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25.3.3: Extremophiles and Biofilms

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Prokaryotes are well adapted to living in all types of conditions, including extreme ones, and prefer to live in colonies called biofilms.

Learning Objectives

• Discuss the distinguishing features of extremophiles and the environments that produce biofilms
• Prokaryotes live in all environments, no matter how extreme they may be.
• Bacteria that prefer very salty environments are called halophiles, while those that live in very acidic environments are called acidophiles.
• An example of a habitat that halophiles can colonize is the Dead Sea, a body of water that is 10 times saltier than regular ocean water.
• A biofilm is a microbial community held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms.
• Biofilms can be found clogging pipes, on kitchen counters, or even on the surface of one’s teeth.
• extremophile : an organism that lives under extreme conditions of temperature, salinity, etc; commercially important as a source of enzymes that operate under similar conditions
• halophile : an organism that lives and thrives in an environment of high salinity, often requiring such an environment; a form of extremophile
• alkaliphile : any organism that lives and thrives in an alkaline environment, such as a soda lake; a form of extremophile

Microbes Are Adaptable: Life in Moderate and Extreme Environments

Some organisms have developed strategies that allow them to survive harsh conditions. Prokaryotes thrive in a vast array of environments; some grow in conditions that would seem very normal to us, whereas others are able to thrive and grow under conditions that would kill a plant or animal. Almost all prokaryotes have a cell wall: a protective structure that allows them to survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are able to form endospores that resist heat and drought, thereby allowing the organism to survive until favorable conditions recur. These adaptations, along with others, allow bacteria to be the most abundant life form in all terrestrial and aquatic ecosystems.

Other bacteria and archaea are adapted to grow under extreme conditions and are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in all kinds of environments: the depth of the oceans, hot springs, the Arctic and the Antarctic, in very dry places, deep inside earth, in harsh chemical environments, and in high radiation environments, just to mention a few. These organisms give us a better understanding of prokaryotic diversity and raise the possibility of finding new prokaryotic species that may lead to the discovery of new therapeutic drugs or have industrial applications. Because they have specialized adaptations that allow them to live in extreme conditions, many extremophiles cannot survive in moderate environments. There are many different groups of extremophiles. They are identified based on the conditions in which they grow best. Several habitats are extreme in multiple ways. For example, a soda lake is both salty and alkaline, so organisms that live in a soda lake must be both alkaliphiles and halophiles. Other extremophiles, like radioresistant organisms, do not prefer an extreme environment (in this case, one with high levels of radiation), but have adapted to survive in it.

Prokaryotes in the Dead Sea

One example of a very harsh environment is the Dead Sea, a hypersaline basin that is located between Jordan and Israel. Hypersaline environments are essentially concentrated seawater. In the Dead Sea, the sodium concentration is 10 times higher than that of seawater. The water also contains high levels of magnesium (about 40 times higher than in seawater) that would be toxic to most living things. Iron, calcium, and magnesium, elements that form divalent ions (Fe 2+ , Ca 2+ , and Mg 2+ ), produce what is commonly referred to as “hard” water. Taken together, the high concentration of divalent cations, the acidic pH (6.0), and the intense solar radiation flux make the Dead Sea a unique, and uniquely hostile, ecosystem.

The Ecology of Biofilms

Until a couple of decades ago, microbiologists used to think of prokaryotes as isolated entities living apart. This model, however, does not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a microbial community held together in a gummy-textured matrix that consists primarily of polysaccharides secreted by the organisms, together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed of prokaryotes, although fungal biofilms have also been described, as well as some composed of a mixture of fungi and bacteria.

Biofilms are present almost everywhere: they can cause the clogging of pipes and readily colonize surfaces in industrial settings. In recent, large-scale outbreaks of bacterial contamination of food, biofilms have played a major role. They also colonize household surfaces, such as kitchen counters, cutting boards, sinks, and toilets, as well as places on the human body, such as the surfaces of our teeth.

Interactions among the organisms that populate a biofilm, together with their protective exopolysaccharidic (EPS) environment, make these communities more robust than free-living, or planktonic, prokaryotes. The sticky substance that holds bacteria together also excludes most antibiotics and disinfectants, making biofilm bacteria hardier than their planktonic counterparts. Overall, biofilms are very difficult to destroy because they are resistant to many common forms of sterilization.

Contributions and Attributions

• OpenStax College, Biology. October 16, 2013. Provided by : OpenStax CNX. Located at : http://cnx.org/content/m44602/latest...ol11448/latest . License : CC BY: Attribution
• Prokaryote. Provided by : Wikipedia. Located at : en.Wikipedia.org/wiki/Prokaryote . License : CC BY-SA: Attribution-ShareAlike
• prokaryote. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/prokaryote . License : CC BY-SA: Attribution-ShareAlike
• archaea. Provided by : Wikipedia. Located at : en.Wikipedia.org/wiki/archaea . License : CC BY-SA: Attribution-ShareAlike
• domain. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/domain . License : CC BY-SA: Attribution-ShareAlike
• OpenStax College, Introduction. October 16, 2013. Provided by : OpenStax CNX. Located at : http://cnx.org/content/m44602/latest...e_22_00_01.jpg . License : CC BY: Attribution
• Archaea. Provided by : Wikipedia. Located at : en.Wikipedia.org/wiki/Archaea . License : CC BY-SA: Attribution-ShareAlike
• OpenStax College, Biology. October 16, 2013. Provided by : OpenStax CNX. Located at : http://cnx.org/content/m44603/latest...ol11448/latest . License : CC BY: Attribution
• stromatolite. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/stromatolite . License : CC BY-SA: Attribution-ShareAlike
• indel. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/indel . License : CC BY-SA: Attribution-ShareAlike
• sacculus. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/sacculus . License : CC BY-SA: Attribution-ShareAlike
• gram-positive. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/gram-positive . License : CC BY-SA: Attribution-ShareAlike
• OpenStax College, Prokaryotic Diversity. October 16, 2013. Provided by : OpenStax CNX. Located at : http://cnx.org/content/m44603/latest...e_22_01_01.jpg . License : CC BY: Attribution
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• extremophile. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/extremophile . License : CC BY-SA: Attribution-ShareAlike
• halophile. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/halophile . License : CC BY-SA: Attribution-ShareAlike
• alkaliphile. Provided by : Wiktionary. Located at : en.wiktionary.org/wiki/alkaliphile . License : CC BY-SA: Attribution-ShareAlike
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Surviving Salt: How Do Extremophiles Do It?

* E-mail: [email protected]

Affiliation Freelance Science Writer, Stillwater, Minnesota, United States of America

Published: December 15, 2009

• https://doi.org/10.1371/journal.pbio.1000258
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Citation: Hoff M (2009) Surviving Salt: How Do Extremophiles Do It? PLoS Biol 7(12): e1000258. https://doi.org/10.1371/journal.pbio.1000258

Copyright: © 2009 Mary Hoff. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Competing interests: The author has declared that no competing interests exist.

