1
|
Seixas MH, Munroe JS, Eggleston EM. Bacterial diversity and geomicrobiology of Winter Wonderland ice cave, Utah, USA. Microbiologyopen 2024; 13:e1426. [PMID: 38995161 PMCID: PMC11241547 DOI: 10.1002/mbo3.1426] [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: 10/23/2023] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
The Winter Wonderland ice cave, located at an elevation of 3140 m above sea level in the Uinta Mountains of northern Utah, USA, maintains a constant sub-zero temperature. Seasonal snowmelt and rain enter the cave, freeze on the surface of the existing ice, and contribute to a 3-m-thick layered ice mass. This ice mass contains organic matter and cryogenic cave carbonates (CCCs) that date back centuries. In this study, samples of ice, liquid water, and exposed CCCs were collected to examine the bacterial communities within the cave and to determine if these communities vary spatially and between sample types. Flow cytometry showed that cell counts are an order of magnitude higher in liquid water samples than in ice. Epifluorescence microscopy and scanning electron microscopy imaging revealed potential coccoid and bacillus microbial morphologies in water samples and putative cells or calcite spherules in the CCCs. The diversity of bacteria associated with soil, identified through sequence-based analysis, supports the hypothesis that water enters the cave by filtering through soil and bedrock. A differential abundance of bacterial taxa was observed between sample types, with the greatest diversity found in CCCs. This supports a geomicrobiological framework where microbes aggregate in the water, sink into a concentrated layer, and precipitate out of the ice with the CCCs, thereby reducing the cell counts in the ice. These CCCs may provide essential nutrients for the bacteria or could themselves be products of biomineralization.
Collapse
Affiliation(s)
- Miranda Herschel Seixas
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
- Biology DepartmentMiddlebury CollegeMiddleburyVermontUSA
| | - Jeffrey S. Munroe
- Department of Earth and Climate SciencesMiddlebury CollegeMiddleburyVermontUSA
| | | |
Collapse
|
2
|
Çil E. Culturable bacterial flora of juveniles of Pelophylax ridibundus (Pallas, 1771) and influence of abiotic factors on diversity. Folia Microbiol (Praha) 2023; 68:939-949. [PMID: 37233886 DOI: 10.1007/s12223-023-01063-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 05/27/2023]
Abstract
This study aims to determine the bacterial flora on the skin surface of the juvenile forms of Pelophylax ridibundus inhabiting three different altitudes and examine potential correlations between bacterial diversity, ecological location, and factors. It was attempted to characterize thirty-two bacteria isolated from the Melet River, Sülük Lake, and Çambaşı Pond through combined biochemical and molecular methods. Canonical correspondence analysis showed that the most important ecological factors for microorganisms to settle on frog skin were determined as water conductivity and dissolved oxygen amount. The most frequently isolated bacteria belonged to the genera Erwinia and Pseudomonas. Altitude positively affected Exiguobacterium. This first report of skin cultivable bacteria from P. ridibundus juvenile forms natural population improves our knowledge of amphibian skin bacterial flora. This study contributes to a better understanding of their ecology and how this species has survived in an environment modulated by altitude.
Collapse
Affiliation(s)
- Elif Çil
- Faculty of Education, Science Education Department, Ordu University, Ordu, Turkey.
| |
Collapse
|
3
|
Kollár J, Kopalová K, Kavan J, Vrbická K, Nývlt D, Nedbalová L, Stibal M, Kohler TJ. Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts. FEMS Microbiol Ecol 2023; 99:fiad087. [PMID: 37516444 PMCID: PMC10446143 DOI: 10.1093/femsec/fiad087] [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: 02/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023] Open
Abstract
Glacier recession is creating new water bodies in proglacial forelands worldwide, including Antarctica. Yet, it is unknown how microbial communities of recently formed "young" waterbodies (originating decades to a few centuries ago) compare with established "old" counterparts (millennia ago). Here, we compared benthic microbial communities of different lake types on James Ross Island, Antarctic Peninsula, using 16S rDNA metabarcoding and light microscopy to explore bacterial and diatom communities, respectively. We found that the older lakes host significantly more diverse bacterial and diatom communities compared to the young ones. To identify potential mechanisms for these differences, linear models and dbRDA analyses suggested combinations of water temperature, pH, and conductivity to be the most important factors for diversity and community structuring, while differences in geomorphological and hydrological stability, though more difficult to quantify, are likely also influential. These results, along with an indicator species analysis, suggest that physical and chemical constraints associated with individual lakes histories are likely more influential to the assembly of the benthic microbial communities than lake age alone. Collectively, these results improve our understanding of microbial community drivers in Antarctic freshwaters, and help predict how the microbial landscape may shift with future habitat creation within a changing environment.
