1
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Tran TV, Hoang T, Jang SH, Lee C. Unraveling the roles of aromatic cluster side-chain interactions on the structural stability and functional significance of psychrophilic Sphingomonas sp. glutaredoxin 3. PLoS One 2023; 18:e0290686. [PMID: 37651358 PMCID: PMC10470887 DOI: 10.1371/journal.pone.0290686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023] Open
Abstract
This study investigates the impact of aromatic cluster side-chain interactions in Grx3 (SpGrx3) from the psychrophilic Arctic bacterium Sphingomonas sp. Grx3 is a class I oxidoreductase with a unique parallel arrangement of aromatic residues in its aromatic cluster, unlike the tetrahedral geometry observed in Trxs. Hydrophilic-to-hydrophobic substitutions were made in the aromatic cluster, in β1 (E5V and Y7F), adjacent β2 (Y32F and Y32L), both β1 and β2 (E5V/Y32L), and short α2 (R47F). The hydrophobic substitutions, particularly those at or near Tyr7 (E5V, Y7F, Y32F, and R47F), increased melting temperatures and conformational stability, whereas disrupting β1-β2 interactions (Y32L and E5V/Y32L) led to structural instability of SpGrx3. However, excessive hydrophobic interactions (Y7F and E5V/Y32L) caused protein aggregation at elevated temperatures. All mutations resulted in a reduction in α-helical content and an increase in β-strand content. The R47F mutant, which formed dimers and exhibited the highest β-strand content, showed increased conformational flexibility and a significant decrease in catalytic rate due to the disturbance of β1-α2 interactions. In summary, the configuration of the aromatic cluster, especially Tyr7 in the buried β1 and Arg47 in the short α2, played crucial roles in maintaining the active conformation of SpGrx3 and preventing its protein aggregation. These modifications, reducing hydrophobicity in the central β-sheet, distinguish Grx3 from other Trx-fold proteins, highlighting evolutionary divergence within the Trx-fold superfamily and its functional versatility.
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Affiliation(s)
- Trang Van Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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Lee H, Cho YJ, Cho A, Kim OS. Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats. J Microbiol 2023; 61:663-672. [PMID: 37615929 DOI: 10.1007/s12275-023-00068-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/25/2023]
Abstract
Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.
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Affiliation(s)
- Hanbyul Lee
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yong-Joon Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ahnna Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ok-Sun Kim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
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Kim W, Jang S, Chae N, Kim M, Yeh JY, Kim S, Lee YM. Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326606 DOI: 10.1099/ijsem.0.005913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467T is distinguishable from H. yonginensis based on average nucleotide identity (91.3 %) and digital DNA-DNA hybridization values (39.3 %). The major fatty acids (>10 %) of strain PAMC 29467T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and summed feature 4 (C17 : 1 iso l and/or anteiso B). The major respiratory quinone was menaquinone-7. The genomic DNA G+C content was 61.5 mol%. Strain PAMC 29467T was separated from the type species in the genus Hymenobacter by its distinct phylogenetic position and some physiological characteristics. As a result, a novel species is proposed, with the name Hymenobacter canadensis sp. nov. (type strain, PAMC 29467T=KCTC 92787T=JCM 35843T).
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Affiliation(s)
- Woohyun Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seonghan Jang
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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Hoang T, Jeong C, Jang SH, Lee C. Tyr76 is essential for the cold adaptation of a class II glutaredoxin 4 with a heat-labile structure from the Arctic bacterium Sphingomonas sp. FEBS Open Bio 2023; 13:500-510. [PMID: 36680400 PMCID: PMC9989929 DOI: 10.1002/2211-5463.13560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023] Open
Abstract
Glutaredoxins (Grxs) are small proteins that share a well-conserved thioredoxin (Trx)-fold and participate in many biological processes. This study examined the cold adaptation mechanism of a Fe-S cluster binding class II Grx4 (SpGrx4) from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621. Three polar residues close to the cis-proline residue (P73) of SpGrx4 form a hydrogen bond network (Q74-S67-Y76) with the cis-proline loop main chain. The hydroxyl group of S67 or Y76 or both is replaced in similar Grxs depending on the temperature of the habitat. Mutants with reduced hydrogen bonds (S67A, Q74A, Y76F, and S67A/Y76W) were more susceptible to urea-induced unfolding and more flexible than the wild-type (WT). By contrast, Y76W, with a bulky indole group, was the most stable. These mutants showed higher melting temperatures than WT as a consequence of increased hydrophobic interactions. These results suggest that the tyrosine residue, Y76, is preferred for the cold adaptation of SpGrx4 with a heat-labile structure despite the rigid cis-proline loop, due to hydrogen bond formation. An aromatic residue on β3 (cis-proline plus3) modulates the stability-flexibility of the cis-proline loop for temperature adaptation of prokaryotic class II Grx4 members via hydrogen bonds and hydrophobic interactions.
