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Microorganisms
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Microbial Diversity in Extreme Environments
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Microbial Diversity in Extreme Environments

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 118752

Special Issue Editors

Dr. Edgardo Rubén Donati

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Guest Editor
CINDEFI (CCT La Plata-CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), Buenos Aires, Argentina
Interests: biomining; bioremediation; extremophiles; acid mine drainage; biotechnology in general
Special Issues, Collections and Topics in MDPI journals
Dr. María Sofía Urbieta

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Guest Editor
CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas—UNLP), Universidad Nacional de La Plata (UNLP), Buenos Aires B8508, Argentina
Interests: environmental microbiology; extremophilic microorganisms; biomining; bioremediation of heavy metals
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Rajesh Kumar Sani

E-Mail Website
Guest Editor
Karen M. Swindler Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, USA
Interests: biomaterials; exopolysaccharides; extremophilic bioprocessing; biocatalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Extreme environments are described as those where one or more physicochemical parameters reach values far from those considered normal for human life. The exploration of remotes corners of the earth has allowed scientists to find microbial life in inhospitable environments like the bottom of the sea, high-altitude deserts, acidic high-temperature hot springs, ice caves in Antarctica, and even in some environments derived from the negative impact of anthropogenic activities, such as acid mine drainage. The assessment of microbial diversity in such extreme environments has increased in the last decades, surely due to the massive use of high-throughput sequencing techniques. Although this kind of assessment is relevant by itself, as microbial diversity is an essential part of the patrimony of each geographic area, it is clear that the driving force to study the microorganisms that inhabit such remarkable environments goes far beyond their mere taxonomic identification. The bacteria, archaea, and the less known eukaryotes that develop in extreme environments open the door to the study of many topics, from their impact on the local biogeochemical cycles or the discovery of novel enzymatic pathways, to the possible biotechnological uses of their species or enzymes. Besides, it is well known that extreme environments are niches of novel species not yet cultured or characterized.

In this context, this Special Issue of Microorganisms invites you to send contributions concerning any aspect related to the microbial diversity found in any extreme environment, natural or of anthropogenic origin, or the potentialities of the bacteria, archaea, or eukaryotes that inhabit them. The topics comprised in this Special Issue are taxonomic diversity assessment, characterization of novel species, biogeochemical interrelationships, temporal/spatial evolution of microbial communities exposed to changes in their environment, and potential biotechnological applications of extremophiles obtained from certain extreme environments.

Prof. Dr. Rajesh K. K. Sani
Dr. Edgardo Rubén Donati
Dr. María Sofía Urbieta
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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17 pages, 2240 KiB  
Article
Influence of Extremophiles on the Generation of Acid Mine Drainage at the Abandoned Pan de Azúcar Mine (Argentina)
by Josefina Plaza-Cazón, Leonardo Benítez, Jésica Murray, Pablo Kirschbaum and Edgardo Donati
Microorganisms 2021, 9(2), 281; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020281 - 29 Jan 2021
Cited by 6 | Viewed by 1936
Abstract
The risk of generation of acid drainages in the tailings of the Pan de Azúcar mine that closed its activities more than three decades ago, was evaluated through biooxidation studies using iron- and sulfur-oxidizing extremophilic leaching consortia. Most of tailings showed a high [...] Read more.
The risk of generation of acid drainages in the tailings of the Pan de Azúcar mine that closed its activities more than three decades ago, was evaluated through biooxidation studies using iron- and sulfur-oxidizing extremophilic leaching consortia. Most of tailings showed a high potential for generating acid drainage, in agreement with the results from net acid generation (NAG) assays. In addition, molecular analysis of the microbial consortia obtained by enrichment of the samples, demonstrated that native leaching microorganisms are ubiquitous in the area and they seemed to be more efficient in the biooxidation of the tailings than the collection microorganisms. The acid drainages detected at the site and those formed by oxidation of the tailings, produced a significant ecotoxicological effect demonstrated by a bioassay. These drainages, even at high dilutions, could seriously affect a nearby Ramsar site (Laguna de Pozuelos) that is connected to the Pan de Azúcar mine through a hydrological route (Cincel River). Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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20 pages, 3246 KiB  
Article
Living Lithic and Sublithic Bacterial Communities in Namibian Drylands
by Steffi Genderjahn, Simon Lewin, Fabian Horn, Anja M. Schleicher, Kai Mangelsdorf and Dirk Wagner
Microorganisms 2021, 9(2), 235; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020235 - 23 Jan 2021
Cited by 8 | Viewed by 2792
Abstract
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering [...] Read more.
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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24 pages, 3328 KiB  
Article
Metagenomics and Culture Dependent Insights into the Distribution of Firmicutes across Two Different Sample Types Located in the Black Hills Region of South Dakota, USA
by Tanvi Govil, Manasi Paste, Dipayan Samanta, Aditi David, Kian Mau Goh, Xiangkai Li, David R. Salem and Rajesh K. Sani
Microorganisms 2021, 9(1), 113; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010113 - 06 Jan 2021
Cited by 9 | Viewed by 2814
Abstract
Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of [...] Read more.