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At the molecular level, proteins that belong to these extremophiles have evolved toward a biased amino acid composition, which reduces the interactions with the solvent. (Image Credit: Luca Galuzzi, http://www.galuzzi.it).

https://doi.org/10.1371/journal.pbio.1000258.g001

Immersed in waters saltier than chicken soup, salt-tolerant “halophilic” microorganisms are able to thrive in conditions that would reduce a less-adapted organism to a shriveled remnant. One way halophilic archaea avoid this fate is by bathing their molecular machinery in a similarly salty intracellular environment that would cause ordinary proteins to lose their shape. How do the proteins inside these cells survive?

At least part of the answer seems to relate to an abundance of certain amino acid residues on the protein surface. Salt-tolerant proteins tend to have lots of aspartic acid, glutamic acid, and other non-hydrophobic residues on their surfaces. They also tend to have fewer lysines than similar proteins from non-halophilic counterparts, their places often being taken by bulkier arginine instead. What traits of these residues make them salt-friendly? One school of thought suggests it's the charge they carry. Another suggests it's not so much charge as the size of the side chain that gives these residues their evolutionary edge in a saline setting.

To determine what allows extremophile proteins to tolerate salt, Oscar Millet, Xavier Tadeo, and colleagues analyzed the structure and thermodynamics of three protein domains under different salt concentrations: Hv 1ALigNm from Haloferax volcanii , a halophile found in places like the Dead Sea and Great Salt Lake; Ec 1ALigN from Escherichia coli ; and ProtL from the mesophilic Streptococcus magnus . They then used site-directed mutagenesis to create three broad classes of domain mutations: mutations in which the amino acid side chain length changed but the charge did not, mutations in which the charge changed but the length did not, and mutations in which both length and charge were altered.

Analyzing the structure and thermodyamics of the altered domains, the investigators found that reducing the size of the residue's side chain without changing its charge improved salt tolerance in both Hv 1ALigN and Ec 1ALigN. Lengthening the side chain had the opposite impact on mutation of all three domains being investigated. Mutations increasing the negative charge of the domain, on the other hand, showed little impact on salt tolerance in any of the three protein domains studied.

The researchers also investigated whether the tendency of halophiles' protein surfaces to have arginine rather than lysine had any effect on the proteins' ability to cope with salt. They found that substituting lysines for arginines or other polar residues with small side chains increased the salt tolerance of ProtL. Introduction of lysine residues, with their long side chains onto the surface of Hv 1ALigN, decreased stability in salty solutions.

To further explore the connections between residue side chains and salt tolerance, the researchers used other types of mutagenic systems to alter a different set of residues on the surface of the proteins. The results indicated that it is the nature of a mutation, and not its location, that alters the proteins' ability to withstand a salt assault.

Interestingly, the researchers also discovered that salt tolerance is not the only characteristic conferred by the particular mix of residues found in halophilic proteins. Their residue substitution experiments also showed that the abundance of aspartic acid and glutamic acid characteristics of halophilic proteins is good not only for salt tolerance but also for solubility—another valuable trait in conditions typical of high-salt environments.

Concluding from their experiments that residue compactness and not charge is what matters most when it comes to surviving in salt, the researchers assessed salt tolerance and (using high-resolution NMR) the accessible solvent surface area in two multiply mutated versions of ProtL, in an attempt to quantify the relationship. They found that a decrease in surface area correlated well with an increase in salt tolerance, indicating that tight packing is the trick for preventing salt from trashing proteins. At the same time, they also discovered that such packing is not a survival skill that's fit for all conditions. When the same mutants were exposed to a low-salt environment, the molecules destabilized, indicating that the mutations that made them better able to tolerate salt also made them less able to tolerate its absence. All together, these findings not only shed light on a fascinating evolutionary trait, but also provide valuable insights into what it takes to survive in a saline environment—information that could be applied to engineer proteins in a way that does not alter their biological function but does confer salt tolerance beyond what they naturally would endure.

Tadeo X, López-Méndez B, Trigueros T, Laín A, Castaño D, et al. (2009) Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea. doi:10.1371/journal.pbio.1000257

EDITORIAL article

Editorial: extremophiles: microbial genomics and taxogenomics.

• 1 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
• 2 State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa, Macau SAR, China
• 3 China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Macau, Macau SAR, China
• 4 School of Life Sciences, University of Nevada, Las Vegas, NV, United States
• 5 Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States

Editorial on the Research Topic Extremophiles: Microbial genomics and taxogenomics

Introduction

Extreme habitats exist across the globe and account for most of our planet's habitable zone by volume ( Gold, 1992 ; Charette and Smith, 2010 ). They vary widely from a physical-chemical perspective as they include diverse types of extremes, such as temperature, pH, salinity, radiation, pressure, water activity, and nutrient availability. Organisms that thrive under conditions that are adverse or lethal for most organisms are called “extremophiles” ( Brock, 1969 ).

All three domains of life are represented in each type of extreme environment. However, the vast majority of extremophiles are bacteria and archaea ( Rampelotto, 2013 ), which is not surprising considering their remarkable diversity and adaptability. The discovery, study, and classification of novel microbial extremophiles is of enormous interest, given their potential biotechnological applications ( Corral et al., 2019 ) and the ever-increasing expectation to find life on other planets, where conditions might be similar to those of extreme environments on Earth ( Gómez et al., 2012 ).

Our understanding of extremophiles on Earth is rooted in studies of pure cultures, but has greatly expanded over the last few decades through both intellectual and technological advancements in molecular ecology, including several next-generation DNA sequencing and bioinformatics applications, which have evolved rapidly over the last decade. Recent developments increasing the fidelity and lowering the cost of both short- and long-read sequencing technologies hold promise for dense, accurate, and inexpensive DNA sequencing studies focused on both microbial pure cultures and microbial communities ( Slatko et al., 2018 ). In parallel, increases in computing power per Moore's law ( Moore, 1965 ) and the development of new bioinformatic tools, machine learning algorithms, and data mining approaches now provide the necessary means to deal with such a huge amount of data ( Gauthier et al., 2019 ; Goodswen et al., 2021 ).

Extreme environments possess a larger than expected microbial diversity, considering the harshness of the conditions that extremophiles need to cope with ( Shu and Huang, 2022 ). Many efforts have been made to characterize and describe prokaryotic and eukaryotic extremophiles and their metabolic functions within these habitats using culture-dependent approaches ( de la Haba et al., 2011 ; Nogi, 2011 ; Yumoto et al., 2011 ; Sorokin et al., 2014 ; Ventosa et al., 2014 ; Deming, 2019 ; Johnson and Aguilera, 2019 ; Nienow, 2019 ; Santos and Antón, 2019 ; Topçuoglu and Holden, 2019 ; Sood et al., 2021 ). Nevertheless, estimates using 16S rRNA gene sequences and fixed similarity cutoffs suggest that around 80 % of microbial genera remain uncultured in non-human-associated environments ( Lloyd et al., 2018 ). Similarly, analysis of shotgun metagenomic data estimated that yet-uncultivated taxa account for ~85 % of the phylogenetic diversity of prokaryotes ( Nayfach et al., 2021 ). Thus, most of the diversity and functions of extremophiles remain poorly understood. Fortunately, high-performance DNA sequencing and computation-based analysis now allow the routine recovery of high-quality metagenome-assembled genomes (MAGs) ( Yang et al., 2021 ) and single-cell genomes ( Rinke et al., 2013 ), in addition to genomes of cultured microorganisms ( Whitman et al., 2015 ). These approaches finally allow us to describe high-quality genomes from extremophilic “microbial dark matter,” which serve as a foundation to guide both field and lab studies of the ecology and physiology of these organisms within the context of the environments and communities they inhabit.

