scholarly journals Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism

2018 ◽  
Author(s):  
Camilla L. Nesbø ◽  
Rhianna Charchuk ◽  
Stephen M. J. Pollo ◽  
Karen Budwill ◽  
Ilya V. Kublanov ◽  
...  
Keyword(s):  
Sulfur Compound ◽  
Anthropogenic Activities ◽  
Genomic Analysis ◽  
Distribution Patterns ◽  
Phylogeographic Structure ◽  
Average Nucleotide Identity ◽  
Genomic Features ◽  
Geographical Separation ◽  
Pyruvate:Ferredoxin Oxidoreductase ◽  
Thiosulfate Reduction

SummaryThe genusMesotoga, the only described mesophilicThermotogaelineage, is common in mesothermic anaerobic hydrocarbon-rich environments. Besides mesophily,Mesotogadisplays lineage-specific phenotypes, such as no or little H2production and dependence on sulfur-compound reduction, which may influence its ecological role. We used comparative genomics of 18Mesotogastrains (pairwise 16S rRNA identity > 99%) and a transcriptome ofM. primato investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage-specific metabolism. We propose thatMesotogaaccomplish H2oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase-complex and that a pyruvate:ferredoxin oxidoreductase acquired fromClostridiais responsible for oxidizing acetate. Phylogenetic analysis revealed three distinctMesotogalineages (89.6-99.9% average nucleotide identity [ANI] within lineages, 79.3-87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra-lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important forMesotogathan hyperthermophilicThermotogaand we hypothesize that distribution ofMesotogais constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expandedMesotogahabitats and dispersal capabilities.Originality-Significance StatementThis study comprises one of the first whole-genome-based phylogeographic analyses of anaerobic mesophiles, and our data suggest that such microbes are more restricted by geography than are thermophiles (and mesophilic aerobes). This is likely to be a general trait for similar anaerobic organisms – and therefore broadly relevant to and testable in other environments. Moreover,Mesotogabacteria are part of the largely understudied subsurface ecosystem that has relatively recently been recognized as a new and important biosphere. Understanding the forces responsible for the distribution of organisms in the subsurface, as well as the identification of genes responsible forMesotoga’s distinct metabolism, will contribute to the understanding of these communities.

scholarly journals Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

mSphere ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Shaomei He ◽  
Sarah L. R. Stevens ◽  
Leong-Keat Chan ◽  
Stefan Bertilsson ◽  
Tijana Glavina del Rio ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Potential Role ◽  
Carbon Sources ◽  
Genomic Analysis ◽  
Distribution Patterns ◽  
Eutrophic Lake ◽  
Genomic Diversity ◽  
Extracellular Electron Transfer ◽  
Different Origins ◽  
Encoding Genes

ABSTRACT Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling. Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called “Planctomycete-specific” cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

scholarly journals Epigenomic, genomic, and transcriptomic landscape of schwannomatosis

2020 ◽  
Vol 141 (1) ◽  
pp. 101-116
Author(s):  
Sheila Mansouri ◽  
Suganth Suppiah ◽  
Yasin Mamatjan ◽  
Irene Paganini ◽  
Jeffrey C. Liu ◽  
...  
Keyword(s):  
Gene Fusion ◽  
Somatic Mutations ◽  
Genomic Analysis ◽  
Germline Mutations ◽  
Tumor Location ◽  
Molecular Signature ◽  
Structural Rearrangements ◽  
Genomic Features ◽  
Cancer Predisposition Syndrome ◽  
Neuronal Tumors