Firmicutes is almost a ubiquitous phylum. Several genera of this group, for instance, Geobacillus, are recognized for decomposing plant organic matter and for producing thermostable ligninolytic enzymes. Amplicon sequencing was used in this study to determine the prevalence and genetic diversity of the Firmicutes in two distinctly related environmental samples—South Dakota Landfill Compost (SDLC, 60 °C), and Sanford Underground Research Facility sediments (SURF, 45 °C). Although distinct microbial community compositions were observed, there was a dominance of Firmicutes in both the SDLC and SURF samples, followed by Proteobacteria. The abundant classes of bacteria in the SDLC site, within the phylum Firmicutes, were Bacilli (83.2%), and Clostridia (2.9%). In comparison, the sample from the SURF mine was dominated by the Clostridia (45.8%) and then Bacilli (20.1%). Within the class Bacilli, the SDLC sample had more diversity (a total of 11 genera with more than 1% operational taxonomic unit, OTU). On the other hand, SURF samples had just three genera, about 1% of the total population: Bacilli, Paenibacillus, and Solibacillus. With specific regard to Geobacillus, it was found to be present at a level of 0.07% and 2.5% in SURF and SDLC, respectively. Subsequently, culture isolations of endospore-forming Firmicutes members from these samples led to the isolation of a total of 117 isolates. According to colony morphologies, and identification based upon 16S rRNA and gyrB gene sequence analysis, we obtained 58 taxonomically distinct strains. Depending on the similarity indexes, a gyrB sequence comparison appeared more useful than 16S rRNA sequence analysis for inferring intra- and some intergeneric relationships between the isolates. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 1954 KiB  
Article
Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia
by Tamara N. Nazina, Salimat K. Bidzhieva, Denis S. Grouzdev, Diyana S. Sokolova, Tatyana P. Tourova, Sofiya N. Parshina, Alexander N. Avtukh, Andrey B. Poltaraus and Azhdar K. Talybly
Microorganisms 2020, 8(12), 1967; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121967 - 11 Dec 2020
Cited by 9 | Viewed by 2810
Abstract
A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the [...] Read more.
A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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20 pages, 10217 KiB  
Article
Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka
by Camille Thomas, Alexander Francke, Hendrik Vogel, Bernd Wagner and Daniel Ariztegui
Microorganisms 2020, 8(11), 1736; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111736 - 05 Nov 2020
Cited by 10 | Viewed by 2557
Abstract
Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated [...] Read more.
Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 12699 KiB  
Article
A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes
by Kshitij Tandon, Bayanmunkh Baatar, Pei-Wen Chiang, Narangarvuu Dashdondog, Bolormaa Oyuntsetseg and Sen-Lin Tang
Microorganisms 2020, 8(11), 1729; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111729 - 04 Nov 2020
Cited by 8 | Viewed by 2514
Abstract
In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily [...] Read more.
In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and -regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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26 pages, 3852 KiB  
Article
The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities
by Hugo Gildardo Castelán-Sánchez, Pablo M. Meza-Rodríguez, Erika Carrillo, David I. Ríos-Vázquez, Arturo Liñan-Torres, Ramón Alberto Batista-García, Ernesto Pérez-Rueda, Norma Elena Rojas-Ruíz and Sonia Dávila-Ramos
Microorganisms 2020, 8(11), 1677; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111677 - 29 Oct 2020
Cited by 9 | Viewed by 3738
Abstract
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, [...] Read more.
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems’ diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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13 pages, 1174 KiB  
Article
Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates
by Pamela Afouda, Grégory Dubourg, Anthony Levasseur, Pierre-Edouard Fournier, Jeremy Delerce, Oleg Mediannikov, Seydina M. Diene, Daniel Nahon, Didier Bourlès, Jean-Marc Rolain and Didier Raoult
Microorganisms 2020, 8(10), 1522; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101522 - 03 Oct 2020
Cited by 6 | Viewed by 3444
Abstract
Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the [...] Read more.
Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 1302 KiB  
Article
Sulfur and Methane-Oxidizing Microbial Community in a Terrestrial Mud Volcano Revealed by Metagenomics
by Andrey V. Mardanov, Vitaly V. Kadnikov, Alexey V. Beletsky and Nikolai V. Ravin
Microorganisms 2020, 8(9), 1333; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091333 - 31 Aug 2020
Cited by 16 | Viewed by 3908
Abstract
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using [...] Read more.