The use of genomic data of both cultured and uncultured extremophiles is also valuable to infer evolutionary relationships and to establish a robust and accurate classification system ( Parks et al., 2022 ), and a formalized code of nomenclature based on genome sequences as nomenclatural types will soon be available ( Murray et al., 2020 ). Most existing taxa of extremophiles were proposed based on classical but increasingly old-fashioned polyphasic studies that included 16S rRNA gene phylogenetic analyses and wet-lab DNA-DNA hybridization approaches, which have limited resolution and suffer from problems with accuracy and reproducibility among laboratories, respectively. These approaches have therefore been overtaken by phylogenomic studies and in silico genome relatedness indices ( Chun and Rainey, 2014 ; Jain et al., 2018 ). Therefore, the current taxonomy of extremophiles needs to be assessed using genomic information. The ever-increasing access to genomic databases and the ever-decreasing cost of next-generation sequencing technologies and computing makes this a particularly timely Research Topic and grants us an exceptional opportunity to address this issue.

The present Research Topic includes 25 manuscripts spanning the discovery and characterization of new microbial extremophiles, the biotechnological applications of their enzymes, the mechanisms of adaptation to harsh environments, their metabolic pathways and potential ecological roles, their evolution, systematics and biodiversity, as well as exciting research on Space Microbiology and the persistence of extremophiles in low-biomass spacecraft assembly cleanrooms. The Research Topic call was well received, with a total of 185 contributing authors from 18 different countries around the world (Australia, China, Czech Republic, Denmark, Egypt, France, Germany, India, Japan, Mexico, Norway, Poland, Russia, Saudi Arabia, Spain, South Korea, United Kingdom, and United States), which reflects global interest on extremophiles. At the time of writing, over 150,000 views of this Research Topic have been recorded. The high impact of this Research Topic has lead us to establish a community series and make a second call for manuscripts to be submitted to Community Series-Extremophiles: Microbial Genomics and Taxogenomics, Volume II.

Discovery of new extremophiles and extremozymes

Considering that only a small fraction of extremophilic taxa possess a cultured representative, it has never been more important to encourage the scientific community to isolate and describe not-yet-cultured extremophiles. New high-throughput cultivation approaches, referred as “culturomics” ( Lagier et al., 2012 ), coupled with focused, genome-guided cultivation efforts ( Tyson et al., 2005 ; Buessecker et al., 2022 ), will broaden our knowledge about extremophiles, as a major complement to metagenomics. This collection of articles contributes to this aim with the description and characterization of new extremophilic isolates belonging to both Bacteria and Archaea, as well as a novel viral genus.

Three papers from the Duroch group describe new taxa of thermophilic cyanobacteria in the family Leptolyngbiaceae , including two new species, Thermoleptolyngbya sichuanensis ( Tang et al. ) and Leptodesmis sichuanensis ( Tang, Du et al. ), and a new genus and species, Leptothermofonsia sichuanensis ( Tang, Shah et al. ). As suggested by their species names, all three were isolated from hot springs in Sichuan Province, China; the morphological, physiological, genomic, and taxonomic data presented in this collection represent a significant expansion of the systematics of the family and of thermophilic cyanobacteria in general. The Research Topic also includes the proposal by Slobodkina et al. of a new member of the class Archaeoglobi , at that time represented by only eight validly published species names ( Parte et al., 2020 ). The new species Archaeoglobus neptunius was isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge and possesses a lithoautotrophic mode of nutrition, although it is also able to grow chemoorganotrophically. This article points to polyphyletic origin of the species currently grouped into the genus Archaeoglobus , necessitating a future review of its taxonomic status.

In addition to thermophiles, new psychrotolerant bacterial species were proposed within this collection. The paper from Králová et al. describes two new psychrotolerant species of Flavobacterium isolated from Antarctica, namely, “ Flavobacterium flabelliforme ” and “ Flavobacterium geliluteum ”, including three and five strains, respectively. As might be expected, both taxa harbor several cold-inducible or cold-adaptation related genes, but surprisingly they also accommodate numerous prophages and displayed a multidrug-resistant phenotype. Genome analysis revealed the presence of unknown biosynthetic gene clusters, which suggests a potential application to synthesize new biomolecules. Another paper combined high-throughput culturomics and mass-spectroscopy screening to successfully isolate only the second phototrophic member of the phylum Gemmatimonadota , “ Gemmatimonas groenlandica ”, from a stream in Greenland ( Zeng et al. ). Although genes encoding the photosynthetic apparatus are closely related to that of Gemmatimonas phototrophica strain AP64 T , the new species is distinct based on average nucleic acid identity, pigment composition and absorption spectra, and high oxygen tolerance.

One significant driver of research in extremophiles is biotechnology, given their well-recognized roles as sources of new biomolecules and applications. Included in this volume, the review by Sysoev et al. provides an overview of culture-independent methods, including sequence-based metagenomics and single-cell genomics, for studying enzymes from extremophiles, with a focus on prokaryotes. Additionally, the authors provide a comprehensive list of extremozymes discovered via metagenomics and single-cell genomics, which is a useful resource for researchers both in academia and industry. Extremophilic viruses are also rich sources of commercially valuable enzymes, particularly nucleic acid-modifying enzymes. One such example is an unusual DNA polymerase A enzyme from an uncultivated, thermophilic virus that has been developed commercially as a high-affinity, thermophilic reverse-transcriptase ( Schoenfeld et al., 2013 ). In this Research Topic, this polA gene and related genes were shown to be encoded by a new family and genus of thermophilic viruses, the genus Pyrovirus , that is inferred to infect diverse members of the Aquificota based on spacers within clustered regularly interspaced short palindromic repeats ( Palmer et al. ). The four species of Pyrovirus proposed based on complete or near-complete genomes is the first study of viruses infecting Aquificota , despite the dominance of Aquificota in many terrestrial and marine thermal systems.

Adaptation to extreme conditions, environmental role and metabolic functions of extremophiles

Mechanisms evolved by extremophiles not just to survive, but to thrive in inhospitable environments are fascinating. Many specialized mechanisms enabling growth under extreme conditions have already been studied while others remain elusive ( Coker, 2019 ; Schmid et al., 2020 ). Some of the manuscripts in this volume expand on such strategies.