AbstractSchwannomatosis (SWNTS) is a genetic cancer predisposition syndrome that manifests as multiple and often painful neuronal tumors called schwannomas (SWNs). While germline mutations in SMARCB1 or LZTR1, plus somatic mutations in NF2 and loss of heterozygosity in chromosome 22q have been identified in a subset of patients, little is known about the epigenomic and genomic alterations that drive SWNTS-related SWNs (SWNTS-SWNs) in a majority of the cases. We performed multiplatform genomic analysis and established the molecular signature of SWNTS-SWNs. We show that SWNTS-SWNs harbor distinct genomic features relative to the histologically identical non-syndromic sporadic SWNs (NS-SWNS). We demonstrate the existence of four distinct DNA methylation subgroups of SWNTS-SWNs that are associated with specific transcriptional programs and tumor location. We show several novel recurrent non-22q deletions and structural rearrangements. We detected the SH3PXD2A-HTRA1 gene fusion in SWNTS-SWNs, with predominance in LZTR1-mutant tumors. In addition, we identified specific genetic, epigenetic, and actionable transcriptional programs associated with painful SWNTS-SWNs including PIGF, VEGF, MEK, and MTOR pathways, which may be harnessed for management of this syndrome.

scholarly journals Genomic analysis revealed a novel genotype of methicillin-susceptible Staphylococcus aureus isolated from a fatal sepsis case in dengue patient

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Soo Tein Ngoi ◽  
Wen Kiong Niek ◽  
Yee Wan Lee ◽  
Sazaly AbuBakar ◽  
Cindy Shuan Ju Teh
Keyword(s):  
Staphylococcus Aureus ◽  
Draft Genome ◽  
Gc Content ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Whole Genome Sequence ◽  
Genomic Features ◽  
Dengue Patient ◽  
Mssa Strain ◽  
Novel Genotype

AbstractStaphylococcus aureus (S. aureus) is an opportunistic pathogen capable of causing serious health implications in susceptible individuals once it invades the host’s protective barriers. Methicillin-susceptible S. aureus (MSSA) often receives lesser attention although it has been frequently associated with serious infections in human. We aim to investigate the genomic features of a highly virulent yet pan susceptible MSSA strain (coded as HS-MSSA) which caused concurrent bacteraemia in a dengue patient, ultimately resulted in sepsis death of the patient. Whole genome sequence analysis was performed. The draft genome of HS-MSSA is approximately 2.78 Mb (GC content = 32.7%) comprising of 2637 predicted coding sequences. In silico genotyping of the HS-MSSA strain revealed a novel combined genotype (t091/ST2990). The HS-MSSA carries a SaPIn1-like pathogenicity island that harbours the staphylococcal enterotoxin and enterotoxin-like genes (sec3 and selL). The strain-specific β-lactamase (blaZ)-bearing plasmid region was identified in HS-MSSA. Core genome phylogeny showed that the HS-MSSA strain shared a common ancestry with the European MRSA clone. We report herein the genomic features of an MSSA lineage with novel genotype previously not reported elsewhere.

scholarly journals Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Natalya Yutin ◽  
Sean Benler ◽  
Sergei A. Shmakov ◽  
Yuri I. Wolf ◽  
Igor Tolstoy ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Human Gut ◽  
Genomic Features ◽  
Viral Genomes ◽  
Founding Member ◽  
Phage Dna ◽  
Conserved Genes ◽  
Phage Genomics ◽  
Self Splicing

AbstractCrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.

scholarly journals Stand Structure, Regeneration Status and Distribution Patterns of Six Important Tree Species along Altitudinal Gradients at the Kilum-Ijim Forest Reserve, Cameroon

2020 ◽  
pp. 41-57
Author(s):  
Franklin Bantar Nworo ◽  
Njoh Roland Ndah ◽  
Egbe Enow Andrew
Keyword(s):  
Tree Species ◽  
Stand Structure ◽  
Anthropogenic Activities ◽  
Elevation Gradient ◽  
Basal Area ◽  
Tree Height ◽  
Distribution Patterns ◽  
Forest Reserve ◽  
Altitudinal Gradients ◽  
Regeneration Status

