101
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Timofeev V, Bahtejeva I, Mironova R, Titareva G, Lev I, Christiany D, Borzilov A, Bogun A, Vergnaud G. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 DOI: 10.1101/486290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 05/28/2023] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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Affiliation(s)
- Vitalii Timofeev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Irina Bahtejeva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Raisa Mironova
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Galina Titareva
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Igor Lev
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - David Christiany
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Alexander Borzilov
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Alexander Bogun
- State Research Center for Applied Microbiology & Biotechnology (FBIS SRCAMB), Obolensk, Russia
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
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102
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Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS One 2019; 14:e0209140. [PMID: 31116737 PMCID: PMC6530834 DOI: 10.1371/journal.pone.0209140] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/07/2019] [Indexed: 12/24/2022] Open
Abstract
This article describes Bacillus anthracis strains isolated during an outbreak of anthrax on the Yamal Peninsula in the summer of 2016 and independently in Yakutia in 2015. A common feature of these strains is their conservation in permafrost, from which they were extracted either due to the thawing of permafrost (Yamal strains) or as the result of paleontological excavations (Yakut strains). All strains isolated on the Yamal share an identical genotype belonging to lineage B.Br.001/002, pointing to a common source of infection in a territory over 250 km in length. In contrast, during the excavations in Yakutia, three genetically different strains were recovered from a single pit. One strain belongs to B.Br.001/002, and whole genome sequence analysis showed that it is most closely related to the Yamal strains in spite of the remoteness of Yamal from Yakutia. The two other strains contribute to two different branches of A.Br.008/011, one of the remarkable polytomies described so far in the B. anthracis species. The geographic distribution of the strains belonging to A.Br.008/011 is suggesting that the polytomy emerged in the thirteenth century, in combination with the constitution of a unified Mongol empire extending from China to Eastern Europe. We propose an evolutionary model for B. anthracis recent evolution in which the B lineage spread throughout Eurasia and was subsequently replaced by the A lineage except in some geographically isolated areas.
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103
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Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
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Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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104
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The Diversity of Pseudomonas species from the Accumulation Zone of Kanchengayao Glacier, North Sikkim, India. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.1.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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105
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Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence. Appl Environ Microbiol 2019; 85:AEM.02646-18. [PMID: 30683748 PMCID: PMC6585489 DOI: 10.1128/aem.02646-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/21/2019] [Indexed: 01/31/2023] Open
Abstract
Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains. Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost. IMPORTANCE Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.
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106
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Šantl-Temkiv T, Gosewinkel U, Starnawski P, Lever M, Finster K. Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states. FEMS Microbiol Ecol 2019; 94:4898009. [PMID: 29481623 DOI: 10.1093/femsec/fiy031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/21/2018] [Indexed: 01/18/2023] Open
Abstract
The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.
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Affiliation(s)
- Tina Šantl-Temkiv
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.,Department of Bioscience, Microbiology Section, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Piotr Starnawski
- Centre for Geomicrobiology, Aarhus University, 116 Ny Munkegade, 8000 Aarhus, Denmark
| | - Mark Lever
- Centre for Geomicrobiology, Aarhus University, 116 Ny Munkegade, 8000 Aarhus, Denmark.,ETH Zürich, Department of Environmental Systems Science, Universitätsstrasse 16, 8092 Zurich, Switzerland
| | - Kai Finster
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus, Denmark.,Department of Bioscience, Microbiology Section, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
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107
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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108
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Margesin R, Collins T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl Microbiol Biotechnol 2019; 103:2537-2549. [PMID: 30719551 PMCID: PMC6443599 DOI: 10.1007/s00253-019-09631-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/28/2022]
Abstract
Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
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109
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Dynamics of microbial communities and CO 2 and CH 4 fluxes in the tundra ecosystems of the changing Arctic. J Microbiol 2019; 57:325-336. [PMID: 30656588 DOI: 10.1007/s12275-019-8661-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
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110
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Martinez MA, Woodcroft BJ, Ignacio Espinoza JC, Zayed AA, Singleton CM, Boyd JA, Li YF, Purvine S, Maughan H, Hodgkins SB, Anderson D, Sederholm M, Temperton B, Bolduc B, Saleska SR, Tyson GW, Rich VI, Saleska SR, Tyson GW, Rich VI. Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Syst Appl Microbiol 2019; 42:54-66. [DOI: 10.1016/j.syapm.2018.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
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111
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Cheptsov VS, Tsypina SI, Minaev NV, Yusupov VI, Chichkov BN. New microorganism isolation techniques with emphasis on laser printing. Int J Bioprint 2018; 5:165. [PMID: 32596530 PMCID: PMC7294688 DOI: 10.18063/ijb.v5i1.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
The study of biodiversity, growth, development, and metabolism of cultivated microorganisms is an integral part of modern microbiological, biotechnological, and medical research. Such studies require the development of new methods of isolation, cultivation, manipulation, and study of individual bacterial cells and their consortia. To this end, in recent years, there has been an active development of different isolation and three-dimensional cell positioning methods. In this review, the optical tweezers, surface heterogeneous functionalization, multiphoton lithography, microfluidic techniques, and laser printing are reviewed. Laser printing is considered as one of the most promising techniques and is discussed in detail.
