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Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative...
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Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Microbial Diversity and Culture Collections".

Deadline for manuscript submissions: closed (30 April 2019) | Viewed by 69682

Special Issue Editors

Dr. Angelina Lo Giudice

E-Mail Website
Guest Editor
Institute of Polar Sciences of the National Research Council (CNR-ISP), 98122 Messina, Italy
Interests: microbial ecology of polar environments; biotechnology of cold-adapted bacteria; bacterial associations with benthic filter feeders; relationships between prokaryotes and chemical contamination
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Concetta Gugliandolo

E-Mail Website
Guest Editor
Dept of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le Ferdinando Stagno D' Alcontres 31, 98166 Messina, Italy
Interests: microbial ecology in extreme environments, microbial biotechnology; biodiversity and biotechnological applications of bacteria from extreme environments
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are inviting you to consider submitting a manuscript to Diversity for a Special Issue on “Microbial Diversity in Extreme Environments: implications for ecological and applicative perspectives”. Extreme environmental niches are characterized by physical and chemical conditions (e.g., low or high temperatures, high ionic strength and/or pressure, lack of sunlight, absence of water, low or high pH values, high level of radiation) that, alone or in combination, are hard to tolerate for most known life forms. Such hostile environments are inhabited by extremophiles (e.g., psychrophiles and thermophiles, halophiles, acidophiles and alkalophiles, piezophiles) that are able to not only survive, but also thrive in different ecosystems thanks to the development of adaptation strategies, involving diverse structural, physiological and metabolic modifications, and also symbiotic associations. Are these life forms adapted to or unique to extreme environments? The application of modern advanced techniques in molecular biology is revealing unexpected high levels of microbial diversity and complexity in extreme environments. Extreme environments represent natural laboratories to investigate the effects of climate changes on the biota and microbiota. Searching for novel extremophiles is largely stimulating the industry’s interest, as molecules from these microorganisms could be transformed into valuable biotechnological compounds.

For this Special Issue, we are looking for experimental studies, reviews, and distributional surveys relating to any aspect of microbial diversity, including the origin of life, ecology, astrobiology, molecular biology, physiology, and biotechnology, related to eukaryotes and prokaryotes in extreme environments. This Special Issue also serves as a memorial to Dr. Luigi Michaud (1974–2014), in recognition of his passion for and contribution to the microbiology of extreme environments.

Thank you for your consideration.

Dr. Angelina Lo Giudice
Prof. Concetta Gugliandolo
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. Diversity 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 2600 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.

Keywords

  • Biotecnonological potentialities
  • Community analysis
  • Community structure and functions
  • Eco-functional diversity of extremophilic microbes in extreme aquatic and terrestrial niches
  • Extremophilic bacteria, archaea and microeukaryotes
  • Microbial life in extreme environments

Published Papers (15 papers)

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Editorial

Jump to: Research, Review

5 pages, 1166 KiB  
Editorial
A Special Issue on Microorganisms from Extreme Environments in Memory of Luigi Michaud (1974–2014)
by Angelina Lo Giudice and Concetta Gugliandolo
Diversity 2020, 12(1), 2; https://doi.org/10.3390/d12010002 - 18 Dec 2019
Cited by 2 | Viewed by 2676
Abstract
A special issue (SI) titled “Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives” has been launched with the aim of showcasing the diversity and biotechnological potential of extremophilic microorganisms. The issue includes 10 research papers and four reviews that mainly [...] Read more.
A special issue (SI) titled “Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives” has been launched with the aim of showcasing the diversity and biotechnological potential of extremophilic microorganisms. The issue includes 10 research papers and four reviews that mainly address prokaryotes inhabiting hyperarid, hypercold, hyperalkaline and hypersaline (or polyextreme) environments, spanning from deserts to meromictic and glacier lakes around the globe. Thermophilic prokaryotes from shallow hydrothermal vents and Antarctic geothermal soils are also treated. The ecology and biotechnological perspectives of eukaryotes are discussed in two review papers and one research paper. This special issue serves as a memorial to Dr. Luigi Michaud (1974–2014), who dramatically passed away in Antarctica during underwater sampling activities. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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Research