Tropical montane forests are considered to be one of the most species diverse ecosystems. These areas pose specific edaphic and environmental characteristics which enable these areas to harbour wide varieties of organisms. Some of these organisms are threatened and others are endemic to the area. The quest for food and other resources has resulted to indiscriminate exploitation of these montane forest. This study aimed to investigate the stand structure, distribution patterns and regeneration status of six tree species (Nuxia congesta, Pittosporum mannii, Podocarpu slatifolius, Prunus africana, Schefflera abyssinica and Syzygium guineense) along altitudinal gradients in the Kilum-Ijim Forest Reserve, Cameroon. A total of six study plots of one hectare (100 x100 m) each were laid across a 120 m elevation gradient. Two plots were established at each altitudinal gradient with elevations 2377 m, 2437 m and 2497 m. Measurements were taken for tree height, diameter at breast height (DBH 1.3 m) for the tree and poles. The digital Vernier callipers were used to measure collar diameters of seedlings and saplings. The highest tree density of 385 stems/ha was recorded for N. congesta at altitude 2497 m while the least was 20 stems/ha for S. abyssinica at altitude 2377m. The highest seedling density was 1563 stems/ha recorded for P. mannii at altitude 2377m and the least was noted for S. abyssinica at all the three altitudinal gradients.  Nuxia congesta had the highest basal area of 8809.23m2/ha at altitude 2437 m and the least of 74.82m2/ha for P. latifolius at altitude 2437 m.  The highest IVI occurred in N. congesta (131.91) was recorded at altitude 2377 m and the least (24.91) occurred in P. latifolius at altitude 2437 m. The spatial distributions of studied tree species were generally clumped and irregular. The regenerations of species were generally poor, though fair regenerations were noticed for N. congesta and P. mannii. The results showed that the six tree species were highly disturbed by anthropogenic activities. It is therefore imperative to develop and implement effective conservation measures to sustain the biodiversity of this reserve.

scholarly journals Evaluation of spatial spreading of phyto-available sulphur and micronutrients in cultivated coastal soils

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258166
Author(s):  
A. K. Shukla ◽  
S. K. Behera ◽  
R. Tripathi ◽  
C. Prakash ◽  
A. K. Nayak ◽  
...  
Keyword(s):  
Soil Ph ◽  
Crop Production ◽  
Agricultural Soils ◽  
Anthropogenic Activities ◽  
Distribution Patterns ◽  
Soil Samples ◽  
Soil Parameters ◽  
Mean Values ◽  
Coastal Soils ◽  
Spatial Spreading

Understanding the spatial spreading patterns of plant-available sulphur (S) (AS) and plant-available micronutrients (available zinc (AZn), available iron (AFe), available copper (ACu), available manganese (AMn) and available boron (AB)) in soils, especially in coastal agricultural soils subjected to various natural and anthropogenic activities, is vital for sustainable crop production by adopting site-specific nutrient management (SSNM) strategies. We studied the spatial distribution patterns of AS, AZn, AFe, ACu, AMn, and AB in cultivated soils of coastal districts of India using geostatistical approaches. Altogether 39,097 soil samples from surface (0 to 15 cm depth) layers were gathered from farm lands of 68 coastal districts. The analysis of soil samples was carried out for soil pH, electrical conductivity (EC), soil organic carbon (SOC) and AS, AZn, AFe, ACu, AMn, and AB. Soil pH, EC and SOC varied from 3.70 to 9.90, 0.01 to 7.45 dS m-1 and 0.02 to 3.74%, respectively. The concentrations of AS, AZn, AFe, ACu, AMn, and AB varied widely in the study area with their corresponding mean values were 37.4±29.4, 1.50±1.53, 27.9±35.1, 2.14±1.74, 16.9±18.4 and 1.34±1.52 mg kg-1, respectively. The coefficient of variation values of analyzed soil parameters varied from 14.6 to 126%. The concentrations of AS, AZn, AFe, ACu, AMn, and AB were negatively and significantly correlated with soil pH and positively and significantly correlated with SOC. The geostatistical analysis indicated stable, Gaussian and exponential best-fit semivariogram models with moderate to strong spatial dependence for available nutrients. The generated spatial spreading maps revealed different distribution patterns for AS, AZn, AFe, ACu, AMn, and AB. There were variations in spatial spreading patterns of AS, AZn, AFe, ACu, AMn, and AB in east- and west-coastal area. About 62, 35, 12, 0.4, 23 and 45% of the study area had deficiency of AS, AZn, AFe, ACu, AMn, and AB, respectively. The spatial spreading maps will be highly useful for SSNM in the cultivated coastal soils of the country. This study could also be used as a base for assessing spatial spreading patterns of soil parameters in cultivated coastal areas of other parts of the world.

