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Dieser M, Smith HJ, Foreman CM. Seven genome sequences of airborne, bacterial isolates from Antarctica. Microbiol Resour Announc 2024; 13:e0112923. [PMID: 38747591 PMCID: PMC11237742 DOI: 10.1128/mra.01129-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/24/2024] [Indexed: 06/12/2024] Open
Abstract
Ice-covered and remote landscapes in the McMurdo Dry Valleys, Antarctica, are likely seeded by aeolian transport of biological material from ice-free local or distant environments. Here, we report the genome sequences of seven bacteria isolated from aerosols collected on top of two dry valley glaciers.
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Affiliation(s)
- Markus Dieser
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Christine M Foreman
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
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Segawa T, Takahashi A, Kokubun N, Ishii S. Spread of antibiotic resistance genes to Antarctica by migratory birds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171345. [PMID: 38447711 DOI: 10.1016/j.scitotenv.2024.171345] [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: 11/03/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Recent studies have highlighted the presence of antibiotic resistance genes (ARGs) in Antarctica, which are typically indicative of human activity. However, these studies have concentrated in the Antarctic Peninsula region, and relatively less is known about ARG prevalence in East Antarctica, where human activity levels are lower compared to the Antarctic Peninsula. In addition, the mechanisms of ARG transmission to Antarctica through natural or anthropogenic pathways remain unclear. In this study, we analyzed the fecal samples of Adélie penguins and South polar skuas by using high-throughput sequencing and microfluidic quantitative PCR to detect potential pathogens and ARGs at their breeding colonies near Syowa Station in East Antarctica. These results revealed the presence of several potential pathogens in the fecal matter of both bird species. However, the HF183 marker, which indicates human fecal contamination, was absent in all samples, as well as seawater sampled near the breeding colonies. This suggests that the human fecal contamination was negligible in our study area. In addition to pathogens, we found a significant number of ARGs and metal resistance genes in the feces of both Adélie penguins and South polar skuas, with higher detection rates in skuas than in penguins. To better understand how these birds acquire and transmit these genes, we analyzed the migratory patterns of Adélie penguins and South polar skuas by geolocator tracking. We found that the skuas migrate to the tropical and subtropical regions of the Indian Ocean during the austral winter. On the other hand, Adélie penguins exhibited a more localized migration pattern, mainly staying within Antarctic waters. Because the Indian Ocean is considered one of the major reservoirs of ARGs, South polar skuas might be exposed to ARGs during their winter migration and transfer these genes to Antarctica.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Akinori Takahashi
- National Institute of Polar Research, Tachikawa, Tokyo, Japan; Department of Polar Science, The Graduate University for Advanced Studies, Tachikawa, Tokyo, Japan
| | - Nobuo Kokubun
- National Institute of Polar Research, Tachikawa, Tokyo, Japan; Department of Polar Science, The Graduate University for Advanced Studies, Tachikawa, Tokyo, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
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Varliero G, Lebre PH, Adams B, Chown SL, Convey P, Dennis PG, Fan D, Ferrari B, Frey B, Hogg ID, Hopkins DW, Kong W, Makhalanyane T, Matcher G, Newsham KK, Stevens MI, Weigh KV, Cowan DA. Biogeographic survey of soil bacterial communities across Antarctica. MICROBIOME 2024; 12:9. [PMID: 38212738 PMCID: PMC10785390 DOI: 10.1186/s40168-023-01719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Pedro H Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton, VA, 3800, Australia
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Paul G Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, 2052, Australia
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, Scotland, UK
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gwynneth Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark I Stevens
- Securing Antarctica's Environmental Future, Earth and Biological Sciences, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katherine V Weigh
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa.
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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [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] [Indexed: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland. Microorganisms 2023; 11:microorganisms11030665. [PMID: 36985243 PMCID: PMC10057085 DOI: 10.3390/microorganisms11030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.
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Perera LJ, Cockell CS. Dispersion of Bacteria by Low-Pressure Boiling: Life Detection in Enceladus' Plume Material. ASTROBIOLOGY 2023; 23:269-279. [PMID: 36689196 DOI: 10.1089/ast.2022.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The plume of Enceladus is thought to originate from the dispersion of a liquid source beneath the icy crust. Cryovolcanic activity on Enceladus may present a direct way of accessing material originating from the potentially habitable subsurface ocean. One way to test the hypothesis of whether life is present within the ocean of Enceladus would be to investigate the plume material for the presence of microbial life. In this study, we investigated the entrainment of Bacillus subtilis within Enceladus-like fluids under boiling conditions caused by exposure of the fluids to low pressure. We show that boiling, associated with exposure of a fluid to low pressure, works as a mechanism for dispersing bacteria in Enceladus plume-like environments. Exposure of Enceladus-type fluids (0.01-0.1 molal Na2CO3 and 0.05-0.2 molal NaCl) to low pressure (5 mbar) results in the dispersion of bacteria in droplets that evaporate to produce particles of salt. We find that, for particles with radius (r) ≤ 10 μm, the number of dispersed particles containing cells was between 7.7% and 10.9%. However, for larger particles 10 < r ≤ 50 μm, 64.4% and 56.4% contained cells for lower and upper end-member solutions, respectively. Our results suggest that the gravity-induced size sorting of plume particles will result in plume deposits closer to the vent source containing a larger volume of biological material than within the plume. If life is present in the ocean of Enceladus, we would expect that it would be effectively entrained and deposited on the surface; therefore, it would be accessible with a surface-lander-based instrument.
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Affiliation(s)
- L J Perera
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, UK
| | - C S Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, UK
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Depta J, Niedźwiedzka-Rystwej P. The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem. Infect Drug Resist 2023; 16:1979-1995. [PMID: 37034396 PMCID: PMC10081531 DOI: 10.2147/idr.s369023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/02/2022] [Indexed: 04/11/2023] Open
Abstract
The increasing prevalence of antibiotic resistance is a global problem in human and animal health. This leads to a reduction in the therapeutic effectiveness of the measures used so far and to the limitation of treatment options, which may pose a threat to human health and life. The problem of phenomenon of antibiotic resistance affects more and more the polar regions. This is due to the increase in tourist traffic and the number of people staying at research stations, unmodernised sewage systems in inhabited areas, as well as the migration of animals or the movement of microplastics, which may contain resistant bacteria. Research shows that the presence of antibiotic resistance genes is more dominant in zones of human and wildlife influence than in remote areas. In a polluted environment, there is evidence of a direct correlation between human activity and the spread and survival of antibiotic-resistant bacteria. Attention should be paid to the presence of resistance to synthetic and semi-synthetic antibiotics in the polar regions, which is likely to be correlated with human presence and activity, and possible steps to be taken. We need to understand many more aspects of this, such as bacterial epigenetics and environmental stress, in order to develop effective strategies for minimizing the spread of antibiotic resistance genes. Studying the diversity and abundance of antibiotic resistance genes in regions with less anthropogenic activity could provide insight into the diversity of primary genes and explain the historical evolution of antibiotic resistance.