Jump to: Editorial, Review

20 pages, 3212 KiB  
Article
Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert
by Johan S. Sáenz, Alessandro Airo, Dirk Schulze-Makuch, Michael Schloter and Gisle Vestergaard
Diversity 2019, 11(11), 205; https://doi.org/10.3390/d11110205 - 31 Oct 2019
Cited by 6 | Viewed by 3886
Abstract
Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function [...] Read more.
Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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18 pages, 3440 KiB  
Article
Exploring the Bacterial Communities of Infernaccio Waterfalls: A Phenotypic and Molecular Characterization of Acinetobacter and Pseudomonas Strains Living in a Red Epilithic Biofilm
by Carolina Chiellini, Sofia Chioccioli, Alberto Vassallo, Stefano Mocali, Elisangela Miceli, Camilla Fagorzi, Giovanni Bacci, Ester Coppini, Donatella Fibbi, Giovanna Bianconi, Francesco Canganella and Renato Fani
Diversity 2019, 11(10), 175; https://doi.org/10.3390/d11100175 - 21 Sep 2019
Cited by 4 | Viewed by 3538
Abstract
Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they [...] Read more.
Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both color and bacterial composition. One is red and is enriched with Pseudomonas strains, while the other one is black and Acinetobacter is the most represented genus. Along the river lay the Infernaccio waterfalls, whose surrounding rocks are covered only by the red epilithon. The bacterial composition of this biofilm was analyzed through high throughput sequencing and compared to those ones of red and black epilithons of Acquarossa river. Moreover, cultivable bacteria were isolated and their phenotype (i.e., resistance against antibiotics and heavy metals) was studied. As previously observed in the case of Acquarossa river, characterization of bacterial composition of the Infernaccio red epilithon revealed that the two most represented genera were Acinetobacter and Pseudomonas. Nonetheless, these strains differed from those isolated from Acquarossa, as revealed by RAPD analysis. This work, besides increasing knowledge about the ecological properties of this site, allowed to isolate new bacterial strains, which could potentially be exploited for biotechnological applications, because of their resistance against environmental pollutants. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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17 pages, 1304 KiB  
Article
Bacterial Communities from Extreme Environments: Vulcano Island
by Camilla Fagorzi, Sara Del Duca, Stefania Venturi, Carolina Chiellini, Giovanni Bacci, Renato Fani and Franco Tassi
Diversity 2019, 11(8), 140; https://doi.org/10.3390/d11080140 - 20 Aug 2019
Cited by 10 | Viewed by 4117
Abstract
Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante [...] Read more.
Although volcanoes represent extreme environments for life, they harbour bacterial communities. Vulcano Island (Aeolian Islands, Sicily) presents an intense fumarolic activity and widespread soil degassing, fed by variable amounts of magmatic gases (dominant at La Fossa Crater) and hydrothermal fluids (dominant at Levante Bay). The aim of this study is to analyse the microbial communities from the different environments of Vulcano Island and to evaluate their possible correlation with the composition of the gas emissions. Microbial analyses were carried out on soils and pioneer plants from both La Fossa Crater and Levante Bay. Total DNA has been extracted from all the samples and sequenced through Illumina MiSeq platform. The analysis of microbiome composition and the gases sampled in the same sites could suggest a possible correlation between the two parameters. We can suggest that the ability of different bacterial genera/species to survive in the same area might be due to the selection of particular genetic traits allowing the survival of these microorganisms. On the other side, the finding that microbial communities inhabiting different sites exhibiting different emission profiles are similar might be explained on the basis of a possible sharing of metabolic abilities related to the gas composition. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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15 pages, 1546 KiB  
Article
Actinobacteria from Extreme Niches in Morocco and Their Plant Growth-Promoting Potentials
by Ahmed Nafis, Anas Raklami, Noura Bechtaoui, Fatima El Khalloufi, Abdelkhalek El Alaoui, Bernard R. Glick, Mohamed Hafidi, Lamfeddal Kouisni, Yedir Ouhdouch and Lahcen Hassani
Diversity 2019, 11(8), 139; https://doi.org/10.3390/d11080139 - 20 Aug 2019
Cited by 60 | Viewed by 6146
Abstract
The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from [...] Read more.
The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from the desert, and from a marine environment. In total, 23 actinobacteria were isolated, 8 from Merzouga sand soil; 5 from Cannabis sativa rhizospheric soil; 5 from Toubkal mountain; 4 from a Draa sfar mining site; and 1 from marine soil. Based on their genotypic classification using 16S rRNA gene sequences, 19 of all belonged to the genus Streptomyces (82%) while the rest are the members of the genera Nocardioides (4.5%), Saccharomonospora (4.5%), Actinomadura (4.5%), and Prauserella (4.5%). Isolates Streptomyces sp. TNC-1 and Streptomyces sp. MNC-1 showed the highest level of phosphorus solubilization activity with 12.39 and 8.56 mg/mL, respectively. All 23 isolates were able to solubilize potassium, and 91% of them could grow under nitrogen-free conditions. The ability of the isolated actinobacteria to form indole-3-acetic acid (IAA) ranged from 6.70 to 75.54 μg/mL with Streptomyces sp. MNC-1 being the best IAA producer. In addition, all of the actinobacteria could produce siderophores, with Saccharomonospora sp. LNS-1 synthesizing the greatest amount (138.92 μg/mL). Principal coordinate analysis revealed that Streptomyces spp. MNC-1, MNT-1, MNB-2, and KNC-5; Saccharomonospora sp. LNS-1; and Nocardioides sp. KNC-3 each showed a variety of high-level plant growth-promoting activities. The extreme environments in Morocco are rich with bioactive actinobacteria that possess a variety of plant growth-promoting potentials that can further benefit green and sustainable agriculture. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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15 pages, 6936 KiB  