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Affiliation(s)
- V S Cheptsov
- Department of Soil Science, Lomonosov Moscow State University, 11999 Moscow, Russia
| | - S I Tsypina
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten, 30167, Hannover
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112
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Li G, Gao P, Zhi B, Fu B, Gao G, Chen Z, Gao M, Wu M, Ma T. The relative abundance of alkane-degrading bacteria oscillated similarly to a sinusoidal curve in an artificial ecosystem model from oil-well products. Environ Microbiol 2018; 20:3772-3783. [DOI: 10.1111/1462-2920.14382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqiang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman OK USA
| | - Peike Gao
- College of Life Sciences; Qufu Normal University; Qufu People's Repubic of China
| | - Bo Zhi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Bing Fu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ge Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Zhaohui Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengli Gao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Mengmeng Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education; College of Life Sciences, Nankai University; Tianjin People's Republic of China
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113
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Sánchez-Soto Jiménez MF, Cerqueda-García D, Montero-Muñoz JL, Aguirre-Macedo ML, García-Maldonado JQ. Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. PeerJ 2018; 6:e5583. [PMID: 30225176 PMCID: PMC6139248 DOI: 10.7717/peerj.5583] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 08/14/2018] [Indexed: 12/31/2022] Open
Abstract
The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto Jiménez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM). Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida. Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Jorge L Montero-Muñoz
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - Ma Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Departamento de Recursos del Mar, Mérida, Yucatán, México
| | - José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida. Departamento de Recursos del Mar, Mérida, Yucatán, México
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Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI. Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. mSystems 2018; 3:e00076-18. [PMID: 30320215 PMCID: PMC6172770 DOI: 10.1128/msystems.00076-18] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/24/2018] [Indexed: 01/10/2023] Open
Abstract
Rapidly thawing permafrost harbors ∼30 to 50% of global soil carbon, and the fate of this carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses could modulate that impact via induced mortality and metabolic controls. Because of the challenges of recovering viruses from soils, little is known about soil viruses or their role(s) in microbial biogeochemical cycling. Here, we describe 53 viral populations (viral operational taxonomic units [vOTUs]) recovered from seven quantitatively derived (i.e., not multiple-displacement-amplified) viral-particle metagenomes (viromes) along a permafrost thaw gradient at the Stordalen Mire field site in northern Sweden. Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. Together, these findings suggest that these soil viruses have distinct ecology, impact host-mediated biogeochemistry, and likely impact ecosystem function in the rapidly changing Arctic. IMPORTANCE This work is part of a 10-year project to examine thawing permafrost peatlands and is the first virome-particle-based approach to characterize viruses in these systems. This method yielded >2-fold-more viral populations (vOTUs) per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum, B. Bolduc, et al., Nat Microbiol 3:870-880, 2018, https://doi.org/10.1038/s41564-018-0190-y). We compared the ecology of the recovered vOTUs along a permafrost thaw gradient and found (i) habitat specificity, (ii) a shift in viral community identity from soil-like to aquatic-like viruses, (iii) infection of dominant microbial hosts, and (iv) carriage of host metabolic genes. These vOTUs can impact ecosystem carbon processing via top-down (inferred from lysing dominant microbial hosts) and bottom-up (inferred from carriage of auxiliary metabolic genes) controls. This work serves as a foundation which future studies can build upon to increase our understanding of the soil virosphere and how viruses affect soil ecosystem services.
