(s):  
Michael P. Ryan ◽  
Shannon Slattery ◽  
J. Tony Pembroke
Keyword(s):  
Comparative Genomics ◽  
De Novo ◽  
Gene Prediction ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Restriction Digestion ◽  
Sequencing Technology ◽  
Phenotypic Analysis ◽  
The United Kingdom ◽  
Integrative And Conjugative Element

The aim of this study was to analyse pMERPH, the first integrative and conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and to determine its relationship to other members of the SXT/R391 family of ICEs. Whole Genome Sequencing of Escherichia coli isolate KH802 (which contains the ICE pMERPH) was performed using Illumina sequencing technology. pMERPH was evaluated by de novo assembly of the sequenced genome, via gene prediction and annotation tools, and phenotypic analysis via comparative genomics to other members of the SXT/R391 ICEs. pMERPH has a size of 110 Kb and has 112 predicted ORFs making it one of the bigger SXT/R391 ICE’s thus far characterised. The “Hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences and heavy metal resistance genes that give resistance to mercury and arsenate. pMERPH is closely related to the SXT-like elements from widely dispersed geographic areas. The sequencing of pMERPH increases the knowledge of the earliest isolated SXT/R391family members and may provide insight on the emergence of such elements.

scholarly journals Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

2020 ◽  
Vol 11 ◽  
Author(s):  
Erika Corretto ◽  
Livio Antonielli ◽  
Angela Sessitsch ◽  
Christoph Höfer ◽  
Markus Puschenreiter ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Comparative Genomics ◽  
Secondary Metabolites ◽  
Heavy Metal Resistance ◽  
Metal Resistance

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 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

scholarly journals Replication of Staphylococcal Multiresistance Plasmids

2000 ◽  
Vol 182 (8) ◽  
pp. 2170-2178 ◽  
Author(s):  
Neville Firth ◽  
Sumalee Apisiridej ◽  
Tracey Berg ◽  
Brendon A. O'Rourke ◽  
Steve Curnock ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Replication Initiation ◽  
Conjugative Plasmid ◽  
Rolling Circle ◽  
Segregational Stability ◽  
Structural And Functional Properties ◽  
Resistance Plasmids ◽  
Genes Encoding

ABSTRACT Based on structural and functional properties, three groups of large staphylococcal multiresistance plasmids have been recognized, viz., the pSK1 family, pSK41-like conjugative plasmids, and β-lactamase–heavy-metal resistance plasmids. Here we describe an analysis of the replication functions of a representative of each of these plasmid groups. The replication initiation genes from theStaphylococcus aureus plasmids pSK1, pSK41, and pI9789::Tn552 were found to be related to each other and to the Staphylococcus xylosus plasmid pSX267 and are also related to rep genes of several plasmids from other gram-positive genera. Nucleotide sequence similarity between pSK1 and pI9789::Tn552 extended beyond theirrep genes, encompassing upstream divergently transcribed genes, orf245 and orf256, respectively. Our analyses revealed that genes encoding proteins related to the deducedorf245 product are variously represented, in several types of organization, on plasmids possessing six seemingly evolutionarily distinct types of replication initiation genes and including both theta-mode and rolling-circle replicons. Construction of minireplicons and subsequent functional analysis demonstrated that orf245is required for the segregational stability of the pSK1 replicon. In contrast, no gene equivalent to orf245 is evident on the conjugative plasmid pSK41, and a minireplicon encoding only the pSK41 rep gene was found to exhibit a segregational stability approaching that of the parent plasmid. Significantly, the results described establish that many of the large multiresistance plasmids that have been identified in clinical staphylococci, which were formerly presumed to be unrelated, actually utilize an evolutionarily related theta-mode replication system.

Screening of heavy metal and antibiotic resistance among Proteus vulgaris isolates from hospital wastewater of Northern India

2021 ◽  
Vol 19 ◽  
Author(s):  
Manzar Alam ◽  
Mohd Imran ◽  
Syed Sayeed Ahmad
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Multiple Drug Resistance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Antibiotics Resistance ◽  
Proteus Vulgaris ◽  
Resistance To Antibiotics ◽  
Transfer Frequency ◽  
Resistance Patterns

Background: Microbial resistance to antibiotics and heavy metals is a rising problem in the world today. All the Proteus vulgaris isolates showed their MIC in between 50-1600 µg/ml. Of 70% and 46% of the isolates showed their MIC at 800-1200 µg/ml against Zn2+ and Cu2+ while 80% of the isolates showed their MIC at 100-200 µg/ml against Ni2+, respectively. All Proteus vulgaris isolates also exhibited multiple resistance patterns (2-7 heavy metals) in different combination of metals. The Multi metal resistance Index (MHMR) ranges were found (0.04-0.5). Methods: A high level of antibiotics resistance was observed against Methicillin (100%) and least to Oflaxicin (6%), Gentamycine and Neomycin (10%). All Proteus vulgaris isolates also showed multiple drug resistance patterns (2-12 antibiotics) in different combination of antibiotics. The MAR index ranges were found (0.02-0.7). Of 98%, 84% and 80% of the total isolates showed urease, gelatinase and amylase activity. Results: The Proteus vulgaris isolates contained plasmid of size ranging from 42.5 to 57.0kb and molecular weight of plasmids ranged from 27.2 to 37.0 MD. Incidences of resistance transfer, 7 pairs of isolates were assessed for the transfer of the antibiotic/ heavy metal resistance markers. The higher (4.4x10-1 and 3.4x10-1) transfer frequency was observed among antibiotic and heavy metal while lower transfer frequency were (5.0x10-2 and 1.0x10-2) showed against antibiotic and heavy metal in both the medium from the entire site tested, respectively. Conclusion: Indicating the high threat of environmental pollution and appearance of heavy metal resistance which may support the enlargement of resistance to antibiotics among the pathogens.

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