Mud volcanoes are prominent geological structures where fluids and gases from the deep subsurface are discharged along a fracture network in tectonically active regions. Microbial communities responsible for sulfur and methane cycling and organic transformation in terrestrial mud volcanoes remain poorly characterized. Using a metagenomics approach, we analyzed the microbial community of bubbling fluids retrieved from an active mud volcano in eastern Crimea. The microbial community was dominated by chemolithoautotrophic Campylobacterota and Gammaproteobacteria, which are capable of sulfur oxidation coupled to aerobic and anaerobic respiration. Methane oxidation could be enabled by aerobic Methylococcales bacteria and anaerobic methanotrophic archaea (ANME), while methanogens were nearly absent. The ANME community was dominated by a novel species of Ca. Methanoperedenaceae that lacked nitrate reductase and probably couple methane oxidation to the reduction of metal oxides. Analysis of two Ca. Bathyarchaeota genomes revealed the lack of mcr genes and predicted that they could grow on fatty acids, sugars, and proteinaceous substrates performing fermentation. Thermophilic sulfate reducers indigenous to the deep subsurface, Thermodesulfovibrionales (Nitrospirae) and Ca. Desulforudis (Firmicutes), were found in minor amounts. Overall, the results obtained suggest that reduced compounds delivered from the deep subsurface support the development of autotrophic microorganisms using various electron acceptors for respiration. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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15 pages, 6385 KiB  
Communication
Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile
by Yoanna Eissler, Cristina Dorador, Brandon Kieft, Verónica Molina and Martha Hengst
Microorganisms 2020, 8(7), 1077; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8071077 - 20 Jul 2020
Cited by 12 | Viewed by 3509
Abstract
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) [...] Read more.
Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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9 pages, 534 KiB  
Article
Characteristics of an Iron-Reducing, Moderately Acidophilic Actinobacterium Isolated from Pyritic Mine Waste, and Its Potential Role in Mitigating Mineral Dissolution in Mineral Tailings Deposits
by Ivan Nancucheo and D. Barrie Johnson
Microorganisms 2020, 8(7), 990; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8070990 - 02 Jul 2020
Cited by 3 | Viewed by 2536
Abstract
Reactive pyritic mine tailings can be populated by chemolithotrophic prokaryotes that enhance the solubilities of many metals, though iron-reducing heterotrophic microorganisms can inhibit the environmental risk posed by tailings by promoting processes that are the reverse of those carried out by pyrite-oxidising autotrophic [...] Read more.
Reactive pyritic mine tailings can be populated by chemolithotrophic prokaryotes that enhance the solubilities of many metals, though iron-reducing heterotrophic microorganisms can inhibit the environmental risk posed by tailings by promoting processes that are the reverse of those carried out by pyrite-oxidising autotrophic bacteria. A strain (IT2) of Curtobacterium ammoniigenes, a bacterium not previously identified as being associated with acidic mine wastes, was isolated from pyritic mine tailings and partially characterized. Strain IT2 was able to reduce ferric iron under anaerobic conditions, but was not found to catalyse the oxidation of ferrous iron or elemental (zero-valent) sulfur, and was an obligate heterotrophic. It metabolized monosaccharides and required small amounts of yeast extract for growth. Isolate IT2 is a mesophilic bacterium, with a temperature growth optimum of 30 °C and is moderately acidophilic, growing optimally at pH 4.0 and between pH 2.7 and 5.0. The isolate tolerated elevated concentrations of many transition metals, and was able to grow in the cell-free spent medium of the acidophilic autotroph Acidithiobacillus ferrooxidans, supporting the hypothesis that it can proliferate in acidic mine tailings. Its potential role in mitigating the production of acidic, metal-rich drainage waters from mine wastes is discussed. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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18 pages, 1709 KiB  
Article
Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature
by Francisco L. Massello, Chia Sing Chan, Kok-Gan Chan, Kian Mau Goh, Edgardo Donati and María Sofía Urbieta
Microorganisms 2020, 8(6), 906; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8060906 - 16 Jun 2020
Cited by 25 | Viewed by 5003
Abstract
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three [...] Read more.
The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities’ profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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9 pages, 539 KiB  
Article
Thermotolerant and Thermophilic Mycobiota in Different Steps of Compost Maturation
by Simone Di Piazza, Jos Houbraken, Martin Meijer, Grazia Cecchi, Bart Kraak, Ester Rosa and Mirca Zotti
Microorganisms 2020, 8(6), 880; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8060880 - 11 Jun 2020
Cited by 21 | Viewed by 3749
Abstract
Composting is a complex process in which various micro-organisms, mainly fungi and bacteria, are involved. The process depends on a large number of factors (biological, chemical, and physical) among which microbial populations play a fundamental role. The high temperatures that occur during the [...] Read more.
Composting is a complex process in which various micro-organisms, mainly fungi and bacteria, are involved. The process depends on a large number of factors (biological, chemical, and physical) among which microbial populations play a fundamental role. The high temperatures that occur during the composting process indicate the presence of thermotolerant and thermophilic micro-organisms that are key for the optimization of the process. However, the same micro-organisms can be harmful (allergenic, pathogenic) for workers that handle large quantities of material in the plant, and for end users, for example, in the indoor environment (e.g., pots in houses and offices). Accurate knowledge of thermotolerant and thermophilic organisms present during the composting stages is required to find key organisms to improve the process and estimate potential health risks. The objective of the present work was to study thermotolerant and thermophilic mycobiota at different time points of compost maturation. Fungi were isolated at four temperatures (25, 37, 45, and 50 °C) from compost samples collected at five different steps during a 21-day compost-maturation period in an active composting plant in Liguria (northwestern Italy). The samples were subsequently plated on three different media. Our results showed a high presence of fungi with an order of magnitude ranging from 1 × 104 to 3 × 105 colony-forming units (CFU) g−1. The isolated strains, identified by means of specific molecular tools (ITS, beta-tubulin, calmodulin, elongation factor 1-alpha, and LSU sequencing), belonged to 45 different species. Several thermophilic species belonging to genera Thermoascus and Thermomyces were detected, which could be key during composting. Moreover, the presence of several potentially harmful fungal species, such as Aspergillus fumigatus, A. terreus, and Scedosporium apiospermum, were found during the whole process, including the final product. Results highlighted the importance of surveying the mycobiota involved in the composting process in order to: (i) find solutions to improve efficiency and (ii) reduce health risks. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 2593 KiB  
Article
Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum
by Rafael Bargiela, Karin Lanthaler, Colin M. Potter, Manuel Ferrer, Alexander F. Yakunin, Bela Paizs, Peter N. Golyshin and Olga V. Golyshina
Microorganisms 2020, 8(5), 759; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050759 - 19 May 2020
Cited by 3 | Viewed by 3027
Abstract
The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. [...] Read more.