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Affiliation(s)
- Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChanSu Jeong
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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Park Y, Noh HJ, Hwang CY, Shin SC, Hong SG, Jin YK, Lee H, Lee YM. Hymenobacter siberiensis sp. nov., isolated from a marine sediment of the East Siberian Sea and Hymenobacter psoromatis sp. nov., isolated from an Antarctic lichen. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005290] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-stain-negative, strictly aerobic, red-pink-coloured, rod-shaped and non-motile bacterial strains PAMC 29290, PAMC 29294T and PAMC 29296 were isolated from marine surface sediment sampled in the East Siberian Sea and strains PAMC 26553 and PAMC 26554T were obtained from an Antarctic lichen. Strains PAMC 29290, PAMC 29294T and PAMC 29296 were closely related to
Hymenobacter artigasi
(98.8 % 16S rRNA gene similarity),
Hymenobacter antarcticus
(97.3 %) and
Hymenobacter glaciei
(96.9 %), and PAMC 26553 and PAMC 26554T showed high similarity to
Hymenobacter ginsengisoli
(97.0 %),
Hymenobacter rivuli
(96.1 %) and
Hymenobacter setariae
(95.9 %). Genomic relatedness analyses showed that strains PAMC 29290, PAMC 29294T and PAMC 29296 could be distinguished from
H. artigasi
by average nucleotide identity (ANI; 93.1–93.2 %) and digital DNA–DNA hybridization (dDDH; 50.3–51.0 %) values. Strains PAMC 26553 and PAMC 26554T could be clearly distinguished from
H. ginsengisoli
with ANI values <79.8 % and dDDH values <23.3 %. The major fatty acids of strains PAMC 29290, PAMC 29294T and PAMC 29296 were C15 : 0 iso (21.0–26.0 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 17.4–18.2 %), C15 : 0 anteiso (12.7–19.1 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 8.6–16.1 %) and those of strains PAMC 26553 and PAMC 26554T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 20.7–22.2 %), C15 : 0 anteiso (17.5–19.7 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 15.5–18.1 %). The major respiratory quinone was MK-7. The genomic DNA G+C contents were 60.6–60.8 mol%. The polar lipids of PAMC 29294T were found to consist of phosphatidylethanolamine, four unidentified aminolipids, an unidentified aminophospholipid and five unidentified lipids; those of PAMC 26554T were phosphatidylethanolamine, three unidentified aminolipids, four unidentified aminophospholipid and two unidentified lipids. The distinct phylogenetic position and some physiological characteristics distinguished the novel strains from closely related type strains in the genus
Hymenobacter
. Thus, two novel species are proposed, with the names Hymenobacter siberiensis sp. nov. (type strain, PAMC 29294T=KCTC 82466T=JCM 34574T) and Hymenobacter psoromatis sp. nov. (type strain, PAMC 26554T=KCTC 82464T=JCM 34572T), respectively.