Collapse
Affiliation(s)
- Jan Kollár
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Kateřina Kopalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Jan Kavan
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Alfred Jahn Cold Regions Research Centre, University of Wroclaw, pl. Uniwersytecki 1, Wroclaw 50-137, Poland
| | - Kristýna Vrbická
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Daniel Nývlt
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Linda Nedbalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Marek Stibal
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| |
Collapse
|
4
|
Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
Collapse
Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| |
Collapse
|
5
|
Sedláček I, Holochová P, Busse HJ, Koublová V, Králová S, Švec P, Sobotka R, Staňková E, Pilný J, Šedo O, Smolíková J, Sedlář K. Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov. Microorganisms 2022; 10:microorganisms10040704. [PMID: 35456753 PMCID: PMC9028926 DOI: 10.3390/microorganisms10040704] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
A group of seven bacterial strains producing blue-purple pigmented colonies on R2A agar was isolated from freshwater samples collected in a deglaciated part of James Ross Island and Eagle Island, Antarctica, from 2017–2019. The isolates were psychrophilic, oligotrophic, resistant to chloramphenicol, and exhibited strong hydrolytic activities. To clarify the taxonomic position of these isolates, a polyphasic taxonomic approach was applied based on sequencing of the 16S rRNA, gyrB and lepA genes, whole-genome sequencing, rep-PCR, MALDI-TOF MS, chemotaxonomy analyses and biotyping. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the entire group are representatives of the genus Massilia. The closest relatives of the reference strain P8398T were Massilia atriviolacea, Massilia violaceinigra, Massilia rubra, Massilia mucilaginosa, Massilia aquatica, Massilia frigida, Massilia glaciei and Massilia eurypsychrophila with a pairwise similarity of 98.6–100% in the 16S rRNA. The subsequent gyrB and lepA sequencing results showed the novelty of the analysed group, and the average nucleotide identity and digital DNA–DNA hybridisation values clearly proved that P8398T represents a distinct Massilia species. After all these results, we nominate a new species with the proposed name Massilia antarctica sp. nov. The type strain is P8398T (= CCM 8941T = LMG 32108T).
Collapse
Affiliation(s)
- Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
- Correspondence: ; Tel.: +420-549-496-922
| | - Pavla Holochová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria;
| | - Vendula Koublová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Roman Sobotka
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.H.); (V.K.); (S.K.); (P.Š.); (E.S.)
| | - Jan Pilný
- Centrum Algatech, Institute of Microbiology, Czech Academy of Sciences, Opatovický mlýn, 379 01 Třeboň, Czech Republic; (R.S.); (J.P.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Jana Smolíková
- Department of Physical Geography and Geoecology, Faculty of Science, Charles University, Albertov 6, 128 00 Praha, Czech Republic;
| | - Karel Sedlář
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic;
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, 803 33 Munich, Germany
| |
Collapse
|
6
|
Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems from James Ross Archipelago (West Antarctica). Polar Biol 2022. [DOI: 10.1007/s00300-021-02997-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
7
|
Krucon T, Dziewit L, Drewniak L. Insight Into Ecology, Metabolic Potential, and the Taxonomic Composition of Bacterial Communities in the Periodic Water Pond on King George Island (Antarctica). Front Microbiol 2021; 12:708607. [PMID: 34690951 PMCID: PMC8531505 DOI: 10.3389/fmicb.2021.708607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Polar regions contain a wide variety of lentic ecosystems. These include periodic ponds that have a significant impact on carbon and nitrogen cycling in polar environments. This study was conducted to assess the taxonomic and metabolic diversity of bacteria found in Antarctic pond affected by penguins and sea elephants and to define their role in ongoing processes. Metabolic assays showed that of the 168 tested heterotrophic bacteria present in the Antarctic periodic pond, 96% are able to degrade lipids, 30% cellulose, 26% proteins, and 26% starch. The taxonomic classification of the obtained isolates differs from that based on the composition of the 16S rRNA relative abundances in the studied pond. The dominant Actinobacteria constituting 45% of isolates represents a low proportion of the community, around 4%. With the addition of run-off, the proportions of inhabiting bacteria changed, including a significant decrease in the abundance of Cyanobacteria, from 2.38 to 0.33%, increase of Firmicutes from 9.32 to 19.18%, and a decreasing richness (Chao1 index from 1299 to 889) and diversity (Shannon index from 4.73 to 4.20). Comparative studies of communities found in different Antarctic environments indicate a great role for penguins in shaping bacterial populations.
Collapse
Affiliation(s)
- Tomasz Krucon
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| |
Collapse
|
8
|
Tahon G, Gök D, Lebbe L, Willems A. Description and functional testing of four species of the novel phototrophic genus Chioneia gen. nov., isolated from different East Antarctic environments. Syst Appl Microbiol 2021; 44:126250. [PMID: 34592543 DOI: 10.1016/j.syapm.2021.126250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Seven Gram-negative, aerobic, non-sporulating, motile strains were isolated from terrestrial (R-67880T, R-67883, R-36501 and R-36677T) and aquatic (R-39604, R-39161T and R-39594T) East Antarctic environments (i.e. soil and aquatic microbial mats), between 2007 and 2014. Analysis of near-complete 16S rRNA gene sequences revealed that the strains potentially form a novel genus in the family Sphingomonadaceae (Alphaproteobacteria). DNA-DNA reassociation and average nucleotide identity values indicated distinction from close neighbors in the family Sphingomonadaceae and showed that the seven isolates form four different species. The main central pathways present in the strains are the glycolysis, tricarboxylic acid cycle and pentose phosphate pathway. The strains can use only a limited number of carbon sources and mainly depend on ammonia and sulfate as a nitrogen and sulfur source, respectively. The novel strains showed the potential of aerobic anoxygenic phototrophy, based on the presence of bacteriochlorophyll a pigments, which was corroborated by the presence of genes for all building blocks for a type 2 photosynthetic reaction center in the annotated genomes. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the strains could be assigned four new species in the novel genus Chioneia gen. nov. in the family Sphingomonadaceae, for which the names C. frigida sp. nov. (R-67880T, R-67883 and R-36501), C. hiemis sp. nov. (R-36677T), C. brumae sp. nov. (R-39161T and R-39604) and C. algoris sp. nov. (R-39594T) are proposed.