Three papers in the Research Topic focused on energy conservation, central carbon metabolism, and piezophily of thermophiles. The paper by Gavrilov et al. focused on mechanisms used by the thermophile Carboxydothermus ferrireducens to use extracellular amorphous ferrihydrite as a terminal electron acceptor for anaerobic respiration, producing large magnetite crystals. Genome sequencing combined with RNA-Seq and proteomic data derived from cultures using different electron acceptors were used to identify three constitutive c-type multiheme cytochromes, including OhmA, which was strongly bound to extracellular magnetite. Another paper by Thomas et al. , focused on carbon metabolism in the thermophile Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales . Despite its chemoheterotrophic metabolism, T. hugenholtzii does not grow on any defined carbon sources, obscuring our understanding of its metabolism. Comparative genomics of the T. hugenholtzii genome with eight related MAGs from geothermal springs revealed a high abundance and strong conservation of peptidases among three species clusters, suggesting a conserved proteolytic metabolism. Exometabolomics and 13 C metabolic probing studies confirmed this metabolism for T. hugenholtzii . The metabolic probing confirmed glycolysis, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways, yet glycolysis and the TCA cycle were uncoupled. Microorganisms living at great depths in the sea must cope with variations in hydrostatic pressure. The classical stress response of piezophiles to changes in hydrostatic pressure consists of up- and down-regulation of several genes. Herein, Moalic et al. suggest that Thermococcus piezophilus , a piezohyperthermophilic archaeon with the widest range of tolerance to high pressure known so far, modulates its energy-conservation process by means of the control of the master transcriptional regulator SurR under non-optimal pressures conditions.

Two additional contributions focused on acidophily and halophily. Genome comparisons by Cortez et al. on bacterial acidophiles affiliated with different phyla and their neutrophilic counterparts demonstrated a correlation between decreases in genome size and adaptation to low-pH ecosystems. This genome streamlining of acidophilic bacteria is mainly due to reduction of average protein size and gene loss, with an unexpected constant number of paralogs compared with studies that claim a relatively lower paralog frequency for other streamlined microorganisms ( Giovannoni et al., 2005 ; Swan et al., 2013 ). According to these authors, other potential mechanisms for acid resistance might be the enrichment in cytoplasmic membrane proteins and those involved in energy conservation, DNA repair, and biofilm formation. The paper by Durán-Viseras et al. uses a culturomics approach to isolate new haloarchaea from the Odiel Saltmarsh, Spain, previously revealed to contain a high proportion of sequences not related to previously cultivated taxa ( Vera-Gargallo and Ventosa, 2018 ). Their approach resulted in the isolation and description of three new species: Halomicroarcula rubra, Halomicroarcula nitratireducens , and Halomicroarcula salinisoli . Ensuing genomic analysis revealed the unexpected identification of complete pathways for the biosynthesis of the compatible solutes trehalose and glycine betaine, not identified before in any other haloarchaea. Although they use a salt-in strategy, this finding might suggest alternative osmoadaptation strategies within this group.

Phylogeny, evolution, classification, and biodiversity of extremophiles

A heated debate exists on the conditions of the environment where the last universal common ancestor (LUCA) of extant life could have inhabited. Although it is not yet clear if the LUCA was an extremophile (i.e., hyperthermophile), the scientific community agrees that extremophily emerged early in the diversification of prokaryotes ( Catchpole and Forterre, 2019 ). Evolution of the thermoacidophilic archaeal family Sulfolobaceae has been a focus of research into this topic. The study by Banerjee et al. revealed a non-symmetric genome evolution within this family, with some species undergoing genome expansion whereas there was gene loss in others, even considering that they share a similar niche. They also detailed a high level of conservation for most of the autotropic pathways across this family.

In the genomic era, systematics has moved forward from gene-based phylogenies to genome-based classifications ( Rosselló-Móra and Whitman, 2019 ; Parks et al., 2022 ). Thus, taxonomic arrangements supported by whole genome data analysis spanning several groups of extremophiles are proposed through this volume. The research conducted by de la Haba et al. sought to solve a well-known issue concerning the taxonomic status of the partially overlapping and contemporaneously described archaeal genera Natrinema and Haloterrigena ( Minegishi et al., 2010 ; Papke et al., 2011 ). Phylogenomic analysis and the use of Overall Genome Relatedness Indexes allowed the authors to clearly differentiate the two genera, and justified transfer several species from Haloterrigena to Natrinema . In the domain Bacteria , the article by Park et al. proposed an average amino-acid identity (AAI) cut-off value of 63.43 ± 0.01% to delineate genera within the Desulfovibrionaceae , following up on recent rearrangements in the family based on a phylogenomic approach ( Galushko and Kuever, 2020 ; Waite et al., 2020 ). As a result, two new genera (i.e., “ Alkalidesulfovibrio” and “ Salidesulfovibrio” ), and one not yet validly published genus name (“ Psychrodesulfovibrio ”) were proposed. On the other hand, Ramírez-Duran et al. revised the taxonomy of the genus Saccharomonospora using a combined approach based on 16S rRNA gene and core-genome sequence phylogenies as well as comparative genomics. Additionally, this article also identifies a wide variety of biosynthetic gene clusters, thus uncovering the potential biotechnological applications of this actinobacterial genus to produce unknown bioactive molecules.

The exploration of natural microbial communities inhabiting extreme environments was the focus of several studies in this Research Topic. These types of studies remain vibrant because they provide insights into the ecology of microorganisms in their natural habitats. As a first example, Liu et al. explored hot springs in Conghua, China, focusing on anaerobic ammonium oxidation (anammox). This is an important process of the nitrogen cycle, and anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remains under-reported. Diverse putative anammox organisms were identified, especially “ Candidatus Brocadia”. In another contribution, Narsing Rao et al. combined culture-dependent and -independent approaches to study seven different hot spring in India. These locations were found to harbor novel microbial groups and some of which produced thermo-stable enzymes. Finally, a separate study focused on benthic microbial community dynamics in an acid saline lake, Lake Magic, Australia, by studying 16S rRNA gene amplicons for prokaryotes and internal transcribed spacer amplicons for fungi over an annual cycle ( Ghori et al. ). The annual cycle included a flooding stage, followed by evapo-concentration of solutes, which led to decreases in bacterial diversity and increases in halotolerant and acid-tolerant taxa, including phylotypes similar to those involved in sulfur cycling.

New frontiers

Research on extremophiles has traditionally been at the forefront of microbiology, boldly opening up new frontiers in our understanding of life and its limits. The reach and impact of such research is now extending beyond our own planet, with increasing relevance in the cross-disciplinary fields of Astrobiology and Space Microbiology. The study of extreme environments on Earth and their inhabitants is one of the main pillars of research supporting the search for life on Mars, the exooceans of the icy moons of the solar system, and beyond (e.g., Jebbar et al., 2020 ; Taubner et al., 2020 ; Changela et al., 2021 ). Studies of terran extremophiles is also increasingly seen as useful for assisting space exploration in activities such as in situ resource utilization (ISRU; Cockell, 2010 ; Dhami et al., 2013 ; Changela et al., 2021 ).