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Affiliation(s)
- Julia Depta
- Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland
| | - Paulina Niedźwiedzka-Rystwej
- Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland
- Correspondence: Paulina Niedźwiedzka-Rystwej, Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland, Tel +48 91 444 15 15, Email
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Malard LA, Avila-Jimenez ML, Schmale J, Cuthbertson L, Cockerton L, Pearce DA. Aerobiology over the Southern Ocean - Implications for bacterial colonization of Antarctica. ENVIRONMENT INTERNATIONAL 2022; 169:107492. [PMID: 36174481 DOI: 10.1016/j.envint.2022.107492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/27/2022] [Accepted: 08/27/2022] [Indexed: 06/16/2023]
Abstract
Parts of the Antarctic are experiencing dramatic ecosystem change due to rapid and record warming, which may weaken biogeographic boundaries and modify dispersal barriers, increasing the risk of biological invasions. In this study, we collected air samples from 100 locations around the Southern Ocean to analyze bacterial biodiversity in the circumpolar air around the Antarctic continent, as understanding dispersal processes is paramount to assessing the risks of microbiological invasions. We also compared the Southern Ocean air bacterial biodiversity to non-polar ecosystems to identify the potential origin of these Southern Ocean air microorganisms. The bacterial diversity in the air had both local and global origins and presented low richness overall but high heterogeneity, compatible with a scenario whereby samples are composed of a suite of different species in very low relative abundances. Only 4% of Amplicon Sequence Variants (ASVs) were identified in both polar and non-polar air masses, suggesting that the polar air mass over the Southern Ocean can act as a selective dispersal filter. Furthermore, both microbial diversity and community structure both varied significantly with meteorological data, suggesting that regional bacterial biodiversity could be sensitive to changes in weather conditions, potentially altering the existing pattern of microbial deposition in the Antarctic.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | | | - Julia Schmale
- Extreme Environments Research Laboratory, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Lewis Cuthbertson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom
| | - Luke Cockerton
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom
| | - David A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom; British Antarctic Survey, Natural Environemnt Research Council, High Cross, Madingley Road, Cambridge BCB3 0ET, United Kingdom.
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Qi J, Ji M, Wang W, Zhang Z, Liu K, Huang Z, Liu Y. Effect of Indian monsoon on the glacial airborne bacteria over the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154980. [PMID: 35378188 DOI: 10.1016/j.scitotenv.2022.154980] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The glacier of the Tibetan Plateau (TP) is influenced by the Indian monsoon and continental westerlies. Wind flow can carry a variety of bacteria and disperse across the TP. Once these bacteria are colonized to the glacier surface, they could affect the biogeochemical cycle of the glacial ecosystems. However, very few studies have focused on the relationships between these airborne bacteria and atmospheric circulation over glaciers of the TP. Here we studied the diversity, taxonomic composition, and community structure of airborne bacteria on six TP glaciers using 16S rRNA gene sequencing. The results revealed an increase in the airborne bacterial diversity over the glaciers under the effect of the Indian monsoon. Airborne bacteria were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while relative abundances of Bacteroidetes and Firmicutes were significantly higher under the influence of the Indian monsoon in the southern and central of the TP, respectively. Moreover, significantly different airborne bacterial community structures were observed over glaciers under the influence of the Indian monsoon, which could be explained by the increased community stochasticity. In addition, the Indian monsoon increases the diversity and relative abundance of potential pathogens, which includes the most notorious bacteria such as Pseudomonas fluorescens, Staphylococcus aureus, and Clostridium butyricum. Our results revealed for the first time that atmospheric circulation influences the composition of airborne bacteria over the glaciers on the TP, this may provide critical insights into the distinct microbial community structure and function in glaciers across the TP.
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Affiliation(s)
- Jing Qi
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Wenqiang Wang
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; School of Life Sciences, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
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11
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Xue Y, Wang L, Zhang Y, Zhao Y, Liu Y. Air pollution: A culprit of lung cancer. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128937. [PMID: 35452993 DOI: 10.1016/j.jhazmat.2022.128937] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Air pollution is a global health problem, especially in the context of rapid economic development and the expansion of urbanization. Herein, we discuss the harmful effects of outdoor and indoor pollution on the lungs. Ambient particulate matters (PMs) from industrial and vehicle exhausts is associated with lung cancer. Workers exposed to asbestos, polycyclic aromatic hydrocarbons (PAHs), and toxic metals are also likely to develop lung cancer. Indoors, cooking fumes, second-hand smoke, and radioactive products from house decoration materials play roles in the development of lung cancer. Bacteria and viruses can also be detrimental to health and are important risk factors in lung inflammation and cancer. Specific effects of lung cancer caused by air pollution are discussed in detail, including inflammation, DNA damage, and epigenetic regulation. In addition, advanced materials for personal protection, as well as the current government policies to prevent air pollution, are summarized. This review provides a basis for future research on the relationship between lung cancer and air pollution.
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Affiliation(s)
- Yueguang Xue
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, PR China; Henan Institute of advanced technology, Zhengzhou University, Zhengzhou 450052, PR China
| | - Liuxiang Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, PR China; Henan Institute of advanced technology, Zhengzhou University, Zhengzhou 450052, PR China
| | - Yiming Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, PR China; Henan Institute of advanced technology, Zhengzhou University, Zhengzhou 450052, PR China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, PR China; GBA National Institute for Nanotechnology Innovation, Guangzhou, Guangdong 510700, PR China.
| | - Ying Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, PR China; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, PR China; GBA National Institute for Nanotechnology Innovation, Guangzhou, Guangdong 510700, PR China.
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12
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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13
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Malard LA, Pearce DA. Bacterial Colonisation: From Airborne Dispersal to Integration Within the Soil Community. Front Microbiol 2022; 13:782789. [PMID: 35615521 PMCID: PMC9125085 DOI: 10.3389/fmicb.2022.782789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
The deposition of airborne microorganisms into new ecosystems is the first stage of colonisation. However, how and under what circumstances deposited microorganisms might successfully colonise a new environment is still unclear. Using the Arctic snowpack as a model system, we investigated the colonisation potential of snow-derived bacteria deposited onto Arctic soils during and after snowmelt using laboratory-based microcosm experiments to mimic realistic environmental conditions. We tested different melting rate scenarios to evaluate the influence of increased precipitation as well as the influence of soil pH on the composition of bacterial communities and on the colonisation potential. We observed several candidate colonisations in all experiments; with a higher number of potentially successful colonisations in acidoneutral soils, at the average snowmelt rate measured in the Arctic. While the higher melt rate increased the total number of potentially invading bacteria, it did not promote colonisation (snow ASVs identified in the soil across multiple sampling days and still present on the last day). Instead, most potential colonists were not identified by the end of the experiments. On the other hand, soil pH appeared as a determinant factor impacting invasion and subsequent colonisation. In acidic and alkaline soils, bacterial persistence with time was lower than in acidoneutral soils, as was the number of potentially successful colonisations. This study demonstrated the occurrence of potentially successful colonisations of soil by invading bacteria. It suggests that local soil properties might have a greater influence on the colonisation outcome than increased precipitation or ecosystem disturbance.
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Affiliation(s)
- Lucie A. Malard
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- *Correspondence: Lucie A. Malard,
| | - David A. Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
- David A. Pearce,
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14
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Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica. Appl Environ Microbiol 2022; 88:e0031522. [PMID: 35499326 DOI: 10.1128/aem.00315-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.
