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Sanyal A, Antony R, Samui G, Thamban M. Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes. J Microbiol 2024:10.1007/s12275-024-00140-1. [PMID: 38814540 DOI: 10.1007/s12275-024-00140-1] [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: 11/03/2023] [Revised: 03/27/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.
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Affiliation(s)
- Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India.
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Goa, 403206, India.
| | - Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- GFZ German Research Centre for Geosciences, 14473, Potsdam, Germany
| | - Gautami Samui
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
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2
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Wang B, Chen C, Xiao Y, Chen K, Wang J, Wang L, Li J, Kang Z, Zhou G. A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus. BMC PLANT BIOLOGY 2023; 23:655. [PMID: 38110871 PMCID: PMC10729362 DOI: 10.1186/s12870-023-04690-1] [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: 10/07/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Although it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau. RESULTS Our results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. CONCLUSIONS Our findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.
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Affiliation(s)
- Bo Wang
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Chen
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yuanming Xiao
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
| | - Kaiyang Chen
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Wang
- Qinghai University, Xining, 810016, China
| | - Lingling Wang
- Resource institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, 550000, China
| | - Jianan Li
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongxiu Kang
- Datong Beichuan Heyuan District National Nature Reserve, Xining, 810100, China
| | - Guoying Zhou
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China.
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3
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Wang H, Yan B, Wu Y, Yin M, Wang M, Fu C. Microbial community diversity and potential functionality in response to dam construction along the Three Gorge Reservoir, China. Front Microbiol 2023; 14:1218806. [PMID: 37799598 PMCID: PMC10547884 DOI: 10.3389/fmicb.2023.1218806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/07/2023] Open
Abstract
River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community.
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Affiliation(s)
- Huan Wang
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
- Chongqing Landscape and Gardening Research Institute, Chongqing, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, China
| | - Bin Yan
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Yan Wu
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Maoyun Yin
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Maoqing Wang
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
| | - Chuan Fu
- Chongqing Key Laboratory of Water Environment Evolution and Pollution Control in Three Gorges Reservoir, Chongqing Three Gorges University, Wanzhou, China
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. ENVIRONMENTAL MICROBIOME 2023; 18:10. [PMID: 36805022 PMCID: PMC9938989 DOI: 10.1186/s40793-023-00470-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Mark Grippo
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Negri
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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6
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Pittino F, Ambrosini R, Seeger M, Azzoni RS, Diolaiuti G, Alviz Gazitua P, Franzetti A. Geographical variability of bacterial communities of cryoconite holes of Andean glaciers. Sci Rep 2023; 13:2633. [PMID: 36788266 PMCID: PMC9929092 DOI: 10.1038/s41598-022-24373-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/14/2022] [Indexed: 02/16/2023] Open
Abstract
Cryoconite holes, ponds full of melting water with sediment on the bottom, are hotspots of biodiversity on glacier surfaces and host dynamic micro-ecosystems. They have been extensively investigated in different areas of the world (e.g., the Arctic, Antarctic, Alps, and Himalaya), but so far no study has described the bacterial communities of the glaciers in the Andes, the world's longest mountain range. In this study, we describe the bacterial communities of three small (< 2 km2) high-elevation (< 4200 m a.s.l.) glaciers of the Central Andes (Iver, East Iver and Morado glaciers) and two large (> 85 km2) glaciers of the Patagonian Andes (Exploradores and Perito Moreno glaciers) whose ablation tongues reach low altitude (< 300 m a.s.l.). Results show that the bacterial communities were generally similar to those observed in the cryoconite holes of other continents, but with few cyanobacteria (0.5% of sequences). The most abundant orders were Betaproteobacteriales, Cytophagales, Chitinophagales, Acetobacterales, Frankiales, Armatimonadales, Sphingobacteriales, Rhizobiales, Bacteroidales, Sphingomonadales, and Micrococcales. The bacterial communities differed between glaciers and both water pH and O2 concentration appeared to influence the bacterial community composition. This work thus provides the first description of the bacterial communities in cryoconite holes of South American glaciers.
