scholarly journals Harnessing the Genetic Diversity and Metabolic Potential of Extremophilic Microorganisms through the Integration of Metagenomics and Single-Cell Genomics

2020 ◽  
Author(s):  
Deepika Goyal ◽  
Shiv Swaroop ◽  
Janmejay Pandey
Keyword(s):  
Microbial Diversity ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Extreme Environments ◽  
Metabolic Potential ◽  
Single Cell Genomics ◽  
Metabolic Characteristics ◽  
Culture Independent ◽  
Synergistic Approach

Microorganisms thriving under extreme environments have proven to be an invaluable resource for metabolic products and processes. While studies carried out on microbial characterization of extremophilic environments during golden era of microbiology adapted a ‘reductionist approach’ and focused on isolation, purification and characterization of individual microbial isolates; the recent studies have implemented a holistic approach using both culture-dependent and culture-independent approaches for characterization of total microbial diversity of the extreme environments. Findings from these studies have unmistakably indicated that microbial diversity within extreme environments is much higher than anticipated. Consequently, unraveling the taxonomic and metabolic characteristics of microbial diversity in extreme environments has emerged as an imposing challenge in the field of microbiology and microbial biotechnology. To a great extent, this challenge has been addressed with inception and advancement of next-generation sequencing and computing methods for NGS data analyses. However, further it has been realized that in order to maximize the exploitation of genetic and metabolic diversity of extremophilic microbial diversity, the metagenomic approaches must be combined synergistically with single-cell genomics. A synergistic approach is expected to provide comprehensions into the biology of extremophilic microorganism, including their metabolic potential, molecular mechanisms of adaptations, unique genomic features including codon reassignments etc.

scholarly journals Transfection of Arctic Bryum sp. KMR5045 as a Model for Genetic Engineering of Cold-Tolerant Mosses

2021 ◽  
Vol 11 ◽  
Author(s):  
Mi Young Byun ◽  
Suyeon Seo ◽  
Jungeun Lee ◽  
Yo-Han Yoo ◽  
Hyoungseok Lee
Keyword(s):  
Molecular Mechanisms ◽  
Extreme Environments ◽  
Temperature Tolerance ◽  
Plant Evolution ◽  
Basic Knowledge ◽  
The Arctic ◽  
Terrestrial Plants ◽  
Moss Species ◽  
Metabolic Characteristics ◽  
Low Temperature Tolerance

Mosses number about 13,000 species and are an important resource for the study of the plant evolution that occurred during terrestrial colonization by plants. Recently, the physiological and metabolic characteristics that distinguish mosses from terrestrial plants have received attention. In the Arctic, in particular, mosses developed their own distinct physiological features to adapt to the harsh environment. However, little is known about the molecular mechanisms by which Arctic mosses survive in extreme environments due to the lack of basic knowledge and tools such as genome sequences and genetic transfection methods. In this study, we report the axenic cultivation and transfection of Arctic Bryum sp. KMR5045, as a model for bioengineering of Arctic mosses. We also found that the inherent low-temperature tolerance of KMR5045 permitted it to maintain slow growth even at 2°C, while the model moss species Physcomitrium patens failed to grow at all, implying that KMR5045 is suitable for studies of cold-tolerance mechanisms. To achieve genetic transfection of KMR5045, some steps of the existing protocol for P. patens were modified. First, protoplasts were isolated using 1% driselase solution. Second, the appropriate antibiotic was identified and its concentration was optimized for the selection of transfectants. Third, the cell regeneration period before transfer to selection medium was extended to 9 days. As a result, KMR5045 transfectants were successfully obtained and confirmed transfection by detection of intracellular Citrine fluorescence derived from expression of a pAct5:Citrine transgene construct. This is the first report regarding the establishment of a genetic transfection method for an Arctic moss species belonging to the Bryaceae. The results of this study will contribute to understanding the function of genes involved in environmental adaptation and to application for production of useful metabolites derived from stress-tolerant mosses.

