Presentación de los contenidos de la revista.Facultad de Ciencias ExactasCentro de Investigación y Desarrollo en Fermentaciones Industriale

Chan, Kok Gan

Donati, Edgardo Rubén

Goh, Kian Mau

Reysenbach, Anna Louise

Sani, Rajesh Kumar

Frontiers in Microbiology

SEDICI - Repositorio de la UNLP

EDITORIAL
published: 03 April 2017
doi: 10.3389/fmicb.2017.00560
Frontiers in Microbiology | www.frontiersin.org 1 April 2017 | Volume 8 | Article 560
Edited by:
Jesse G. Dillon,
California State University,
Long Beach, USA
Reviewed by:
Jesse G. Dillon,
California State University,
Long Beach, USA
Matthew Schrenk,
Michigan State University, USA
*Correspondence:
Kian Mau Goh
gohkianmau@utm.my
Specialty section:
This article was submitted to
Extreme Microbiology,
a section of the journal
Frontiers in Microbiology
Received: 09 February 2017
Accepted: 17 March 2017
Published: 03 April 2017
Citation:
Goh KM, Chan K-G, Sani RK,
Donati ER and Reysenbach A-L
(2017) Editorial: Genetics, Genomics
and –Omics of Thermophiles.
Front. Microbiol. 8:560.
doi: 10.3389/fmicb.2017.00560
Editorial: Genetics, Genomics and
–Omics of Thermophiles
Kian Mau Goh 1*, Kok-Gan Chan 2, Rajesh Kumar Sani 3, Edgardo Rubén Donati 4 and
Anna-Louise Reysenbach 5
1 Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Malaysia, 2Division of Genetics and
Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia,
3Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA,
4CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata,
Argentina, 5Department of Biology, Portland State University, Portland, OR, USA
Keywords: comparative genomics, extremophile, hot spring, hyperthermophile, thermozyme, metagenome
Editorial on the Research Topic
Genetics, Genomics and –Omics of Thermophiles
Thermophilic Archaea and Bacteria occupy heated environments. Advancement of next-generation
sequencing (NGS), single-cell analyses, and combinations of –omics and microscopic technologies
have resulted in the discovery of new thermophiles. This e-book consists of a review, and 10
original articles authored by 94 authors. The main aim of this Research Topic of Frontiers in
Microbiology was to provide a platform for researchers to describe recent findings on the ecology
of thermophiles using NGS, functional genomics, comparative genomics, gene evolution, and
extremozyme discovery.
The review by DeCastro et al. discussed the approaches currently available in assessing the
taxonomy and functional metagenomics of thermophiles in high temperature environments.
The review also provides limitations or challenges for each approach in the discovery of novel
thermozymes that include lipolytic enzymes, glycosidases, proteases, and oxidoreductases.
Nearly 50 years ago, Thomas Brock was among the earliest researchers who elucidated the
existence of living organisms in hot springs in Yellowstone National Park, YNP (Brock, 1967). In
this e-book, Thiel et al. revisited Mushroom Spring (60◦C) and examined the microbial diversity
in the orange-colored undermat using NGS shotgun sequencing and 16S rRNA amplicon analyses.
The phylumChloroflexi dominated 49% of total OTUs, followed by Thermotogae,Armatimonadetes
(previously known as candidate division OP10), Aquificae, Cyanobacteria, Atribacteria (candidate
phylumOP-9/JS1),Nitrospirae and others. Thiel et al. showed that the dominant taxon, Roseoflexus,
had high microdiversity of the 16S rRNA gene sequences which most likely represent different
ecotypes with specific ecological adaptations. In a separate article, Saxena et al. performed
shotgun metagenomic and 16S rRNA amplicons sequencing from samples collected from three
Indian hot springs (43.5–98◦C, pH 7.5–7.8). The alpha- and beta-diversity of thermophiles in
seven distinct sites were compared and the authors concluded that the temperatures significantly
affected the microbial community structure. These sites were dominated by phyla Proteobacteria,
Thermi, Chloroflexi, Bacteroidetes, Firmicutes, and Thermotogae. Data from shotgun metagenome
sequencing were used to assess hydrocarbon degradation pathways in the Anhoni hot spring. One
of the interesting insights from Saxena et al. is that all enzymes involved in a particular hydrocarbon
degradation pathway were not found in a single microbial species; therefore, the degradation could
only be completed by consortium members of the microbial community.
Goh et al. Editorial: Genetics, Genomics and –Omics of Thermophiles
Genomes of several hyper- and thermophilic bacteria
were sequenced and reported in this e-book. Dictyoglomus
turgidum has an optimum growth temperature (OGT) of 72◦C.
Brumm et al. analyzed genome content of D. turgidum from
multiple aspects including metabolic pathways, polysaccharides
degradation and transport, energy generation, DNA repair
