scholarly journals Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils

2021 ◽  
Author(s):  
Adrian Gorecki ◽  
Stine Holm ◽  
Mikolaj Dziurzynski ◽  
Matthias Winkel ◽  
Sizhong Yang ◽  
...  
Keyword(s):  
Active Layer ◽  
Bacterial Communities ◽  
Extraction Methods ◽  
Metal Resistance ◽  
Rapid Adaptation ◽  
Tundra Soils ◽  
Genetic Traits ◽  
Functional Potential ◽  
Stress Response Genes ◽  
Genes Encoding

AbstractPlasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.

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.

scholarly journals Chromosomal rearrangements and protein globularity changes inMycobacterium tuberculosisisolates from cerebrospinal fluid

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2484 ◽  
Author(s):  
Seow Hoon Saw ◽  
Joon Liang Tan ◽  
Xin Yue Chan ◽  
Kok Gan Chan ◽  
Yun Fong Ngeow
Keyword(s):  
Cerebrospinal Fluid ◽  
Chromosomal Rearrangements ◽  
Genome Sequences ◽  
Genetic Traits ◽  
Genomic Features ◽  
Synonymous Snps ◽  
Genome Wide ◽  
Genes Encoding ◽  
Transcription Regulators ◽  
Central Nervous System Invasion

BackgroundMeningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains ofMycobacterium tuberculosis(Mtb) might have genetic traits associated with neurotropism.MethodsIn this study, we generated whole genome sequences of eight clinical strains ofMtbthat were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratoryMtbgenomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratoryMtb.ResultsGenome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratoryMtbgenomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated withStreptococcus pneumoniaemeningitis andNeisseria meningitidisvirulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study.DiscussionThe occurrence of in silico genetic differences in CSF-derived but not respiratoryMtbsuggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infection is more likely to be related to the expression of multiple virulence factors on interaction with host defences than to CNS tropism associated with specific genetic traits.

scholarly journals Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nojood A. Aalismail ◽  
David K. Ngugi ◽  
Rubén Díaz-Rúa ◽  
Intikhab Alam ◽  
Michael Cusack ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Sequences ◽  
Biofilm Formation ◽  
Atmospheric Transport ◽  
Taxonomic Diversity ◽  
Functional Metagenomics ◽  
Genetic Traits ◽  
Gene Catalogue ◽  
Range Transport ◽  
Genes Encoding

Abstract Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

scholarly journals Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Jana Voříšková ◽  
Bo Elberling ◽  
Anders Priemé
Keyword(s):  
Organic Matter ◽  
Seasonal Variation ◽  
Snow Cover ◽  
Bacterial Communities ◽  
Winter Precipitation ◽  
Fungal Communities ◽  
Tundra Soils ◽  
Short Term ◽  
Fungal Community Composition ◽  
Climate Manipulation

Abstract Background Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season. Results The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted. Conclusions We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.

scholarly journals Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Ankita Kothari ◽  
Drishti Soneja ◽  
Albert Tang ◽  
Hans K. Carlson ◽  
Adam M. Deutschbauer ◽  
...  
Keyword(s):  
Natural Transformation ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Metal Resistance ◽  
Mercury Resistance ◽  
Bacterial Isolates ◽  
Rapid Adaptation ◽  
Bacterial Strains ◽  
Content Type ◽  
Native Plasmid

ABSTRACT Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli. Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses. IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

scholarly journals Phenotypic and Transcriptomic Analyses Demonstrate Interactions between the Transcriptional Regulators CtsR and Sigma B in Listeria monocytogenes

2007 ◽  
Vol 73 (24) ◽  
pp. 7967-7980 ◽  
Author(s):  
Yuewei Hu ◽  
Sarita Raengpradub ◽  
Ute Schwab ◽  
Chris Loss ◽  
Renato H. Orsi ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Response ◽  
Heat Resistance ◽  
Parent Strain ◽  
Inducible Promoter ◽  
Heat Sensitivity ◽  
Intestinal Epithelial ◽  
Class Iii ◽  
Stress Response Genes ◽  
Genes Encoding

ABSTRACT Listeria monocytogenes σB positively regulates the transcription of class II stress response genes; CtsR negatively regulates class III stress response genes. To identify interactions between these two stress response systems, we constructed L. monocytogenes ΔctsR and ΔctsR ΔsigB strains, as well as a ΔctsR strain expressing ctsR in trans under the control of an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible promoter. These strains, along with a parent and a ΔsigB strain, were assayed for motility, heat resistance, and invasion of human intestinal epithelial cells, as well as by whole-genome transcriptomic and quantitative real-time PCR analyses. Both ΔctsR and ΔctsR ΔsigB strains had significantly higher thermotolerances than the parent strain; however, full heat sensitivity was restored to the ΔctsR strain when ctsR was expressed in trans. Although log-phase ΔctsR was not reduced in its ability to infect human intestinal cells, the ΔctsR ΔsigB strain showed significantly lower invasion efficiency than either the parent strain or the ΔsigB strain, indicating that interactions between CtsR and σB contribute to invasiveness. Statistical analyses also confirmed interactions between the ctsR and the sigB null mutations in both heat resistance and invasion phenotypes. Microarray transcriptomic analyses and promoter searches identified (i) 42 CtsR-repressed genes, (ii) 22 genes with lower transcript levels in the ΔctsR strain, and (iii) at least 40 genes coregulated by both CtsR and σB, including genes encoding proteins with confirmed or plausible roles in virulence and stress response. Our data demonstrate that interactions between CtsR and σB play an important role in L. monocytogenes stress resistance and virulence.

scholarly journals Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings

2011 ◽  
Vol 193 (22) ◽  
pp. 6408-6409 ◽  
Author(s):  
Yanbing Lin ◽  
Xiuli Hao ◽  
Laurel Johnstone ◽  
Susan J. Miller ◽  
David A. Baltrus ◽  
...  
Keyword(s):  
Mine Tailings ◽  
Draft Genome ◽  
Metal Resistance ◽  
Content Type ◽  
Resistant Species ◽  
Number Of Genes ◽  
Genes Encoding ◽  
Zinc Mine ◽  
Copper Zinc ◽  
High Level

A draft genome sequence of Streptomyces zinciresistens K42, a novel Streptomyces species displaying a high level of resistance to zinc and cadmium, is presented here. The genome contains a large number of genes encoding proteins predicted to be involved in conferring metal resistance. Many of these genes appear to have been acquired through horizontal gene transfer.

scholarly journals Rampant prophage movement among transient competitors drives rapid adaptation during infection

2021 ◽  
Author(s):  
Christopher W. Marshall ◽  
Erin S. Gloag ◽  
Christina Lim ◽  
Daniel J. Wozniak ◽  
Vaughn S. Cooper
Keyword(s):  
Microbial Communities ◽  
Chronic Infection ◽  
Evolutionary Dynamics ◽  
Functional Genes ◽  
Rapid Adaptation ◽  
Chronic Infections ◽  
Global Regulators ◽  
New Genes ◽  
Biofilm Production ◽  
Genes Encoding

AbstractInteractions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny. Here, we show that active lysogeny can fuel rapid, parallel adaptations in establishing a chronic infection. These recombination events repeatedly disrupted genes encoding global regulators, leading to increased cyclic-di-GMP levels and elevated biofilm production. The implications of prophage-mediated adaptation are broad, as even transient members of microbial communities can alter the course of evolution and generate persistent phenotypes associated with poor clinical outcomes.One Sentence SummaryBacteriophage act as genetic regulators that are key to establishing chronic infections and are rapidly shared among co-infecting strains.

Sign in / Sign up

Export Citation Format

Share Document