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Affiliation(s)
- F. Pittino
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy ,grid.419754.a0000 0001 2259 5533WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - R. Ambrosini
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - M. Seeger
- grid.12148.3e0000 0001 1958 645XMolecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Valparaiso, Chile
| | - R. S. Azzoni
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Earth Science “Ardito Desio”, Università degli Studi di Milano, Milan, Italy
| | - G. Diolaiuti
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - P. Alviz Gazitua
- grid.442234.70000 0001 2295 9069Departamento de Ciencias Biológicas, Universidad de los Lagos, Osorno, Chile
| | - A. Franzetti
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy
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Zoumplis A, Kolody B, Kaul D, Zheng H, Venepally P, McKnight DM, Takacs-Vesbach C, DeVries A, Allen AE. Impact of meltwater flow intensity on the spatiotemporal heterogeneity of microbial mats in the McMurdo Dry Valleys, Antarctica. ISME COMMUNICATIONS 2023; 3:3. [PMID: 36690784 PMCID: PMC9870883 DOI: 10.1038/s43705-022-00202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 01/24/2023]
Abstract
The meltwater streams of the McMurdo Dry Valleys are hot spots of biological diversity in the climate-sensitive polar desert landscape. Microbial mats, largely comprised of cyanobacteria, dominate the streams which flow for a brief window of time (~10 weeks) over the austral summer. These communities, critical to nutrient and carbon cycling, display previously uncharacterized patterns of rapid destabilization and recovery upon exposure to variable and physiologically detrimental conditions. Here, we characterize changes in biodiversity, transcriptional responses and activity of microbial mats in response to hydrological disturbance over spatiotemporal gradients. While diverse metabolic strategies persist between marginal mats and main channel mats, data collected from 4 time points during the austral summer revealed a homogenization of the mat communities during the mid-season peak meltwater flow, directly influencing the biogeochemical roles of this stream ecosystem. Gene expression pattern analyses identified strong functional sensitivities of nitrogen-fixing marginal mats to changes in hydrological activities. Stress response markers detailed the environmental challenges of each microhabitat and the molecular mechanisms underpinning survival in a polar desert ecosystem at the forefront of climate change. At mid and end points in the flow cycle, mobile genetic elements were upregulated across all mat types indicating high degrees of genome evolvability and transcriptional synchronies. Additionally, we identified novel antifreeze activity in the stream microbial mats indicating the presence of ice-binding proteins (IBPs). Cumulatively, these data provide a new view of active intra-stream diversity, biotic interactions and alterations in ecosystem function over a high-flow hydrological regime.
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Affiliation(s)
- A Zoumplis
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - B Kolody
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - D Kaul
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - H Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - P Venepally
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - D M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - C Takacs-Vesbach
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - A DeVries
- Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - A E Allen
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA.