Space itself can be seen as an extreme environment, with a combination of multiple conditions and with a range of effects on microbes that are not yet fully explored. Observed changes in the characteristics of pathogens and conditional pathogens in space, namely increased pathogenicity and virulence, are a significant concern when discussing long-term crewed mission or human presence in space ( Simões and Antunes, 2021 ). The impact of the space environment seems to vary between species, so the need for further studies has been stressed by several authors.

The current volume of our special topic addresses this issue with a study by Su et al. , focusing on the conditional pathogen Stenotrophomonas maltophilia , an understudied emerging Gram-stain-negative multidrug-resistant species. This paper constitutes the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in this species under simulated microgravity. Results from this investigation showed that microgravity led to an increased growth rate, enhanced biofilm formation, increased swimming motility, and metabolic alterations. This study further increases our understanding of the effects of space conditions on microbial physiology, metabolism, and pathogenicity and may help to provide new ideas for the prevention and treatment of infections in future missions.

Bijlani et al. describe in this article collection the new species Methylobacterium ajmalii , isolated from the International Space Station as part of an on-going microbial tracking experiment that retrieved a few strains from the family Methylobacteriaceae ( Checinska Sielaff et al., 2019 ). In addition to the full characterization and description of this new species of Methylobacterium using polyphasic taxonomy, the paper further analyses whole genome sequencing data with identification of some specific features with potential relevance for biotechnology.

Another important link between microbiology and space exploration is the study of persistent species in spacecraft assembly cleanrooms. Despite their inhospitable conditions and intense precautions taken within these facilities, different types of microbes are known to persist and are a major source of concern regarding planetary protection measures focused on preventing potential biological contamination of other parts of the solar system (e.g., Rettberg et al., 2019 ). Within such studies, fungi are frequently overlooked despite the fact that they are known for their resilience and might pose a threat to closed habitats (biocorrosion) as well as their immunocompromised occupants (pathogenicity).

In this sense, Blachowicz et al. deal with isolation and characterization of rare mycobiome associated with spacecraft assembly cleanrooms. The study aimed to help address two current gaps in understanding fungi populations under such settings. On one hand, the majority of previous reports were based on cultivation-based approaches, while culture-independent mycobiome analyses were scarce. On the other, the authors highlighted the need for more efficient cultivation methods when analyzing cleanrooms, particularly as isolation is essential for thorough analysis and characterization of fungi. Metagenomic reads were dominated by Ascomycota and Basidiomycota , with significant differences between distant locations, and the detection of several potential novel species. This paper is presented as a first step toward characterizing cultivable and viable fungal populations in cleanrooms to assess fungal potential as biocontaminants during interplanetary exploration, in addition to other cleanroom settings, such as intensive care units, operating rooms, or in the semiconducting and pharmaceutical industries.

Schultzhaus et al. also focused on fungi with an eye toward extreme conditions relevant to space exploration, namely ionizing radiation. By studying the phenotypic and transcriptomic responses of the radioresistant yeast Exophiala dermatitidis to three different radiation sources (i.e., protons, deuterons, and α-particles), a common theme of induction of DNA repair and DNA replication genes and repression of ribosome and protein synthesis emerged. Yet, differences also emerged, most notably that particle irradiation resulted in greater changes in gene expression and an upregulation of genes involved in autophagy and protein catabolism.

This collection contains a manuscript by Wood et al. that highlights concerns about inconsistent results of different short-read metagenomic pipelines to assess the microbial diversity of the aforementioned cleanrooms. Although all four used pipelines detected extremophiles and spore-forming bacteria, they did not yield the same microbial profile based on the same raw dataset, which raises doubts of the reliability of using a single pipeline. The paper also presents a roadmap aimed at validating future studies on planetary protection-related microorganisms.

Final remarks

As evidenced by the success of this Research Topic, after over 50 years of research focused on extreme environments, extremophiles are still the subject of enormous interest for the scientific community and for biotechnology. The more we learn about extremophiles, the more fascinating they become, and each new discovery reveals more of their secrets, but also opens up new questions. After all, they are one of the most ancient dwellers on Earth and they will certainly remain here, and possibly beyond our planet, once all of us are gone.

Author contributions

RH, AA, and BH wrote the first draft of the editorial article, and they also reviewed and approved the final version of the manuscript.

Acknowledgments

We thank all contributing authors for submission of their articles to this Research Topic. We are grateful to reviewers for the valuable comments on the manuscript.

Conflict of interest

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.

Publisher's note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

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Keywords: extremophiles, taxonomy, genomics, metagenomics, adaptation, Space Microbiology, extremozymes, biodiversity

Citation: de la Haba RR, Antunes A and Hedlund BP (2022) Editorial: Extremophiles: Microbial genomics and taxogenomics. Front. Microbiol. 13:984632. doi: 10.3389/fmicb.2022.984632

Received: 02 July 2022; Accepted: 15 July 2022; Published: 02 August 2022.

Edited and reviewed by: Andreas Teske , University of North Carolina at Chapel Hill, United States

Copyright © 2022 de la Haba, Antunes and Hedlund. 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) and the copyright owner(s) 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.

*Correspondence: Rafael R. de la Haba, rrh@us.es ; André Antunes, aglantunes@must.edu.mo ; Brian P. Hedlund, brian.hedlund@unlv.edu

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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• TECHNOLOGY FEATURE
• 02 November 2020

Studying life at the extremes

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Researchers are looking for microbes in soil samples from this flaming gas crater in Turkmenistan, known as the Door to Hell. Credit: Stefan Green/XMP

Microbes cling to life in some of Earth’s most extreme environments, from toxic hot springs to high-altitude deserts. These ‘extremophiles’ include organisms that can survive near-boiling heat or near-freezing cold, high pressure or high salt, as well as environments steeped in acids, alkalis, metals or radioactivity.

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August 11, 2021

Extremophiles: Resilient microorganisms that help us understand our past and future

by Jaz L. Millar, The Conversation

In the infamous words of Jurassic Park consultant Dr. Ian Malcolm, "life finds a way" . In the depths of the ocean, in volcanic springs, under four meters of ice: almost anywhere scientists can think of to look for life on Earth, we have found it.

The methods these organisms employ to survive the extreme have taught us how to protect our bodies better, how to copy DNA to better diagnose illnesses and how life survived 100 million years of a global Ice Age .

Throughout my career, I have been collecting organisms from extreme environments . The first was a single-celled alga, known as Dunaliella salina , that inhabits salt pans: wide, flat expanses of land where water has evaporated to leave behind very high concentrations of salt. Salt may not seem like an obvious cause of biological stress , but it can draw out enough moisture from a cell to burst it, killing the organism.

My work aimed to find whether D. salina is an "extremophile" (a lover of extreme conditions) or simply tolerant of highly salty conditions, with a preference for less salt. The latter certainly wasn't the case: in fact, I never found its optimum state, as the more salt was added, the more it grew. It was a true extremophile.

D. salina compensates for salt stress by carrying high levels of glycerol (a sweet-tasting liquid chemical) within its cell, balancing the direction in which water is pulled to stop water from being drawn out of its cell through osmosis. It also has to contend with incredibly high levels of UV radiation in the dry, exposed salt pans where it lives. That's why it carries high concentrations of beta-carotene —a form of vitamin A, which protect it from UV damage.