Article
Community Structures of Bacteria, Archaea, and Eukaryotic Microbes in the Freshwater Glacier Lake Yukidori-Ike in Langhovde, East Antarctica
by Aoi Chaya, Norio Kurosawa, Akinori Kawamata, Makiko Kosugi and Satoshi Imura
Diversity 2019, 11(7), 105; https://doi.org/10.3390/d11070105 - 06 Jul 2019
Cited by 14 | Viewed by 4044
Abstract
Since most studies about community structures of microorganisms in Antarctic terrestrial lakes using molecular biological tools are mainly focused on bacteria, limited information is available about archaeal and eukaryotic microbial diversity. In this study, the biodiversity of microorganisms belonging to all three domains [...] Read more.
Since most studies about community structures of microorganisms in Antarctic terrestrial lakes using molecular biological tools are mainly focused on bacteria, limited information is available about archaeal and eukaryotic microbial diversity. In this study, the biodiversity of microorganisms belonging to all three domains in a typical Antarctic freshwater glacier lake (Yukidori-Ike) was revealed using small subunit ribosomal RNA (SSU rRNA) clone library analysis. The bacterial clones were grouped into 102 operational taxonomic units (OTUs) and showed significant biodiversity. Betaproteobacteria were most frequently detected, followed by Cyanobacteria, Bacteroidetes, and Firmicutes as major lineages. In contrast to the bacterial diversity, much lower archaeal diversity, consisting of only two OTUs of methanogens, was observed. In the eukaryotic microbial community consisting of 20 OTUs, Tardigradal DNA was remarkably frequently detected. Genera affiliated with the phyla Ciliophora, Cryptomycota, Chlorophyta, Bacillariophyta, and Apusozoa were also detected. The biodiversity and species compositions of the whole microbial community of Lake Yukidori-Ike are similar to those of freshwater environments in temperate regions but are different from saline lakes in Antarctica, indicating that the salinity seems to affect the microbial composition more than the temperature. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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16 pages, 3168 KiB  
Article
Microbial Community in Hyperalkaline Steel Slag-Fill Emulates Serpentinizing Springs
by J. Ingemar Ohlsson, Jay T. Osvatic, Eric D. Becraft and Wesley D. Swingley
Diversity 2019, 11(7), 103; https://doi.org/10.3390/d11070103 - 30 Jun 2019
Cited by 8 | Viewed by 3511
Abstract
To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions offer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. [...] Read more.
To date, a majority of studies of microbial life in hyperalkaline settings focus on environments that are also highly saline (haloalkaline). Haloalkaline conditions offer microbes abundant workarounds to maintain pH homeostasis, as salt ions can be exchanged for protons by dedicated antiporter proteins. Yet hyperalkaline freshwater systems also occur both naturally and anthropogenically, such as the slag fill aquifers around former Lake Calumet (Chicago, IL, USA). In this study, 16S rRNA gene sequences and metagenomic sequence libraries were collected to assess the taxonomic composition and functional potential of microbes present in these slag-polluted waterways. Relative 16S rRNA gene abundances in Calumet sediment and water samples describe community compositions not significantly divergent from those in nearby circumneutral conditions. Major differences in composition are mainly driven by Proteobacteria, primarily one sequence cluster closely related to Hydrogenophaga, which comprises up to 85% of 16S rRNA gene abundance in hyperalkaline surface sediments. Sequence identity indicates this novel species belongs to the recently established genus Serpentinomonas, a bacterial lineage associated with natural freshwater hyperalkaline serpentinizing springs. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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19 pages, 5531 KiB  
Article
Impacts of Elevated CO2 Levels on the Soil Bacterial Community in a Natural CO2-Enhanced Oil Recovery Area
by Jing Ma, Zhanbin Luo, Fu Chen, Run Chen, Qianlin Zhu and Shaoliang Zhang
Diversity 2019, 11(5), 77; https://doi.org/10.3390/d11050077 - 11 May 2019
Cited by 11 | Viewed by 3343
Abstract
Knowledge of the interactions among different microorganisms is important to understand how ecological function transformation is affected by elevated CO2 levels in CO2-enhanced oil recovery (CO2-EOR) sites. Molecular ecological networks were established to reveal the interactions among different [...] Read more.
Knowledge of the interactions among different microorganisms is important to understand how ecological function transformation is affected by elevated CO2 levels in CO2-enhanced oil recovery (CO2-EOR) sites. Molecular ecological networks were established to reveal the interactions among different microbes of the soil bacterial community with the high-throughput sequencing data of 16S rRNA genes. The results showed that these networks are a powerful tool to identify and explain the interactions and keystone species in the communities under elevated CO2 pressure. The structures of networks under different CO2 leakage concentrations were different as a result of the networks’ topology properties, such as node numbers, topological roles of individual nodes, and network hubs. These indicators imply that the interactions among different groups were obviously changed. Moreover, changes in the network structure were significantly correlated with soil pH value, which might suggest that the large CO2 leakage affected the soil ecosystem functions by changing the network interactions. Additionally, the key microbial populations such as Bacteroidetes and Proteobacteria were distinguished based on network topology to reveal community structure and ecosystem functioning. The work developed in this study could help microbiologists to address some research questions that could not be approached previously, and, hence, might represent a new area of research for microbial ecology. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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Graphical abstract