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
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Lian WH, Mohamad OAA, Dong L, Zhang LY, Wang D, Liu L, Han MX, Li S, Wang S, Antunes A, Fang BZ, Jiao JY, Li WJ. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems. ENVIRONMENTAL MICROBIOME 2023; 18:4. [PMID: 36639807 PMCID: PMC9840269 DOI: 10.1186/s40793-023-00463-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/08/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Yu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong Wang
- College of Life Science and Technology, Honghe University, Mengzi, 661199, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, People's Republic of China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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The First Comprehensive Biodiversity Study of Culturable Fungal Communities Inhabiting Cryoconite Holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic). BIOLOGY 2022; 11:biology11081224. [PMID: 36009851 PMCID: PMC9405543 DOI: 10.3390/biology11081224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Cryoconite holes on glacier surfaces are a source of cold-adapted microorganisms, but little is known about their fungal inhabitants. Here, we provide the first report of distinctive fungal communities in cryoconite holes in the Werenskiold Glacier on Spitsbergen (Svalbard Archipelago, Arctic). Due to a combination of two incubation temperatures (7 °C and 24 ± 0.5 °C) and two media during isolation (PDA, YPG), as well as classical and molecular identification approaches, we were able to identify 23 different fungi (21 species and 2 unassigned species). Most of the fungi cultured from cryoconite sediment were ascomycetous filamentous micromycetes. However, four representatives of macromycetes were also identified (Bjerkandera adusta, Holwaya mucida, Orbiliaceae sp., and Trametes versicolor). Some of the described fungi possess biotechnological potential (Aspergillus pseudoglaucus, A. sydowii, Penicillium expansum, P. velutinum, B. adusta, and T. versicolor), thus, we propose the Arctic region as a source of new strains for industrial applications. In addition, two phytopathogenic representatives were present (P. sumatraense, Botrytis cinerea), as well as one potentially harmful to humans (Cladosporium cladosporioides). To the best of our knowledge, we are the first to report the occurrence of A. pseudoglaucus, C. allicinum, C. ramotenellum, P. sumatraense, P. velutinum, P. cumulodentata, B. adusta, and T. versicolor in polar regions. In all likelihood, two unassigned fungus species (Orbiliaceae and Dothideomycetes spp.) might also be newly described in such environments. Additionally, due to experimenting with 10 sampling sites located at different latitudes, we were able to conclude that the number of fungal spores decreases as one moves down the glacier. Considering the prevalence and endangerment of glacial environments worldwide, such findings suggest their potential as reservoirs of fungal diversity, which should not be overlooked.
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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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Darcy JL, Amend AS, Swift SOI, Sommers PS, Lozupone CA. specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data. ENVIRONMENTAL MICROBIOME 2022; 17:34. [PMID: 35752802 PMCID: PMC9233361 DOI: 10.1186/s40793-022-00426-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables. RESULTS We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well. CONCLUSIONS specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.
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Affiliation(s)
- John L. Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
| | - Anthony S. Amend
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, HI USA
| | - Sean O. I. Swift
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI USA
| | - Pacifica S. Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO USA
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
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Łokas E, Wachniew P, Baccolo G, Gaca P, Janko K, Milton A, Buda J, Komędera K, Zawierucha K. Unveiling the extreme environmental radioactivity of cryoconite from a Norwegian glacier. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152656. [PMID: 34954174 DOI: 10.1016/j.scitotenv.2021.152656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/29/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
This study is a first survey of the occurrence of artificial (137Cs, 241Am, 207Bi, Pu isotopes) and natural (210Pb, 228Ac, 214Bi, 40K) radionuclides in Norwegian cryoconite. Cryoconite samples were collected before (12 samples) and after (5 samples) a rainfall event, after which 7 cryoconite holes dissapeared. The concentrations of radionuclides in cryoconite samples from the Blåisen Glacier are compared with data from the Arctic and Alpine glaciers. Cryoconite samples from the studied glacier had extremely high activity concentrations of 137Cs, 241Am, 207Bi and 239+240Pu (up to 25,000 Bq/kg, 58 Bq/kg, 13 Bq/kg and 131 Bq/kg, respectively) and also high concentrations of organic matter (OM), comparing to other Scandinavian and Arctic glaciers, reaching up to ~40% of total mass. The outstandingly high concentrations of 137Cs, 241Am, Pu isotopes, and 207Bi on the Blåisen Glacier are primarily related to bioaccumulation of radionuclides in organic-rich cryoconite and might be enhanced by additional transfers of contamination from the tundra by lemmings during their population peaks. The presumed influence of intense rainfall on radionuclide concentrations in the cryoconite was not confirmed.
