Extreme Environments: Microbial and Biochemical Diversity

Topic Information

Dear Colleagues,

Terrestrial and marine environments comprise a large variety of extreme habitats, which can permit life only characterized by the highest degree of adaptation. These life frontiers include, for instance, the McMurdo Dry Valleys in Antarctica, the highest mountains, the deep oceanic trenches and biosphere, the permafrost regions, the hydrothermal vents, and the hyper-saline, hyper-alkaline and hyper-acidic environments. Here, microorganisms (extremophiles or poly-extremophiles) often represent the last boundary of life, where the highly stressful conditions have forced them to evolve a plethora of adaptations at the taxonomical, morphological and biochemical levels. This has resulted in very broad microbial diversity that allows microbes to cope with highly stressful environmental parameters, such as very high/low temperatures, high salinity, extreme pH and high hydrostatic pressure. In addition, particularly in some marine environments, the combination of different stressful parameters makes live even more difficult, which requires unique adaptation strategies. The unique features of extremophilic microbial diversity could be investigated both at the ecological and biotechnological level. At the ecological level, it is important to describe the communities harboured by these habitats, their adaptation strategies and relations with the environments. On the other hand, members of these communities show very interesting chemical/biochemical diversity, which could be exploited in traditional and new fields of biotechnology. However, since the majority of the microbial communities are represented by unculturable fractions, molecular (culture-independent) methods are often requested in their characterization. The topic on “Extreme Environments: Microbial and Biochemical Diversity” aims to offer a wide framework for the diffusion of advanced research that investigates both the microbial diversity and its biochemical peculiarities in extreme environments. In this context, every high-quality contribution, by basic or applied scientists, that addresses new aspects of the extremophilic microbial life, together with review papers reporting the “state of the art” of specific parts of this subject, will be considered.

Prof. Dr. Massimiliano Fenice
Dr. Susanna Gorrasi
Dr. Marcella Pasqualetti
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Biology biology	3.6	5.7	2012	16.4 Days	CHF 2700
Diversity diversity	2.1	3.4	2009	18.3 Days	CHF 2100
Microorganisms microorganisms	4.1	7.4	2013	11.7 Days	CHF 2700
Molecules molecules	4.2	7.4	1996	15.1 Days	CHF 2700
Life life	3.2	4.3	2011	17.8 Days	CHF 2600

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Published Papers (8 papers)

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Open AccessArticle

Endolithic Fungal Diversity in Antarctic Oligocene Rock Samples Explored Using DNA Metabarcoding

by Natana G. Rabelo, Vívian N. Gonçalves, Marcelo A. Carvalho, Sandro M. Scheffler, Gustavo Santiago, Paula A. Sucerquia, Fabio S. Oliveira, Larissa P. Campos, Fabyano A. C. Lopes, Karita C. R. Santos, Micheline C. Silva, Peter Convey, Paulo E. A. S. Câmara and Luiz H. Rosa

Biology 2024, 13(6), 414; https://doi.org/10.3390/biology13060414 - 5 Jun 2024

Cited by 2 | Viewed by 1582

Abstract

In this study, we evaluated the fungal diversity present associated with cores of Oligocene rocks using a DNA metabarcoding approach. We detected 940,969 DNA reads grouped into 198 amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, [...] Read more.

In this study, we evaluated the fungal diversity present associated with cores of Oligocene rocks using a DNA metabarcoding approach. We detected 940,969 DNA reads grouped into 198 amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Mucoromycota, Rozellomycota, Blastocladiomycota, Monoblepharomycota, Zoopagomycota, Aphelidiomycota (Fungi) and the fungal-like Oomycota (Stramenopila), in rank abundance order. Pseudogymnoascus pannorum, Penicillium sp., Aspergillus sp., Cladosporium sp., Aspergillaceae sp. and Diaporthaceae sp. were assessed to be dominant taxa, with 22 fungal ASVs displaying intermediate abundance and 170 being minor components of the assigned fungal diversity. The data obtained displayed high diversity indices, while rarefaction indicated that the majority of the diversity was detected. However, the diversity indices varied between the cores analysed. The endolithic fungal community detected using a metabarcoding approach in the Oligocene rock samples examined contains a rich and complex mycobiome comprising taxa with different lifestyles, comparable with the diversity reported in recent studies of a range of Antarctic habitats. Due to the high fungal diversity detected, our results suggest the necessity of further research to develop strategies to isolate these fungi in culture for evolutionary, physiological, and biogeochemical studies, and to assess their potential role in biotechnological applications. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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13 pages, 2652 KiB  