Geochemistry and environmental effects of rare earth elements in laterites from Yunnan province, southwest China

2021 ◽  
pp. geochem2021-039
Author(s):  
Bin Liang ◽  
Guilin Han ◽  
Jie Zeng ◽  
Rui Qu ◽  
Man Liu ◽  
...  
Keyword(s):  
Rare Earth ◽  
Rare Earth Elements ◽  
Environmental Effects ◽  
Inductively Coupled Plasma ◽  
Anthropogenic Activities ◽  
Distribution Patterns ◽  
Content Type ◽  
Tropical Regions ◽  
Supplementary Material ◽  
And Migration

Rare earth elements (REEs) in soils are influenced by pedogenic processes and anthropogenic activities. To interpret the fractionation and migration of REEs during weathering in (sub-) tropical regions, the distribution, fractionation patterns, and environmental effects of REEs in laterites were investigated in this study. Soil samples from two laterite profiles (labeled with S1 and S2) were collected and the concentration of REEs were measured with an inductively coupled plasma mass spectrometer (ICP-MS). The results suggested that the ΣREEs of S2 (119 ± 10 mg/kg to 209 ± 10 mg/kg) has a higher concentration and a wider variation than that of S1 (114 ± 5 mg/kg to 154 ± 8 mg/kg). The REEs in both laterite profiles are enriched with the order of HREEs > LREEs > MREEs. The distribution patterns of laterite profiles show evidence of inheritance from parent granites. The laterites preferentially incorporated HREEs, and besides, secondary Fe2O3 and clay minerals were likely to affect the fractionation of REEs in laterites. The enrichment factor of REEs varies from 11.1 to 18.9 for S1 and 10.0 to 27.6 for S1, indicating potential pollution by REEs. The accumulation of REEs in laterites by mining activities should be a concern of environmental agencies of governments.Supplementary material:https://doi.org/10.6084/m9.figshare.c.5609234

scholarly journals Adult high-grade B-cell lymphoma with Burkitt lymphoma signature: genomic features and potential therapeutic targets

Blood ◽  
2017 ◽  
Vol 130 (16) ◽  
pp. 1819-1831 ◽  
Author(s):  
Alyssa Bouska ◽  
Chengfeng Bi ◽  
Waseem Lone ◽  
Weiwei Zhang ◽  
Ambreen Kedwaii ◽  
...  
Keyword(s):  
B Cell ◽  
Copy Number ◽  
Cell Lymphoma ◽  
Genomic Analysis ◽  
B Cell Lymphoma ◽  
High Grade ◽  
Potential Therapeutic Target ◽  
Genomic Features ◽  
Key Points ◽  
Bcr Signaling

Key Points Adult-mBLs have distinct and more frequent DNA copy number abnormalities compared with pediatric-mBL. Comprehensive genomic analysis revealed that the BCR signaling pathway is a potential therapeutic target in adult-mBL.

scholarly journals Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons

2021 ◽  
Author(s):  
Yaqian Xiao ◽  
Ruhan Jiang ◽  
Xiaoxiong Wu ◽  
Qi Zhong ◽  
Yi Li ◽  
...  
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Natural Environments ◽  
Genomic Features ◽  
Content Type ◽  
The Core ◽  
Core Function ◽  
Polycyclic Aromatic

This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable.

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