Collapse
Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Duygu Gök
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| |
Collapse
|
9
|
Rigauts C, Aizawa J, Taylor S, Rogers GB, Govaerts M, Cos P, Ostyn L, Sims S, Vandeplassche E, Sze M, Dondelinger Y, Vereecke L, Van Acker H, Simpson JL, Burr L, Willems A, Tunney MM, Cigana C, Bragonzi A, Coenye T, Crabbé A. Rothia mucilaginosa is an anti-inflammatory bacterium in the respiratory tract of patients with chronic lung disease. Eur Respir J 2021; 59:13993003.01293-2021. [PMID: 34588194 PMCID: PMC9068977 DOI: 10.1183/13993003.01293-2021] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
Background Chronic airway inflammation is the main driver of pathogenesis in respiratory diseases such as severe asthma, chronic obstructive pulmonary disease, cystic fibrosis (CF) and bronchiectasis. While the role of common pathogens in airway inflammation is widely recognised, the influence of other microbiota members is still poorly understood. Methods We hypothesised that the lung microbiota contains bacteria with immunomodulatory activity which modulate net levels of immune activation by key respiratory pathogens. Therefore, we assessed the immunomodulatory effect of several members of the lung microbiota frequently reported as present in CF lower respiratory tract samples. Results We show that Rothia mucilaginosa, a common resident of the oral cavity that is also often detectable in the lower airways in chronic disease, has an inhibitory effect on pathogen- or lipopolysaccharide-induced pro-inflammatory responses, in vitro (three-dimensional cell culture model) and in vivo (mouse model). Furthermore, in a cohort of adults with bronchiectasis, the abundance of Rothia species was negatively correlated with pro-inflammatory markers (interleukin (IL)-8 and IL-1β) and matrix metalloproteinase (MMP)-1, MMP-8 and MMP-9 in sputum. Mechanistic studies revealed that R. mucilaginosa inhibits NF-κB pathway activation by reducing the phosphorylation of IκBα and consequently the expression of NF-κB target genes. Conclusions These findings indicate that the presence of R. mucilaginosa in the lower airways potentially mitigates inflammation, which could in turn influence the severity and progression of chronic respiratory disorders. A commensal bacterium of the lower airways, Rothia mucilaginosa, inhibits inflammation by NF-κB pathway inactivation. R. mucilaginosa abundance inversely correlates with sputum pro-inflammatory markers in chronic lung disease, indicating a beneficial role.https://bit.ly/3lNT9th
Collapse
Affiliation(s)
- Charlotte Rigauts
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Juliana Aizawa
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Steven Taylor
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Matthias Govaerts
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Sarah Sims
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Mozes Sze
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Yves Dondelinger
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Lars Vereecke
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Rheumatology, Ghent University, Gent, Belgium
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Jodie L Simpson
- Faculty of Health and Medicine, Priority Research Centre for Healthy Lungs, University of Newcastle, Callaghan, New South Wales, Australia
| | - Lucy Burr
- Department of Respiratory Medicine, Mater Health Services, South Brisbane, QLD, Australia.,Mater Research - University of Queensland, Aubigny Place, South Brisbane, QLD, Australia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael M Tunney
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Cristina Cigana
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| |
Collapse
|
10
|
Chen X, Liu X, Jia H, Jin J, Kong W, Huang Y. Inverse hydrogen isotope fractionation indicates heterotrophic microbial production of long-chain n-alkyl lipids in desolate Antarctic ponds. GEOBIOLOGY 2021; 19:394-404. [PMID: 33799312 DOI: 10.1111/gbi.12441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Long-chain (>C25 ) n-alkyl lipids have long been considered biomarkers for higher plant leaf waxes and widely applied for paleoclimate and paleoenvironmental reconstructions. However, recent experimental and lacustrine sediment studies suggest long-chain n-alkanes and n-alkanoic acids can also be produced by aerobic microbes, probably heterotrophic microbes based on carbon isotope data. Here we show that sedimentary long-chain n-alkanes and n-alkanoic acids in two desolate Antarctic ponds where vascular plants are absent in the surroundings display hydrogen isotopic values up to 300 per mil higher than those of lake water. It is the first time that such strongly inverse or reduced hydrogen isotopic fractionation of lipid biomarkers is observed in natural sediment samples. Based on recent extensive experimental data on microbial hydrogen isotopic fractionation, our data can only be explained by the predominant production of long-chain n-alkanes and n-alkanoic acids from heterotrophic micro-organisms. Together with preliminary 16S rRNA gene sequencing data, our results represent the first unambiguous example of predominant heterotrophic microbial production of long-chain n-alkyl waxes in a natural environment.