The archaeon Cuniculiplasma divulgatum is ubiquitous in acidic environments with low-to-moderate temperatures. However, molecular mechanisms underlying its ability to thrive at lower temperatures remain unexplored. Using mass spectrometry (MS)-based proteomics, we analysed the effect of short-term (3 h) exposure to cold. The C. divulgatum genome encodes 2016 protein-coding genes, from which 819 proteins were identified in the cells grown under optimal conditions. In line with the peptidolytic lifestyle of C. divulgatum, its intracellular proteome revealed the abundance of proteases, ABC transporters and cytochrome C oxidase. From 747 quantifiable polypeptides, the levels of 582 proteins showed no change after the cold shock, whereas 104 proteins were upregulated suggesting that they might be contributing to cold adaptation. The highest increase in expression appeared in low-abundance (0.001–0.005 fmol%) proteins for polypeptides’ hydrolysis (metal-dependent hydrolase), oxidation of amino acids (FAD-dependent oxidoreductase), pyrimidine biosynthesis (aspartate carbamoyltransferase regulatory chain proteins), citrate cycle (2-oxoacid ferredoxin oxidoreductase) and ATP production (V type ATP synthase). Importantly, the cold shock induced a substantial increase (6% and 9%) in expression of the most-abundant proteins, thermosome beta subunit and glutamate dehydrogenase. This study has outlined potential mechanisms of environmental fitness of Cuniculiplasma spp. allowing them to colonise acidic settings at low/moderate temperatures. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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18 pages, 4972 KiB  
Article
High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea
by Qing-Lei Sun, Jian Zhang, Min-Xiao Wang, Lei Cao, Zeng-Feng Du, Yuan-Yuan Sun, Shi-Qi Liu, Chao-Lun Li and Li Sun
Microorganisms 2020, 8(5), 687; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050687 - 08 May 2020
Cited by 26 | Viewed by 4095
Abstract
In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing [...] Read more.
In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (<97%) of the gene sequence with its close phylogenetic species. Further, a draft genome of Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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15 pages, 1824 KiB  
Article
Staphylococcus sciuri Strain LCHXa is a Free-Living Lithium-Tolerant Bacterium Isolated from Salar de Atacama, Chile
by Camila Salazar-Ardiles, Tamara Caimanque, Alexandra Galetović, Claudia Vilo, Jorge E. Araya, Nataly Flores and Benito Gómez-Silva
Microorganisms 2020, 8(5), 668; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050668 - 05 May 2020
Cited by 4 | Viewed by 3589
Abstract
In addition to the industrial and biomedical applications of lithium, information on the tolerance of microorganisms to high Li concentrations in natural biological systems is limited. Strain LCHXa is a novel free-living Gram-positive, non-motile bacterium strain isolated from water samples taken at Laguna [...] Read more.
In addition to the industrial and biomedical applications of lithium, information on the tolerance of microorganisms to high Li concentrations in natural biological systems is limited. Strain LCHXa is a novel free-living Gram-positive, non-motile bacterium strain isolated from water samples taken at Laguna Chaxa, a non-industrial water body with the highest soluble Li content (33 mM LiCl) within the Salar de Atacama basin in northern Chile. Enrichment was conducted in Luria-Bertani (LB) medium supplemented with 1 M LiCl. Strain LCHXa was a Novobiocin-resistant and coagulase negative Staphylococcus. Phylogenetically, strain LCHXa belongs to the species Staphylococcus sciuri. Strain LCHXa grew optimally in LB medium at pH 6–8 and 37 °C, and it was able to sustain growth at molar Li concentrations at 2 M LiCl, with a decrease in the specific growth rate of 85%. Osmoregulation in strain LCHXa partially involves glycine betaine and glycerol as compatible solutes. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 962 KiB  
Article
Taxogenomics of the Genus Cyclobacterium: Cyclobacterium xiamenense and Cyclobacterium halophilum as Synonyms and Description of Cyclobacterium plantarum sp. nov.
by Azadeh Shahinpei, Mohammad Ali Amoozegar, Leila Mirfeizi, Mahdi Moshtaghi Nikou, Antonio Ventosa and Cristina Sánchez-Porro
Microorganisms 2020, 8(4), 610; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8040610 - 23 Apr 2020
Cited by 4 | Viewed by 2837
Abstract
The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA–DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to [...] Read more.