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Affiliation(s)
- Gareth Trubl
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ho Bin Jang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Joanne B. Emerson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Dean R. Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Jared Ellenbogen
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Ben J. Woodcroft
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Scott R. Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queensland, Australia
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
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115
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Kramshøj M, Albers CN, Holst T, Holzinger R, Elberling B, Rinnan R. Biogenic volatile release from permafrost thaw is determined by the soil microbial sink. Nat Commun 2018; 9:3412. [PMID: 30143640 PMCID: PMC6109083 DOI: 10.1038/s41467-018-05824-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
Abstract
Warming in the Arctic accelerates thawing of permafrost-affected soils, which leads to a release of greenhouse gases to the atmosphere. We do not know whether permafrost thaw also releases non-methane volatile organic compounds that can contribute to both negative and positive radiative forcing on climate. Here we show using proton transfer reaction-time of flight-mass spectrometry that substantial amounts of ethanol and methanol and in total 316 organic ions were released from Greenlandic permafrost soils upon thaw in laboratory incubations. We demonstrate that the majority of this release is taken up in the active layer above. In an experiment using 14C-labeled ethanol and methanol, we demonstrate that these compounds are consumed by microorganisms. Our findings highlight that the thawing permafrost soils are not only a considerable source of volatile organic compounds but also that the active layer regulates their release into the atmosphere.
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Affiliation(s)
- Magnus Kramshøj
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.,Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Christian N Albers
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark.,Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Thomas Holst
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.,Department of Physical Geography & Ecosystem Science, Lund University, Sölvegatan 12, S-22362, Lund, Sweden
| | - Rupert Holzinger
- Institute for Marine and Atmospheric Research (IMAU), Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands
| | - Bo Elberling
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Riikka Rinnan
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark. .,Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark.
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116
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Müller O, Bang-Andreasen T, White RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol 2018; 20:4328-4342. [PMID: 29971895 DOI: 10.1111/1462-2920.14348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.
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Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway
| | - Toke Bang-Andreasen
- Department of Environmental Science, Aarhus University, DK-4000, Roskilde, Denmark.,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
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117
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Genome-centric view of carbon processing in thawing permafrost. Nature 2018; 560:49-54. [PMID: 30013118 DOI: 10.1038/s41586-018-0338-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/05/2018] [Indexed: 11/09/2022]
Abstract
As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.
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118
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Bottos EM, Kennedy DW, Romero EB, Fansler SJ, Brown JM, Bramer LM, Chu RK, Tfaily MM, Jansson JK, Stegen JC. Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. FEMS Microbiol Ecol 2018; 94:5037918. [DOI: 10.1093/femsec/fiy110] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eric M Bottos
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC, V2C 0C8, Canada
| | - David W Kennedy
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Elvira B Romero
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Sarah J Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Joseph M Brown
- Computational Biology, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - James C Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
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119
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Ballard ZS, Brown C, Ozcan A. Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome. ACS NANO 2018; 12:3065-3082. [PMID: 29553706 DOI: 10.1021/acsnano.7b08660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbiome has been heralded as a gauge of and contributor to both human health and environmental conditions. Current challenges in probing, engineering, and harnessing the microbiome stem from its microscopic and nanoscopic nature, diversity and complexity of interactions among its members and hosts, as well as the spatiotemporal sampling and in situ measurement limitations induced by the restricted capabilities and norm of existing technologies, leaving some of the constituents of the microbiome unknown. To facilitate significant progress in the microbiome field, deeper understanding of the constituents' individual behavior, interactions with others, and biodiversity are needed. Also crucial is the generation of multimodal data from a variety of subjects and environments over time. Mobile imaging and sensing technologies, particularly through smartphone-based platforms, can potentially meet some of these needs in field-portable, cost-effective, and massively scalable manners by circumventing the need for bulky, expensive instrumentation. In this Perspective, we outline how mobile sensing and imaging technologies could lead the way to unprecedented insight into the microbiome, potentially shedding light on various microbiome-related mysteries of today, including the composition and function of human, animal, plant, and environmental microbiomes. Finally, we conclude with a look at the future, propose a computational microbiome engineering and optimization framework, and discuss its potential impact and applications.
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120
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Ren B, Hu Y, Chen B, Zhang Y, Thiele J, Shi R, Liu M, Bu R. Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China. Sci Rep 2018; 8:5619. [PMID: 29618759 PMCID: PMC5884794 DOI: 10.1038/s41598-018-24040-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/26/2018] [Indexed: 12/21/2022] Open
Abstract
In the permafrost region of northeastern China, vegetation and soil environment have showed response to permafrost degradation triggered by global warming, but the corresponding variation of the soil microbial communities remains poorly investigated. Here, a field investigation in the continuous permafrost region was conducted to collect 63 soil samples from 21 sites along a latitudinal gradient to assess the distribution pattern of microbial communities and their correlation with environmental factors. High-throughput Illumina sequencing revealed that bacterial communities were dominated by Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria. Both microbial richness and phylogenetic diversity decreased initially and then increased as the latitude increased. UniFrac analysis of microbial communities detected significant differences among latitudes. Variation partitioning analysis and structural equation models revealed that environmental variables, including geographic factors, plant-community factors and soil physicochemical factors, all played non-negligible roles in affecting the microbial community structures directly or indirectly. Redundancy analysis and boosted regression tree analysis further highlighted the influences of soil pH and plant richness on microbial community compositions and diversity patterns. Taken together, these results suggest that the distribution pattern of soil microbial communities shows distinct changes along the latitudinal gradients in northeastern China and is predominantly mediated by soil pH and plant diversity.
