Diversity analysis and metagenomic insights into the Antibiotic Resistance and Metal Resistances among Hot Spring Bacteriobiome-insinuating inherent environmental baseline levels of Antibiotic and Metal tolerance (original) (raw)
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Journal of Global Antimicrobial Resistance, 2020
Mechanisms of occurrence and expression of antibiotic resistance genes (ARGs) in thermophilic bacteria are still unknown owing to limited research and data. In this research, comparative profiling of antibiotic resistance genes and metal tolerance genes among the thermophilic bacteria been done by functional metagenomic methods. Methods: Short gun metagenomic sequence data were generated using Illumina HiSeq 4000. Putative ARGs from the PROKKA predicted genes were identified with the ardbAnno V.1.0 script available from the ARDB (Antibiotic Resistance Genes Database) consortium using the non-redundant resistance genes as a reference. Putative MRGs were identified by using BacMetScan V.1.0. The whole-genome sequencing for bacterial isolate was performed using Illumina HiSeq 4000 sequencing technology with a paired-end sequencing module. Results: Metagenomic analysis showed the dominance of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes in two hot springs of Sikkim. ARG analysis through shotgun gene sequencing was found to be negative in the case of thermophilic bacteria. However, few genes were detected but they were showing maximum similarity with mesophilic bacteria. Concurrently, metal resistance genes were also detected in the metagenome sequence of hot springs. Detection of metal resistance gene and absence of ARG's investigated by whole genome sequencing, in the reference genome sequence of thermophilic Geobacillus also conveyed the same message. Conclusion: The study of ARGs and MRGs (Heavy metal resistance gene) among culturable and nonculturable bacteria from the hot springs of Sikkim via metagenomics showed a preferential selection of MRGs over ARGs. The absence of ARGs also declines the fact of co-selection of ARGs and MRGs in these environments. This evolutionary selection of metal resistance over antibiotic genes may have been necessary to survive in the geological craters which are full of different metals from earth sediments rather than antibiotics. Furthermore, the selection could be environment driven depending on the susceptibility of ARGs in thermophilic environment as it reduces the chances of horizontal gene transfer.
Characterization and 16S rDNA Identification of Thermo-tolerant Bacteria Isolated from Hot Springs
2007
High water temperature exerts selection pressure on microbial species leading to specific flora that survives and tolerates heat stress. A total of 229 bacterial cultures were isolated from ten different hot springs at Siwa, Matrouh, Egypt. The number and percentage of heat tolerant bacteria were assessed. Only 13 (5.6%) of bacterial isolates were able to tolerate and survive 65°C. These bacterial isolates were genetically diverse according to RAPD and Box-PCR analyses using different primers. RAPD, Box-PCR and 16S rRNA sequence analysis confirmed the abundance of bacterial genotypes and that they were closely related to Bacillus licheniformis and Bacillus pumilus, based on 100% similarity in their 16S rDNA gene sequences. Bacillus licheniformis responded to one hour of thermal stress at elevated temperature from 30°C to 65°C by synthesizing different heat shock proteins (HSPs) with molecular weights ranging between .30-120 kDa.
2022
The hot spring microbiome is a complex assemblage of micro- and macro- organisms, however, the understanding and projection of enzymatic repertoire that access earth’s integral ecosystem processes remains limited. The composite microbial communities drive global carbon, sulfur, oxygen, iron and nitrogen cycles and other metabolic mechanism involved in heavy metal tolerance and degradation. Interestingly, the Khirganga hot spring microbiome displayed an astounding taxonomical diversity revealed by examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) from at least 12 bacterial and 2 archaeal phyla. Over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorous, sulfur and 598 genes encoding enzymes for metals resistance from cadmium, zinc, chromium, arsenic and copper. The MAGs also possess 229 biosynthetic gene clusters dominated by bacteriocins and terpenes could be exploited in medicinal industries. Their metabolic roles ...
DECIPHERING THE MICROBIAL DIVERSITY OF TATTAPANI HOT WATER SPRING USING METAGENOMIC APPROACH
Heat stress due to changing environmental conditions is a problem as it negatively affects plant growth and development leading to reduction in crop yield. Thermal springs are major source of potentially significant but untapped microbial diversity encoding novel genes related to high temperature tolerance. The genes involved in the heat tolerance mechanism of thermophiles can serve as a valuable resource to improve high temperature tolerance in crop plants. Metagenomics bypasses the need for isolation or cultivation of microorganisms as it deals with direct isolation of nucleic acids from environmental samples. The present study was designed to analyse the profile of microbial community inhabiting hot water spring Tattapani, Himachal Pradesh, India. The spring water temperature at the discharge point was recorded as 65°C and pH 7.5. Two sets of universal 16S rRNA gene specific primers namely U789F-U1053R and MGUF-MGUR were used to amplify partial 16S rRNA gene (from V5-V6 and V3-V6 regions respectively) from metagenomic DNA. Sequencing and bioinformatic analysis revealed that bacterial phylum Proteobacteria was most abundant, constituting 36% and 40% of the total bacteria identified using V5-V6 and V3-V6 regions, respectively. Other phyla Thermodesulfobacteria (9.3%), Firmicutes (7.5%), Deinococcus-thermus (7%), Bacteriodates (2.5%), Aquificae (2%) were assigned to sequences amplified from V5-V6 region while phyla Firmicutes (18%), Bacteriodates (6%), Chloroflexi (2%) were assigned to sequences amplified from V3-V6 region. A significant number of sequences (30.5% and 20.5%) from region V3-V6 and V5-V6 respectively did not show homology with existing database and were recorded as unclassified Bacteria. The information generated in this study will help us in understanding the microbial ecology of hot springs.