The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA–DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to this genus and constitute a coherent phylogenomic group, but with species forming two separate branches. In addition, the genome-based analyses revealed that Cyclobacterium xiamenense and Cyclobacterium halophilum are members of the same species. Besides, we carried out a taxonomic characterization of the new strain GBPx2T, isolated from the halophytic plant Salicornia sp. Analysis of its 16S rRNA gene sequence showed the highest sequence similarity (97.5%) to Cyclobacterium lianum HY9T. Percentages of GGDC and OrthoANI between strain GBPx2T and species of the genus Cyclobacterium were lower than the threshold value for species delineation. The DNA G+C content was 43.0 mol%. The polar lipids included phosphatidylethanolamine as well as one unidentified phospholipid and four unidentified lipids, and its major cellular fatty acids were iso-C15:0 and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The only quinone present was menaquinone 7. Based on a combination of phenotypic, chemotaxonomic, and phylogenomic features, the GBPx2T strain represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium plantarum sp. nov. is proposed. The type strain of Cyclobacterium plantarum is GBPx2T (= IBRC-M 10634T = LMG 28551T). Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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16 pages, 2953 KiB  
Article
Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern
by Ana Durán-Viseras, Cristina Sánchez-Porro and Antonio Ventosa
Microorganisms 2020, 8(4), 605; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8040605 - 21 Apr 2020
Cited by 9 | Viewed by 2970
Abstract
A halophilic archaeon, strain F20-122T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w [...] Read more.
A halophilic archaeon, strain F20-122T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w/v) total salts (optimum 25% salts). The phylogenetic analyses based on the 16S rRNA and rpoB’ genes showed its affiliation with the genus Natronomonas and suggested its placement as a new species within this genus. The in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) analyses of this strain against closely related species supported its placement in a new taxon. The DNA G + C content of this isolate was 63.0 mol%. The polar lipids of strain F20-122T were phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol (PG), and phosphatidylglycerol sulfate (PGS). Traces of biphosphatidylglycerol (BPG) and other minor phospholipids and unidentified glycolipids were also present. Based on the phylogenetic, genomic, phenotypic, and chemotaxonomic characterization, we propose strain F20-122T (= CCM 8891T = CECT 9564T = JCM 33320T) as the type strain of a new species within the genus Natronomonas, with the name Natronomonas salsuginis sp. nov. Rhodopsin-like sequence analysis of strain F20-122T revealed the presence of haloarchaeal proton pumps, suggesting a light-mediated ATP synthesis for this strain and a maximum wavelength absorption in the green spectrum. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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22 pages, 2131 KiB  
Article
Adaptive Development of Soil Bacterial Communities to Ecological Processes Caused by Mining Activities in the Loess Plateau, China
by Zhanbin Luo, Jing Ma, Fu Chen, Xiaoxiao Li, Qi Zhang and Yongjun Yang
Microorganisms 2020, 8(4), 477; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8040477 - 27 Mar 2020
Cited by 26 | Viewed by 3038
Abstract
Microorganisms are the driving force behind the circulation and transformation of the soil substance. The development of soil bacterial communities is critical for ecosystem restoration and evolution. In the Loess Plateau, coal mining activities have aggravated the deterioration of the fragile local ecological [...] Read more.
Microorganisms are the driving force behind the circulation and transformation of the soil substance. The development of soil bacterial communities is critical for ecosystem restoration and evolution. In the Loess Plateau, coal mining activities have aggravated the deterioration of the fragile local ecological environment. The adaptive development of soil bacterial communities in response to different ecological processes caused by coal mining activities was explored through high-throughput sequencing technology and an ecological network analysis of the mining subsidence area of the Daliuta Coal Mine and vegetation rehabilitation area of the Heidaigou Coal Mine in the Loess Plateau. The results showed that while mining subsidence was inhibited, vegetation rehabilitation promoted the soil physicochemical properties. Soil organic matter, available phosphorus and available potassium in the subsidence area decreased significantly (P < 0.05), while soil organic matter, soil water, pH and EC in the vegetation rehabilitation area increased significantly (P < 0.05). The diversity index in the subsidence area decreased by about 20%, while that in the vegetation rehabilitation area increased by 63%. Mining subsidence and vegetation rehabilitation had a distinct influence on the molecular ecological networks of the soil bacteria, which tended to be more complex after the mining subsidence, and the number of connections in the network increased otherwise significantly enhanced interactive relationships. After the vegetation rehabilitation, the number of modules in the ecological network increased, but the contents of modules tended to be simpler. Soil bacterial communities adapted to the changes by changing the relationships between bacteria in response to different ecological processes. This study provides new insights into the monitoring and abatement of the damaged ecological environment in mines. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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15 pages, 4736 KiB  
Article
High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments
by Mei Zhuang, Edmond Sanganyado, Liang Xu, Jianming Zhu, Ping Li and Wenhua Liu
Microorganisms 2020, 8(2), 233; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020233 - 09 Feb 2020
Cited by 12 | Viewed by 2761
Abstract
Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a [...] Read more.
Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase (azoR), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr (p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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20 pages, 6102 KiB  
Article
Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System
by Vilma Pérez, Johanna Cortés, Francisca Marchant, Cristina Dorador, Verónica Molina, Marcela Cornejo-D’Ottone, Klaudia Hernández, Wade Jeffrey, Sergio Barahona and Martha B. Hengst
Microorganisms 2020, 8(2), 208; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020208 - 03 Feb 2020
Cited by 4 | Viewed by 3268
Abstract
Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of [...] Read more.
Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42–72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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15 pages, 2611 KiB  
Article
Haloglomus irregulare gen. nov., sp. nov., a New Halophilic Archaeon Isolated from a Marine Saltern
by Ana Durán-Viseras, Cristina Sánchez-Porro and Antonio Ventosa
Microorganisms 2020, 8(2), 206; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020206 - 02 Feb 2020
Cited by 7 | Viewed by 3397
Abstract
A halophilic archaeal strain, designated F16-60T, was isolated from Isla Cristina marine saltern in Huelva, Spain. Cells were pleomorphic, irregular, non-motile, and Gram-stain-negative. It produced red-pigmented colonies on agar plates. Strain F16-60T was extremely halophilic (optimum at 30% (w [...] Read more.
A halophilic archaeal strain, designated F16-60T, was isolated from Isla Cristina marine saltern in Huelva, Spain. Cells were pleomorphic, irregular, non-motile, and Gram-stain-negative. It produced red-pigmented colonies on agar plates. Strain F16-60T was extremely halophilic (optimum at 30% (w/v) NaCl) and neutrophilic (optimum pH 7.5). Phylogenetic tree reconstructions based on 16S rRNA and rpoB´ gene sequences revealed that strain F16-60T was distinct from species of the related genera Natronomonas, Halomarina, and Halomicrobium, of the order Halobacteriales. The polar lipids are phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and one glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). The DNA G+C content is 68.0 mol%. The taxonomic study, based on a combination of phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, suggest that strain F16-60T (= CECT 9635T = JCM 33318T), represents a novel species of a new genus within the family Haloarculaceae and the order Halobacteriales, for which the name Haloglomus irregulare gen. nov., sp. nov. is proposed. Metagenomic fragment recruitment analysis revealed the worldwide distribution of members of this genus and suggested the existence of other closely related species to be isolated. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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14 pages, 2627 KiB  
Article
A Deeper Look into the Biodiversity of the Extremely Acidic Copahue volcano-Río Agrio System in Neuquén, Argentina
by Germán Lopez Bedogni, Francisco L. Massello, Alejandra Giaveno, Edgardo Rubén Donati and María Sofía Urbieta
Microorganisms 2020, 8(1), 58; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8010058 - 29 Dec 2019
Cited by 13 | Viewed by 3595
Abstract
The Copahue volcano-Río Agrio system, on Patagonia Argentina, comprises the naturally acidic river Río Agrio, that runs from a few meters down the Copahue volcano crater to more than 40 km maintaining low pH waters, and the acidic lagoon that sporadically forms on [...] Read more.
The Copahue volcano-Río Agrio system, on Patagonia Argentina, comprises the naturally acidic river Río Agrio, that runs from a few meters down the Copahue volcano crater to more than 40 km maintaining low pH waters, and the acidic lagoon that sporadically forms on the crater of the volcano, which is studied for the first time in this work. We used next-generation sequencing of the 16S rRNA gene of the entire prokaryotic community to study the biodiversity of this poorly explored extreme environment. The correlation of the operational taxonomic units (OTUs)s presence with physicochemical variables showed that the system contains three distinct environments: the crater lagoon, the Upper Río Agrio, and the Salto del Agrio waterfall, a point located approximately 12 km down the origin of the river, after it emerges from the Caviahue lake. The prokaryotic community of the Copahue Volcano-Río Agrio system is mainly formed by acidic bacteria and archaea, such as Acidithiobacillus, Ferroplasma, and Leptospirillum, which have been isolated from similar environments around the world. These results support the idea of a ubiquitous acidic biodiversity; however, this highly interesting extreme environment also has apparently autochthonous species such as Sulfuriferula, Acidianus copahuensis, and strains of Acidibacillus and Alicyclobacillus. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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25 pages, 5065 KiB  
Article
Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes
by Benito Gómez-Silva, Claudia Vilo-Muñoz, Alexandra Galetović, Qunfeng Dong, Hugo G. Castelán-Sánchez, Yordanis Pérez-Llano, María del Rayo Sánchez-Carbente, Sonia Dávila-Ramos, Nohemí Gabriela Cortés-López, Liliana Martínez-Ávila, Alan D. W. Dobson and Ramón Alberto Batista-García
Microorganisms 2019, 7(12), 619; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7120619 - 27 Nov 2019
Cited by 23 | Viewed by 5914
Abstract
Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In [...] Read more.