Open AccessArticle

Low Bacterial Diversity and Nitrate Levels in Cores from Deep Boreholes in Pristine Karst

by Janez Mulec, Sara Skok and Lejla Pašić

Life 2024, 14(6), 677; https://doi.org/10.3390/life14060677 - 24 May 2024

Viewed by 1081

Abstract

This study investigates the nitrate gradients within the deep biosphere of karst carbonate rocks and their resident microbiota. Samples were taken from borehole cores at depths down to 350 m below the surface, collected during geological site investigations for proposed railway tunnels and [...] Read more.

This study investigates the nitrate gradients within the deep biosphere of karst carbonate rocks and their resident microbiota. Samples were taken from borehole cores at depths down to 350 m below the surface, collected during geological site investigations for proposed railway tunnels and analysed using 16S rRNA amplicon sequencing. 16S rRNA amplicon sequencing analysis revealed relatively low microbial diversity, which can serve as a reliable indicator of the pristine nature of deep karst. However, some local hotspots of diversity are independent of depth. Pseudomonadota dominated the samples, with Gammaproteobacteria dominating at the class level. The low nitrate content in deep karst, in contrast to higher values closer to the surface, serves as an additional marker of its undisturbed and unpolluted status. Based on the prediction of functional profiles from 16S rRNA sequencing data, nitrates remain low due to indigenous microbial denitrification and assimilatory nitrate reduction. Pathways related to nitrogen fixation, ammonia assimilation, and nitrification were not confirmed. When elevated nitrate levels are observed in karst, they are most probably related to anthropogenic activities. Environmental factors other than depth and nitrate content play an important role in shaping bacterial communities. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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14 pages, 2718 KiB  

Open AccessEditor’s ChoiceArticle

Characterization of Lacinutrix neustonica sp. nov., Isolated from the Sea Surface Microlayer of Brackish Lake Shihwa, South Korea

by Jy Young Choi, Soo Yoon Kim, Yeon Woo Hong, Bok Jin Kim, Dong Young Shin, Jin Kyeong Kang, Byung Cheol Cho and Chung Yeon Hwang

Diversity 2023, 15(9), 1004; https://doi.org/10.3390/d15091004 - 9 Sep 2023

Cited by 1 | Viewed by 2183

Abstract

A Gram-negative, strictly aerobic, non-motile, slightly curved rod-shaped bacterial strain, designated as HL-RS19^T, was isolated from a sea surface microlayer (SML) sample of the brackish Lake Shihwa. Here, we characterized the new strain HL-RS19^T using a polyphasic approach to determine [...] Read more.

A Gram-negative, strictly aerobic, non-motile, slightly curved rod-shaped bacterial strain, designated as HL-RS19^T, was isolated from a sea surface microlayer (SML) sample of the brackish Lake Shihwa. Here, we characterized the new strain HL-RS19^T using a polyphasic approach to determine its taxonomic position. A phylogenetic analysis of its 16S rRNA gene sequence revealed that strain HL-RS19^T belonged to the genus Lacinutrix and was closely related to L. mariniflava AKS432^T (97.9%), L. algicola AKS293^T (97.8%), and other Lacinutrix species (<97.3%). The complete genome sequence of strain HL-RS19^T comprised a circular chromosome of 3.9 Mbp with a DNA G+C content of 35.2%. Genomic comparisons based on the average nucleotide identity and digital DNA-DNA hybridization showed that strain HL-RS19^T was consistently discriminated from its closely related taxa in the genus Lacinutrix. Strain HL-RS19^T showed optimal growth at 20–25 °C, pH 6.5–7.0, and 3.0–3.5% (w/v) sea salts. The major fatty acids (>5%) of strain HL-RS19^T were identified as iso-C_15:1 G (16.5%), iso-C_16:0 3-OH (12.9%), anteiso-C_15:1 A (9.9%), anteiso-C_15:0 (9.7%), iso-C_15:0 (9.0%), and iso-C_15:0 3-OH (8.3%). The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid, and two unidentified lipids. The major respiratory quinone was MK-6. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic data, strain HL-RS19^T represents a novel species belonging to the genus Lacinutrix, for which the name Lacinutrix neustonica sp. nov. is proposed. The type strain is HL-RS19^T (=KCCM 90497^T = JCM 35710^T). The genome sequence analysis of strain HL-RS19^T suggests that it may be well adapted to a harsh SML environment and is likely involved in arsenic cycling, potentially contributing to the bioremediation of anthropogenic arsenic pollution. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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18 pages, 2454 KiB  