Metagenomic Analysis: Microbial Diversity of Hot Spring Water Near Mumbai Region (India)
2018
A large diversity of microorganisms are being harbored by natural environments and most of them have not yet been identified /or characterized. Extremophilic microorganisms are known to survive in diverse extreme conditions, such as high or low temperatures, high salinity etc.Thermophiles and hyper-thermophiles have the ability to survive in environments with very high temperature such as in hot springs. Sample was collected from hot spring near Nimbavali village, Ganeshpuri, Mumbai region, Maharashtra, India. The bacterial diversity as determined by sequencing the hypervariable region V3 of the 16S rRNA belonging to the microbial community of the Ganeshpuri (Nimbavali) hot spring is presented here. In the taxonomy classification of OTUs, only top ten OTUs were selected and rests were shown as others. Top ten OTUs at phylum level wereProteobacteria, Firmicutes,Bacteriodetes;class-Gammaprotobactera, Betaprotobacteria, Clostridia; Order-Clostridiales, Bacteriodales, Rhodothermales; family-Halobacteriaece,Comamondaceae; genus-Protovella, Oscillospira;and species-Bifidobacteriumadolescentis. In all of the above significant percentage of OTUs were found to be unknown or not yet classified. These unknown microbes could serve as the source of novel products. Our data provide new information on hot spring bacteria and shed light on their abundance, diversity, distribution and coexisting organisms.
Frontiers in Microbiology
Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51 • C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39 • C vs. Deinococcus at 51 • C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an
Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection
The ISME Journal, 2016
The high frequency of antibiotic resistance is a global public health concern. More seriously, widespread metal pressure in the environment may facilitate the proliferation of antibiotic resistance via coselection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Given the lack of comprehensive understanding of the ARG and MRG coselection, in this study both abundance relationship and genetic linkage between ARGs and MRGs were rigorously investigated by performing a genomic analysis of a large complete genome collection. Many more ARGs were enriched in human-associated bacteria compared with those subjected to less anthropogenic interference. The signatures of ARG and MRG co-occurrence were much more frequent and the distance linkages between ARGs and MRGs were much more intimate in human pathogens than those less human-associated bacteria. Moreover, the co-occurrence structures in the habitat divisions were significantly different, which could be attributed to their distinct gene transfer potentials. More exogenous ARGs and MRGs on the genomes of human pathogens indicated the importance of recent resistance acquisition in resistome development of human commensal flora. Overall, the study emphasizes the potential risk associated with ARG and MRG coselection of both environmental and medical relevance.
Bioresource technology, 2017
This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed. Partial redundancy analysis (RDA) showed that shifts in temperature were the key factors affecting a decrease in ARGs. Shifts in temperature led to decreased amounts of ARGs by reducing resistome and bacterial diversity, rather than by lowering horizontal transfer potential via intI1 or co-resistance via MRGs.
Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis
MicrobiologyOpen, 2017
A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP(®) ). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%. Eukaryotic microorganisms were detected but with varying abundances (0.6%-15%). Because most of the detected sequences were found to belong to the domain of bacteria (196,936 sequences out 288,452), the bacterial sequences were utilized for further microbial analyses. With respect to alpha and beta diversity, samples were rarefied to 30,000 sequences and bootstrapped at 10,000...
Deciphering the diversity of culturable thermotolerant bacteria from Manikaran hot springs
The aim of this study was to analyze and characterize the diversity of culturable thermotolerant bacteria in Manikaran hot springs. A total of 235 isolates were obtained employing different media, and screened for temperature tolerance (40 °C–70 °C). A set of 85 isolates tolerant to 45 °C or above were placed in 42 phylogenetic clusters after amplified ribosomal DNA restriction analysis (16S rRNA-ARDRA). Sequencing of the 16S rRNA gene of 42 representative isolates followed by BLAST search revealed that the majority of isolates belonged to Firmicutes, followed by equal representation of Actinobacteria and Proteobacteria. Screening of representative isolates (42 ARDRA phylotypes) for amylase activity revealed that 26 % of the isolates were positive, while 45 % exhibited protease activity, among which one amylase and six protease producers were tolerant up to 70 °C. BIOLOG-based identification of 13 isolates exhibiting temperature tolerance up to 70 °C, using carbon utilization patterns and sensitivity to chemicals, revealed a high degree of correlation with identification based on 16S rRNA gene sequencing for all isolates, except one (M48). These promising isolates showing a range of useful metabolic attributes demand to be explored further for industrial and agricultural applications.