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Affiliation(s)
- Yerin Park
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hyun-Ju Noh
- Division of Microbiology, Honam National Institute of Biological Resources, 99 Gohadoan-gil, Mokpo-si, Jeollanam-do, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Chung Yeon Hwang
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Young Keun Jin
- Division of Earth-System Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hyoungseok Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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Diversity and Physiological Characteristics of Antarctic Lichens-Associated Bacteria. Microorganisms 2021; 9:microorganisms9030607. [PMID: 33804278 PMCID: PMC8001610 DOI: 10.3390/microorganisms9030607] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/23/2022] Open
Abstract
The diversity of lichen-associated bacteria from lichen taxa Cetraria, Cladonia, Megaspora, Pseudephebe, Psoroma, and Sphaerophorus was investigated by sequencing of 16S rRNA gene amplicons. Physiological characteristics of the cultured bacterial isolates were investigated to understand possible roles in the lichen ecosystem. Proteobacteria (with a relative abundance of 69.7–96.7%) were mostly represented by the order Rhodospirillales. The 117 retrieved isolates were grouped into 35 phylotypes of the phyla Actinobacteria (27), Bacteroidetes (6), Deinococcus-Thermus (1), and Proteobacteria (Alphaproteobacteria (53), Betaproteobacteria (18), and Gammaproteobacteria (12)). Hydrolysis of macromolecules such as skim milk, polymer, and (hypo)xanthine, solubilization of inorganic phosphate, production of phytohormone indole-3-acetic acid, and fixation of atmospheric nitrogen were observed in different taxa. The potential phototrophy of the strains of the genus Polymorphobacter which were cultivated from a lichen for the first time was revealed by the presence of genes involved in photosynthesis. Altogether, the physiological characteristics of diverse bacterial taxa from Antarctic lichens are considered to imply significant roles of lichen-associated bacteria to allow lichens to be tolerant or competitive in the harsh Antarctic environment.
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Rizzo C, Lo Giudice A. The Variety and Inscrutability of Polar Environments as a Resource of Biotechnologically Relevant Molecules. Microorganisms 2020; 8:microorganisms8091422. [PMID: 32947905 PMCID: PMC7564310 DOI: 10.3390/microorganisms8091422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with peculiar properties to be exploited in a number of biotechnological fields. This review aims at highlighting the biotechnological potentialities of bacteria from Arctic and Antarctic habitats, both biotic and abiotic. In addition to cold-enzymes, which have been intensively analysed, relevance is given to recent advances in the search for less investigated biomolecules, such as biosurfactants, exopolysaccharides and antibiotics.
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Affiliation(s)
- Carmen Rizzo
- Stazione Zoologica Anton Dohrn, Department Marine Biotechnology, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
- Correspondence:
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy;
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8
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Tran KN, Pham N, Jang SH, Lee C. Purification and characterization of a novel medium-chain ribitol dehydrogenase from a lichen-associated bacterium Sphingomonas sp. PLoS One 2020; 15:e0235718. [PMID: 32639976 PMCID: PMC7343156 DOI: 10.1371/journal.pone.0235718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/20/2020] [Indexed: 11/27/2022] Open
Abstract
Sugar alcohols (polyols) are abundant carbohydrates in lichen-forming algae and transported to other lichen symbionts, fungi, and bacteria. Particularly, ribitol is an abundant polyol in the lichen Cetraria sp. Polyols have important physiological roles in lichen symbiosis, but polyol utilization in lichen-associated bacteria has been largely unreported. Herein, we purified and characterized a novel ribitol dehydrogenase (RDH) from a Cetraria sp.-associated bacterium Sphingomonas sp. PAMC 26621 grown on a minimal medium containing D-ribitol (the RDH hereafter referred to as SpRDH). SpRDH is present as a trimer in its native form, and the molecular weight of SpRDH was estimated to be 39 kDa by SDS-PAGE and 117 kDa by gel filtration chromatography. SpRDH converted D-ribitol to D-ribulose using NAD+ as a cofactor. As far as we know, SpRDH is the first RDH belonging to the medium-chain dehydrogenase/reductase family. Multiple sequence alignments indicated that the catalytic amino acid residues of SpRDH consist of Cys37, His65, Glu66, and Glu157, whereas those of short-chain RDHs consist of Ser, Tyr, and Lys. Furthermore, unlike other short-chain RDHs, SpRDH did not require divalent metal ions for its catalytic activity. Despite SpRDH originating from a psychrophilic Arctic bacterium, Sphingomonas sp., it had maximum activity at 60°C and exhibited high thermal stability within the 4-50°C range. Further studies on the structure/function relationship and catalytic mechanism of SpRDH will expand our understanding of its role in lichen symbiosis.