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Affiliation(s)
- Edyta Łokas
- Department of Mass Spectrometry, Institute of Nuclear Physics Polish Academy of Sciences, Kraków, Poland.
| | - Przemysław Wachniew
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Kraków, Poland
| | - Giovanni Baccolo
- Department of Environmental and Earth Sciences, University of Milano-Bicocca, Milano, Italy
| | - Paweł Gaca
- GAU-Radioanalytical Laboratories, Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton, United Kingdom
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov, Czech Republic; Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Andrew Milton
- GAU-Radioanalytical Laboratories, Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton, United Kingdom
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz Unversity, Poznań, Poland
| | - Kamila Komędera
- Mössbauer Spectroscopy Laboratory, Institute of Physics, Pedagogical University, Kraków, Poland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz Unversity, Poznań, Poland
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Schulte NO, Khan AL, Smith EW, Zoumplis A, Kaul D, Allen AE, Adams BJ, McKnight DM. Blowin' in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica. JOURNAL OF PHYCOLOGY 2022; 58:36-54. [PMID: 34817069 DOI: 10.1111/jpy.13223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Diatom metacommunities are structured by environmental, historical, and spatial factors that are often attributed to organism dispersal. In the McMurdo Sound region (MSR) of Antarctica, wind connects aquatic habitats through delivery of inorganic and organic matter. We evaluated the dispersal of diatoms in aeolian material and its relation to the regional diatom metacommunity using light microscopy and 18S rRNA high-throughput sequencing. The concentration of diatoms ranged from 0 to 8.76 * 106 valves · g-1 dry aeolian material. Up to 15% of whole cells contained visible protoplasm, indicating that up to 3.43 * 104 potentially viable individuals could be dispersed in a year to a single 2 -cm2 site. Diatom DNA and RNA was detected at each site, reinforcing the likelihood that we observed dispersal of viable diatoms. Of the 50 known morphospecies in the MSR, 72% were identified from aeolian material using microscopy. Aeolian community composition varied primarily by site. Meanwhile, each aeolian community was comprised of morphospecies found in aquatic communities from the same lake basin. These results suggest that aeolian diatom dispersal in the MSR is spatially structured, is predominantly local, and connects local aquatic habitats via a shared species pool. Nonetheless, aeolian community structure was distinct from that of aquatic communities, indicating that intrahabitat dispersal and environmental filtering also underlie diatom metacommunity dynamics. The present study confirms that a large number of diatoms are passively dispersed by wind across a landscape characterized by aeolian processes, integrating the regional flora and contributing to metacommunity structure and landscape connectivity.
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Affiliation(s)
- Nicholas O Schulte
- Institute of Arctic and Alpine Research, University of Colorado, Campus Box 450, Boulder, Colorado, 80309, USA
| | - Alia L Khan
- Department of Environmental Sciences, Western Washington University, Bellingham, Washington, 98225, USA
| | - Emma W Smith
- Division of the Biological Sciences, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Angela Zoumplis
- Scripps Institution of Oceanography, University of California, La Jolla, California, USA
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Drishti Kaul
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California, La Jolla, California, USA
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Byron J Adams
- Department of Biology, Evolutionary Ecology Laboratories and Monte L. Bean Museum, Brigham Young University, Provo, Utah, 84602, USA
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Campus Box 450, Boulder, Colorado, 80309, USA
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14
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Raymond-Bouchard I, Maggiori C, Brennan L, Altshuler I, Manchado JM, Parro V, Whyte LG. Assessment of Automated Nucleic Acid Extraction Systems in Combination with MinION Sequencing As Potential Tools for the Detection of Microbial Biosignatures. ASTROBIOLOGY 2022; 22:87-103. [PMID: 34962136 DOI: 10.1089/ast.2020.2349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The utilization of nanopore technologies for the detection of organic biogenic compounds has garnered significant focus in recent years. Oxford Nanopore Technologies' (ONT) MinION instrument, which can detect and sequence nucleic acids (NAs), is one such example. These technologies have much promise for unambiguous life detection but require significant development in terms of methods for extraction and preparation of NAs for biosignature detection and their feasibility for use in astrobiology-focused field missions. In this study, we tested pre-existing, automated, or semiautomated NA extraction technologies, coupled with automated ONT VolTRAX NA sample preparation, and verification with Nanopore MinION sequencing. All of the extraction systems tested (SuperFastPrep2, ClaremontX1, and SOLID-Sample Preparation Unit) showed potential for extracting DNA from Canadian High Arctic environments analogous to Mars, Europa, and Enceladus, which could subsequently be detected and sequenced with the MinION. However, they differed with regard to efficacy, yield, purity, and sequencing and annotation quality. Overall, bead beating-based systems performed the best for these parameters. In addition, we showed that the MinION could sequence unpurified DNA contained in crude cell lysates. This is valuable from an astrobiology perspective because purification steps are time-consuming and complicate the requirements for an automated extraction and life detection system. Our results indicate that semiautomated NA extraction and preparation technologies hold much promise, and with increased optimization and automation could be coupled to a larger platform incorporating nanopore detection and sequencing of NAs for life detection applications.