In one of history's biggest biotechnology success stories, D. salina is now commercially cultivated for dietary supplements and skincare products: especially for foundation and face creams that protect skin from UV radiation. Effectively, scientists have stolen the "superpower" of these microbes—being able to survive UV radiation—to save our skins.

But perhaps even more significant discoveries have come from "thermophiles," or heat-loving organisms. It is from these thermophilic microorganisms that scientists have extracted thermostable proteins able to hold their molecular form above 60°C, the temperature required to pull apart and replicate DNA in order to examine it. If you have had a COVID PCR test, for example, your DNA sample has been through this process. This ability to replicate, or "amplify," DNA to levels we can detect has revolutionized biological and medical science.

At the University of York, I studied the cellular mechanisms of a hyper-thermophilic microorganism known as Sulfolobus . These amazing microbes belong to the archaea domain , the third branch of life alongside bacteria and eukaryotes.

Sulfolobus are not only at home in the 75-80°C heat of active volcanoes, they're also able to flourish in the highly acidic pH 2-3 environment of volcanic springs —roughly the same as lemon juice or vinegar. Learning their secrets may help us discover molecules that can remain stable at even higher temperatures, providing even more versatile analysis that could help us make strides forward in healthcare, genetics and environmental research .

From hot to cold

Since working with thermophiles, my research has taken me to the other extreme of life on our planet. For the last four years I have been studying the microorganisms living in the Arctic and Antarctic. Although from a distance the Earth's poles may seem pristine and untouched by life, microorganisms persist and even thrive.

Many of these microorganisms add patches of bright color to the landscape, thanks to their lurid photosynthetic pigments. One example is the pink and green algae snow blooms known as "watermelon snow" . Drill through the surface of frozen lakes such as Lake Untersee in Antarctica and you will find bright purple mats of photosynthetic cyanobacteria, so colored because of the low levels of light under the ice. Their purple pigment allows them to absorb green light—the main wavelength that penetrates deep water and thick ice—more efficiently.

Remarkably—despite the low availability of light and nutrients—blue-green cyanobacteria can even be found clinging to tiny pores within and underneath rocks in the polar regions. In such a hostile environment with so little photosynthetic life producing energy to feed into the food chain, these cyanobacteria are a key foundation of the local ecosystem.

While my colleagues at the Natural History Museum in London have been working on those colorful communities, I have been studying the "black holes of the cryosphere" (frozen water zones) known as cryoconite holes . Cryoconite holes are small meltwater pockets containing dark sediment that give the melt zones of glaciers a spotted appearance. Although they are often only 5-20cm wide, my colleagues and I have found hundreds of species of microscopic organisms in each one.

It has been proposed that these hotspots of species diversity could have provided refuge for a range of microorganisms during the Snowball Earth period, a global Ice Age that occurred 720-635 million years ago—just before the appearance of animals in the fossil record. Our planet has endured many periods of glaciation, but the Cryogenian Snowball Earth was especially severe, with ice reaching all the way to the equator.

To test cryoconite organisms' ability to survive Snowball Earth, we compared the growth of cryoconite organisms incubated at a constant Antarctic summer temperature (0.5°C) to cryoconites frozen at -5°C for 12 hours within each 24-hour period. After one month, our initial results showed there was no observable difference between the 0.5°C and -5°C groups. Amazingly, being completely frozen each night did not even slow down the growth of these organisms.

Hopefully, this research will help us learn not only about how life survived extreme climates of the past, but how modern-day connections between climate and microbial ecosystems work.

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Extremophiles Reveal a New Dimension of the Genome

Distantly related extremophiles share genetic signatures, a product of their adaptation to a specific “harsh” environment..

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Extremophiles, as their name suggests, are organisms that can live in extreme conditions, many of which are inhospitable for other terrestrial organisms.

These fascinating organisms have been discovered deep within the Earth’s crust, in extremely acidic or basic conditions, under high pressures and in environments with blisteringly hot or freezing cold temperatures.

Extremophiles have intrigued scientists for many years; how do they not only survive, but thrive in such harsh environments? Advances in next-generation sequencing are helping to answer this question, providing insights into their genetic composition.

Professor Lila Kari from the Cheriton School of Computer Science has studied genetic signatures since the early 2000s. In a bid to understand whether an organism’s genome might contain information beyond taxonomic and evolutionary insights – i.e., its ancestry and how it is related to other organisms – she turned to extremophiles.

Using machine learning algorithms, Kari and colleagues compared genetic signatures across 700 microbial extremophiles. Their findings, published in Scientific Reports , were so unexpected that the team “couldn’t believe their eyes.” 1

Typically, the more similar an organism’s DNA is to another organism, the more closely related those organisms are. But Kari and colleagues found some extremophiles had very similar DNA, despite being very distantly related.

This suggests that an environmental “signature” exists within the extremophiles’ genome. Two extremophiles – though distantly related – could share similar genome signatures if they have adapted to survive in the same harsh conditions, such as extreme temperature or pH.

“Our study has revealed, in some sense, a new dimension of the genome: The DNA of extremophiles contains, in addition to ancestry information, information associated with the extreme environment where they live,” said Kari.

Technology Networks recently had the pleasure of interviewing Kari, where we learned more about the backstory of this study and the significance of its findings.

Molly Campbell (MC): Why did you decide to focus on extremophiles in this study? Why are they so interesting, and are there any examples of extremophiles that you think are particularly fascinating?

Lila Kari (LK): Extremophiles are very interesting creatures, as they live at the edges of survivability and beyond. Besides being fascinating to young and old people alike (my younger daughter loves tardigrades!), it is of great interest to discover the biological mechanisms that allow them to survive and even thrive in incredibly hostile environments.

Cool examples of extremophiles are the super-cute tardigrades (also known as water bears or moss piglets) that can survive exposure to extreme temperatures, extreme pressures, air deprivation, radiation, dehydration and starvation. Or the microbe Deinococcus radiodurans, which can survive in outer space.

The study of extremophiles has become a hot topic in recent years, when humanity is exploring outer space and searching for organisms that can survive the extremely hostile conditions of outer space, to be sent to Mars or on other space missions.

We had different reason for choosing to study extremophiles. Our group has studied “genomic signatures” since the 2000s; that is, patterns in the genomes of organisms that allow us to identify them and classify and position them correctly on the Tree of Life.

To elaborate, from a mathematical point of view:

• A genome is a long string made up of “letters” from a four-letter alphabet (A, C, G and T).
• A “DNA word” is a sequence of such letters (for example, GGAATC a six-letter DNA word.
• A “pattern” refers to a pattern of frequencies of such DNA words in a given genome.

These frequency patterns form a so-called “genomic signature” of an organism, and they allow us to identify the species and the degree of relatedness to other species. Intuitively, this is akin to being able to tell the difference between a French book and an English book by noticing that the English one has a high frequency of the three-letter word “the”, while the French one has a high frequency of the three-letter word, “les”.