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Affiliation(s)
- Kiet N. Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Nhung Pham
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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9
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Hotaling S, Foley ME, Zeglin LH, Finn DS, Tronstad LM, Giersch JJ, Muhlfeld CC, Weisrock DW. Microbial assemblages reflect environmental heterogeneity in alpine streams. GLOBAL CHANGE BIOLOGY 2019; 25:2576-2590. [PMID: 31077498 DOI: 10.1111/gcb.14683] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Alpine streams are dynamic habitats harboring substantial biodiversity across small spatial extents. The diversity of alpine stream biota is largely reflective of environmental heterogeneity stemming from varying hydrological sources. Globally, alpine stream diversity is under threat as meltwater sources recede and stream conditions become increasingly homogeneous. Much attention has been devoted to macroinvertebrate diversity in alpine headwaters, yet to fully understand the breadth of climate change threats, a more thorough accounting of microbial diversity is needed. We characterized microbial diversity (specifically Bacteria and Archaea) of 13 streams in two disjunct Rocky Mountain subranges through 16S rRNA gene sequencing. Our study encompassed the spectrum of alpine stream sources (glaciers, snowfields, subterranean ice, and groundwater) and three microhabitats (ice, biofilms, and streamwater). We observed no difference in regional (γ) diversity between subranges but substantial differences in diversity among (β) stream types and microhabitats. Within-stream (α) diversity was highest in groundwater-fed springs, lowest in glacier-fed streams, and positively correlated with water temperature for both streamwater and biofilm assemblages. We identified an underappreciated alpine stream type-the icy seep-that are fed by subterranean ice, exhibit cold temperatures (summer mean <2°C), moderate bed stability, and relatively high conductivity. Icy seeps will likely be important for combatting biodiversity losses as they contain similar microbial assemblages to streams fed by surface ice yet may be buffered against climate change by insulating debris cover. Our results show that the patterns of microbial diversity support an ominous trend for alpine stream biodiversity; as meltwater sources decline, stream communities will become more diverse locally, but regional diversity will be lost. Icy seeps, however, represent a source of optimism for the future of biodiversity in these imperiled ecosystems.
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Affiliation(s)
- Scott Hotaling
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Mary E Foley
- Department of Biology, University of Kentucky, Lexington, Kentucky
- Biology Department, Rutgers, The State University of New Jersey, Camden, New Jersey
| | - Lydia H Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Debra S Finn
- Department of Biology, Missouri State University, Springfield, Missouri
| | - Lusha M Tronstad
- Wyoming Natural Diversity Database, University of Wyoming, Laramie, Wyoming
| | - J Joseph Giersch
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana
| | - Clint C Muhlfeld
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, Montana
- Flathead Lake Biological Station, The University of Montana, Polson, Montana
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, Kentucky
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10
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Koo H, Hakim JA, Morrow CD, Crowley MR, Andersen DT, Bej AK. Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems. Life (Basel) 2018; 8:life8030029. [PMID: 29997353 PMCID: PMC6161096 DOI: 10.3390/life8030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/16/2022] Open
Abstract
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus, Anaeromyxobacter, Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes. Among CIPs, genes necessary for DNA replication, translation initiation, and transcription termination were highly abundant in all metagenomes. However, genes for fatty acid desaturase (FAD) and trehalose synthase (TS) were common in the soil and lake sediment metagenomes. Interestingly, the Lake Untersee water and sediment metagenome samples contained histone-like nucleoid structuring protein (H-NS) and all genes for CIPs. As for the CASPs, high abundances of a wide range of genes for cryo- and osmo-protectants (glutamate, glycine, choline, and betaine) were identified in all metagenomes. However, genes for exopolysaccharide biosynthesis were dominant in Lake Untersee water, sediment, and other soil metagenomes. The results from this study indicate that although diverse microbial communities are present in various metagenomes, they share common cold-responsive stress genes necessary for their survival and sustenance in the extreme Antarctic conditions.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, California, CA 94043, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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11
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Perfumo A, Banat IM, Marchant R. Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications. Trends Biotechnol 2018; 36:277-289. [PMID: 29428461 DOI: 10.1016/j.tibtech.2017.10.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/17/2022]
Abstract
Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.
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Affiliation(s)
- Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.