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Affiliation(s)
- Baihui Ren
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Yuanman Hu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Baodong Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Zhang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Jan Thiele
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Rongjiu Shi
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Miao Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Rencang Bu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.
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121
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Shmakova LA, Karpov SA, Malavin SA, Smirnov AV. Morphology, biology and phylogeny of Phalansterium arcticum sp. n. (Amoebozoa, Variosea), isolated from ancient Arctic permafrost. Eur J Protistol 2018; 63:117-129. [PMID: 29574284 DOI: 10.1016/j.ejop.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
A new species, Phalansterium arcticum sp. n., was isolated from an 8580-year-old Arctic permafrost layer. This organism typically lives as a sedentary uniflagellated cell enclosed in a thin flexible mucilaginous sheath, but can form naked swimming cells and amoeboid cells with eruptive pseudopodia accompanied with the formation of short, filopodia-like projections. In an SSU rDNA phylogenetic tree, it robustly groups with other species of this genus. Along with a description of the species, we also add new details to the description of the cell division of Phalansterium and the feeding process in this organism.
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Affiliation(s)
- Lyubov A Shmakova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya 2, 142290, Pushchino, Moscow Region, Russian Federation.
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russian Federation; St. Petersburg State University, St. Petersburg 199034, Russian Federation
| | - Stanislav A Malavin
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya 2, 142290, Pushchino, Moscow Region, Russian Federation
| | - Alexey V Smirnov
- St. Petersburg State University, St. Petersburg 199034, Russian Federation
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122
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Robak MJ, Richards-Zawacki CL. Temperature-Dependent Effects of Cutaneous Bacteria on a Frog's Tolerance of Fungal Infection. Front Microbiol 2018; 9:410. [PMID: 29563909 PMCID: PMC5845872 DOI: 10.3389/fmicb.2018.00410] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/21/2018] [Indexed: 11/27/2022] Open
Abstract
Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community affect the susceptibility of amphibian hosts to infection by Batrachochytrium dendrobatidis (Bd), one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (Acris crepitans), prior to exposing these animals to Bd under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, Stenotrophomonas maltophilia, and one in which the frog’s skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of Bd infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to Bd infection and chytridiomycosis. However, we also predicted that this interaction would be temperature dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in Bd-exposed frogs. Whether temperature affected survival; however, it differed among our skin microbial treatment groups, with animals having more S. maltophilia on their skin surviving longer at 14 but not at 26°C. Our results suggest that temperature was the predominant factor influencing Bd’s ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host’s ability to survive (i.e., tolerate) a heavy Bd infection.
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Affiliation(s)
- Matthew J Robak
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - Corinne L Richards-Zawacki
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
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123
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Landscape topography structures the soil microbiome in arctic polygonal tundra. Nat Commun 2018; 9:777. [PMID: 29472560 PMCID: PMC5823929 DOI: 10.1038/s41467-018-03089-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 01/18/2018] [Indexed: 11/08/2022] Open
Abstract
In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions. The role of ecosystem structure in microbial activity related to greenhouse gas production is poorly understood. Here, Taş and colleagues show that microbial communities and ecosystem function vary across fine-scale topography in a polygonal tundra.
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124
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Wei S, Cui H, Zhu Y, Lu Z, Pang S, Zhang S, Dong H, Su X. Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes. Extremophiles 2018; 22:447-459. [PMID: 29429010 DOI: 10.1007/s00792-018-1007-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/05/2018] [Indexed: 11/28/2022]
Abstract
Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.
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Affiliation(s)
- Shiping Wei
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China. .,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.
| | - Hongpeng Cui
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Youhai Zhu
- Oil and Gas Survey, Geological Survey, Beijing, 100029, China
| | - Zhenquan Lu
- Oil and Gas Survey, Geological Survey, Beijing, 100029, China
| | - Shouji Pang
- Oil and Gas Survey, Geological Survey, Beijing, 100029, China
| | - Shuai Zhang
- Oil and Gas Survey, Geological Survey, Beijing, 100029, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China. .,School of Marine Sciences, China University of Geosciences, Beijing, 100083, China.