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15
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Hawkins JH, Zeglin LH. Microbial Dispersal, Including Bison Dung Vectored Dispersal, Increases Soil Microbial Diversity in a Grassland Ecosystem. Front Microbiol 2022; 13:825193. [PMID: 35432281 PMCID: PMC9009311 DOI: 10.3389/fmicb.2022.825193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities display biogeographical patterns that are driven by local environmental conditions and dispersal limitation, but the relative importance of underlying dispersal mechanisms and their consequences on community structure are not well described. High dispersal rates can cause soil microbial communities to become more homogenous across space and therefore it is important to identify factors that promote dispersal. This study experimentally manipulated microbial dispersal within different land management treatments at a native tallgrass prairie site, by changing the relative openness of soil to dispersal and by simulating vector dispersal via bison dung addition. We deployed experimental soil bags with mesh open or closed to dispersal, and placed bison dung over a subset of these bags, to areas with three different land managements: active bison grazing and annual fire, annual fire but no bison grazing, and no bison grazing with infrequent fire. We expected microbial dispersal to be highest in grazed and burned environments, and that the addition of dung would consistently increase overall microbial richness and lead to homogenization of communities over time. Results show that dispersal rates, as the accumulation of taxa over the course of the 3-month experiment, increase taxonomic richness similarly in all land management treatments. Additionally, bison dung seems to be serving as a dispersal and homogenization vector, based on the consistently higher taxon richness and increased community similarity across contrasting grazing and fire treatments when dung is added. This finding also points to microbial dispersal as an important function that herbivores perform in grassland ecosystems, and in turn, as a function that was lost at a continental scale following bison extermination across the Great Plains of North America in the nineteenth century. This study is the first to detect that dispersal and vector dispersal by grazing mammals promote grassland soil microbial diversity and affect microbial community composition.
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Affiliation(s)
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, KS, United States
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16
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Yan D, Zhang T, Bai JL, Su J, Zhao LL, Wang H, Fang XM, Zhang YQ, Liu HY, Yu LY. Isolation, Characterization, and Antimicrobial Activity of Bacterial and Fungal Representatives Associated With Particulate Matter During Haze and Non-haze Days. Front Microbiol 2022; 12:793037. [PMID: 35087495 PMCID: PMC8787346 DOI: 10.3389/fmicb.2021.793037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 12/07/2022] Open
Abstract
Particulate matter (PM) has been a threat to the environment and public health in the metropolises of developing industrial countries such as Beijing. The microorganisms associated with PM have an impact on human health if they are exposed to the respiratory tract persistently. There are few reports on the microbial resources collected from PM and their antimicrobial activities. In this study, we greatly expanded the diversity of available commensal organisms by collecting 1,258 bacterial and 456 fungal isolates from 63 PM samples. A total of 77 bacterial genera and 35 fungal genera were included in our pure cultures, with Bacillus as the most prevalent cultured bacterial genus, Aspergillus, and Penicillium as the most prevalent fungal ones. During heavy-haze days, the numbers of colony-forming units (CFUs) and isolates of bacteria and fungi were decreased. Bacillus, Paenibacillus, and Chaetomium were found to be enriched during haze days, while Kocuria, Microbacterium, and Penicillium were found to be enriched during non-haze days. Antimicrobial activity against common pathogens have been found in 40 bacterial representatives and 1 fungal representative. The collection of airborne strains will provide a basis to greatly increase our understanding of the relationship between bacteria and fungi associated with PM and human health.
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Affiliation(s)
- Dong Yan
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Tao Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing-Lin Bai
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Su
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Li Zhao
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Wang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao-Mei Fang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu-Qin Zhang
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong-Yu Liu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Yan Yu
- China Pharmaceutical Culture Collection, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Millar JL, Bagshaw EA, Edwards A, Poniecka EA, Jungblut AD. Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera. Front Microbiol 2021; 12:738451. [PMID: 34899626 PMCID: PMC8660574 DOI: 10.3389/fmicb.2021.738451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a "core group" of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.
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Affiliation(s)
- Jasmin L Millar
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Elizabeth A Bagshaw
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, United Kingdom
| | - Ewa A Poniecka
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Anne D Jungblut
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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18
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Salawu-Rotimi A, Lebre PH, Vos HC, Fister W, Kuhn N, Eckardt FD, Cowan DA. Gone with the Wind: Microbial Communities Associated with Dust from Emissive Farmlands. MICROBIAL ECOLOGY 2021; 82:859-869. [PMID: 33656686 DOI: 10.1007/s00248-021-01717-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Dust is a major vehicle for the dispersal of microorganisms across the globe. While much attention has been focused on microbial dispersal in dust plumes from major natural dust sources, very little is known about the fractionation processes that select for the "dust microbiome." The recent identification of highly emissive, agricultural land dust sources in South Africa has provided the opportunity to study the displacement of microbial communities through dust generation and transport. In this study, we aimed to document the microbial communities that are carried in the dust from one of South Africa's most emissive locations, and to investigate the selective factors that control the partitioning of microbial communities from soil to dust. For this purpose, dust samples were generated at different emission sources using a Portable In-Situ Wind Erosion Lab (PI-SWERL), and the taxonomic composition of the resulting microbiomes was compared with the source soils. Dust emission processes resulted in the clear fractionation of the soil bacterial community, where dust samples were significantly enriched in spore-forming taxa. Conversely, little fractionation was observed in the soil fungal communities, such that the dust fungal fingerprint could be used to identify the source soil. Dust microbiomes were also found to vary according to the emission source, suggesting that land use significantly affected the structure and fractionation of microbial communities transported in dust plumes. In addition, several potential biological allergens of fungal origin were detected in the dust microbiomes, highlighting the potential detrimental effects of dust plumes emitted in South Africa. This study represents the first description of the fractionation of microbial taxa occurring at the source of dust plumes and provides a direct link between land use and its impact on the dust microbiome.
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Affiliation(s)
- Adeola Salawu-Rotimi
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa.
| | - Heleen Cornelia Vos
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Wolfgang Fister
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Nikolaus Kuhn
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Frank D Eckardt
- Department of Environmental and Geographical Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
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19
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Miaow K, Lacap-Bugler D, Buckley HL. Identifying optimal bioinformatics protocols for aerosol microbial community data. PeerJ 2021; 9:e12065. [PMID: 34703658 PMCID: PMC8487624 DOI: 10.7717/peerj.12065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Microbes are fundamental to Earth’s ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next generation sequencing (NGS) data generated from these molecular approaches; however, there are numerous options and choices in the process. These choices can markedly affect key aspects of the data output including relative abundances, diversity, and taxonomy. Bioaerosol samples have relatively little DNA, and often contain novel and proportionally high levels of contaminant organisms, that are difficult to identify. Therefore, bioinformatics choices are of crucial importance. A bioaerosol dataset for bacteria and fungi based on the 16S rRNA gene (16S) and internal transcribed spacer (ITS) DNA sequencing from parks in the metropolitan area of Auckland, Aotearoa New Zealand was used to develop a process for determining the bioinformatics pipeline that would maximize the data amount and quality generated. Two popular tools (Dada2 and USEARCH) were compared for amplicon sequence variant (ASV) inference and generation of an ASV table. A scorecard was created and used to assess multiple outputs and make systematic choices about the most suitable option. The read number and ASVs were assessed, alpha diversity was calculated (Hill numbers), beta diversity (Bray–Curtis distances), differential abundance by site and consistency of ASVs were considered. USEARCH was selected, due to higher consistency in ASVs identified and greater read counts. Taxonomic assignment is highly dependent on the taxonomic database used. Two popular taxonomy databases were compared in terms of number and confidence of assignments, and a combined approach developed that uses information in both databases to maximize the number and confidence of taxonomic assignments. This approach increased the assignment rate by 12–15%, depending on amplicon and the overall assignment was 77% for bacteria and 47% for fungi. Assessment of decontamination using “decontam” and “microDecon” was performed, based on review of ASVs identified as contaminants by each and consideration of the probability of them being legitimate members of the bioaerosol community. For this example, “microDecon’s” subtraction approach for removing background contamination was selected. This study demonstrates a systematic approach to determining the optimal bioinformatics pipeline using a multi-criteria scorecard for microbial bioaerosol data. Example code in the R environment for this data processing pipeline is provided.
