Metagenomics of extreme environments

Cowan, Don A.; Ramond, Jean‐Baptiste; Makhalanyane, Thulani P.; Maayer, Pieter De

doi:10.1016/j.mib.2015.05.005

Cited by 112 publications

(54 citation statements)

References 54 publications

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“…Regardless of the actual figures, microorganisms are highly abundant and, thanks in part to culture independent methods and the so-called 'omic' approaches, we now have realistic estimates of the true depth of microbial diversity, and their functional capacity. Through application of metagenomic approaches (Figure 1), it is now known that most extreme environments harbour lower levels of microbial diversity (species richness and relative abundance), than more 'benign' ecosystems [16,17]. This is thought to be due to the requirement for specific physiological adaptations, which allow organisms to exploit the combination of physical and biochemical stressors, but result in simplified ecosystems dominated by a relatively few taxa [18,19].…”

Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 99%

“…Although Proteobacteria, Actinobacteria and Acidobacteria are the most numerically abundant, Cyanobacteria are also significant colonists of cold soils [16]. Cyanobacteria, mostly affiliated to Nostoc commune, are prevalent in both Arctic and Antarctic soils and appear to drive most functional processes related to carbon and nitrogen cycling [48][49][50].…”

Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 99%

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Microbial diversity and functional capacity in polar soils

Makhalanyane

Goethem

Cowan

2016

Current Opinion in Biotechnology

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Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions. AddressCentre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa Corresponding author: Cowan, Don Arthur (don.cowan@up.ac.za) IntroductionThe Congress of Parties (COP) 21 meeting in Paris (November 2015) highlighted the urgency of global climate change, and the critical need to reduce global average temperatures through curbing greenhouse gas emissions [1]. Nowhere are the effects of global change more apparent than in cold environments (polar and alpine regions), which are subject to accelerated rates of warming compared to other ecosystems [2 ,3]. Climatic models have predicted that temperatures in high latitude regions of the Northern Hemisphere are likely to increase by between 0.38C and 4.88C before the end of the twenty first century [4]. There is also evidence that regions in the Southern Hemisphere have experienced the fastest warming globally, with average increases of as much as 2.48C in the last fifty years [5].A major consequence of climate change in cold environments is the thawing of submerged and surface ice, which alters the hydrology of the systems and may have adverse effects on microbial processes [6 ]. In cold environments, microorganisms (bacteria, archaea and fungi) are major constituents of the total biomass, and are estimated to mediate the cycling of key biogeochemical elements such as nitrogen and carbon, with potentially important implications for the productivity of these systems [7]. Although the precise contribution of microbial processes to global change processes are not well known, there are efforts to incorporate biological processes into Earth systems models with the realization that they may be crucial in regulating soil organic matter (SOM) [8 ]. For instance, permafrost (defined as ground which remains frozen for at least two years) in cold environments stores roughly 1600 Pg of carbon, which if released would significantly contribute towards increasing global CO 2 levels [9]. The current contribution of microbial communities to constraining carbon losses in permafrost and the influence on CO 2 levels remains virtually unknown. In ...

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Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 99%

Section: Microbial Diversity In Cold Environmentsmentioning

confidence: 99%

Microbial diversity and functional capacity in polar soils

Makhalanyane

Goethem

Cowan

2016

Current Opinion in Biotechnology

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“…However, recent advances in 'omics' technologies, particularly within a system biology context, allowed significant progress in this field. These include the prediction of microbial consortia functionality in situ and the access to enzymes with important potential applications in biotechnology (Cowan et al 2015). Metagenomics is particularly relevant in geothermal environments since most extremophilic microorganisms are recalcitrant to cultivation-based approaches (Amann et al 1995;Lorenz et al 2002).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, metagenomic datasets can provide novel, and even unexpected insights into community dynamics. For example, surprisingly, it has been found that both extreme thermophiles and hyperthermophiles showed a statistically significant higher number of clustered regularly interspaced short palindromic repeats (CRISPR) sequences in their genomes than mesophiles, suggesting that viruses/phages may play an important role in shaping composition and function of thermophiles communities as well as in driving their evolution (Cowan et al 2015). In addition, functional metagenomic strategies, exploiting expression libraries in conventional microbes, are powerful alternatives to conventional genomic approaches for producing novel enzymes for industrial applications.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al. 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al. 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged A. Strazzulli Á M. Moracci Á P. Contursi

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“…[133,134], are popular targets for bioprospecting on the basis that their gene products are very likely to be adapted to function optimally under the specific extreme conditions [135][136][137]. A number of AcXEs have been identified from thermophiles and hyperthermophiles, including Caldicellulosiruptor owensensis [103], Thermomonospora fusca [138], Thermoanaerobacterium sp.…”

Section: Acxes From Extremophilesmentioning

confidence: 99%

Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

Adesioye

Makhalanyane

Biely

et al. 2016

Enzyme and Microbial Technology

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Highlights• AcXEs occur in several CAZy families, and show promiscuous substrate specificities.• A strong AcXE sequence to specificity link would be a valuable functional predictor.• There is a clear need for novel AcXE enzymes with detailed substrate specificity data.• Functional metagenomics would be the most effective means for identifying new AcXEs.• A lack of suitable substrates limits high throughput metagenomic biomining of AcXEs.

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Metagenomics of extreme environments

Cited by 112 publications

References 54 publications

Microbial diversity and functional capacity in polar soils

Microbial diversity and functional capacity in polar soils

Metagenomics of microbial and viral life in terrestrial geothermal environments

Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

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