Open AccessArticle

Altitudinal Gradient and Soil Depth as Sources of Variations in Fungal Communities Revealed by Culture-Dependent and Culture-Independent Methods in the Negev Desert, Israel

by Isabella Grishkan, Giora J. Kidron, Natalia Rodriguez-Berbel, Isabel Miralles and Raúl Ortega

Microorganisms 2023, 11(7), 1761; https://doi.org/10.3390/microorganisms11071761 - 5 Jul 2023

Cited by 2 | Viewed by 1566

Abstract

We examined fungal communities in soil profiles of 0–10 cm depth along the altitudinal gradient of 250–530–990 m.a.s.l. at the Central Negev Desert, Israel, which benefit from similar annual precipitation (95 mm). In the soil samples collected in the summer of 2020, a [...] Read more.

We examined fungal communities in soil profiles of 0–10 cm depth along the altitudinal gradient of 250–530–990 m.a.s.l. at the Central Negev Desert, Israel, which benefit from similar annual precipitation (95 mm). In the soil samples collected in the summer of 2020, a mycobiota accounting for 169 species was revealed by both culture-dependent and culture-independent (DNA-based) methodologies. The impact of soil depth on the variations in fungal communities was stronger than the impact of altitude. Both methodologies displayed a similar tendency in the composition of fungal communities: the prevalence of melanin-containing species with many-celled large spores (mainly Alternaria spp.) in the uppermost layers and the depth-wise increase in the proportion of light-colored species producing a high amount of small one-celled spores. The culturable and the DNA-based fungal communities had only 13 species in common. The differences were attributed to the pros and cons of each method. Nevertheless, despite the drawbacks, the employment of both methodologies has an advantage in providing a more comprehensive picture of fungal diversity in soils. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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16 pages, 2915 KiB  

Open AccessArticle

Critical Role of Monooxygenase in Biodegradation of 2,4,6-Trinitrotoluene by Buttiauxella sp. S19-1

by Miao Xu, Lei He, Ping Sun, Ming Wu, Xiyan Cui, Dong Liu, Amma G. Adomako-Bonsu, Min Geng, Guangming Xiong, Liquan Guo and Edmund Maser

Molecules 2023, 28(4), 1969; https://doi.org/10.3390/molecules28041969 - 19 Feb 2023

Cited by 7 | Viewed by 2530

Abstract

2,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for bioremediation of TNT has received much attention from scholars. In this paper, transcriptome analysis of the efficient degrading bacterium Buttiauxella [...] Read more.

2,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for bioremediation of TNT has received much attention from scholars. In this paper, transcriptome analysis of the efficient degrading bacterium Buttiauxella sp. S19-1 revealed that the monooxygenase gene (BuMO) was significantly up-regulated during TNT degradation. S-ΔMO (absence of BuMO gene in S19-1 mutant) degraded TNT 1.66-fold less efficiently than strain S19-1 (from 71.2% to 42.9%), and E-MO mutant (Escherichia coli BuMO-expressing strain) increased the efficiency of TNT degradation 1.33-fold (from 52.1% to 69.5%) for 9 h at 180 rpm at 27 °C in LB medium with 1.4 µg·mL⁻¹ TNT. We predicted the structure of BuMO and purified recombinant BuMO (rBuMO). Its specific activity was 1.81 µmol·min⁻¹·mg⁻¹ protein at pH 7.5 and 35 °C. The results of gas chromatography mass spectrometry (GC–MS) analysis indicated that 4-amino-2,6-dinitrotoluene (ADNT) is a metabolite of TNT biodegradation. We speculate that MO is involved in catalysis in the bacterial degradation pathway of TNT in TNT-polluted environment. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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20 pages, 4243 KiB  

Open AccessArticle

Microbiological Study in Petrol-Spiked Soil

by Agata Borowik, Jadwiga Wyszkowska and Jan Kucharski

Molecules 2021, 26(9), 2664; https://doi.org/10.3390/molecules26092664 - 1 May 2021

Cited by 17 | Viewed by 3133

Abstract

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 [...] Read more.