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Affiliation(s)
- Katie Miaow
- School of Science, Auckland University of Technology, Auckland, Auckland, New Zealand
| | | | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, Auckland, New Zealand
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20
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Rosa LH, Pinto OHB, Convey P, Carvalho-Silva M, Rosa CA, Câmara PEAS. DNA Metabarcoding to Assess the Diversity of Airborne Fungi Present over Keller Peninsula, King George Island, Antarctica. MICROBIAL ECOLOGY 2021; 82:165-172. [PMID: 33161522 DOI: 10.1007/s00248-020-01627-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 05/06/2023]
Abstract
We assessed fungal diversity present in air samples obtained from King George Island, Antarctica, using DNA metabarcoding through high-throughput sequencing. We detected 186 fungal amplicon sequence variants (ASVs) dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, and Chytridiomycota. Fungi sp. 1, Agaricomycetes sp. 1, Mortierella parvispora, Mortierella sp. 2, Penicillium sp., Pseudogymnoascus roseus, Microdochium lycopodinum, Mortierella gamsii, Arrhenia sp., Cladosporium sp., Mortierella fimbricystis, Moniliella pollinis, Omphalina sp., Mortierella antarctica, and Pseudogymnoascus appendiculatus were the most dominant ASVs. In addition, several ASVs could only be identified at higher taxonomic levels and may represent previously unknown fungi and/or new records for Antarctica. The fungi detected in the air displayed high indices of diversity, richness, and dominance. The airborne fungal diversity included saprophytic, mutualistic, and plant and animal opportunistic pathogenic taxa. The diversity of taxa detected reinforces the hypothesis that the Antarctic airspora includes fungal propagules of both intra- and inter-continental origin. If regional Antarctic environmental conditions ameliorate further in concert with climate warming, these fungi might be able to reactivate and colonize different Antarctic ecosystems, with as yet unknown consequences for ecosystem function in Antarctica. Further aeromycological studies are necessary to understand how and from where these fungi arrive and move within Antarctica and if environmental changes will encourage the development of non-native fungal species in Antarctica.
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Affiliation(s)
- Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, CB3 0ET, Cambridge, UK
| | | | - Carlos Augusto Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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21
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Canini F, Geml J, Buzzini P, Turchetti B, Onofri S, D’Acqui LP, Ripa C, Zucconi L. Growth Forms and Functional Guilds Distribution of Soil Fungi in Coastal Versus Inland Sites of Victoria Land, Antarctica. BIOLOGY 2021; 10:biology10040320. [PMID: 33920495 PMCID: PMC8070035 DOI: 10.3390/biology10040320] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022]
Abstract
In Victoria Land, Antarctica, ice-free areas are restricted to coastal regions and dominate the landscape of the McMurdo Dry Valleys. These two environments are subjected to different pressures that determine the establishment of highly adapted fungal communities. Within the kingdom of fungi, filamentous, yeasts and meristematic/microcolonial growth forms on one side and different lifestyles on the other side may be considered adaptive strategies of particular interest in the frame of Antarctic constraints. In this optic, soil fungal communities from both coastal and Dry Valleys sites, already characterized thorough ITS1 metabarcoding sequencing, have been compared to determine the different distribution of phyla, growth forms, and lifestyles. Though we did not find significant differences in the richness between the two environments, the communities were highly differentiated and Dry Valleys sites had a higher evenness compared to coastal ones. Additionally, the distribution of different growth forms and lifestyles were well differentiated, and their diversity and composition were likely influenced by soil abiotic parameters, among which soil granulometry, pH, P, and C contents were the potential main determinants.
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Affiliation(s)
- Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
- Correspondence: ; Tel.: +39-0761357138
| | - József Geml
- Biodiversity Dynamics Research Group, Naturalis Biodiversity Center, 2300 RA Leiden, The Netherlands;
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, H-3300 Eger, Hungary
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (P.B.); (B.T.)
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (P.B.); (B.T.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
| | - Luigi Paolo D’Acqui
- Research Institute of Terrestrial Ecosystems, National Research Council of Italy (IRET-CNR), 50019 Sesto Fiorentino, Italy;
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (S.O.); (C.R.); (L.Z.)
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22
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Rosa LH, Pinto OHB, Šantl-Temkiv T, Convey P, Carvalho-Silva M, Rosa CA, Câmara PEAS. DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica. Sci Rep 2020; 10:21793. [PMID: 33311553 PMCID: PMC7733504 DOI: 10.1038/s41598-020-78630-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/19/2020] [Indexed: 01/04/2023] Open
Abstract
We assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.
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Affiliation(s)
- Luiz Henrique Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil.
| | | | - Tina Šantl-Temkiv
- Department of Bioscience, Aarhus University, Building 1540 Office 124, 116 Ny Munkegade, 8000, Aarhus C, Denmark
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | | | - Carlos Augusto Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, P.O. Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil
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Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC. Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica. FEMS Microbiol Ecol 2020; 96:5815075. [PMID: 32239205 DOI: 10.1093/femsec/fiaa042] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.
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Affiliation(s)
- Eric M Bottos
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Daniel C Laughlin
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Craig W Herbold
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Charles K Lee
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Ian R McDonald
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - S Craig Cary
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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24
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Wagner M, Bathke AC, Cary SC, Green TGA, Junker RR, Trutschnig W, Ruprecht U. Myco- and photobiont associations in crustose lichens in the McMurdo Dry Valleys (Antarctica) reveal high differentiation along an elevational gradient. Polar Biol 2020. [DOI: 10.1007/s00300-020-02754-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AbstractClimatically extreme regions such as the polar deserts of the McMurdo Dry Valleys (78° S) in Continental Antarctica are key areas for a better understanding of changes in ecosystems. Therefore, it is particularly important to analyze and communicate current patterns of biodiversity in these sensitive areas, where precipitation mostly occurs in form of snow and liquid water is rare. Humidity provided by dew, clouds, and fog are the main water sources, especially for rock-dwelling crustose lichens as one of the most common vegetation-forming organisms. We investigated the diversity and interaction specificity of myco-/photobiont associations of 232 crustose lichen specimens, collected along an elevational gradient (171–959 m a.s.l.) within the McMurdo Dry Valleys. The mycobiont species and photobiont OTUs were identified by using three markers each (nrITS, mtSSU, RPB1, and nrITS, psbJ-L, COX2). Elevation, positively associated with water availability, turned out to be the key factor explaining most of the distribution patterns of the mycobionts. Pairwise comparisons showed Lecidea cancriformis and Rhizoplaca macleanii to be significantly more common at higher elevations and Carbonea vorticosa and Lecidea polypycnidophora at lower elevations. Lichen photobionts were dominated by the globally distributed Trebouxia OTU, Tr_A02 which occurred at all habitats. Network specialization resulting from myco-/photobiont bipartite network structure varied with elevation and associated abiotic factors. Along an elevational gradient, the spatial distribution, diversity, and genetic variability of the lichen symbionts appear to be mainly influenced by improved water relations at higher altitudes.