| | - Ibrahim M Banat
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
| | - Roger Marchant
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
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12
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Kashif A, Tran LH, Jang SH, Lee C. Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1. ACS OMEGA 2017; 2:8760-8769. [PMID: 31457406 PMCID: PMC6645578 DOI: 10.1021/acsomega.7b01435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/23/2017] [Indexed: 06/10/2023]
Abstract
The aromatic amino acids, Tyr or Trp, which line the active-site walls of esterases, stabilize the catalytic His loop via hydrogen bonding. A Tyr residue is preferred in extremophilic esterases (psychrophilic or hyperthermophilic esterases), whereas a Trp residue is preferred in moderate-temperature esterases. Here, we provide evidence that Tyr and Trp play distinct roles in cold adaptation of the psychrophilic esterase EstSP1 isolated from an Arctic bacterium Sphingomonas glacialis PAMC 26605. Stern-Volmer plots showed that the mutation of Tyr191 to Ala, Phe, Trp, and His resulted in reduced conformational flexibility of the overall protein structure. Interestingly, the Y191W and Y191H mutants showed increased thermal stability at moderate temperatures. All Tyr191 mutants showed reduced catalytic activity relative to wild-type EstSP1. Our results indicate that Tyr with its phenyl hydroxyl group is favored for increased conformational flexibility and high catalytic activity of EstSP1 at low temperatures at the expense of thermal stability. The results of this study suggest that, in the permanently cold Arctic zone, enzyme activity has been selected for psychrophilic enzymes over thermal stability. The results presented herein provide novel insight into the roles of Tyr and Trp residues for temperature adaptation of enzymes that function at low, moderate, and high temperatures.
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Affiliation(s)
| | | | | | - ChangWoo Lee
- E-mail: . Tel: +82-53-850-6464. Fax: +82-53-850-6469
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13
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14
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Genome Sequence of Deinococcus marmoris PAMC 26562 Isolated from Antarctic Lichen. GENOME ANNOUNCEMENTS 2017; 5:5/12/e00013-17. [PMID: 28336585 PMCID: PMC5364210 DOI: 10.1128/genomea.00013-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Deinococcus marmoris strain PAMC 26562 was isolated from Usnea sp., a lichen collected from King George Island, Antarctica. We report here the draft genome sequence of strain PAMC 26562, which has xanthorhodopsin and carbon monoxide dehydrogenase genes in addition to major metabolic pathways presented in deinococcal genomes.
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15
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Hong DK, Jang SH, Lee C. Gene cloning and characterization of a psychrophilic phthalate esterase with organic solvent tolerance from an Arctic bacterium Sphingomonas glacialis PAMC 26605. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Lee YM, Yang JY, Baek K, Han SJ, Shin SC, Hwang CY, Hong SG, Lee HK. Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter. Int J Syst Evol Microbiol 2016; 66:1068-1073. [DOI: 10.1099/ijsem.0.000841] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. M. Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
- School of Biological Sciences, College of Natural Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-747, Republic of Korea
| | - J. Y. Yang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - K. Baek
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - S. J. Han
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - S. C. Shin
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - C. Y. Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - S. G. Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - H. K. Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
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17
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Gyeong HR, Baek K, Hwang CY, Park KH, Kim HM, Lee HK, Lee YK. Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus. Int J Syst Evol Microbiol 2015; 65:3407-3412. [PMID: 26296675 DOI: 10.1099/ijsem.0.000429] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.
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Affiliation(s)
- Hye Ryeon Gyeong
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Kiwoon Baek
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Chung Yeon Hwang
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Key Hun Park
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hye Min Kim
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hong Kum Lee
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, KIOST, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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18
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Arbel J, King CK, Raymond B, Winsley T, Mengersen KL. Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil. Ecol Evol 2015; 5:2633-45. [PMID: 26257876 PMCID: PMC4523359 DOI: 10.1002/ece3.1493] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 02/21/2015] [Accepted: 03/10/2015] [Indexed: 11/12/2022] Open
Abstract
Ecotoxicology is primarily concerned with predicting the effects of toxic substances on the biological components of the ecosystem. In remote, high latitude environments such as Antarctica, where field work is logistically difficult and expensive, and where access to adequate numbers of soil invertebrates is limited and response times of biota are slow, appropriate modeling tools using microbial community responses can be valuable as an alternative to traditional single-species toxicity tests. In this study, we apply a Bayesian nonparametric model to a soil microbial data set acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. We model community change in terms of OTUs (operational taxonomic units) in response to a range of total petroleum hydrocarbon (TPH) concentrations. The Shannon diversity of the microbial community, clustering of OTUs into groups with similar behavior with respect to TPH, and effective concentration values at level x, which represent the TPH concentration that causes x% change in the community, are presented. This model is broadly applicable to other complex data sets with similar data structure and inferential requirements on the response of communities to environmental parameters and stressors.