Collapse
Affiliation(s)
- Xin Chen
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaodong Liu
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Hongzeng Jia
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Jing Jin
- Anhui Province Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Yongsong Huang
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
| |
Collapse
|
11
|
Antarctic Rahnella inusitata: A Producer of Cold-Stable β-Galactosidase Enzymes. Int J Mol Sci 2021; 22:ijms22084144. [PMID: 33923711 PMCID: PMC8074230 DOI: 10.3390/ijms22084144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 11/18/2022] Open
Abstract
There has been a recent increase in the exploration of cold-active β-galactosidases, as it offers new alternatives for the dairy industry, mainly in response to the current needs of lactose-intolerant consumers. Since extremophilic microbial compounds might have unique physical and chemical properties, this research aimed to study the capacity of Antarctic bacterial strains to produce cold-active β-galactosidases. A screening revealed 81 out of 304 strains with β-galactosidase activity. The strain Se8.10.12 showed the highest enzymatic activity. Morphological, biochemical, and molecular characterization based on whole-genome sequencing confirmed it as the first Rahnella inusitata isolate from the Antarctic, which retained 41–62% of its β-galactosidase activity in the cold (4 °C–15 °C). Three β-galactosidases genes were found in the R. inusitata genome, which belong to the glycoside hydrolase families GH2 (LacZ and EbgA) and GH42 (BglY). Based on molecular docking, some of these enzymes exhibited higher lactose predicted affinity than the commercial control enzyme from Aspergillus oryzae. Hence, this work reports a new Rahnella inusitata strain from the Antarctic continent as a prominent cold-active β-galactosidase producer.
Collapse
|
12
|
Buetti-Dinh A, Ruinelli M, Czerski D, Scapozza C, Martignier A, Roman S, Caminada A, Tonolla M. Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps. PLoS One 2021; 16:e0248877. [PMID: 33784327 PMCID: PMC8009434 DOI: 10.1371/journal.pone.0248877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 03/07/2021] [Indexed: 12/02/2022] Open
Abstract
The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.
Collapse
Affiliation(s)
- Antoine Buetti-Dinh
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (ABD); (MT)
| | - Michela Ruinelli
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Dorota Czerski
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Cristian Scapozza
- Institute of Earth Sciences, University of Applied Sciences of Southern Switzerland (SUPSI), Trevano, Canobbio, Switzerland
| | - Agathe Martignier
- Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
| | - Annapaola Caminada
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology (LMA), Department of Environment, Constructions and Design (DACD), University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, Switzerland
- Alpine Biology Center Foundation, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (ABD); (MT)
| |
Collapse
|
13
|
Núñez-Montero K, Quezada-Solís D, Khalil ZG, Capon RJ, Andreote FD, Barrientos L. Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds. Biomolecules 2020; 10:E673. [PMID: 32349314 PMCID: PMC7277857 DOI: 10.3390/biom10050673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new "-omics" comparative approaches for drug discovery.
Collapse
Affiliation(s)
- Kattia Núñez-Montero
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
- Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica
| | - Damián Quezada-Solís
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil;
| | - Leticia Barrientos
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| |
Collapse
|
14
|
Mohammed A, Abdul-Wahab MF, Hashim M, Omar AH, Md Reba MN, Muhamad Said MF, Soeed K, Alias SA, Smykla J, Abba M, Ibrahim Z. Biohydrogen Production by Antarctic Psychrotolerant Klebsiella sp. ABZ11. Pol J Microbiol 2019; 67:283-290. [PMID: 30451444 PMCID: PMC7255690 DOI: 10.21307/pjm-2018-033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
Lower temperature biohydrogen production has always been attractive, due to the lower energy requirements. However, the slow metabolic rate of psychrotolerant biohydrogen-producing bacteria is a common problem that affects their biohydrogen yield. This study reports on the improved substrate synthesis and biohydrogen productivity by the psychrotolerant Klebsiella sp. strain ABZ11, isolated from Antarctic seawater sample. The isolate was screened for biohydrogen production at 30°C, under facultative anaerobic condition. The isolate is able to ferment glucose, fructose and sucrose with biohydrogen production rate and yield of 0.8 mol/l/h and 3.8 mol/g, respectively at 10 g/l glucose concentration. It also showed 74% carbohydrate uptake and 95% oxygen uptake ability, and a wide growth temperature range with optimum at 37°C. Klebsiella sp. ABZ11 has a short biohydrogen production lag phase, fast substrate uptake and is able to tolerate the presence of oxygen in the culture medium. Thus, the isolate has a potential to be used for lower temperature biohydrogen production process.