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IF_G); index of petrol effect on soil microorganisms and enzymes (IF_P); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (ID_H). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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20 pages, 1929 KiB  

Open AccessArticle

Role of Bacillus cereus in Improving the Growth and Phytoextractability of Brassica nigra (L.) K. Koch in Chromium Contaminated Soil

by Nosheen Akhtar, Noshin Ilyas, Humaira Yasmin, R. Z. Sayyed, Zuhair Hasnain, Elsayed A. Elsayed and Hesham A. El Enshasy

Molecules 2021, 26(6), 1569; https://doi.org/10.3390/molecules26061569 - 12 Mar 2021

Cited by 73 | Viewed by 5627

Abstract

Plant growth-promoting rhizobacteria (PGPR) mediate heavy metal tolerance and improve phytoextraction potential in plants. The present research was conducted to find the potential of bacterial strains in improving the growth and phytoextraction abilities of Brassica nigra (L.) K. Koch. in chromium contaminated soil. [...] Read more.

Plant growth-promoting rhizobacteria (PGPR) mediate heavy metal tolerance and improve phytoextraction potential in plants. The present research was conducted to find the potential of bacterial strains in improving the growth and phytoextraction abilities of Brassica nigra (L.) K. Koch. in chromium contaminated soil. In this study, a total of 15 bacterial strains were isolated from heavy metal polluted soil and were screened for their heavy metal tolerance and plant growth promotion potential. The most efficient strain was identified by 16S rRNA gene sequencing and was identified as Bacillus cereus. The isolate also showed the potential to solubilize phosphate and synthesize siderophore, phytohormones (indole acetic acid, cytokinin, and abscisic acid), and osmolyte (proline and sugar) in chromium (Cr⁺³) supplemented medium. The results of the present study showed that chromium stress has negative effects on seed germination and plant growth in B. nigra while inoculation of B. cereus improved plant growth and reduced chromium toxicity. The increase in seed germination percentage, shoot length, and root length was 28.07%, 35.86%, 19.11% while the fresh and dry biomass of the plant increased by 48.00% and 62.16%, respectively, as compared to the uninoculated/control plants. The photosynthetic pigments were also improved by bacterial inoculation as compared to untreated stress-exposed plants, i.e., increase in chlorophyll a, chlorophyll b, chlorophyll a + b, and carotenoid was d 25.94%, 10.65%, 20.35%, and 44.30%, respectively. Bacterial inoculation also resulted in osmotic adjustment (proline 8.76% and sugar 28.71%) and maintained the membrane stability (51.39%) which was also indicated by reduced malondialdehyde content (59.53% decrease). The antioxidant enzyme activities were also improved to 35.90% (superoxide dismutase), 59.61% (peroxide), and 33.33% (catalase) in inoculated stress-exposed plants as compared to the control plants. B. cereus inoculation also improved the uptake, bioaccumulation, and translocation of Cr in the plant. Data showed that B. cereus also increased Cr content in the root (2.71-fold) and shoot (4.01-fold), its bioaccumulation (2.71-fold in root and 4.03-fold in the shoot) and translocation (40%) was also high in B. nigra. The data revealed that B. cereus is a multifarious PGPR that efficiently tolerates heavy metal ions (Cr⁺³) and it can be used to enhance the growth and phytoextraction potential of B. nigra in heavy metal contaminated soil. Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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21 pages, 5127 KiB  

Open AccessArticle

Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy)

by Susanna Gorrasi, Andrea Franzetti, Roberto Ambrosini, Francesca Pittino, Marcella Pasqualetti and Massimiliano Fenice

Molecules 2021, 26(5), 1338; https://doi.org/10.3390/molecules26051338 - 2 Mar 2021

Cited by 16 | Viewed by 3069

Abstract

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial [...] Read more.

The “Saline di Tarquinia” salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds). Full article

(This article belongs to the Topic Extreme Environments: Microbial and Biochemical Diversity)

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