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Affiliation(s)
| | - Catherine K King
- Australian Antarctic DivisionKingston, Tasmania, 7050, Australia
| | - Ben Raymond
- Australian Antarctic DivisionKingston, Tasmania, 7050, Australia
| | - Tristrom Winsley
- Australian Antarctic DivisionKingston, Tasmania, 7050, Australia
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Baek K, Lee YM, Hwang CY, Park H, Jung YJ, Kim MK, Hong SG, Kim JH, Lee HK. Psychroserpens jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment. Int J Syst Evol Microbiol 2015; 65:183-188. [DOI: 10.1099/ijs.0.069740-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, yellow-pigmented, aerobic, rod-shaped and non-motile bacterium, PAMC 27130T, was isolated from the marine sediment of the Ross Sea, Antarctica. The temperature, pH and NaCl tolerance ranges for growth were 4–20 °C, pH 6.0–9.0 and 0.5–5.0 % (w/v) NaCl, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PAMC 27130T belonged to the genus
Psychroserpens
and was closely related to
Psychroserpens mesophilus
,
Psychroserpens damuponensis
and
Psychroserpens burtonensis
with 97.2, 94.7 and 94.2 % sequence similarities, respectively. Genomic relatedness analyses based on average nucleotide identity and genome-to-genome distance showed that strain PAMC 27130T could be clearly distinguished from other species of the genus
Psychroserpens
. The genomic DNA G+C content was 32.7 mol%. The major fatty acids (>10 %) were C20 : 4ω6c (13.2 %), iso-C15 : 0 (12.3 %), iso-C15 : 1 G (11.7 %) and iso-C15 : 0 3-OH (10.0 %). The major respiratory isoprenoid quinone was menaquinone-6 (MK-6) and the polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified aminophospholipid and three unidentified lipids. On the basis of genotypic and phenotypic data collected in this study, it is proposed that strain PAMC 27130T represents a novel species of the genus
Psychroserpens
, for which the name Psychroserpens jangbogonensis sp. nov. is proposed. The type strain is PAMC 27130T ( = KCTC 42128T = JCM 30228T).
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Affiliation(s)
- Kiwoon Baek
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Yung Mi Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-747, Republic of Korea
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Chung Yeon Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Hyun Park
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - You-Jung Jung
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Mi-Kyeong Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Ji Hee Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Hong Kum Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 406-840, Republic of Korea
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Cappa F, Suciu N, Trevisan M, Ferrari S, Puglisi E, Cocconcelli PS. Bacterial diversity in a contaminated Alpine glacier as determined by culture-based and molecular approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 497-498:50-59. [PMID: 25117971 DOI: 10.1016/j.scitotenv.2014.07.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 06/03/2023]
Abstract
Glaciers are important ecosystems, hosting bacterial communities that are adapted to cold conditions and scarcity of available nutrients. Several works focused on the composition of bacterial communities in glaciers and on the long-range atmospheric deposition of pollutants in glaciers, but it is not clear yet if ski resorts can represent a source of point pollution in near-by glaciers, and if these pollutants can influence the residing bacterial communities. To test these hypotheses, 12 samples were analyzed in Madaccio Glacier, in a 3200 ma.s.l. from two areas, one undisturbed and one close to a summer ski resort that is active since the 1930s. Chemical analyses found concentrations up to 43 ng L(-1) for PCBs and up to 168 μg L(-1) for PAHs in the contaminated area: these values are significantly higher than the ones found in undisturbed glaciers because of long-range atmospheric deposition events, and can be explained as being related to the near-by ski resort activities. Isolation of strains on rich medium plates and PCR-DGGE analyses followed by sequencing of bands allowed the identification of a bacterial community with phylogenetic patterns close to other glacier environments, with Proteobacteria and Actinobacteria the mostly abundant phyla, with Acidobacteria, Firmicutes and Cyanobacteria also represented in the culture-independent analyses. A number of isolates were identified by molecular and biochemical methods as phylogenetic related to known xenobiotic-degrading strains: glaciers subjected to chemical contamination can be important reservoirs of bacterial strains with potential applications in bioremediation.