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25
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Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing. Sci Rep 2020; 10:12406. [PMID: 32699373 PMCID: PMC7376176 DOI: 10.1038/s41598-020-68933-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/03/2020] [Indexed: 02/01/2023] Open
Abstract
To study the size-resolved characteristics of airborne bacterial community composition, diversity, and abundance, outdoor aerosol samples were analysed by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing with Illumina MiSeq. The samples were collected using size-resolved samplers between August and October 2016, at a suburban site in Toyama City and an urban site in Yokohama City, Japan. The bacterial communities were found to be dominated by Actinobacteria, Firmicutes, and Proteobacteria. At the genus level, we found a high abundance of human skin-associated bacteria, such as Propionibacterium, Staphylococcus, and Corynebacterium, in the urban site. Whereas, a high abundance of bacteria associated with soil and plants, such as Methylobacterium and Sphingomonas, was observed in the suburban site. Furthermore, our data revealed a shift in the bacterial community structure, diversity, and abundance of total bacteria at a threshold of 1.1-µm diameter. Interestingly, we observed that Legionella spp., the causal agents of legionellosis in humans, were mainly detected in > 2.1 µm coarse particles. Our data indicate that local environmental factors including built environments could influence the outdoor airborne bacterial community at each site. These results provide a basis for understanding the size-resolved properties of bacterial community composition, diversity, and abundance in outdoor aerosol samples and their potential influence on human health.
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26
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Trout-Haney JV, Heindel RC, Virginia RA. Picocyanobacterial cells in near-surface air above terrestrial and freshwater substrates in Greenland and Antarctica. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:296-305. [PMID: 32134187 DOI: 10.1111/1758-2229.12832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Bioaerosols are an important component of the total atmospheric aerosol load, with implications for human health, climate feedbacks and the distribution and dispersal of microbial taxa. Bioaerosols are sourced from marine, freshwater and terrestrial surfaces, with different mechanisms potentially responsible for releasing biological particles from these substrates. Little is known about the production of freshwater and terrestrial bioaerosols in polar regions. We used portable collection devices to test for the presence of picocyanobacterial aerosols above freshwater and soil substrates in the southwestern Greenland tundra and the McMurdo Dry Valleys of Antarctica. We show that picocyanobacterial cells are present in the near-surface air at concentrations ranging from 2,431 to 28,355 cells m-3 of air, with no significant differences among substrates or between polar regions. Our concentrations are lower than those measured using the same methods in temperate ecosystems. We suggest that aerosolization is an important process linking terrestrial and aquatic ecosystems in these polar environments, and that future work is needed to explore aerosolization mechanisms and taxon-specific aerosolization rates. Our study is a first step toward understanding the production of bioaerosols in extreme environments dominated by microbial life.
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Affiliation(s)
- Jessica V Trout-Haney
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, Hanover, NH, 03755
| | - Ruth C Heindel
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO
| | - Ross A Virginia
- Environmental Studies Program and Institute of Arctic Studies, Dartmouth College, Hanover, NH, 03755
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Marone A, Kane CT, Mbengue M, Jenkins GS, Niang DN, Drame MS, Gernand JM. Characterization of Bacteria on Aerosols From Dust Events in Dakar, Senegal, West Africa. GEOHEALTH 2020; 4:e2019GH000216. [PMID: 32490303 PMCID: PMC7262684 DOI: 10.1029/2019gh000216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/01/2020] [Accepted: 04/15/2020] [Indexed: 05/31/2023]
Abstract
We identify bacteria types on collected dust samples in Dakar Senegal, a region that experiences frequent Saharan dust events. We use classical techniques to identify bacteria types from dust samples. Seventy-seven bacteria types are identified from samples collected by spatula and the QuickTake® 30 air sampling pump. The dominant groups in the first batch of 51 bacteria (collected via deposition) are Micrococcus (33.33%), Bacillus (13.73%), Kytococcus (11.76%), Pseudomonas (9.80%), and Burkholderia (7.84%) and dominants in the second batch of 26 bacteria (collected with aerosol sampling vacuum pump): Pseudomonas (38.61%), Burkholderia (26.92%), Micrococcus (11.54%), and Brucella spp (7.69%). These bacteria are found in earlier studies from desert sources and can potentially cause respiratory diseases to exposed populations. Future work will use molecular methods is necessary to search for additional pathogens, including viruses on dust aerosols.
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Affiliation(s)
- Alioune Marone
- Laboratory of Applied Microbiology and Industrial Engineering, École Supériure Polytechnique (ESP)Cheikh Anta Diop UniversityDakarSenegal
| | - Coumba Touré Kane
- Laboratory of Applied Microbiology and Industrial Engineering, École Supériure Polytechnique (ESP)Cheikh Anta Diop UniversityDakarSenegal
- Institute of Health ResearchEpidemiological Surveillance and Training (IRESSEF)DiamniadioSenegal
| | - Malick Mbengue
- Laboratory of Applied Microbiology and Industrial Engineering, École Supériure Polytechnique (ESP)Cheikh Anta Diop UniversityDakarSenegal
| | - Gregory S. Jenkins
- Department of Meteorology and Atmospheric SciencePennsylvania State UniversityUniversity ParkPAUSA
| | - Demba Ndao Niang
- Laboratory for Atmospheric‐Oceanic Physics Simeon Fongang, École Supériure Polytechnique (ESP)Cheikh Anta Diop UniversityDakarSenegal
| | - Mamadou Simina Drame
- Laboratory for Atmospheric‐Oceanic Physics Simeon Fongang, École Supériure Polytechnique (ESP)Cheikh Anta Diop UniversityDakarSenegal
| | - Jeremy M. Gernand
- Department of Mineral EngineeringThe Pennsylvania State UniversityUniversity ParkPAUSA
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Shukla SP, Kvíderová J, Adamec L, Elster J. Ecophysiological Features of Polar Soil Unicellular Microalgae 1. JOURNAL OF PHYCOLOGY 2020; 56:481-495. [PMID: 31833070 DOI: 10.1111/jpy.12953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Due to their ecological, physiological, and molecular adaptations to low and varying temperatures, as well as varying seasonal irradiances, polar non-marine eukaryotic microalgae could be suitable for low-temperature biotechnology. Adaptations include the synthesis of compounds from different metabolic pathways that protect them against stress. Production of biological compounds and various biotechnological applications, for instance, water treatment technology, are of interest to humans. To select prospective strains for future low-temperature biotechnology in polar regions, temperature and irradiance of growth requirements (Q10 and Ea of 10 polar soil unicellular strains) were evaluated. In terms of temperature, three groups of strains were recognized: (i) cold-preferring where temperature optima ranged between 10.1 and 18.4°C, growth rate 0.252 and 0.344 · d-1 , (ii) cold- and warm-tolerating with optima above 10°C and growth rate 0.162-0.341 · d-1 , and (iii) warm-preferring temperatures above 20°C and growth rate 0.249-0.357 · d-1 . Their light requirements were low. Mean values Q10 for specific growth rate ranged from 0.7 to 3.1. The lowest Ea values were observed on cold-preferring and the highest in the warm-preferring strains. One strain from each temperature group was selected for PN and RD measurements. The PN :RD ratio of the warm-preferring strains was less affected by temperature similarly as Q10 and Ea. For future biotechnological applications, the strains with broad temperature tolerance (i.e., the group of cold- and warm-tolerating and warm-preferring strains) will be most useful.