In the research to date, including our own, scientists have obtained highly accurate classifications of genomes of organisms based on this method, which led to the tentative conclusion that this “genomic signature” contains exclusively taxonomic information regarding biological relatedness.

However, we had the idea that perhaps the genome contains information other than taxonomic/evolutionary, and we wanted to explore this question. For example, could it be possible that the genome also has patterns that reflect the environment in which an organism lives?

We realized that if such an “environmental signal” would exist at all, it would probably be very faint, and that our only hope to discover such a signal would be to search for it in organisms that live in extreme environments, that is – you guessed it – in extremophiles.

MC: Can you explain the purpose of using machine learning methods in this study, and how you used them?

LK: Machine learning is a very powerful methodology for classification problems, such as the taxonomic classification problem we are exploring (given a DNA fragment, what species of organism does it belong to, and how closely it is related to other species).

In supervised classification, you “train” the machine learning algorithm with examples, each consisting of a DNA fragment and the species label of that organism. At the end of training, you present the algorithm with a new DNA fragment and ask it: what is its taxonomic label? The algorithm gives you the answer based on what it has “learned” during training.

Machine learning trained with genomic signatures of DNA fragments has proved to yield highly accurate classifications of very large biological datasets (tens of thousands, or even much larger). Note that taxonomic identification and classification is a very important problem for biodiversity research, given that 95% of the multicellular species on Earth have yet to be taxonomically classified.

For our extremophile research, we used both supervised and unsupervised machine learning. In the latter, the algorithm is simply given a large dataset of DNA fragments and is asked to discover what various DNA fragments have in common and group them in clusters based on their similarities, whatever those may be. In other words, unsupervised machine learning is a “blind” algorithm that is given some unlabeled DNA fragments and no other information, and is told to “go there and find something,” and group the organisms in clusters based on whatever similarities it finds.

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MC: Your data show that the environment creates a “mark” in the genome of an organism living in it, meaning organisms that are distantly related might have similarities in their genomes if they occupy similar “harsh” environments. Can you talk more about this finding and its significance?

LK: To our great astonishment, we discovered that besides the expected taxonomic signature (DNA word patterns that allow us to identify a species, and how it is related to other species), the extremophile genomes also exhibit an environmental signature. That is, word patterns that are associated with the type of environment that the extremophile lives in (e.g., certain common DNA patterns are found in extremophiles who live in very hot environments, even though taxonomically they are as distant as they can be in the Tree of Life).

It is as if, until now, we thought that the DNA/genome of an organism is like a “book”. Now we discovered that it is actually like sheet music where the lyrics (the taxonomic information) are interwoven with music (the environmental information), both encoded with the same alphabet. Moreover, we discovered that, at times (e.g., in some extremophiles), the environmental signal is louder than the evolutionary signal.

This is a bit like, say, trying to classify songs of different genres, sung in different languages. Most of the time what stands out in a song is the language of the lyrics, but sometimes the music is so loud that you can only tell that both belong to the same genre (e.g. rock, or heavy metal) but you cannot tell in which language they are sung.

Overall, I cannot stress enough how unexpected this discovery is: It is akin to discovering a completely new “dimension” of the genome.

MC: Are there any examples of extremophiles with similar genome patterns that you think are particularly “surprising” or exciting?

LK: Yes, we found several concrete examples of completely unrelated organisms with similar genomic signatures caused by the environment. Now I am exaggerating a bit here, since all life on Earth is related, as descendants of the “Last Universal Common Ancestor”. What I mean is that they are as distantly related as they can be, i.e., some being bacteria and some archaea, with bacteria and archaea being two of the only three distinct “domains” of life” alongside eukaryotes.

These unrelated organisms were grouped together as similar by all the machine learning algorithms we used, including the “blind” unsupervised ones, in spite of being more different taxonomically from each other than a lichen is from a polar bear.

The only feature that these grouped-together extremophiles had in common was that they were all thermophiles, that is, they lived in extremely hot environments. Among them is one of my favourite extremophiles, the archaeon Pyrococcus furiosus . You have to love that name, which comes from the Greek “pyrococcus”, meaning fireball, and the Latin “furiosus”, meaning furiously, and refers to its furious swimming at temperatures of over 100 °C!

P. furiosus was grouped together with three thermophile bacteria, which was completely jaw-dropping given how different they are taxonomically.

MC: Are there any limitations to this research that you think it is important to highlight? If so, how could future work overcome such limitations?

LK: Every method has limitations, including machine learning algorithms. First, their classification/clustering accuracies, while high, are almost never 100%, so we are working on improving the accuracy of the machine learning methods that we used in this study.

In addition, a limitation of machine learning algorithms is that they are “black box” methods, in the sense that while they output a classification or clustering, they do not offer a rationale for their output. More research is needed to be able to understand and interpret the results of the machine learning classifications/clustering.

MC: What are your next research steps?

LK: We are currently working on several research directions, including the exploration of the existence of an environmental signature in radiation-resistant extremophiles, such as Deinococcus radiodurans , which was recently proved by scientists to be able to survive outer space conditions for one to three years. 2 , 3

The next steps would then be to extend our exploration to polyextremophiles (organisms that thrive under multiple stresses in extreme environments, e.g., both high temperature and high acidity), and to multicellular extremophilic organisms such as tardigrades or extremophilic plants.

References:

1. Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Sci Rep. 2023;13(1):16105. doi: 10.1038/s41598-023-42518-y

2. Ott E, Kawaguchi Y, Kölbl D, et al. Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission. Microbiome . 2020;8(1):150. doi: 10.1186/s40168-020-00927-5

3. Kawaguchi Y, Shibuya M, Kinoshita I, et al. DNA damage and survival time course of deinococcal cell pellets during 3 years of exposure to outer space. Front Microbiol . 2020;11. doi: 10.3389/fmicb.2020.02050

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Yellowstone: 1 ft Sea Vents on the East Pacific Ridge: 1.5 miles Atacama Desert, Chile: 1ft Lake Vostok, Antarctica: 2 miles

The driest parts of Chile's Atacama high desert get rain once every few decades, and are blasted with high levels of ultraviolet radiation. These and other circumstances make the Atacama an excellent terrestrial model for conditions on Mars. Yet, extreme microbial life exists a few inches below the surface. In this image, researcher Jay Quade samples the soil for key compounds. Credit: Julio L. Betancourt, U.S. Geological Survey

Antarctica is another site in which researchers study extreme life forms adapted to survive fiercely hostile environments. Investigators with NSF's Long-Term Ecological Research program have identified a number of novel species, including microbes (shown in scanning electron microscope inset) in lake ice from the ultra-cold Dry Valleys in East Antarctica. Credit: Peter West, National Science Foundation; courtesy of the Priscu Research Group, Montana State University at Bozeman

Antarctica's Dry Valleys contain a number of lakes that are ice-covered year-round. Although they harbor some liquid water, their conditions are drastically different from those in temperate lakes. There is almost no circulation and the water is cut off from air and light. To see what kind of microbes might survive this environment, investigators from Montana State University lowered a sediment trap. Credit: Courtesy of the Priscu Research Group, Montana State University at Bozeman