12 pages, 1550 KiB  
Article
The Polyextreme Ecosystem, Salar de Huasco at the Chilean Altiplano of the Atacama Desert Houses Diverse Streptomyces spp. with Promising Pharmaceutical Potentials
by Carlos Cortés-Albayay, Johanna Silber, Johannes F. Imhoff, Juan A. Asenjo, Barbara Andrews, Imen Nouioui and Cristina Dorador
Diversity 2019, 11(5), 69; https://doi.org/10.3390/d11050069 - 28 Apr 2019
Cited by 17 | Viewed by 5368
Abstract
Salar de Huasco at the Chilean Altiplano of the Atacama Desert is considered a polyextreme environment, where solar radiation, salinity and aridity are extremely high and occur simultaneously. In this study, a total of 76 bacterial isolates were discovered from soil samples collected [...] Read more.
Salar de Huasco at the Chilean Altiplano of the Atacama Desert is considered a polyextreme environment, where solar radiation, salinity and aridity are extremely high and occur simultaneously. In this study, a total of 76 bacterial isolates were discovered from soil samples collected at two different sites in the east shoreline of Salar de Huasco, including H0 (base camp next to freshwater stream in the north part) and H6 (saline soils in the south part). All isolated bacteria were preliminarily identified using some of their phenotypic and genotypic data into the genera Streptomyces (86%), Nocardiopsis (9%), Micromonospora (3%), Bacillus (1%), and Pseudomonas (1%). Streptomyces was found dominantly in both sites (H0 = 19 isolates and H6 = 46 isolates), while the other genera were found only in site H0 (11 isolates). Based on the genotypic and phylogenetic analyses using the 16S rRNA gene sequences of all Streptomyces isolates, 18% (12 isolates) revealed <98.7% identity of the gene sequences compared to those in the publicly available databases and were determined as highly possibly novel species. Further studies suggested that many Streptomyces isolates possess the nonribosomal peptide synthetases-coding gene, and some of which could inhibit growth of at least two test microbes (i.e., Gram-positive and Gram-negative bacteria and fungi) and showed also the cytotoxicity against hepatocellular carcinoma and or mouse fibroblast cell lines. The antimicrobial activity and cytotoxicity of these Streptomyces isolates were highly dependent upon the nutrients used for their cultivation. Moreover, the HPLC-UV-MS profiles of metabolites produced by the selected Streptomyces isolates unveiled apparent differences when compared to the public database of existing natural products. With our findings, the polyextreme environments like Salar de Huasco are promising sources for exploring novel and valuable bacteria with pharmaceutical potentials. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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17 pages, 2489 KiB  
Article
Prokaryotic Dynamics in the Meromictic Coastal Lake Faro (Sicily, Italy)
by Carmela Raffa, Carmen Rizzo, Marc Strous, Emilio De Domenico, Marilena Sanfilippo, Luigi Michaud and Angelina Lo Giudice
Diversity 2019, 11(3), 37; https://doi.org/10.3390/d11030037 - 06 Mar 2019
Cited by 7 | Viewed by 3587
Abstract
Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution [...] Read more.
Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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20 pages, 2723 KiB  
Article
The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers
by Bex L. Kemp, Erin M. Tabish, Adam J. Wolford, Daniel L. Jones, Jaimi K. Butler and Bonnie K. Baxter
Diversity 2018, 10(4), 124; https://doi.org/10.3390/d10040124 - 27 Nov 2018
Cited by 15 | Viewed by 10317
Abstract
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that [...] Read more.
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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Review