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Affiliation(s)
- Satya P Shukla
- Central Institute of Fisheries and Education, Indian Council of Agricultural Research, Panch Marg, Off. Yari Road, Versova, Andheri (west), Mumbai, 400 061, India
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82, Třeboň, Czech Republic
| | - Jana Kvíderová
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82, Třeboň, Czech Republic
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, Na Zlaté Stoce 3, 370 05, České Budějovice, Czech Republic
| | - Lubomír Adamec
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82, Třeboň, Czech Republic
| | - Josef Elster
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82, Třeboň, Czech Republic
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, Na Zlaté Stoce 3, 370 05, České Budějovice, Czech Republic
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Molina-Montenegro MA, Ballesteros GI, Castro-Nallar E, Meneses C, Gallardo-Cerda J, Torres-Díaz C. A first insight into the structure and function of rhizosphere microbiota in Antarctic plants using shotgun metagenomic. Polar Biol 2019. [DOI: 10.1007/s00300-019-02556-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Weisleitner K, Perras A, Moissl-Eichinger C, Andersen DT, Sattler B. Source Environments of the Microbiome in Perennially Ice-Covered Lake Untersee, Antarctica. Front Microbiol 2019; 10:1019. [PMID: 31134036 PMCID: PMC6524460 DOI: 10.3389/fmicb.2019.01019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022] Open
Abstract
Ultra-oligotrophic Lake Untersee is among the largest and deepest surface lakes of Central Queen Maud Land in East Antarctica. It is dammed at its north end by the Anuchin Glacier and the ice-cover dynamics are controlled by sublimation - not melt - as the dominating ablation process and therefore surface melt during austral summer does not provide significant amounts of water for recharge compared to subsurface melt of the Anuchin Glacier. Several studies have already described the structure and function of the microbial communities within the water column and benthic environments of Lake Untersee, however, thus far there have been no studies that examine the linkages between the lake ecosystem with that of the surrounding soils or the Anuchin Glacier. The glacier may also play an important role as a major contributor of nutrients and biota into the lake ecosystem. Based on microbial 16S rRNA amplicon sequencing, we showed that the dominant bacterial signatures in Lake Untersee, the Anuchin Glacier and its surrounding soils were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Aerosol and local soil depositions on the glacier surface resulted in distinct microbial communities developing in glacier ice and cryoconite holes. Based on a source tracking algorithm, we found that cryoconite microbial assemblages were a potential source of organisms, explaining up to 36% of benthic microbial mat communities in the lake. However, the major biotic sources for the lake ecosystem are still unknown, illustrating the possible importance of englacial and subglacial zones. The Anuchin Glacier may be considered as a vector in a biological sense for the bacterial colonization of the perennially ice-covered Lake Untersee. However, despite a thick perennial ice cover, observed "lift-off" microbial mats escaping the lake make a bidirectional transfer of biota plausible. Hence, there is an exchange of biota between Lake Untersee and connective habitats possible despite the apparent sealing by a perennial ice cover and the absence of moat areas during austral summer.
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Affiliation(s)
- Klemens Weisleitner
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexandra Perras
- Center for Medical Research (ZMF), Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Joint Facilities, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | | | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
- Austrian Polar Research Institute, Vienna, Austria
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Niederberger TD, Bottos EM, Sohm JA, Gunderson T, Parker A, Coyne KJ, Capone DG, Carpenter EJ, Cary SC. Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils. Front Microbiol 2019; 10:621. [PMID: 31019494 PMCID: PMC6458288 DOI: 10.3389/fmicb.2019.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical "high-productivity" MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted.
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Affiliation(s)
- Thomas D Niederberger
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Eric M Bottos
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand.,Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jill A Sohm
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Troy Gunderson
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Alex Parker
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Kathryn J Coyne
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Douglas G Capone
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Edward J Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Stephen Craig Cary
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand
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Malard LA, Šabacká M, Magiopoulos I, Mowlem M, Hodson A, Tranter M, Siegert MJ, Pearce DA. Spatial Variability of Antarctic Surface Snow Bacterial Communities. Front Microbiol 2019; 10:461. [PMID: 30972032 PMCID: PMC6443967 DOI: 10.3389/fmicb.2019.00461] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
It was once a long-held view that the Antarctic was a pristine environment with low biomass, low biodiversity and low rates of microbial activity. However, as the intensity of scientific investigation has increased, so these views have started to change. In particular, the role and impact of human activity toward indigenous microbial communities has started to come under more intense scrutiny. During the Subglacial Lake Ellsworth exploration campaign in December 2012, a microbiological survey was conducted to determine the extent and likelihood of exogenous input into the subglacial lake system during the hot-water drilling process. Snow was collected from the surface to represent that used for melt water production for hot-water drilling. The results of this study showed that snow used to provide melt water differed in its microbiological composition from that of the surrounding area and raised the question of how the biogeography of snow-borne microorganisms might influence the potential outcome of scientific analyses. In this study, we investigated the biogeography of microorganisms in snow around a series of Antarctic logistic hubs, where human activity was clearly apparent, and from which scientific investigations have been undertaken. A change in microbial community structure with geographical location was apparent and, notably, a decrease in alpha diversity at more remote southern latitudes. Soil-related microorganisms dominated microbial assemblages suggesting terrestrial input, most likely from long-range aeolian transport into continental Antarctica. We also observed that relic DNA was not a major issue when assessing snow samples. Overall, our observations might have profound implications for future scientific activities in Antarctica, such as the need to establish "no-go" protected areas, the need for better characterization of field sites and improved protocols for sterilization and verification of ice drilling equipment.
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Affiliation(s)
- Lucie A. Malard
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle upon Tyne, United Kingdom
| | - Marie Šabacká
- Centre for Polar Ecology, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Iordanis Magiopoulos
- Institute of Oceanography, Hellenic Centre for Marine Research, Heraklion, Greece
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, United Kingdom
| | - Matt Mowlem
- Ocean Technology and Engineering Group, National Oceanography Centre Southampton, Southampton, United Kingdom
| | - Andy Hodson
- Arctic Geology, University Centre in Svalbard, Longyearbyen, Norway
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Martyn Tranter
- Bristol Glaciology Centre, University of Bristol, Bristol, United Kingdom
| | - Martin J. Siegert
- Grantham Institute, Department of Earth Science and Engineering, Imperial College London, London, United Kingdom
| | - David A. Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle upon Tyne, United Kingdom
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
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Airborne microbial transport limitation to isolated Antarctic soil habitats. Nat Microbiol 2019; 4:925-932. [DOI: 10.1038/s41564-019-0370-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/15/2019] [Indexed: 11/08/2022]
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34
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Airborne Microorganisms in Antarctica: Transport, Survival and Establishment. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Lee KC, Caruso T, Archer SD, Gillman LN, Lau MC, Cary SC, Lee CK, Pointing SB. Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica. Front Microbiol 2018; 9:2619. [PMID: 30450087 PMCID: PMC6225844 DOI: 10.3389/fmicb.2018.02619] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
Antarctic soil supports surface microbial communities that are dependent on ephemeral moisture. Understanding the response to availability of this resource is essential to predicting how the system will respond to climate change. The McMurdo Dry Valleys are the largest ice-free soil region in Antarctica. They are a hyper-arid polar desert with extremely limited moisture availability. Microbial colonization dominates this ecosystem but surprisingly little is known about how communities respond to changing moisture regimes. We utilized the natural model system provided by transiently wetted soil at lake margins in the Dry Valleys to interrogate microbial responses along a well-defined contiguous moisture gradient and disentangle responses between and within phyla. We identified a striking non-linear response among bacteria where at low moisture levels small changes resulted in a large impact on diversity. At higher moister levels community responses were less pronounced, resulting in diversity asymptotes. We postulate that whilst the main drivers of observed community diversity were deterministic, a switch in the major influence occurred from abiotic factors at low moisture levels to biotic interactions at higher moisture. Response between and within phyla was markedly different, highlighting the importance of taxonomic resolution in community analysis. Furthermore, we resolved apparent stochasticity at high taxonomic ranks as the result of deterministic interactions taking place at finer taxonomic and spatial scales. Overall the findings provide new insight on the response to moisture and this will be useful in advancing understanding of potential ecosystem responses in the threatened McMurdo Dry Valleys system.