Collapse
Affiliation(s)
- Abdullahi Mohammed
- Ibrahim Badamasi Babangida University, Lapai, Niger State, Nigeria ; Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Mazlan Hashim
- Geoscience and Digital Earth Centre (INSTeG), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Abdul Hafidz Omar
- Sports Innovation Technology Centre (SITC), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Mohd Nadzri Md Reba
- Geoscience and Digital Earth Centre (INSTeG), Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Kamaruzaman Soeed
- Sports Innovation Technology Centre (SITC), Universiti Teknologi Malaysia, Johor, Malaysia
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia ; National Antarctic Research Centre, Institute of Graduate Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Jerzy Smykla
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, USA ; Department of Biodiversity, Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Mustapha Abba
- Department of Microbiology, Bauchi State University Gadau, Bauchi, Nigeria
| | - Zaharah Ibrahim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
| |
Collapse
|
15
|
Carotenoids from heterotrophic bacteria isolated from Fildes Peninsula, King George Island, Antarctica. ACTA ACUST UNITED AC 2019; 21:e00306. [PMID: 30705834 PMCID: PMC6348148 DOI: 10.1016/j.btre.2019.e00306] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/23/2022]
Abstract
Carotenoids are isoprenoid pigments used by pharmaceutical, cosmetic, food and feed industry as antioxidants and colorants. Although traditional sources of carotenoids are fruits, vegetables and chemical synthesis, prospecting for alternative sinks of common and/or unusual carotenoids is important for the development of natural carotenoid industry. In this work, 30 pigmented bacterial strains from Fildes Peninsula in King George Island, Antarctica, were isolated and identified by 16S rRNA gene sequencing and classified in three phyla, Bacteroidetes, Firmicutes and Actinobacteria. After cells extraction, ten different carotenoids were identified based on the chromatographic and spectroscopic characteristic obtained by HPLC-PDA and HPLC-PDA-APCI-MS analyses. Strains assigned to Bacteroidetes affiliated to Flavobacterium, Chryseobacterium and Zobellia genera, presented a pigment profile composed of zeaxanthin, β-cryptoxanthin and β-carotene. Firmicutes strains of Planococcus genus produced a C50 carotenoid, identified as C.p. 450 glucoside. Actinobacteria isolates were mainly assigned to Arthrobacter genus, and few to Salinibacterium and Cryobacterium genera. Arthrobacter strains produced C50 carotenoids such as decaprenoxanthin and its glucosylated derivatives, as well as some C40 carotenoids such as lycopene which is used as synthesis precursors of the C50 carotenoids. Salinibacterium and Cryobacterium genera produced C.p. 450 free form and its glucosylated derivatives. Although most isolates produce carotenoids similar in diversity and quantity than those already reported in the literature, novel sources for C50 carotenoids results from this work. According to their carotenoid content, all isolates could be promising candidates for carotenoids production.
Collapse
|
16
|
Vigneron A, Cruaud P, Mohit V, Martineau MJ, Culley AI, Lovejoy C, Vincent WF. Multiple Strategies for Light-Harvesting, Photoprotection, and Carbon Flow in High Latitude Microbial Mats. Front Microbiol 2018; 9:2881. [PMID: 30564204 PMCID: PMC6288179 DOI: 10.3389/fmicb.2018.02881] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/09/2018] [Indexed: 12/27/2022] Open
Abstract
Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection, and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communities in shallow water habitats, we sampled cyanobacterial mats in the thawed littoral zone of two lakes situated at the northern and southern limits of the Canadian Arctic permafrost zone. We applied a multiphasic approach using pigment profiles from high performance liquid chromatography, Illumina MiSeq sequencing of the 16S and 18S rRNA genes, and metagenomic analysis. The mats shared a taxonomic and functional core microbiome, dominated by oxygenic cyanobacteria with light-harvesting and photoprotective pigments, bacteria with bacteriochlorophyll, and bacteria with light-driven Type I rhodopsins. Organisms able to use light for energy related processes represented up to 85% of the total microbial community, with 15–30% attributable to cyanobacteria and 55–70% attributable to other bacteria. The proportion of genes involved in anaplerotic CO2 fixation was greater than for genes associated with oxygenic photosynthesis. Diverse heterotrophic bacteria, eukaryotes (including metazoans and fungi) and viruses co-occurred in both communities. The results indicate a broad range of strategies for capturing sunlight and CO2, and for the subsequent flow of energy and carbon in these complex, light-driven microbial ecosystems.
Collapse
Affiliation(s)
- Adrien Vigneron
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
| | - Vani Mohit
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Marie-Josée Martineau
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada
| | - Alexander I Culley
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Centre d'Études Nordiques, Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.,Département de Biologie, Université Laval, Québec, QC, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| |
Collapse
|
17
|
Cornet L, Bertrand AR, Hanikenne M, Javaux EJ, Wilmotte A, Baurain D. Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures. Microb Genom 2018; 4. [PMID: 30136922 PMCID: PMC6202449 DOI: 10.1099/mgen.0.000212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.
