Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics

Zaikova, Elena; Goerlitz, David; Tighe, Scott; Wagner, Nicole Yasmin; Bai, Yu; Hall, Brenda L.; Bevilacqua, J. G.; Weng, M. M.; Samuels-Fair, Maya; Johnson, S. S.

doi:10.3389/fevo.2019.00001

Cited by 39 publications

(14 citation statements)

References 96 publications

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“…Yuan et al ( 2019 ) found macrolide resistance genes in soil samples, but all of them encoded efflux pumps rather than acetyltransferases. Similarly,Zaikova et al ( 2019 ) found macrolides efflux pumps in 5 assembled genomes recovered from fossil microbial mats, but not vat genes. Also, Fitzpatrick & Walsh ( 2016 ) performed a meta‐analysis of metagenomes recovered from different environments, identifying 11 non‐efflux‐pump‐mediated genes that conferred resistance to macrolides in 23 metagenomes, but none in the metagenome of an Antarctic aquatic sample, included in the search.…”

Section: Discussionmentioning

confidence: 93%

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

Antelo

Giménez

Azziz³

et al. 2021

MicrobiologyOpen

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The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high‐throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non‐Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside‐modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β‐lactamase (blaOXA‐205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase ( aadA6 ), and the other is a qacG2 gene.

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Section: Discussionmentioning

confidence: 93%

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

Antelo

Giménez

Azziz³

et al. 2021

MicrobiologyOpen

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“…These techniques have reduced the cost and time required for sequencing and generate numerous sequences for each sample [10]. Moreover, these new methods can identify the predominant bacteria in a sample and permit the discovery of minor taxa in the bacterial community; importantly, minor taxa may play substantive roles in any given bacterial community or, if not, the minor taxa may be relics of an ancient ecosystem that underwent a shift in environmental conditions [11]. Analysis of the 16S rRNA gene amplicon remains the standard method for culture-independent studies of microbial diversity, and this approach has made it clear that there exist enormous numbers of unculturable (and therefore uncharacterized) microbes whose metabolic capacities, life cycles and relative ecosystem impact remain largely undefined.…”

Section: Introductionmentioning

confidence: 99%

Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

Oyewusi

Wahab

Edbeib³

et al. 2020

Biotechnology & Biotechnological Equipment

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The 16S rRNA amplicon sequencing technique is a key aspect of studies of microbial communities but does not provide direct evidence of a community's functional capabilities. This work aimed to assess the structure of the uncultured bacterial communities from two locations in Lake Tuz in Turkey to provide information on their roles in the lake ecosystem. The most abundant phyla in the lake water were Firmicutes (84%) for lake sample site 1 (TG1), 70% for lake sample site 2 (TG2), Fusobacteria (9% for TG1, 22% for TG2) and Proteobacteria (6% for TG1, 7% for TG2). The most abundant genera were Romboutsia (45% for TG1, 35% for TG2), Clostridium sensu stricto 1 (8% for TG1, 8% for TG2), Cetobacterium (9% for TG1, 22% for TG2) and Photobacterium (2% for TG1, 3% for TG2). PICRUSt constitutes a novel bioinformatics tool to establish profiles for bacterial protein functions based on metagenomic 16S rRNA data for a community of unculturable bacteria. PICRUSt also provides information on whole-community metabolic functions related to adaptation, bioremediation potential and the ability of various groups of microorganisms to survive in highly saline water. The overall results provide an effective strategy for assessing the metabolic capacities of microbes in situ in a high-salt aquatic environment such as Lake Tuz and the potential of these microbes to serve as bioremediation agents. This approach provides useful insights into predictive metagenomics of an unculturable microbial community for which only marker-gene surveys are currently available.

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“…Permafrost environments are dominated by the hostile-to-life conditions of constant freezing, desiccation and starvation [15]. In line with findings from Arctic and Antarctic environments [20, 23, 63, 64], the higher potential of the MBP permafrost microorganisms to synthesize cold-shock proteins and chaperones could indicate their ability to survive prolonged freezing, as these proteins ensure the integrity of the cell components and the continuing functioning of the cells under environmental stress [65].…”

Section: Discussionmentioning

confidence: 95%

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

Perez-Mon

Vikram

et al. 2021

Microbial Genomics

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The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil–climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

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Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics

Cited by 39 publications

References 96 publications

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

Metagenomic strategies identify diverse integron‐integrase and antibiotic resistance genes in the Antarctic environment

Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

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