and recombination, and stress responses. D. turgidum has an
abundance of glycosyl hydrolases, 16 of which were examined
for their activities. D. turgidum can utilize most plant-based
polysaccharides, except crystalline cellulose. Zarafeta et al.
isolated a Dictyoglomus sp. Ch5.6.S from an in situ enrichment
culture containing xanthan gum established in a Yunnan hot
spring. A new hyperthermostable esterolytic enzyme (EstDZ3)
was identified from the genome sequence. The EstDZ3 is likely
a carboxylesterase as it reacts best on fatty acid esters with
short to medium chain lengths. The enzyme exhibited a half-
life of more than 24 h when incubated at 80◦C. Clearly, both
articles suggested Dictyoglomus is an interesting genus with
biotechnological potential.
Three articles in this Research Topic provide novel insights
into sulfur-metabolizing prokaryotes. Zhang et al. studied the
evolution of sixAcidithiobacillus caldus strains using comparative
genomic approaches. The authors identifiedmanymobile genetic
elements and showed that gene gains and losses all drive the
genomic diversification in this species. Dai et al. compared the
genome of Sulfolobus sp. A20 with the Sulfolobus solfataricus,
Sulfolobus acidocaldarius, Sulfolobus islandicus, and Sulfolobus
tokodaii, and identified 1,801 core genes sequences. Genes
in central carbon metabolism and ammonium assimilation
are highly conserved in Sulfolobus. The genes for sulfur
oxygenase/reductase and inorganic nitrogen utilization which
are less conserved probably due to the presence or remnants of
insertion sequence elements. The anaerobic Thermosulfurimonas
dismutans S95T was isolated from a deep-sea hydrothermal
vent by Mardanov et al. and they showed that T. dismutans
had the sulfur-disproportionating capability even without the
need of direct contact of the cells to solid elemental sulfur.
It is therefore likely that the soluble glutathione persulfide is
the actual substrate entering the disproportionation pathway.
Mardanov et al. proposed a model of sulfur metabolism and
related pathways in T. dismutans.
Goh et al. reported the isolation and genome description
of a new bacterium strain RA (OGT: 50–60◦C) in the
Rhodothermaceae. The strain RA is likely to be a new genus due to
its low 16S rRNA and housekeeping genes (e.g., recA, rpoD, and
gyrB) similarity to other genera in Rhodothermaceae. Goh et al.
also compared the genome of this bacterium with Rhodothermus
marinus DSM 4252T and Salinibacter ruber DSMT and showed
that it has putative genes for adaptation to osmotic stress
and survival in a high sulfidic hot springs. Using phylogenetic
analyses and sequence similarity networks, Cardenas et al.
reported the phylogenomic analysis of 2,631 representative
rubrerythrins, a group of proteins involved in oxidative stress
defense. The authors proposed that “aerobic-type” rubrerythrins
underwent a separate adaptation process than that of the
“cyanobacterial group.” Lastly, Irla et al. compared four different
plasmids that were able to replicate in Bacillus methanolicus.
They reported the effects of copy number, expression levels
and stability of these plasmids in B. methanolicus. The article
provided new tools for genetic engineering of B. methanolicus.
We hope that this e-book can stimulate the research community
to integrate –omics and bioinformatics tools in understanding
the biology of heated environments and thermophiles.
AUTHOR CONTRIBUTIONS
All authors listed, have made substantial, direct and intellectual
contribution to the work, and approved it for publication.
ACKNOWLEDGMENTS
KG is supported by the UTM GUP grants (14H67 and 15H50).
KC gratefully acknowledges the financial support provided
by University of Malaya—Ministry of Higher Education High
Impact Research Grant (UM.C/625/1/HIR/MOHE/CHAN/01
Grant No. A-000001-50001 and UM.C/625/1/HIR/MOHE/
CHAN/14/1 Grant No. H-50001-A000027). RS gratefully
acknowledges the financial support provided by National
Aeronautics and Space Administration (Grant #NNX16AQ98A).
ED is thankful to grant PICT 2013-0630. This was supported
by grants to AR (NASA grant #NNX16AJ66G and NSF DEB
1134877).
REFERENCES
Brock, T. D. (1967). Life at high temperatures. Science 158, 1012–1019.
Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Copyright © 2017 Goh, Chan, Sani, Donati and Reysenbach. This is an open-
access article distributed under the terms of the Creative Commons Attribution
License (CC BY). The use, distribution or reproduction in other forums is permitted,
provided the original author(s) or licensor are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice.
No use, distribution or reproduction is permitted which does not comply with these
terms.
Frontiers in Microbiology | www.frontiersin.org 2 April 2017 | Volume 8 | Article 560