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125
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Perfumo A, Banat IM, Marchant R. Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications. Trends Biotechnol 2018; 36:277-289. [PMID: 29428461 DOI: 10.1016/j.tibtech.2017.10.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/17/2022]
Abstract
Approximately 80% of the Earth's biosphere is cold, at an average temperature of 5°C, and is populated by a diversity of microorganisms that are a precious source of molecules with high biotechnological potential. Biosurfactants from cold-adapted organisms can interact with multiple physical phases - water, ice, hydrophobic compounds, and gases - at low and freezing temperatures and be used in sustainable (green) and low-energy-impact (cold) products and processes. We review the biodiversity of microbial biosurfactants produced in cold habitats and provide a perspective on the most promising future applications in environmental and industrial technologies. Finally, we encourage exploring the cryosphere for novel types of biosurfactants via both culture screening and functional metagenomics.
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Affiliation(s)
- Amedea Perfumo
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.
| | - Ibrahim M Banat
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
| | - Roger Marchant
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, UK
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126
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Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, Grigoriev MN, Knoblauch C, Mangelsdorf K, Wagner D, Liebner S. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep 2018; 8:1291. [PMID: 29358665 PMCID: PMC5778128 DOI: 10.1038/s41598-018-19505-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022] Open
Abstract
Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.
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Affiliation(s)
- Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany.
| | - Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Pier P Overduin
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Periglacial Research, 14473, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Maria Winterfeld
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Geochemistry, 27570, Bremerhaven, Germany
| | - Ruud Rijkers
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | | | | | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
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127
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Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep 2018; 8:504. [PMID: 29323168 PMCID: PMC5765012 DOI: 10.1038/s41598-017-18777-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.
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128
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Pratama AA, van Elsas JD. The 'Neglected' Soil Virome - Potential Role and Impact. Trends Microbiol 2018; 26:649-662. [PMID: 29306554 DOI: 10.1016/j.tim.2017.12.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Accepted: 12/11/2017] [Indexed: 12/29/2022]
Abstract
Bacteriophages are among the most abundant and diverse biological units in the biosphere. They have contributed to our understanding of the central dogma of biology and have been instrumental in the evolutionary success of bacterial pathogens. In contrast to our current understanding of marine viral communities, the soil virome and its function in terrestrial ecosystems has remained relatively understudied. Here, we examine, in a comparative fashion, the knowledge gathered from studies performed in soil versus marine settings. We address the information with respect to the abundance, diversity, ecological significance, and effects of, in particular, bacteriophages on their host's evolutionary trajectories. We also identify the main challenges that soil virology faces and the studies that are required to accompany the current developments in marine settings.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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129
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Cabrol NA. The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures. ASTROBIOLOGY 2018; 18:1-27. [PMID: 29252008 PMCID: PMC5779243 DOI: 10.1089/ast.2017.1756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/27/2017] [Indexed: 05/09/2023]
Abstract
Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.
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130
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Yuan MM, Zhang J, Xue K, Wu L, Deng Y, Deng J, Hale L, Zhou X, He Z, Yang Y, Van Nostrand JD, Schuur EAG, Konstantinidis KT, Penton CR, Cole JR, Tiedje JM, Luo Y, Zhou J. Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil. GLOBAL CHANGE BIOLOGY 2018; 24:297-307. [PMID: 28715138 DOI: 10.1111/gcb.13820] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 05/27/2023]
Abstract
Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
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Affiliation(s)
- Mengting M Yuan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jin Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Kai Xue
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- University of Chinese Academy of Sciences, Beijing, China
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ye Deng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jie Deng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Xishu Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Edward A G Schuur
- Center for Ecosystem Sciences and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Christopher R Penton
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- School of Environment, Tsinghua University, Beijing, China
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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131
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Chen YL, Deng Y, Ding JZ, Hu HW, Xu TL, Li F, Yang GB, Yang YH. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Mol Ecol 2017; 26:6608-6620. [DOI: 10.1111/mec.14396] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 09/29/2017] [Accepted: 10/13/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Yong-Liang Chen
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Jin-Zhi Ding
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Tian-Le Xu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Gui-Biao Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Yuan-He Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
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132
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Madigan MT, Kempher ML, Bender KS, Sullivan P, Matthew Sattley W, Dohnalkova AC, Joye SB. Characterization of a cold-active bacterium isolated from the South Pole "Ice Tunnel". Extremophiles 2017; 21:891-901. [PMID: 28681112 DOI: 10.1007/s00792-017-0950-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/23/2017] [Indexed: 11/26/2022]
Abstract
Extremely cold microbial habitats on Earth (those below -30 °C) are rare and have not been surveyed for microbes as extensively as environments in the 0 to -20 °C range. Using cryoprotected growth media incubated at -5 °C, we enriched a cold-active Pseudomonas species from -50 °C ice collected from a utility tunnel for wastewater pipes under Amundsen-Scott South Pole Station, Antarctica. The isolate, strain UC-1, is related to other cold-active Pseudomonas species, most notably P. psychrophila, and grew at -5 °C to +34-37 °C; growth of UC-1 at +3 °C was significantly faster than at +34 °C. Strain UC-1 synthesized a surface exopolymer and high levels of unsaturated fatty acids under cold growth conditions. A 16S rRNA gene diversity screen of the ice sample that yielded strain UC-1 revealed over 1200 operational taxonomic units (OTUs) distributed across eight major classes of Bacteria. Many of the OTUs were Clostridia and Bacteriodia and some of these were probably of wastewater origin. However, a significant fraction of the OTUs were Proteobacteria and Actinobacteria of likely environmental origin. Our results shed light on the lower temperature limits to life and the possible existence of functional microbial communities in ultra-cold environments.