Collapse
Affiliation(s)
- Luc Cornet
- 1InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.,2UR Geology - Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Amandine R Bertrand
- 1InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.,3InBioS - PhytoSYSTEMS, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Marc Hanikenne
- 3InBioS - PhytoSYSTEMS, Functional Genomics and Plant Molecular Imaging, University of Liège, Liège, Belgium
| | - Emmanuelle J Javaux
- 2UR Geology - Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Annick Wilmotte
- 4InBioS - CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Denis Baurain
- 1InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| |
Collapse
|
18
|
Cornet L, Meunier L, Van Vlierberghe M, Léonard RR, Durieu B, Lara Y, Misztak A, Sirjacobs D, Javaux EJ, Philippe H, Wilmotte A, Baurain D. Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLoS One 2018; 13:e0200323. [PMID: 30044797 PMCID: PMC6059444 DOI: 10.1371/journal.pone.0200323] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
Collapse
Affiliation(s)
- Luc Cornet
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Loïc Meunier
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Mick Van Vlierberghe
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Raphaël R. Léonard
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- InBioS–CIP, Macromolecular Crystallography, University of Liège, Liège, Belgium
| | - Benoit Durieu
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Agnieszka Misztak
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- Intercollegiate Faculty of Biotechnology UG-MUG, Gdansk, Poland
| | - Damien Sirjacobs
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Emmanuelle J. Javaux
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, Moulis, France
| | - Annick Wilmotte
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- * E-mail:
| |
Collapse
|
19
|
Callejas C, Azziz G, Souza EM, Gill PR, Batista S. Prokaryotic diversity in four microbial mats on the Fildes Peninsula, King George Island, maritime Antarctica. Polar Biol 2018. [DOI: 10.1007/s00300-018-2256-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
20
|
Pessi IS, Lara Y, Durieu B, Maalouf PDC, Verleyen E, Wilmotte A. Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS Microbiol Ecol 2018; 94:4935156. [DOI: 10.1093/femsec/fiy042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Igor S Pessi
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Yannick Lara
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Benoit Durieu
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Pedro de C Maalouf
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Elie Verleyen
- Research Group Protistology and Aquatic Ecology, Department of Biology, Ghent University, Campus Sterre, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Annick Wilmotte
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| |
Collapse
|
21
|
Prieto-Barajas CM, Valencia-Cantero E, Santoyo G. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
22
|
Tahon G, Willems A. Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica. Syst Appl Microbiol 2017; 40:357-369. [DOI: 10.1016/j.syapm.2017.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/24/2022]
|
23
|
González-Rocha G, Muñoz-Cartes G, Canales-Aguirre CB, Lima CA, Domínguez-Yévenes M, Bello-Toledo H, Hernández CE. Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective. PLoS One 2017. [PMID: 28632790 PMCID: PMC5478107 DOI: 10.1371/journal.pone.0179390] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.
Collapse
Affiliation(s)
- Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Gabriel Muñoz-Cartes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristian B. Canales-Aguirre
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue 6 km, Puerto Montt, Chile
| | - Celia A. Lima
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristián E. Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- * E-mail:
| |
Collapse
|
24
|
Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep 2017; 7:46160. [PMID: 28397816 PMCID: PMC5387419 DOI: 10.1038/srep46160] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 01/07/2023] Open
Abstract
The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
Collapse
Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T Visscher
- Department of Marine Sciences, University of Connecticut, USA.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Richard Allen White
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | | | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| |
Collapse
|
25
|
Freshwater diatom biogeography and the genus Luticola: an extreme case of endemism in Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2090-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
26
|
Van Horn DJ, Wolf CR, Colman DR, Jiang X, Kohler TJ, McKnight DM, Stanish LF, Yazzie T, Takacs-Vesbach CD. Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw148. [PMID: 27495241 DOI: 10.1093/femsec/fiw148] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2016] [Indexed: 12/26/2022] Open
Abstract
Microbial consortia dominate glacial meltwater streams from polar regions, including the McMurdo Dry Valleys (MDV), where they thrive under physiologically stressful conditions. In this study, we examined microbial mat types and sediments found in 12 hydrologically diverse streams to describe the community diversity and composition within and across sites. Sequencing of the 16S rRNA gene from 129 samples revealed ∼24 000 operational taxonomic units (<97% DNA similarity), making streams the most biodiverse habitat in the MDV. Principal coordinate analyses revealed significant but weak clustering by mat type across all streams (ANOSIM R-statistic = 0.28) but stronger clustering within streams (ANOSIM R-statistic from 0.28 to 0.94). Significant relationships (P < 0.05) were found between bacterial diversity and mat ash-free dry mass, suggesting that diversity is related to the hydrologic regimes of the various streams, which are predictive of mat biomass. However, correlations between stream chemistry and community members were weak, possibly reflecting the importance of internal processes and hydrologic conditions. Collectively, these results suggest that localized conditions dictate bacterial community composition of the same mat types and sediments from different streams, and while MDV streams are hotspots of biodiversity in an otherwise depauperate landscape, controls on community structure are complex and site specific.