English

Editorial: Genetics, genomics and -omics of thermophiles

Servicio de Difusión de la Creación Intelectual

EDITORIALpublished: 03 April 2017doi: 10.3389/fmicb.2017.00560Frontiers in Microbiology | www.frontiersin.org 1 April 2017 | Volume 8 | Article 560Edited by:Jesse G. Dillon,California State University,Long Beach, USAReviewed by:Jesse G. Dillon,California State University,Long Beach, USAMatthew Schrenk,Michigan State University, USA*Correspondence:Kian Mau Gohgohkianmau@utm.mySpecialty section:This article was submitted toExtreme Microbiology,a section of the journalFrontiers in MicrobiologyReceived: 09 February 2017Accepted: 17 March 2017Published: 03 April 2017Citation:Goh KM, Chan K-G, Sani RK,Donati ER and Reysenbach A-L(2017) Editorial: Genetics, Genomicsand –Omics of Thermophiles.Front. Microbiol. 8:560.doi: 10.3389/fmicb.2017.00560Editorial: Genetics, Genomics and–Omics of ThermophilesKian Mau Goh 1*, Kok-Gan Chan 2, Rajesh Kumar Sani 3, Edgardo Rubén Donati 4 andAnna-Louise Reysenbach 51 Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Malaysia, 2Division of Genetics andMolecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia,3Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA,4CINDEFI (CCT, La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata,Argentina, 5Department of Biology, Portland State University, Portland, OR, USAKeywords: comparative genomics, extremophile, hot spring, hyperthermophile, thermozyme, metagenomeEditorial on the Research TopicGenetics, Genomics and –Omics of ThermophilesThermophilic Archaea and Bacteria occupy heated environments. Advancement of next-generationsequencing (NGS), single-cell analyses, and combinations of –omics and microscopic technologieshave resulted in the discovery of new thermophiles. This e-book consists of a review, and 10original articles authored by 94 authors. The main aim of this Research Topic of Frontiers inMicrobiology was to provide a platform for researchers to describe recent findings on the ecologyof thermophiles using NGS, functional genomics, comparative genomics, gene evolution, andextremozyme discovery.The review by DeCastro et al. discussed the approaches currently available in assessing thetaxonomy and functional metagenomics of thermophiles in high temperature environments.The review also provides limitations or challenges for each approach in the discovery of novelthermozymes that include lipolytic enzymes, glycosidases, proteases, and oxidoreductases.Nearly 50 years ago, Thomas Brock was among the earliest researchers who elucidated theexistence of living organisms in hot springs in Yellowstone National Park, YNP (Brock, 1967). Inthis e-book, Thiel et al. revisited Mushroom Spring (60◦C) and examined the microbial diversityin the orange-colored undermat using NGS shotgun sequencing and 16S rRNA amplicon analyses.The phylumChloroflexi dominated 49% of total OTUs, followed by Thermotogae,Armatimonadetes(previously known as candidate division OP10), Aquificae, Cyanobacteria, Atribacteria (candidatephylumOP-9/JS1),Nitrospirae and others. Thiel et al. showed that the dominant taxon, Roseoflexus,had high microdiversity of the 16S rRNA gene sequences which most likely represent differentecotypes with specific ecological adaptations. In a separate article, Saxena et al. performedshotgun metagenomic and 16S rRNA amplicons sequencing from samples collected from threeIndian hot springs (43.5–98◦C, pH 7.5–7.8). The alpha- and beta-diversity of thermophiles inseven distinct sites were compared and the authors concluded that the temperatures significantlyaffected the microbial community structure. These sites were dominated by phyla Proteobacteria,Thermi, Chloroflexi, Bacteroidetes, Firmicutes, and Thermotogae. Data from shotgun metagenomesequencing were used to assess hydrocarbon degradation pathways in the Anhoni hot spring. Oneof the interesting insights from Saxena et al. is that all enzymes involved in a particular hydrocarbondegradation pathway were not found in a single microbial species; therefore, the degradation couldonly be completed by consortium members of the microbial community.Goh et al. Editorial: Genetics, Genomics and –Omics of ThermophilesGenomes of several hyper- and thermophilic bacteriawere sequenced and reported in this e-book. Dictyoglomusturgidum has an optimum growth temperature (OGT) of 72◦C.Brumm et al. analyzed genome content of D. turgidum frommultiple aspects including metabolic pathways, polysaccharidesdegradation and transport, energy generation, DNA repairand recombination, and stress responses. D. turgidum has anabundance of glycosyl hydrolases, 16 of which were examinedfor their activities. D. turgidum can utilize most plant-basedpolysaccharides, except crystalline