Halites, which are typically found in various Atacama locations, are evaporitic rocks that are considered as micro-scaled salterns. Both structural and functional metagenomic analyses of halite nodules were performed. Structural analyses indicated that the halite microbiota is mainly composed of NaCl-adapted microorganisms. In addition, halites appear to harbor a limited diversity of fungal families together with a biodiverse collection of protozoa. Functional analysis indicated that the halite microbiome possesses the capacity to make an extensive contribution to carbon, nitrogen, and sulfur cycles, but possess a limited capacity to fix nitrogen. The halite metagenome also contains a vast repertory of carbohydrate active enzymes (CAZY) with glycosyl transferases being the most abundant class present, followed by glycosyl hydrolases (GH). Amylases were also present in high abundance, with GH also being identified. Thus, the halite microbiota is a potential useful source of novel enzymes that could have biotechnological applicability. This is the first metagenomic report of fungi and protozoa as endolithobionts of halite nodules, as well as the first attempt to describe the repertoire of CAZY in this community. In addition, we present a comprehensive functional metagenomic analysis of the metabolic capacities of the halite microbiota, providing evidence for the first time on the sulfur cycle in Atacama halites. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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18 pages, 4281 KiB  
Article
Life in High Salt Concentrations with Changing Environmental Conditions: Insights from Genomic and Phenotypic Analysis of Salinivibrio sp.
by Jojy John, Vinu Siva, Kumari Richa, Aditya Arya and Amit Kumar
Microorganisms 2019, 7(11), 577; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7110577 - 19 Nov 2019
Cited by 7 | Viewed by 4603
Abstract
Life in salt pans with varying chemical compositions require special adaptation strategies at both the physiological and molecular level. The Marakkanam salt pan in South India is characterized with a high fluctuation in salinity (19–490 ppt), Ultravioletradiation, and heavy metal concentrations. Several bacterial [...] Read more.
Life in salt pans with varying chemical compositions require special adaptation strategies at both the physiological and molecular level. The Marakkanam salt pan in South India is characterized with a high fluctuation in salinity (19–490 ppt), Ultravioletradiation, and heavy metal concentrations. Several bacterial species have been isolated and identified in the view of phylogenetic analysis and for the subsequent production of industrially important enzymes. However, limited information exists on the genomic basis of their survival under variable environmental conditions. To this extent, we sequenced the whole genome of the Salinivibrio sp. HTSP, a moderately halophilic bacterium. We analysed the physiological and genomic attributes of Salinivibrio sp. HTSP to elucidate the strategies of adaptation under various abiotic stresses. The genome size is estimated to be 3.39 Mbp with a mean G + C content of 50.6%, including 3150 coding sequences. The genome possessed osmotic stress-related coding sequences, and genes involved in different pathways of DNA repair mechanisms and genes related to the resistance to toxic metals were identified. The periplasmic stress response genes and genes of different oxidative stress mechanisms were also identified. The tolerance capacity of the bacterial isolates to heavy metals, UV-radiation, and salinity was also confirmed through appropriate laboratory experiments under controlled conditions. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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14 pages, 3061 KiB  
Article
Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica
by Yanhong Lu, Xiaomin Xia, Shunyan Cheung, Hongmei Jing and Hongbin Liu
Microorganisms 2019, 7(10), 453; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100453 - 15 Oct 2019
Cited by 8 | Viewed by 2776
Abstract
Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A [...] Read more.
Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40–3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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17 pages, 4555 KiB  
Article
Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)
by Magdalena Dyda, Adam Pyzik, Ewa Wilkojc, Beata Kwiatkowska-Kopka and Aleksandra Sklodowska
Microorganisms 2019, 7(10), 416; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100416 - 03 Oct 2019
Cited by 17 | Viewed by 3664
Abstract
Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in [...] Read more.
Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e.g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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25 pages, 1483 KiB  
Article
Microbial Assemblages in Pressurized Antarctic Brine Pockets (Tarn Flat, Northern Victoria Land): A Hotspot of Biodiversity and Activity
by Maria Papale, Angelina Lo Giudice, Antonella Conte, Carmen Rizzo, Alessandro C. Rappazzo, Giovanna Maimone, Gabriella Caruso, Rosabruna La Ferla, Maurizio Azzaro, Concetta Gugliandolo, Rodolfo Paranhos, Anderson S. Cabral, Vincenzo Romano Spica and Mauro Guglielmin
Microorganisms 2019, 7(9), 333; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7090333 - 09 Sep 2019
Cited by 18 | Viewed by 4094
Abstract
Two distinct pressurized hypersaline brine pockets (named TF4 and TF5), separated by a thin ice layer, were detected below an ice-sealed Antarctic lake. Prokaryotic (bacterial and archaeal) diversity, abundances (including virus-like particles) and metabolic profiles were investigated by an integrated approach, including traditional [...] Read more.