scholarly journals Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
L. V. Alteio ◽  
F. Schulz ◽  
R. Seshadri ◽  
N. Varghese ◽  
W. Rodriguez-Reillo ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Single Cell ◽  
Forest Soil ◽  
Carbon Metabolism ◽  
Cell Sorting ◽  
Phylogenetic Diversity ◽  
Metabolic Potential ◽  
Shotgun Metagenomics ◽  
Rare Biosphere ◽  
Depth Analysis

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes. Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

scholarly journals Single-cell genomics to understand disease pathogenesis

2020 ◽  
Vol 66 (1) ◽  
pp. 75-84
Author(s):  
Seitaro Nomura
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Disease Pathogenesis ◽  
Single Cell Genomics ◽  
Molecular Systems ◽  
Biological Phenomena ◽  
Molecular Behavior ◽  
Unbiased Manner

AbstractCells are minimal functional units in biological phenomena, and therefore single-cell analysis is needed to understand the molecular behavior leading to cellular function in organisms. In addition, omics analysis technology can be used to identify essential molecular mechanisms in an unbiased manner. Recently, single-cell genomics has unveiled hidden molecular systems leading to disease pathogenesis in patients. In this review, I summarize the recent advances in single-cell genomics for the understanding of disease pathogenesis and discuss future perspectives.

scholarly journals Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the amoebozoa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yonas I. Tekle ◽  
Janae M. Lyttle ◽  
Maya G. Blasingame ◽  
Fang Wang
Keyword(s):  
Public Health ◽  
Single Cell ◽  
Pathogenic Bacteria ◽  
Health Concern ◽  
Human Pathogens ◽  
Single Cell Genomics ◽  
Bacterial Phyla ◽  
Published Evidence ◽  
Culture Independent ◽  
Bacterial Replication

AbstractThe Amoebozoa, a group containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics/transcriptomics to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (64) and human pathogen genera (51) associated with the Amoebozoa. Using single cell genomics/transcriptomics we were able to determine up to 24 potential endosymbiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multi-drug resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.

scholarly journals ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles

2018 ◽  
Author(s):  
Xin Gao ◽  
Deqing Hu ◽  
Madelaine Gogol ◽  
Hua Li
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Population Level ◽  
Marker Genes ◽  
Rna Seq ◽  
Matching Problem ◽  
Cut Method ◽  
Underlying Mechanisms

AbstractSingle cell RNA-Seq facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging. We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides “similarity” as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric “separability” to summarize sub-population changes among all sample pairs. In three case studies, we demonstrate that ClusterMap has the ability to offer us further insight into the different molecular mechanisms of cellular sub-populations across different conditions. ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap.

scholarly journals Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods

2007 ◽  
Vol 59 (2) ◽  
pp. 513-523 ◽  
Author(s):  
Blaire Steven ◽  
Geoffrey Briggs ◽  
Chris P. McKay ◽  
Wayne H. Pollard ◽  
Charles W. Greer ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Arctic ◽  
Canadian High Arctic ◽  
Culture Independent ◽  
Culture Dependent

scholarly journals Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils

2012 ◽  
Vol 78 (21) ◽  
pp. 7527-7537 ◽  
Author(s):  
David R. Andrew ◽  
Robert R. Fitak ◽  
Adrian Munguia-Vega ◽  
Adriana Racolta ◽  
Vincent G. Martinson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Sonoran Desert ◽  
Abiotic Factors ◽  
Extreme Environments ◽  
Community Diversity ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterial Phyla ◽  
Culture Independent

ABSTRACTHigh-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundantCrenarchaeotaclassThermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phylaProteobacteria,Actinobacteria,Planctomycetes,Firmicutes,Bacteroidetes,Chloroflexi, andAcidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.

Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis

2019 ◽  
pp. 33-49
Author(s):  
Rama Kant Dubey ◽  
Vishal Tripathi ◽  
Ratna Prabha ◽  
Rajan Chaurasia ◽  
Dhananjaya Pratap Singh ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Single Cell ◽  
Diversity Analysis ◽  
Single Cell Genomics
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