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Affiliation(s)
- Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Megan L Kempher
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Kelly S Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Paul Sullivan
- United States Antarctic Program, Amundsen-Scott Station, Antarctica
| | - W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | | | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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133
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La Ferla R, Azzaro M, Michaud L, Caruso G, Lo Giudice A, Paranhos R, Cabral AS, Conte A, Cosenza A, Maimone G, Papale M, Rappazzo AC, Guglielmin M. Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica). MICROBIAL ECOLOGY 2017; 74:402-415. [PMID: 28289836 DOI: 10.1007/s00248-017-0955-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 104-105) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.
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Affiliation(s)
- Rosabruna La Ferla
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy.
| | - Maurizio Azzaro
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Gabriella Caruso
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Angelina Lo Giudice
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Rodolfo Paranhos
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Anderson S Cabral
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Cosenza
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Giovanna Maimone
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Ciro Rappazzo
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant 3, Varese, Italy
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134
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Mackelprang R, Burkert A, Haw M, Mahendrarajah T, Conaway CH, Douglas TA, Waldrop MP. Microbial survival strategies in ancient permafrost: insights from metagenomics. ISME JOURNAL 2017; 11:2305-2318. [PMID: 28696425 PMCID: PMC5607373 DOI: 10.1038/ismej.2017.93] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/25/2017] [Accepted: 04/27/2017] [Indexed: 01/14/2023]
Abstract
In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.
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Affiliation(s)
- Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Alexander Burkert
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Monica Haw
- US Geological Survey, Menlo Park, CA, USA
| | - Tara Mahendrarajah
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | | | - Thomas A Douglas
- US Army Cold Regions Research and Engineering Laboratory, Fort Wainwright, AK, USA
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135
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Abstract
Antibiotic resistance is an ancient biological mechanism in bacteria, although its proliferation in our contemporary world has been amplified through antimicrobial therapy. Recent studies conducted on ancient environmental and human samples have uncovered numerous antibiotic-resistant bacteria and resistance genes. The resistance genes that have been reported from the analysis of ancient bacterial DNA include genes coding for several classes of antibiotics, such as glycopeptides, β-lactams, tetracyclines, and macrolides. The investigation of the resistome of ancient bacteria is a recent and emerging field of research, and technological advancements such as next-generation sequencing will further contribute to its growth. It is hoped that the knowledge gained from this research will help us to better understand the evolution of antibiotic resistance genes and will also be used in drug design as a proactive measure against antibiotic resistance.
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136
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Abstract
Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.
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Affiliation(s)
- Matthew D Surette
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
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137
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Cryosphere and Psychrophiles: Insights into a Cold Origin of Life? Life (Basel) 2017; 7:life7020025. [PMID: 28604605 PMCID: PMC5492147 DOI: 10.3390/life7020025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 11/23/2022] Open
Abstract
Psychrophiles thrive permanently in the various cold environments on Earth. Their unsuspected ability to remain metabolically active in the most extreme low temperature conditions provides insights into a possible cold step in the origin of life. More specifically, metabolically active psychrophilic bacteria have been observed at −20 °C in the ice eutectic phase (i.e., the liquid veins between sea ice crystals). In the context of the RNA world hypothesis, this ice eutectic phase would have provided stability to the RNA molecules and confinement of the molecules in order to react and replicate. This aspect has been convincingly tested by laboratory experiments.