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Affiliation(s)
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | | | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
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15
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Antarctica as a reservoir of planetary analogue environments. Extremophiles 2021; 25:437-458. [PMID: 34586500 DOI: 10.1007/s00792-021-01245-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
One of the main objectives of astrobiological research is the investigation of the habitability of other planetary bodies. Since space exploration missions are expensive and require long-term organization, the preliminary study of terrestrial environments is an essential step to prepare and support exploration missions. The Earth hosts a multitude of extreme environments whose characteristics resemble celestial bodies in our Solar System. In these environments, the physico-chemical properties partly match extraterrestrial environments and could clarify limits and adaptation mechanisms of life, the mineralogical or geochemical context, and support and interpret data sent back from planetary bodies. One of the best terrestrial analogues is Antarctica, whose conditions lie on the edge of habitability. It is characterized by a cold and dry climate (Onofri et al., Nova Hedwigia 68:175-182, 1999), low water availability, strong katabatic winds, salt concentration, desiccation, and high radiation. Thanks to the harsh conditions like those in other celestial bodies, Antarctica offers good terrestrial analogues for celestial body (Mars or icy moons; Léveillé, CR Palevol 8:637-648, https://doi.org/10.1016/j.crpv.2009.03.005 , 2009). The continent could be distinguished into several habitats, each with characteristics similar to those existing on other bodies. Here, we reported a description of each simulated parameter within the habitats, in relation to each of the simulated extraterrestrial environments.
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16
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Solon AJ, Mastrangelo C, Vimercati L, Sommers P, Darcy JL, Gendron EMS, Porazinska DL, Schmidt SK. Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica. Front Microbiol 2021; 12:654135. [PMID: 34177836 PMCID: PMC8222675 DOI: 10.3389/fmicb.2021.654135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Claire Mastrangelo
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado-Anschutz Medical Campus, Denver, CO, United States
| | - Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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17
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Rojas-Gätjens D, Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Fuentes-Schweizer P, Pieper DH, Chavarría M. Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments. Extremophiles 2021; 25:85-99. [PMID: 33416983 DOI: 10.1007/s00792-020-01213-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/16/2020] [Indexed: 01/22/2023]
Abstract
Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microorganisms to early planet life conditions. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in Costa Rica. Both locations hold a low pH (1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO42- = 1170-2460 mg/L), but significant differences in their temperature (90.0-95.0 ºC in the seepages at Poas Volcano, 19.1-26.6 ºC in Agrio River) and in the elemental sulfur content. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp. represented more than half of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by Leptospirillum and members of the archaeal order Thermoplasmatales. Both environments share some chemical characteristics and part of their microbiota, however, the temperature and the reduced sulfur are likely the main distinguishing features, ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Alejandro Arce-Rodríguez
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Eduardo Libby
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Raúl Mora-Amador
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica.,Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, San José, 11501-2060, Costa Rica
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Paola Fuentes-Schweizer
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.,Centro de Investigación en Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica. .,Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica. .,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.
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Greco C, Andersen DT, Hawes I, Bowles AMC, Yallop ML, Barker G, Jungblut AD. Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica. Front Microbiol 2020; 11:607251. [PMID: 33362751 PMCID: PMC7759091 DOI: 10.3389/fmicb.2020.607251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/20/2020] [Indexed: 01/04/2023] Open
Abstract
Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.