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Affiliation(s)
- Kevin C. Lee
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Stephen D.J. Archer
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Len N. Gillman
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Maggie C.Y. Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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36
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Smith HJ, Dieser M, McKnight DM, SanClements MD, Foreman CM. Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments. FEMS Microbiol Ecol 2018; 94:4995909. [DOI: 10.1093/femsec/fiy090] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- HJ Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
| | - M Dieser
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717, USA
| | - DM McKnight
- INSTAAR, University of Colorado Boulder, Boulder, CO 80303, USA
| | - MD SanClements
- INSTAAR, University of Colorado Boulder, Boulder, CO 80303, USA
- National Ecological Observatory Network, Boulder, CO 80301, USA
| | - CM Foreman
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717, USA
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37
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Tandon K, Yang SH, Wan MT, Yang CC, Baatar B, Chiu CY, Tsai JW, Liu WC, Tang SL. Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan. Microbes Environ 2018; 33:120-126. [PMID: 29681561 PMCID: PMC6031399 DOI: 10.1264/jsme2.me17148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Very few studies have attempted to profile the microbial communities in the air above freshwater bodies, such as lakes, even though freshwater sources are an important part of aquatic ecosystems and airborne bacteria are the most dispersible microorganisms on earth. In the present study, we investigated microbial communities in the waters of two high mountain sub-alpine montane lakes—located 21 km apart and with disparate trophic characteristics—and the air above them. Although bacteria in the lakes had locational differences, their community compositions remained constant over time. However, airborne bacterial communities were diverse and displayed spatial and temporal variance. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria were dominant in both lakes, with different relative abundances between lakes, and Parcubacteria (OD1) was dominant in air samples for all sampling times, except two. We also identified certain shared taxa between lake water and the air above it. The results obtained on these communities in the present study provide putative candidates to study how airborne communities shape lake water bacterial compositions and vice versa.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University
| | | | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd
| | | | | | | | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University
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38
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Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days. Appl Environ Microbiol 2018; 84:AEM.00004-18. [PMID: 29549101 DOI: 10.1128/aem.00004-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM2.5 [<2.5 μm], PM10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions (R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus, Tumebacillus, and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO2 concentration, relative humidity, PM10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM10 samples (Dokdonella, Caenimonas, Geminicoccus, and Sphingopyxis) and PM2.5 samples (Cellulomonas and Rhizobacter), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus, Kocuria, and Sphingomonas Network analysis indicated that Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days.IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus, Tumebacillus, and Desulfurispora) increased significantly on heavy-haze days. In addition, Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze.
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39
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Van Goethem MW, Pierneef R, Bezuidt OKI, Van De Peer Y, Cowan DA, Makhalanyane TP. A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils. MICROBIOME 2018; 6:40. [PMID: 29471872 PMCID: PMC5824556 DOI: 10.1186/s40168-018-0424-5] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/11/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. METHODS We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. RESULTS In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = - 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. CONCLUSIONS ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.
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Affiliation(s)
- Marc W Van Goethem
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Rian Pierneef
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Oliver K I Bezuidt
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Yves Van De Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences Building 2, Lynnwood Road, Pretoria, 0028, South Africa.
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40
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Lacap-Bugler DC, Lee KK, Archer S, Gillman LN, Lau MCY, Leuzinger S, Lee CK, Maki T, McKay CP, Perrott JK, de Los Rios-Murillo A, Warren-Rhodes KA, Hopkins DW, Pointing SB. Global Diversity of Desert Hypolithic Cyanobacteria. Front Microbiol 2017; 8:867. [PMID: 28559886 PMCID: PMC5432569 DOI: 10.3389/fmicb.2017.00867] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/28/2017] [Indexed: 12/02/2022] Open
Abstract
Global patterns in diversity were estimated for cyanobacteria-dominated hypolithic communities that colonize ventral surfaces of quartz stones and are common in desert environments. A total of 64 hypolithic communities were recovered from deserts on every continent plus a tropical moisture sufficient location. Community diversity was estimated using a combined t-RFLP fingerprinting and high throughput sequencing approach. The t-RFLP analysis revealed desert communities were different from the single non-desert location. A striking pattern also emerged where Antarctic desert communities were clearly distinct from all other deserts. Some overlap in community similarity occurred for hot, cold and tundra deserts. A further observation was that the producer-consumer ratio displayed a significant negative correlation with growing season, such that shorter growing seasons supported communities with greater abundance of producers, and this pattern was independent of macroclimate. High-throughput sequencing of 16S rRNA and nifH genes from four representative samples validated the t-RFLP study and revealed patterns of taxonomic and putative diazotrophic diversity for desert communities from the Taklimakan Desert, Tibetan Plateau, Canadian Arctic and Antarctic. All communities were dominated by cyanobacteria and among these 21 taxa were potentially endemic to any given desert location. Some others occurred in all but the most extreme hot and polar deserts suggesting they were relatively less well adapted to environmental stress. The t-RFLP and sequencing data revealed the two most abundant cyanobacterial taxa were Phormidium in Antarctic and Tibetan deserts and Chroococcidiopsis in hot and cold deserts. The Arctic tundra displayed a more heterogenous cyanobacterial assemblage and this was attributed to the maritime-influenced sampling location. The most abundant heterotrophic taxa were ubiquitous among samples and belonged to the Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria. Sequencing using nitrogenase gene-specific primers revealed all putative diazotrophs were Proteobacteria of the orders Burkholderiales, Rhizobiales, and Rhodospirillales. We envisage cyanobacterial carbon input to the system is accompanied by nitrogen fixation largely from non-cyanobacterial taxa. Overall the results indicate desert hypoliths worldwide are dominated by cyanobacteria and that growing season is a useful predictor of their abundance. Differences in cyanobacterial taxa encountered may reflect their adaptation to different moisture availability regimes in polar and non-polar deserts.
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Affiliation(s)
- Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Kevin K Lee
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Stephen Archer
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Len N Gillman
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, PrincetonNJ, USA
| | - Sebastian Leuzinger
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of WaikatoHamilton, New Zealand
| | - Teruya Maki
- Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
| | - Christopher P McKay
- National Aeronautics and Space Administration Ames Research Center, Moffett FieldCA, USA
| | - John K Perrott
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand
| | | | | | | | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Science, Auckland University of TechnologyAuckland, New Zealand.,Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
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41
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Moon KL, Chown SL, Fraser CI. Reconsidering connectivity in the sub-Antarctic. Biol Rev Camb Philos Soc 2017; 92:2164-2181. [DOI: 10.1111/brv.12327] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Katherine L. Moon
- School of Biological Sciences; Monash University; Clayton 3800 Australia
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
| | - Steven L. Chown
- School of Biological Sciences; Monash University; Clayton 3800 Australia
| | - Ceridwen I. Fraser
- Fenner School of Environment and Society; Australian National University; Acton 2601 Australia
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42
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Chen Y, Li XK, Si J, Wu GJ, Tian LD, Xiang SR. Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China. Front Microbiol 2016; 7:1716. [PMID: 27847503 PMCID: PMC5088206 DOI: 10.3389/fmicb.2016.01716] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/13/2016] [Indexed: 02/02/2023] Open
Abstract
In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups.