Jump to: Editorial, Research

20 pages, 4312 KiB  
Review
Limnology and Aquatic Microbial Ecology of Byers Peninsula: A Main Freshwater Biodiversity Hotspot in Maritime Antarctica
by Carlos Rochera and Antonio Camacho
Diversity 2019, 11(10), 201; https://doi.org/10.3390/d11100201 - 21 Oct 2019
Cited by 9 | Viewed by 3623
Abstract
Here we present a comprehensive review of the diversity revealed by research in limnology and microbial ecology conducted in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) during the last two decades. The site constitutes one of the largest ice-free areas within the [...] Read more.
Here we present a comprehensive review of the diversity revealed by research in limnology and microbial ecology conducted in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) during the last two decades. The site constitutes one of the largest ice-free areas within the Antarctic Peninsula region. Since it has a high level of environmental protection, it is less human-impacted compared to other sites within the South Shetland archipelago. The main investigations in Byers Peninsula focused on the physical and chemical limnology of the lakes, ponds, rivers, and wetlands, as well as on the structure of their planktonic and benthic microbial communities, and on the functional ecology of the microbial food webs. Lakes and ponds in Byers range along a productivity gradient that extends from the less productive lakes located upland to the eutrophic coastal lakes. Their planktonic assemblages include viruses, bacteria, a metabolically diverse community of protists (i.e., autotrophs, heterotrophs, and mixotrophs), and a few metazooplankton species. Most of the studies conducted in the site demonstrate the strong influence of the physical environment (i.e., temperature, availability of light, and water) and nutrient availability in structuring these microbial communities. However, top-down biotic processes may occur in summer, when predation by zooplankton can exert a strong influence on the abundance of protists, including flagellates and ciliated protozoa. As a consequence, bacterioplankton could be partly released from the grazing pressure exerted by these protists, and proliferates fueled by external nutrient subsidies from the lake’s catchment. As summer temperatures in this region are slightly above the melting point of water, biotic processes, such as those related to the productivity of lakes during ice-free periods, could become even more relevant as warming induced by climate change progresses. The limnological research carried out at the site proves that Byers Peninsula deserves special attention in the framework of the research in extreme environments. Together with nearby sites, such as Signy Island, Byers Peninsula comprises a featuring element of the Maritime Antarctic region that represents a benchmark area relative to the global distribution and diversity of aquatic microorganisms. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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20 pages, 4125 KiB  
Review
Phylogenetic Diversity of Archaea in Shallow Hydrothermal Vents of Eolian Islands, Italy
by Concetta Gugliandolo and Teresa L. Maugeri
Diversity 2019, 11(9), 156; https://doi.org/10.3390/d11090156 - 05 Sep 2019
Cited by 20 | Viewed by 4374
Abstract
Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant [...] Read more.
Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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23 pages, 2532 KiB  
Review
Parageobacillus thermantarcticus, an Antarctic Cell Factory: From Crop Residue Valorization by Green Chemistry to Astrobiology Studies
by Ilaria Finore, Licia Lama, Paola Di Donato, Ida Romano, Annabella Tramice, Luigi Leone, Barbara Nicolaus and Annarita Poli
Diversity 2019, 11(8), 128; https://doi.org/10.3390/d11080128 - 07 Aug 2019
Cited by 11 | Viewed by 4610
Abstract
Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from [...] Read more.
Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition. In addition to the biotechnological potential due to the production of exopolysaccharides and thermostable enzymes, successful studies have demonstrated its use in the green chemistry for the transformation and valorization of residual biomass and its employment as a suitable microbial model for astrobiology studies. The recent acquisition of its genome sequence opens up new opportunities for the use of this versatile bacterium in still unexplored biotechnology sectors. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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23 pages, 922 KiB  
Review
Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins
by Giulio Barone, Stefano Varrella, Michael Tangherlini, Eugenio Rastelli, Antonio Dell’Anno, Roberto Danovaro and Cinzia Corinaldesi
Diversity 2019, 11(7), 113; https://doi.org/10.3390/d11070113 - 16 Jul 2019
Cited by 26 | Viewed by 4891
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively [...] Read more.
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential. Full article
(This article belongs to the Special Issue Microbial Diversity in Extreme Environments: Implications for Ecological and Applicative Perspectives)
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