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Affiliation(s)
- Carla Greco
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | | | - Marian L Yallop
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Anne D Jungblut
- Department of Life Sciences, Natural History Museum, London, United Kingdom
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19
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Sommers P, Porazinska DL, Darcy JL, Gendron EMS, Vimercati L, Solon AJ, Schmidt SK. Microbial Species-Area Relationships in Antarctic Cryoconite Holes Depend on Productivity. Microorganisms 2020; 8:E1747. [PMID: 33171740 PMCID: PMC7694949 DOI: 10.3390/microorganisms8111747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.
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Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Dorota L. Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - John L. Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA;
| | - Eli M. S. Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Adam J. Solon
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
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20
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Zawierucha K, Buda J, Jaromerska TN, Janko K, Gąsiorek P. Integrative approach reveals new species of water bears (Pilatobius, Grevenius, and Acutuncus) from Arctic cryoconite holes, with the discovery of hidden lineages of Hypsibius. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Zawierucha K, Porazinska DL, Ficetola GF, Ambrosini R, Baccolo G, Buda J, Ceballos JL, Devetter M, Dial R, Franzetti A, Fuglewicz U, Gielly L, Łokas E, Janko K, Novotna Jaromerska T, Kościński A, Kozłowska A, Ono M, Parnikoza I, Pittino F, Poniecka E, Sommers P, Schmidt SK, Shain D, Sikorska S, Uetake J, Takeuchi N. A hole in the nematosphere: tardigrades and rotifers dominate the cryoconite hole environment, whereas nematodes are missing. J Zool (1987) 2020. [DOI: 10.1111/jzo.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- K. Zawierucha
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - D. L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville FL USA
| | - G. F. Ficetola
- Department of Environmental Science and Policy University of Milan Milan Italy
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - R. Ambrosini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - G. Baccolo
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - J. Buda
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. L. Ceballos
- Institute of Hydrology, Meteorology and Environmental Studies IDEAM Bogota' Colombia
| | - M. Devetter
- Institute of soil Biology Biology Centre CAS České Budějovice Czech Republic
- Centre for Polar Ecology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - R. Dial
- Institute of Culture and the Environment Alaska Pacific University Anchorage AK USA
| | - A. Franzetti
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | | | - L. Gielly
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - E. Łokas
- Department of Mass Spectroscopy Institute of Nuclear Physics Polish Academy of Sciences Kraków Poland
| | - K. Janko
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Libechov Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | | | - A. Kozłowska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - M. Ono
- Graduate School of Science and Engineering Chiba University Chiba Japan
| | - I. Parnikoza
- State Institution National Antarctic Center of Ministry of Education and Science of Ukraine Kyiv Ukraine
- Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - F. Pittino
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - E. Poniecka
- School of Earth and Ocean Sciences Cardiff University Cardiff UK
| | - P. Sommers
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - S. K. Schmidt
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - D. Shain
- Biology Department Rutgers, The State University of New Jersey Camden NJ USA
| | - S. Sikorska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. Uetake
- The Arctic Environment Research Center National Institute of Polar Research Tachikawa Japan
| | - N. Takeuchi
- Department of Earth Sciences Graduate School of Science Chiba University Chiba Japan
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22
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Bellas CM, Schroeder DC, Edwards A, Barker G, Anesio AM. Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems. Nat Commun 2020; 11:4403. [PMID: 32879312 PMCID: PMC7468147 DOI: 10.1038/s41467-020-18236-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage. Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.