Collapse
Affiliation(s)
- David J Van Horn
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Caitlin R Wolf
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Daniel R Colman
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Xiaoben Jiang
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Prague 2, Prague, Czech Republic
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA
| | - Lee F Stanish
- National Ecological Observatory Network, 1685 38th Street, Boulder, CO, 80301
| | - Terrill Yazzie
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | | |
Collapse
|
27
|
|
28
|
Archer SDJ, McDonald IR, Herbold CW, Lee CK, Niederberger TS, Cary C. Temporal, regional and geochemical drivers of microbial community variation in the melt ponds of the Ross Sea region, Antarctica. Polar Biol 2016. [DOI: 10.1007/s00300-015-1780-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
29
|
Chong CW, Pearce DA, Convey P. Emerging spatial patterns in Antarctic prokaryotes. Front Microbiol 2015; 6:1058. [PMID: 26483777 PMCID: PMC4588704 DOI: 10.3389/fmicb.2015.01058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
Collapse
Affiliation(s)
- Chun-Wie Chong
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur Malaysia ; National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia
| | - David A Pearce
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne UK ; University Centre in Svalbard, Longyearbyen Norway ; British Antarctic Survey, Cambridge UK
| | - Peter Convey
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; British Antarctic Survey, Cambridge UK
| |
Collapse
|
30
|
Puja G, Jyoti V. Culturable bacterial diversity and hydrolytic enzymes from drass, a cold desert in India. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajmr2015.7424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
31
|
Archer SDJ, McDonald IR, Herbold CW, Lee CK, Cary CS. Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds. Front Microbiol 2015; 6:485. [PMID: 26074890 PMCID: PMC4444838 DOI: 10.3389/fmicb.2015.00485] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 05/03/2015] [Indexed: 11/13/2022] Open
Abstract
The numerous perennial meltwater ponds distributed throughout Antarctica represent diverse and productive ecosystems central to the ecological functioning of the surrounding ultra oligotrophic environment. The dominant taxa in the pond benthic communities have been well described however, little is known regarding their regional dispersal and local drivers to community structure. The benthic microbial communities of 12 meltwater ponds in the McMurdo Sound of Antarctica were investigated to examine variation between pond microbial communities and their biogeography. Geochemically comparable but geomorphologically distinct ponds were selected from Bratina Island (ice shelf) and Miers Valley (terrestrial) (<40 km between study sites), and community structure within ponds was compared using DNA fingerprinting and pyrosequencing of 16S rRNA gene amplicons. More than 85% of total sequence reads were shared between pooled benthic communities at different locations (OTU0.05), which in combination with favorable prevailing winds suggests aeolian regional distribution. Consistent with previous findings Proteobacteria and Bacteroidetes were the dominant phyla representing over 50% of total sequences; however, a large number of other phyla (21) were also detected in this ecosystem. Although dominant Bacteria were ubiquitous between ponds, site and local selection resulted in heterogeneous community structures and with more than 45% of diversity being pond specific. Potassium was identified as the most significant contributing factor to the cosmopolitan community structure and aluminum to the location unique community based on a BEST analysis (Spearman's correlation coefficient of 0.632 and 0.806, respectively). These results indicate that the microbial communities in meltwater ponds are easily dispersed regionally and that the local geochemical environment drives the ponds community structure.
Collapse
Affiliation(s)
- Stephen D J Archer
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato Hamilton, New Zealand
| | - Ian R McDonald
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato Hamilton, New Zealand
| | - Craig W Herbold
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato Hamilton, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato Hamilton, New Zealand
| | - Craig S Cary
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato Hamilton, New Zealand
| |
Collapse
|
32
|
Venkatachalam S, Gowdaman V, Prabagaran SR. Culturable and culture-independent bacterial diversity and the prevalence of cold-adapted enzymes from the Himalayan mountain ranges of India and Nepal. MICROBIAL ECOLOGY 2015; 69:472-91. [PMID: 25204748 DOI: 10.1007/s00248-014-0476-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/28/2014] [Indexed: 05/18/2023]
Abstract
Bacterial diversity of soil samples collected from different geographical regions of Himalayan mountains was studied through culturable (13 samples) and culture-independent approaches (5 samples based on abundance of diversity indices in each ecological niche). Shannon-Wiener diversity index and total bacterial count ranged from 1.50 ± 0.1 to 2.57 ± 0.15 and 7.8 ± 1.6 × 10(5) to 30.9 ± 1.7 × 10(5) cfu ml(-1) of soil, respectively. Based on morphology and pigmentation, 406 isolates were selected by culturing in different cultivable media at various strengths and concentrations. All the strains were subjected to amplified ribosomal DNA restriction analysis and the representative isolates from each cluster were chosen for 16S rRNA gene sequence-based identification. Soil habitat in Himalayan foot hills was dominated by the genera Arthrobacter, Exiguobacterium, Bacillus, Cedecea, Erwinia, and Pseudomonas. Five 16S rRNA gene libraries from the selected five samples yielded 268 clones and were grouped into 53 phylotypes covering 25 genera including the genus of Ferribacterium, Rothia, and Wautersiella, which were reported for the first time in Himalayan tracks. Principal coordinates analysis indicates that all the clone libraries were clearly separated and found to be significantly different from each other. Further, extracellular investigation of cold-active enzymes showed activity of cellulase (23.71%), pectinase (20.24%), amylase (17.32%), phytase (13.87%), protease (12.72%), and lipase (23.71%) among the isolates. Four isolates namely Exiguobacterium mexicanum (BSa14), Exiguobacterium sibiricum (BZa11), Micrococcus antarcticus (BSb10), and Bacillus simplex (BZb3) showed multiple enzyme activity for five different types of enzymes. In addition, various genera like Exiguobacterium, Erwinia, Mycetecola, Cedecea, Pantoea, and Trichococcus have also shown novel hydrolytic enzyme activity in the Himalayan foothills.