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138
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Hotaling S, Hood E, Hamilton TL. Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate. Environ Microbiol 2017; 19:2935-2948. [PMID: 28419666 DOI: 10.1111/1462-2920.13766] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 11/29/2022]
Abstract
Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation. Here, we provide a modern synthesis of the microbial ecology of mountain glacier ecosystems, and particularly those at low- to mid-latitudes. We focus on five ecological zones: the supraglacial surface, englacial interior, subglacial bedrock-ice interface, proglacial streams and glacier forefields. For each, we discuss the role of microbiota in biogeochemical cycling and outline ecological and hydrological connections among zones, underscoring the interconnected nature of these ecosystems. Collectively, we highlight the need to: better document the biodiversity and functional roles of mountain glacier microbiota; describe the ecological implications of rapid glacial retreat under climate change and resolve the relative contributions of ecological zones to broader ecosystem function.
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Affiliation(s)
- Scott Hotaling
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - Eran Hood
- Department of Natural Science, University of Alaska Southeast, Juneau, AK, 99801, USA
| | - Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
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139
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Paranjape AR, Hall BD. Recent advances in the study of mercury methylation in aquatic systems. Facets (Ott) 2017. [DOI: 10.1139/facets-2016-0027] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
With increasing input of neurotoxic mercury to environments as a result of anthropogenic activity, it has become imperative to examine how mercury may enter biotic systems through its methylation to bioavailable forms in aquatic environments. Recent development of stable isotope-based methods in methylation studies has enabled a better understanding of the factors controlling methylation in aquatic systems. In addition, the identification and tracking of the hgcAB gene cluster, which is necessary for methylation, has broadened the range of known methylators and methylation-conducive environments. Study of abiotic factors in methylation with new molecular methods (the use of stable isotopes and genomic methods) has helped elucidate the confounding influences of many environmental factors, as these methods enable the examination of their direct effects instead of merely correlative observations. Such developments will be helpful in the finer characterization of mercury biogeochemical cycles, which will enable better predictions of the potential effects of climate change on mercury methylation in aquatic systems and, by extension, the threat this may pose to biota.
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Affiliation(s)
- Avnee R. Paranjape
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Britt D. Hall
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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140
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Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS, Burns BP, Ferrari BC. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods. Front Microbiol 2017; 8:591. [PMID: 28439263 PMCID: PMC5383709 DOI: 10.3389/fmicb.2017.00591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/22/2017] [Indexed: 01/07/2023] Open
Abstract
Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.
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Affiliation(s)
- Sarita Pudasaini
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - John Wilson
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Anne S Palmer
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
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141
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Potential microbial contamination during sampling of permafrost soil assessed by tracers. Sci Rep 2017; 7:43338. [PMID: 28230151 PMCID: PMC5322388 DOI: 10.1038/srep43338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/25/2017] [Indexed: 11/08/2022] Open
Abstract
Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.
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142
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Kashuba E, Dmitriev AA, Kamal SM, Melefors O, Griva G, Römling U, Ernberg I, Kashuba V, Brouchkov A. Ancient permafrost staphylococci carry antibiotic resistance genes. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1345574. [PMID: 28959177 PMCID: PMC5614383 DOI: 10.1080/16512235.2017.1345574] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/14/2017] [Indexed: 10/26/2022]
Abstract
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences. Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome. Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.
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Affiliation(s)
- Elena Kashuba
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Laboratory of Cancer Genetics, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU, Kyiv, Ukraine
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, New Cairo, Egypt
| | - Ojar Melefors
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Gennady Griva
- Siberian Branch of RAS, Institute of the Earth Cryosphere, Tyumen, Russia
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Anatoli Brouchkov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
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143
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Diversity and abundance of microbial eukaryotes in stream sediments from Svalbard. Polar Biol 2017; 40:1835-1843. [PMID: 32009726 PMCID: PMC6961512 DOI: 10.1007/s00300-017-2106-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 03/08/2017] [Accepted: 03/10/2017] [Indexed: 10/25/2022]
Abstract
Microbial eukaryotes are increasingly being recognised for their role in global biogeochemical cycles, yet very few studies have focussed on their distribution in high-latitude stream sediments, an important habitat which influences stream water nutrient chemistry. In this study, we present the first comparison of microbial eukaryotes from two different polar habitats by determining the abundance and taxonomic affiliation of 18S rRNA gene fragments recovered from four sediment samples in Svalbard: two from a glaciated catchment and two from an unglaciated permafrost-dominated catchment. Whilst there was no difference between the two catchments in terms of Rao's phylogenetic diversity (0.18±0.04, 1SD), the glaciated catchment samples had slightly higher richness (138-139) than the unglaciated catchment samples (67-106). At the phylum level, Ciliophora had the highest relative abundance in the samples from the glaciated catchment (32-63%), but only comprised 0-17% of the unglaciated catchment samples. Bacillariophyta was the most abundant phylum in one of the samples from the unglaciated catchment (43%) but phototrophic microbial eukaryotes only formed a minor component of the glaciated catchment samples (<2%), suggesting that in these environments the microbial eukaryotes are predominantly heterotrophic (chemotrophic). This is in contrast to previously published data from Robertson Glacier, Canada where the relative abundance of chlorophyta (phototrophs) in three samples was 48-57%. The contrast may be due to differences in glacial hydrology and/or geology, highlighting the variation in microbial eukaryote communities between nominally similar environments.