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Affiliation(s)
- Christopher M Bellas
- Department of Ecology, Lake and Glacier Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN, 55108, USA.,School of Biological Sciences, University of Reading, Reading, UK
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
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23
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Buda J, Łokas E, Pietryka M, Richter D, Magowski W, Iakovenko NS, Porazinska DL, Budzik T, Grabiec M, Grzesiak J, Klimaszyk P, Gaca P, Zawierucha K. Biotope and biocenosis of cryoconite hole ecosystems on Ecology Glacier in the maritime Antarctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138112. [PMID: 32408434 DOI: 10.1016/j.scitotenv.2020.138112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Despite recent great interest in glacier ecosystems in the continental Antarctic, little is known about their maritime counterparts. Our study presents descriptive data on cryoconite sediments and cryoconite holes on Ecology Glacier (King George Island) to accomplish three main objectives: (a) to identify main eukaryotic (algae, invertebrates) and prokaryotic (cyanobacteria) components of microbial communities; (b) to provide a "baseline" of community composition, organic matter and artificial contamination; and (c) to identify key abiotic factors that might be important in community assembly. Cryoconite holes were sampled along an altitudinal gradient of Ecology Glacier in January, mid Austral Summer 2017. Cryoconite holes located in lower altitude were deeper than those located in the middle and the highest altitude. Seventeen species of algae and cyanobacteria with biomass of 0.79 to 5.37 μg/cm3 have been found in sediments. Dominant species were cyanobacterial Pseudanabaena frigida and Bacillariophyceae Microcostaus sp. Biomass of Bacillariophyceae was significantly higher than that of Chlorophyta and Cyanobacteria. We found three species of rotifers (potentially two new to science) and for the first time a glacier dwelling Acari (suspension feeder, Nanorchestes nivalis). Organic matter content ranged from 5.4% to 7.6%. Investigated artificial radionuclides included 137Cs, 238Pu, 239+240Pu and 241Am. 210Pb seems to be related to organic matter content. Overall, cryoconite holes on Ecology Glacier present unique habitats that serve as biodiversity hotspots of psychrophiles, source of organic matter, matrices for radioactivity tracking and model for observing changes in supraglacial ecosystems in the maritime Antarctic.
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Affiliation(s)
- Jakub Buda
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Edyta Łokas
- Department of Mass Spectrometry, Institute of Nuclear Physics Polish Academy of Sciences, Radzikowskiego 152, 31-342 Kraków, Poland
| | - Mirosława Pietryka
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Science, pl. Grunwaldzki 24a, 50-363 Wrocław, Poland
| | - Dorota Richter
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Science, pl. Grunwaldzki 24a, 50-363 Wrocław, Poland
| | - Wojciech Magowski
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Nataliia S Iakovenko
- Czech University of Life Sciences Prague, Faculty of Forestry and Wood Sciences, Kamýcká 129, CZ - 165 21 Praha 6, Suchdol, Czech Republic
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Tomasz Budzik
- Institute of Earth Sciences, University of Silesia in Katowice, Będzińska 60, 41-200 Sosnowiec, Poland
| | - Mariusz Grabiec
- Institute of Earth Sciences, University of Silesia in Katowice, Będzińska 60, 41-200 Sosnowiec, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Piotr Klimaszyk
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Paweł Gaca
- Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, United Kingdom
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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24
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Sommers P, Fontenele RS, Kringen T, Kraberger S, Porazinska DL, Darcy JL, Schmidt SK, Varsani A. Single-Stranded DNA Viruses in Antarctic Cryoconite Holes. Viruses 2019; 11:E1022. [PMID: 31689942 PMCID: PMC6893807 DOI: 10.3390/v11111022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Tayele Kringen
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Dorota L Porazinska
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA.
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa.
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25
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Sommers P, Porazinska DL, Darcy JL, Zamora F, Fountain AG, Schmidt SK. Experimental cryoconite holes as mesocosms for studying community ecology. Polar Biol 2019. [DOI: 10.1007/s00300-019-02572-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Zulkefli NS, Kim KH, Hwang SJ. Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16183339. [PMID: 31510040 PMCID: PMC6765872 DOI: 10.3390/ijerph16183339] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022]
Abstract
Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.
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Affiliation(s)
| | - Keon-Hee Kim
- Human & Eco-Care Center, Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
| | - Soon-Jin Hwang
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
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