Collapse
Affiliation(s)
- Siddarthan Venkatachalam
- Molecular Microbiology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641046, Tamil Nadu, India
| | | | | |
Collapse
|
33
|
Tam HK, Wong CMVL, Yong ST, Blamey J, González M. Multiple-antibiotic-resistant bacteria from the maritime Antarctic. Polar Biol 2015. [DOI: 10.1007/s00300-015-1671-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
34
|
Adaptational properties and applications of cold-active lipases from psychrophilic bacteria. Extremophiles 2014; 19:235-47. [PMID: 25472009 DOI: 10.1007/s00792-014-0710-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Psychrophilic microorganisms are cold-adapted with distinct properties from other thermal classes thriving in cold conditions in large areas of the earth's cold environment. Maintenance of functional membranes, evolving cold-adapted enzymes and synthesizing a range of structural features are basic adaptive strategies of psychrophiles. Among the cold-evolved enzymes are the cold-active lipases, a group of microbial lipases with inherent stability-activity-flexibility property that have engaged the interest of researchers over the years. Current knowledge regarding these cold-evolved enzymes in psychrophilic bacteria proves a display of high catalytic efficiency with low thermal stability, which is a differentiating feature with that of their mesophilic and thermophilic counterparts. Improvement strategies of their adaptive structural features have significantly benefited the enzyme industry. Based on their homogeneity and purity, molecular characterizations of these enzymes have been successful and their properties make them unique biocatalysts for various industrial and biotechnological applications. Although, strong association of lipopolysaccharides from Antarctic microorganisms with lipid hydrolases pose a challenge in their purification, heterologous expression of the cold-adapted lipases with affinity tags simplifies purification with higher yield. The review discusses these cold-evolved lipases from bacteria and their peculiar properties, in addition to their potential biotechnological and industrial applications.
Collapse
|
35
|
Tytgat B, Verleyen E, Obbels D, Peeters K, De Wever A, D’hondt S, De Meyer T, Van Criekinge W, Vyverman W, Willems A. Bacterial diversity assessment in Antarctic terrestrial and aquatic microbial mats: a comparison between bidirectional pyrosequencing and cultivation. PLoS One 2014; 9:e97564. [PMID: 24887330 PMCID: PMC4041716 DOI: 10.1371/journal.pone.0097564] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/21/2014] [Indexed: 12/26/2022] Open
Abstract
The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1–22.2%) and OTU (3.5–3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1–V2 and V3–V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity.
Collapse
Affiliation(s)
- Bjorn Tytgat
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Dagmar Obbels
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Karolien Peeters
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Aaike De Wever
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie D’hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
36
|
Convey P, Chown SL, Clarke A, Barnes DKA, Bokhorst S, Cummings V, Ducklow HW, Frati F, Green TGA, Gordon S, Griffiths HJ, Howard-Williams C, Huiskes AHL, Laybourn-Parry J, Lyons WB, McMinn A, Morley SA, Peck LS, Quesada A, Robinson SA, Schiaparelli S, Wall DH. The spatial structure of Antarctic biodiversity. ECOL MONOGR 2014. [DOI: 10.1890/12-2216.1] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
37
|
|
38
|
Characterization and comparison of potential denitrifiers in microbial mats from King George Island, Maritime Antarctica. Polar Biol 2013. [DOI: 10.1007/s00300-013-1440-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
39
|
Bacterial composition of soils of the Lake Wellman area, Darwin Mountains, Antarctica. Extremophiles 2013; 17:775-86. [PMID: 23820800 DOI: 10.1007/s00792-013-0560-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/18/2013] [Indexed: 10/26/2022]
Abstract
The aim of this study was to examine the bacterial composition of high latitude soils from the Darwin-Hatherton glacier region of Antarctica. Four soil pits on each of four glacial drift sheets were sampled for chemical and microbial analyses. The four drifts-Hatherton, Britannia, Danum, and Isca-ranged, respectively, from early Holocene (10 ky) to mid-Quaternary (ca 900 ky). Numbers of culturable bacteria were low, with highest levels detected in soils from the younger Hatherton drift. DNA was extracted and 16S rRNA gene clone libraries prepared from samples below the desert pavement for each of the four drift sheets. Between 31 and 262 clones were analysed from each of the Hatherton, Britannia, and Danum drifts. Bacterial sequences were dominated by members of the phyla Deinococcus-Thermus, Actinobacteria, and Bacteroidetes. Culturable bacteria, including some that clustered with soil clones (e.g., members of the genera Arthrobacter, Adhaeribacter, and Pontibacter), belonged to Actinobacteria and Bacteroidetes. The isolated bacteria are ideal model organisms for genomic and phenotypic investigations of those attributes that allow bacteria to survive and/or grow in Antarctic soils because they have close relatives that are not tolerant of these conditions.
Collapse
|
40
|
Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R. Key microbial drivers in Antarctic aquatic environments. FEMS Microbiol Rev 2013; 37:303-35. [DOI: 10.1111/1574-6976.12007] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/11/2012] [Accepted: 10/01/2012] [Indexed: 11/27/2022] Open
|