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Affiliation(s)
- Fabrizio Cappa
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Nicoleta Suciu
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Marco Trevisan
- Istituto di Chimica Agraria ed Ambientale, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Susanna Ferrari
- Centro Ricerche Biotecnologiche, Università Cattolica del Sacro Cuore, Via Milano 24, 26100 Cremona, Italy
| | - Edoardo Puglisi
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Pier Sandro Cocconcelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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Lacinutrix jangbogonensis sp. nov., a psychrophilic bacterium isolated from Antarctic marine sediment and emended description of the genus Lacinutrix. Antonie van Leeuwenhoek 2014; 106:527-33. [PMID: 25038886 DOI: 10.1007/s10482-014-0221-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 10/25/2022]
Abstract
A Gram-negative, strictly aerobic, non-motile, rod-shaped and psychrophilic bacterial strain, PAMC 27137(T), was isolated from the marine sediment of the Ross Sea, Antarctica. Strain PAMC 27137(T) was observed to grow at 4-10 °C, at pH 6.5-7.5 and in the presence of 2.5-4.0 % (w/v) sea salts. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain PAMC 27137(T) belongs to the genus Lacinutrix showing the high similarities with Lacinutrix mariniflava JCM 13824(T) (97.6 %) and Lacinutrix algicola JCM 13825(T) (97.1 %). Genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 27137(T) is clearly distinguished from the most closely related Lacinutrix species. The major fatty acids (>5 %) were identified as iso-C15:1 G (19.9 %), iso-C15:0 (19.3 %), iso-C17:0 3-OH (11.3 %), summed feature 9 (C16:0 10-methyl and/or iso-C17:1 ω9c as defined by MIDI, 9.1 %), iso-C15:0 3-OH (7.5 %), and anteiso-C15:1 A (5.8 %). The polar lipids were found to consist of phosphatidylethanolamine, an unidentified aminolipid, an unidentified aminophospholipid, and five unidentified phospholipids. The major respiratory quinone was identified as MK-6. The genomic DNA G+C content was determined to be 32.1 mol%. Based on the data from this polyphasic taxonomic study, strain PAMC 27137(T) is considered to represent a novel species of the genus Lacinutrix, for which the name Lacinutrix jangbogonensis sp. nov. is proposed. The type strain is PAMC 27137(T) (=KCTC 32573(T)=JCM 19883(T)).
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Biodiversity and physiological characteristics of Antarctic and Arctic lichens-associated bacteria. World J Microbiol Biotechnol 2014; 30:2711-21. [PMID: 25001073 DOI: 10.1007/s11274-014-1695-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
Abstract
The diversity and physiological characteristics of culturable bacteria associated with lichens from different habitats of the Arctic and Antarctica were investigated. The 68 retrieved isolates could be grouped on the basis of their 16S rRNA gene sequences into 26 phylotypes affiliated with the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes and with the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Isolates belonging to the Alphaproteobacteria were the most abundant, followed by those belonging to Actinobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus. Phylogenetic analysis showed that approximately 21 % of the total isolates represented a potentially novel species or genus (≤97 % sequence similarity). Strains belonging to the genera Sphingomonas, Frondihabitans, Hymenobacter, and Burkholderia were recovered from lichen samples from both geographic locations, implying common and important bacterial functions within lichens. Extracellular protease activities were detected in six isolates, affiliated with Burkholderia, Frondihabitans, Hymenobacter, Pseudomonas, and Rhodanobacter. Extracellular lipase activities were detected in 37 isolates of the genera Burkholderia, Deinococcus, Frondihabitans, Pseudomonas, Rhodanobacter, Sphingomonas, and Subtercola. This is the first report on the culturable bacterial diversity present within lichens from Arctic and Antarctica and the isolates described herein are valuable resources to decode the functional and ecological roles of bacteria within lichens. In addition, the low similarity (≤97 %) of the recovered isolates to known species and their production of cold-active enzymes together suggest that lichens are noteworthy sources of novel bacterial strains for use in biotechnological applications.
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Kim D, Yoo M, Kim E, Hong SG. Anthranilate degradation by a cold-adaptedPseudomonassp. J Basic Microbiol 2013; 55:354-62. [DOI: 10.1002/jobm.201300079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/13/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Dockyu Kim
- Division of Life Sciences; Korea Polar Research Institute; Incheon Korea
| | - Miyoun Yoo
- Department of Systems Biology; Yonsei University; Seoul Korea
- Yonsei/Paris-Sud Project; Yonsei International Campus; Incheon Korea
| | - Eungbin Kim
- Department of Systems Biology; Yonsei University; Seoul Korea
- Yonsei/Paris-Sud Project; Yonsei International Campus; Incheon Korea
| | - Soon Gyu Hong
- Division of Life Sciences; Korea Polar Research Institute; Incheon Korea
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