cellulose. Zarafeta et al.isolated a Dictyoglomus sp. Ch5.6.S from an in situ enrichmentculture containing xanthan gum established in a Yunnan hotspring. A new hyperthermostable esterolytic enzyme (EstDZ3)was identified from the genome sequence. The EstDZ3 is likelya carboxylesterase as it reacts best on fatty acid esters withshort to medium chain lengths. The enzyme exhibited a half-life of more than 24 h when incubated at 80◦C. Clearly, botharticles suggested Dictyoglomus is an interesting genus withbiotechnological potential.Three articles in this Research Topic provide novel insightsinto sulfur-metabolizing prokaryotes. Zhang et al. studied theevolution of sixAcidithiobacillus caldus strains using comparativegenomic approaches. The authors identifiedmanymobile geneticelements and showed that gene gains and losses all drive thegenomic diversification in this species. Dai et al. compared thegenome of Sulfolobus sp. A20 with the Sulfolobus solfataricus,Sulfolobus acidocaldarius, Sulfolobus islandicus, and Sulfolobustokodaii, and identified 1,801 core genes sequences. Genesin central carbon metabolism and ammonium assimilationare highly conserved in Sulfolobus. The genes for sulfuroxygenase/reductase and inorganic nitrogen utilization whichare less conserved probably due to the presence or remnants ofinsertion sequence elements. The anaerobic Thermosulfurimonasdismutans S95T was isolated from a deep-sea hydrothermalvent by Mardanov et al. and they showed that T. dismutanshad the sulfur-disproportionating capability even without theneed of direct contact of the cells to solid elemental sulfur.It is therefore likely that the soluble glutathione persulfide isthe actual substrate entering the disproportionation pathway.Mardanov et al. proposed a model of sulfur metabolism andrelated pathways in T. dismutans.Goh et al. reported the isolation and genome descriptionof a new bacterium strain RA (OGT: 50–60◦C) in theRhodothermaceae. The strain RA is likely to be a new genus due toits low 16S rRNA and housekeeping genes (e.g., recA, rpoD, andgyrB) similarity to other genera in Rhodothermaceae. Goh et al.also compared the genome of this bacterium with Rhodothermusmarinus DSM 4252T and Salinibacter ruber DSMT and showedthat it has putative genes for adaptation to osmotic stressand survival in a high sulfidic hot springs. Using phylogeneticanalyses and sequence similarity networks, Cardenas et al.reported the phylogenomic analysis of 2,631 representativerubrerythrins, a group of proteins involved in oxidative stressdefense. The authors proposed that “aerobic-type” rubrerythrinsunderwent a separate adaptation process than that of the“cyanobacterial group.” Lastly, Irla et al. compared four differentplasmids that were able to replicate in Bacillus methanolicus.They reported the effects of copy number, expression levelsand stability of these plasmids in B. methanolicus. The articleprovided new tools for genetic engineering of B. methanolicus.We hope that this e-book can stimulate the research communityto integrate –omics and bioinformatics tools in understandingthe biology of heated environments and thermophiles.AUTHOR CONTRIBUTIONSAll authors listed, have made substantial, direct and intellectualcontribution to the work, and approved it for publication.ACKNOWLEDGMENTSKG is supported by the UTM GUP grants (14H67 and 15H50).KC gratefully acknowledges the financial support providedby University of Malaya—Ministry of Higher Education HighImpact Research Grant (UM.C/625/1/HIR/MOHE/CHAN/01Grant No. A-000001-50001 and UM.C/625/1/HIR/MOHE/CHAN/14/1 Grant No. H-50001-A000027). RS gratefullyacknowledges the financial support provided by NationalAeronautics and Space Administration (Grant #NNX16AQ98A).ED is thankful to grant PICT 2013-0630. This was supportedby grants to AR (NASA grant #NNX16AJ66G and NSF DEB1134877).REFERENCESBrock, T. D. (1967). Life at high temperatures. Science 158, 1012–1019.Conflict of Interest Statement: The authors declare that the research wasconducted in the absence of any commercial or financial relationships that couldbe construed as a potential conflict of interest.Copyright © 2017 Goh, Chan, Sani, Donati and Reysenbach. This is an open-access article distributed under the terms of the Creative Commons AttributionLicense (CC BY). The use, distribution or reproduction in other forums is permitted,provided the original author(s) or licensor are credited and that the originalpublication in this journal is cited, in accordance with accepted academic practice.No use, distribution or reproduction is permitted which does not comply with theseterms.Frontiers in Microbiology | www.frontiersin.org 2 April 2017 | Volume 8 | Article 560

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