Researchers have removed ice cores from an ice-capped body of water called Lake Vida in Antarctica's Dry Valleys. The cores contained microbes nearly 3,000 years old, with DNA that has been extremely well preserved. Once thought to be frozen down to its bottom, Lake Vida has been shown to have a small amount of liquid water that is seven times saltier than the sea, enabling it to remain liquid at -10 C. Credit: Courtesy of the Priscu Research Group, Montana State University at Bozeman

In the middle of East Antarctica, buried two miles beneath the surface of the massive ice sheet, is an underground freshwater lake the size of Lake Ontario. Called Lake Vostok, it may contain organisms that have been completely isolated for 500,000 years. This image, taken from ice cores obtained above the lake, reveals numerous microorganisms. Credit: Courtesy of the Priscu Research Group, Montana State University at Bozeman

The Arctic region holds its share of extreme life forms. In this image from an expedition near Greenland, researchers remove the filter head from a pump. The device was designed to pump hundreds of liters of seawater from a given depth across a set of filters with pore sizes small enough to collect aggregates of material and associated microbes (shown in inset). Credit: Melanie Simard; Shelly Carpenter (inset)

In the 1970s, researchers discovered that seafloor vents—cracks in the Earth's crust that release superheated water and thick clouds of minerals—are home to a host of extremophile organisms. This photo shows a typical formation. The inset photo is a scanning electron microscope image of organisms (both bacteria and archaea) inhabiting the interior of the vent chimney. Credit: University of Washington, Center for Environmental Visualization

Researchers monitor organisms in the Colorado Rockies at one of several sites in the Alpine Microbial Observatory program. Participants study the seasonal dynamics of soil microorganisms across a wide range of elevations and geography, from mountain forests at around 9000 feet to tundra and rocky cliffs at 12,000 feet. Credit: Ken Wilson, EBIO Department, University of Colorado

For more than 40 years, Yellowstone National Park, with its remarkable range of microenvironments, has proven to be an unflagging source for extremophile organisms. This photo shows one such environment, a geothermal spring called Black Sand Basin, named for the small granules of obsidian distributed throughout the area. Credit: Gwendolyn E. Morgan

A scientist collects samples from Obsidian Pool, a hot spring in Yellowstone National Park that has provided investigators with a broad spectrum of extremophile diversity over the years. The genetic differences among various microbes in this environment is a subject of intense study. Credit: Jeff Walker

This sandstone-like sample from the Norris Geyser Basin in Yellowstone National Park has a surprise occupant: A number of microbes (the greenish layer) that have learned to survive in the pores of rock that is acidic enough to dissolve nails and heated by surrounding water to about 95 F. Inset luminescence image shows microbes as pink and rock as blue. Credit: John R. Spear; Jeff Walker (inset)

Another category of extreme microbes, called "halophiles," is adapted to high-salt conditions of the sort found in ponds of the Guerrero Negro area of Baja California, shown here. A research team from the University of Colorado, using genetic identification techniques, found a variety of novel microorganisms that thrive in this locale. The inset photo shows a piece of gypsum from the brine ponds. Each color indicates the presence of a different kind of microorganism. Credit: John R. Spear (both)

Researchers take samples from the bubbling mud around a collapsed volcano in Russia's remote Kamchatka peninsula. The site features a remarkable diversity of extremophile activity, and is studied by scientists from around the world. Credit: Noah Whitman, ©Exploratorium, www.exploratorium.edu

Kamchatka microbial samples, sealed in blue-topped test tubes, incubate in a hot spring among hairy-looking filamentous bacteria. Credit: Noah Whitman, ©Exploratorium, www.exploratorium.edu

Researchers take samples from the Henderson Mine in Empire, Colorado. Among the many questions to be answered in such deep underground locations is: Are particular kinds of deep-dwelling extremophiles associated with different kinds of mineral composition in the surrounding rock? Credit: John R. Spear

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Any opinions, findings, conclusions or recommendations presented in this material are only those of the presenter grantee/researcher, author, or agency employee; and do not necessarily reflect the views of the National Science Foundation.

Extremophiles: the species that evolve and survive under hostile conditions

• Review Article
• Published: 25 August 2023
• Volume 13 , article number  316 , ( 2023 )

Cite this article

• Bhagwan Narayan Rekadwad 4 , 5   nAff2 ,
• Wen-Jun Li   ORCID: orcid.org/0000-0002-7391-7093 1 ,
• Juan M. Gonzalez 3 ,
• Rekha Punchappady Devasya 2 ,
• Arun Ananthapadmanabha Bhagwath 2 , 6 ,
• Ruchi Urana 7 &
• Khalid Parwez 8  

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Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

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Acknowledgements

This research was supported by Key-Area Research and Development Program of Guangdong Province (2022B0202110001), National Natural Science Foundation of China (Nos: 31972856 and 32061143043) and Yenepoya (Deemed to be University), India (No. YU/SeedGrant/104-2021). All authors duly acknowledge Dr. Manik Prabhu Narsing Rao (former affiliation: Sun Yat-Sen University, Guangzhou 510275, PR China) for his advice during preparation of the manuscript.

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Bhagwan Narayan Rekadwad

Present address: Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, Karnataka, India

Authors and Affiliations

State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, Karnataka, India

Rekha Punchappady Devasya & Arun Ananthapadmanabha Bhagwath

Microbial Diversity and Microbiology of Extreme Environments Research Group, Agencia Estatal Consejo Superior De Investigaciones Científicas, IRNAS-CSIC, Avda. Reina Mercedes, 10, 41012, Seville, Spain

Juan M. Gonzalez

National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007, Maharashtra, India

Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU), Ganeshkhind Road, Pune, 411007, Maharashtra, India

Yenepoya Institute of Arts, Science, Commerce and Management, A Constituent Unit of Yenepoya (Deemed to be University), Yenepoya Complex, Balmatta, Mangalore, 575002, Karnataka, India

Arun Ananthapadmanabha Bhagwath

Department of Environmental Science and Engineering, Faculty of Environmental and Bio Sciences and Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India

Ruchi Urana

Department of Microbiology, Shree Narayan Medical Institute and Hospital, Saharsa, Bihar, 852201, India

Khalid Parwez

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Rekadwad, B., Li, WJ., Gonzalez, J.M. et al. Extremophiles: the species that evolve and survive under hostile conditions. 3 Biotech 13 , 316 (2023). https://doi.org/10.1007/s13205-023-03733-6

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A young researcher wants to test how well extremophilies, orpanisms that thrive in extreme conditions, live in different environments. She will do this by putting extremophiles of different species into different solvents. Because of limited lab space, she can rum only one sample at a time, and each sample must remain undisturbed for 7 days. To reduce the total time needed to process all samples, the researcher decides to use two acidic solutions along with a control. The information below includes the extremophiies and the solvents the researcher will use in her tests. Extremophiles Species of Solvents Based on the tables, how many days will all of the researcher's experiments take? You may use the caiculator A. 7 B. 21 C. 45 D. 56

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