Two distinct pressurized hypersaline brine pockets (named TF4 and TF5), separated by a thin ice layer, were detected below an ice-sealed Antarctic lake. Prokaryotic (bacterial and archaeal) diversity, abundances (including virus-like particles) and metabolic profiles were investigated by an integrated approach, including traditional and new-generation methods. Although similar diversity indices were computed for both Bacteria and Archaea, distinct bacterial and archaeal assemblages were observed. Bacteroidetes and Gammaproteobacteria were more abundant in the shallowest brine pocket, TF4, and Deltaproteobacteria, mainly represented by versatile sulphate-reducing bacteria, dominated in the deepest, TF5. The detection of sulphate-reducing bacteria and methanogenic Archaea likely reflects the presence of a distinct synthrophic consortium in TF5. Surprisingly, members assigned to hyperthermophilic Crenarchaeota and Euryarchaeota were common to both brines, indicating that these cold habitats host the most thermally tolerant Archaea. The patterns of microbial communities were different, coherently with the observed microbiological diversity between TF4 and TF5 brines. Both the influence exerted by upward movement of saline brines from a sub-surface anoxic system and the possible occurrence of an ancient ice remnant from the Ross Ice Shelf were the likely main factors shaping the microbial communities. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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11 pages, 539 KiB  
Article
Characterization of Salinivibrio socompensis sp. nov., A New Halophilic Bacterium Isolated from the High-Altitude Hypersaline Lake Socompa, Argentina
by Cristina Galisteo, Cristina Sánchez-Porro, Rafael R. de la Haba, Clara López-Hermoso, Ana B. Fernández, María E. Farias and Antonio Ventosa
Microorganisms 2019, 7(8), 241; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7080241 - 05 Aug 2019
Cited by 15 | Viewed by 4177
Abstract
The genus Salinivibrio belongs to the family Vibrionaceae and includes Gram-stain-negative, motile by a polar flagellum, and facultatively anaerobic curved rods. They are halophilic bacteria commonly found in hypersaline aquatic habitats and salted foods. This genus includes five species and two subspecies. A [...] Read more.
The genus Salinivibrio belongs to the family Vibrionaceae and includes Gram-stain-negative, motile by a polar flagellum, and facultatively anaerobic curved rods. They are halophilic bacteria commonly found in hypersaline aquatic habitats and salted foods. This genus includes five species and two subspecies. A presumed novel species, strain S35T, was previously isolated from the high-altitude volcanic, alkaline, and saline lake Socompa (Argentinean Andes). In this study we carried out a complete taxonomic characterization of strain S35T, including the 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANIb, ANIm, and orthoANI), and in silico DNA–DNA hybridization (GGDC), as well as the phenotypic and chemotaxonomic characterization. It grew at 3%–20% (w/v) NaCl, pH 6–10, and 10–42 °C, with optimum growth at 7.0%–7.5% (w/v) NaCl, pH 8.0, and 37 °C, respectively. Strain S35T was oxidase- and catalase-positive, able to produce acid from D-glucose and other carbohydrates. Hydrolysis of DNA, methyl red test, and nitrate and nitrite reduction were positive. Its main fatty acids were C16:0, C16:1 ω7c and C16:1 ω6c, and C18:1 ω7c and/or C18:1 ω6c. ANI, GGDC, and core-genome analysis determined that strain S35T constitutes a novel species of the genus Salinivibrio, for which the name Salinivibrio socompensis sp. nov. is proposed. The type strain is S35T (= CECT 9634T = BNM 0535T). Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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22 pages, 3253 KiB  
Article
Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica
by Merry Sailonga Faluaburu, Ryosuke Nakai, Satoshi Imura and Takeshi Naganuma
Microorganisms 2019, 7(7), 203; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7070203 - 18 Jul 2019
Cited by 11 | Viewed by 4598
Abstract
Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera [...] Read more.
Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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Review

Jump to: Research

17 pages, 2497 KiB  
Review
Microbial Ecology from the Himalayan Cryosphere Perspective
by Kusum Dhakar and Anita Pandey
Microorganisms 2020, 8(2), 257; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8020257 - 14 Feb 2020
Cited by 32 | Viewed by 6809
Abstract
Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments [...] Read more.
Cold-adapted microorganisms represent a large fraction of biomass on Earth because of the dominance of low-temperature environments. Extreme cold environments are mainly dependent on microbial activities because this climate restricts higher plants and animals. Himalaya is one of the most important cold environments on Earth as it shares climatic similarities with the polar regions. It includes a wide range of ecosystems, from temperate to extreme cold, distributed along the higher altitudes. These regions are characterized as stressful environments because of the heavy exposure to harmful rays, scarcity of nutrition, and freezing conditions. The microorganisms that colonize these regions are recognized as cold-tolerant (psychrotolerants) or/and cold-loving (psychrophiles) microorganisms. These microorganisms possess several structural and functional adaptations in order to perform normal life processes under the stressful low-temperature environments. Their biological activities maintain the nutrient flux in the environment and contribute to the global biogeochemical cycles. Limited culture-dependent and culture-independent studies have revealed their diversity in community structure and functional potential. Apart from the ecological importance, these microorganisms have been recognized as source of cold-active enzymes and novel bioactive compounds of industrial and biotechnological importance. Being an important part of the cryosphere, Himalaya needs to be explored at different dimensions related to the life of the inhabiting extremophiles. The present review discusses the distinct facts associated with microbial ecology from the Himalayan cryosphere perspective. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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Graphical abstract

25 pages, 4289 KiB  
Review
Current Status and Potential Applications of Underexplored Prokaryotes
by Kian Mau Goh, Saleha Shahar, Kok-Gan Chan, Chun Shiong Chong, Syazwani Itri Amran, Mohd Helmi Sani, Iffah Izzati Zakaria and Ummirul Mukminin Kahar
Microorganisms 2019, 7(10), 468; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100468 - 18 Oct 2019
Cited by 15 | Viewed by 5977
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains [...] Read more.
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments)
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