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Affiliation(s)
- Yong Chen
- School of Life Science, Lanzhou University, Lanzhou China
| | - Xiang-Kai Li
- School of Life Science, Lanzhou University, Lanzhou China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou China
| | - Guang-Jian Wu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Li-De Tian
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
| | - Shu-Rong Xiang
- School of Life Science, Lanzhou University, LanzhouChina; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, BeijingChina; Laboratory of Ice Core and Cold Regions Environment, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, LanzhouChina
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43
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Wei STS, Lacap-Bugler DC, Lau MCY, Caruso T, Rao S, de Los Rios A, Archer SK, Chiu JMY, Higgins C, Van Nostrand JD, Zhou J, Hopkins DW, Pointing SB. Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1642. [PMID: 27812351 PMCID: PMC5071352 DOI: 10.3389/fmicb.2016.01642] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/03/2016] [Indexed: 12/04/2022] Open
Abstract
The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.
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Affiliation(s)
- Sean T S Wei
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - Tancredi Caruso
- School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland
| | - Subramanya Rao
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, China
| | - Asunción de Los Rios
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales Madrid, Spain
| | - Stephen K Archer
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University Hong Kong, China
| | - Colleen Higgins
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - David W Hopkins
- School of Agriculture, Food and Environment, The Royal Agricultural University Gloucestershire, UK
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of TechnologyAuckland, New Zealand; Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
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44
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Stamper CE, Hoisington AJ, Gomez OM, Halweg-Edwards AL, Smith DG, Bates KL, Kinney KA, Postolache TT, Brenner LA, Rook GAW, Lowry CA. The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2016; 131:289-323. [PMID: 27793224 DOI: 10.1016/bs.irn.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It is increasingly evident that inflammation is an important determinant of cognitive function and emotional behaviors that are dysregulated in stress-related psychiatric disorders, such as anxiety and affective disorders. Inflammatory responses to physical or psychological stressors are dependent on immunoregulation, which is indicated by a balanced expansion of effector T-cell populations and regulatory T cells. This balance is in part driven by microbial signals. The hygiene or "old friends" hypothesis posits that exposure to immunoregulation-inducing microorganisms is reduced in modern urban societies, leading to an epidemic of inflammatory disease and increased vulnerability to stress-related psychiatric disorders. With the global trend toward urbanization, humans are progressively spending more time in built environments, thereby, experiencing limited exposures to these immunoregulatory "old friends." Here, we evaluate the implications of the global trend toward urbanization, and how this transition may affect human microbial exposures and human behavior.
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Affiliation(s)
- C E Stamper
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - A J Hoisington
- US Air Force Academy, Colorado Springs, CO, United States; Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States
| | - O M Gomez
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | | | - D G Smith
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States
| | - K L Bates
- US Air Force Academy, Colorado Springs, CO, United States
| | - K A Kinney
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; University of Texas Austin, Austin, TX, United States
| | - T T Postolache
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; University of Maryland School of Medicine, Baltimore, MD, United States; VISN 5 Mental Illness Research Education and Clinical Center (MIRECC), Baltimore, MD, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States
| | - L A Brenner
- Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States; University of Colorado, Aurora, CO, United States
| | - G A W Rook
- Center for Clinical Microbiology, UCL (University College London), London, United Kingdom
| | - C A Lowry
- Center for Neuroscience, University of Colorado Boulder, Boulder, CO, United States; Military and Veteran Microbiome Consortium for Research and Education (MVM-CoRE), Denver, CO, United States; Rocky Mountain Mental Illness Research Education and Clinical Center, Denver, CO, United States; University of Colorado, Aurora, CO, United States.
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45
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Goordial J, Davila A, Greer CW, Cannam R, DiRuggiero J, McKay CP, Whyte LG. Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert. Environ Microbiol 2016; 19:443-458. [DOI: 10.1111/1462-2920.13353] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Rebecca Cannam
- McGill University Macdonald Campus; Ste-Anne-de-Bellevue Quebec Canada
| | | | | | - Lyle G. Whyte
- McGill University Macdonald Campus; Ste-Anne-de-Bellevue Quebec Canada
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46
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Hodač L, Hallmann C, Spitzer K, Elster J, Faßhauer F, Brinkmann N, Lepka D, Diwan V, Friedl T. Widespread green algae Chlorella and Stichococcus exhibit polar-temperate and tropical-temperate biogeography. FEMS Microbiol Ecol 2016; 92:fiw122. [PMID: 27279416 DOI: 10.1093/femsec/fiw122] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
Chlorella and Stichococcus are morphologically simple airborne microalgae, omnipresent in terrestrial and aquatic habitats. The minute cell size and resistance against environmental stress facilitate their long-distance dispersal. However, the actual distribution of Chlorella- and Stichococcus-like species has so far been inferred only from ambiguous morphology-based evidence. Here we contribute a phylogenetic analysis of an expanded SSU and ITS2 rDNA sequence dataset representing Chlorella- and Stichococcus-like species from terrestrial habitats of polar, temperate and tropical regions. We aim to uncover biogeographical patterns at low taxonomic levels. We found that psychrotolerant strains of Chlorella and Stichococcus are closely related with strains originating from the temperate zone. Species closely related to Chlorella vulgaris and Muriella terrestris, and recovered from extreme terrestrial environments of polar regions and hot deserts, are particularly widespread. Stichococcus strains from the temperate zone, with their closest relatives in the tropics, differ from strains with the closest relatives being from the polar regions. Our data suggest that terrestrial Chlorella and Stichococcus might be capable of intercontinental dispersal; however, their actual distributions exhibit biogeographical patterns.
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Affiliation(s)
- Ladislav Hodač
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, 37073 Göttingen, Germany
| | - Christine Hallmann
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
| | - Karolin Spitzer
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, 37005 České Budějovice, Czech Republic Institute of Botany, Phycology Centrum, Academy of Sciences of the Czech Republic, 37982 Třeboň, Czech Republic
| | - Fabian Faßhauer
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
| | - Nicole Brinkmann
- Department of Forest Botany, University of Göttingen, 37077 Göttingen, Germany
| | - Daniela Lepka
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
| | - Vaibhav Diwan
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, 37073 Göttingen, Germany
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Leung MHY, Lee PKH. The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. MICROBIOME 2016; 4:21. [PMID: 27216717 PMCID: PMC4877933 DOI: 10.1186/s40168-016-0165-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/11/2016] [Indexed: 05/10/2023]
Abstract
Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
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48
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Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region. Polar Biol 2016. [DOI: 10.1007/s00300-016-1921-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lang-Yona N, Mazar Y, Pardo M, Rudich Y. Air-sampled Filter Analysis for Endotoxins and DNA Content. J Vis Exp 2016. [PMID: 27023725 DOI: 10.3791/53444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Outdoor aerosol research commonly uses particulate matter sampled on filters. This procedure enables various characterizations of the collected particles to be performed in parallel. The purpose of the method presented here is to obtain a highly accurate and reliable analysis of the endotoxin and DNA content of bio-aerosols extracted from filters. The extraction of high molecular weight organic molecules, such as lipopolysaccharides, from sampled filters involves shaking the sample in a pyrogen-free water-based medium. The subsequent analysis is based on an enzymatic reaction that can be detected using a turbidimetric measurement. As a result of the high organic content on the sampled filters, the extraction of DNA from the samples is performed using a commercial DNA extraction kit that was originally designed for soils and modified to improve the DNA yield. The detection and quantification of specific microbial species using quantitative polymerase chain reaction (q-PCR) analysis are described and compared with other available methods.
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Affiliation(s)
- Naama Lang-Yona
- Department of Earth and Planetary Sciences, Weizmann Institute of Science; Multiphase Chemistry Department, Max Planck Institute
| | - Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science
| | - Michal Pardo
- Department of Earth and Planetary Sciences, Weizmann Institute of Science
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science;
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Van Goethem MW, Makhalanyane TP, Valverde A, Cary SC, Cowan DA. Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw051. [DOI: 10.1093/femsec/fiw051] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
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