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144
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Brevik EC, Steffan JJ, Burgess LC, Cerdà A. Links Between Soil Security and the Influence of Soil on Human Health. PROGRESS IN SOIL SCIENCE 2017. [DOI: 10.1007/978-3-319-43394-3_24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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145
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Vishnyakov IE, Borchsenius SN, Kayumov AR, Rivkina EM. Mycoplasma Diversity in Arctic Permafrost. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-016-0280-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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146
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Kim HM, Lee MJ, Jung JY, Hwang CY, Kim M, Ro HM, Chun J, Lee YK. Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra. J Microbiol 2016; 54:713-723. [DOI: 10.1007/s12275-016-6294-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/29/2016] [Accepted: 09/20/2016] [Indexed: 01/14/2023]
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147
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Crevecoeur S, Vincent WF, Lovejoy C. Environmental selection of planktonic methanogens in permafrost thaw ponds. Sci Rep 2016; 6:31312. [PMID: 27501855 PMCID: PMC4977513 DOI: 10.1038/srep31312] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/18/2016] [Indexed: 01/07/2023] Open
Abstract
The warming and thermal erosion of ice-containing permafrost results in thaw ponds that are strong emitters of methane to the atmosphere. Here we examined methanogens and other Archaea, in two types of thaw ponds that are formed by the collapse of either permafrost peat mounds (palsas) or mineral soil mounds (lithalsas) in subarctic Quebec, Canada. Using high-throughput sequencing of a hypervariable region of 16S rRNA, we determined the taxonomic structure and diversity of archaeal communities in near-bottom water samples, and analyzed the mcrA gene transcripts from two sites. The ponds at all sites were well stratified, with hypoxic or anoxic bottom waters. Their archaeal communities were dominated by Euryarchaeota, specifically taxa in the methanogenic orders Methanomicrobiales and Methanosarcinales, indicating a potentially active community of planktonic methanogens. The order Methanomicrobiales accounted for most of the mcrA transcripts in the two ponds. The Archaeal communities differed significantly between the lithalsa and palsa ponds, with higher alpha diversity in the organic-rich palsa ponds, and pronounced differences in community structure. These results indicate the widespread occurrence of planktonic, methane-producing Archaea in thaw ponds, with environmental selection of taxa according to permafrost landscape type.
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Affiliation(s)
- Sophie Crevecoeur
- Département de Biologie, Centre d'études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
| | - Warwick F Vincent
- Département de Biologie, Centre d'études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada
| | - Connie Lovejoy
- Département de Biologie, Centre d'études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, QC G1V 0A6, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada.,Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada
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148
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Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes. Trends Microbiol 2016; 24:600-610. [DOI: 10.1016/j.tim.2016.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 11/24/2022]
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149
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Silva LCR, Sun G, Zhu-Barker X, Liang Q, Wu N, Horwath WR. Tree growth acceleration and expansion of alpine forests: The synergistic effect of atmospheric and edaphic change. SCIENCE ADVANCES 2016; 2:e1501302. [PMID: 27652334 PMCID: PMC5020709 DOI: 10.1126/sciadv.1501302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 08/08/2016] [Indexed: 05/30/2023]
Abstract
Many forest ecosystems have experienced recent declines in productivity; however, in some alpine regions, tree growth and forest expansion are increasing at marked rates. Dendrochronological analyses at the upper limit of alpine forests in the Tibetan Plateau show a steady increase in tree growth since the early 1900s, which intensified during the 1930s and 1960s, and have reached unprecedented levels since 1760. This recent growth acceleration was observed in small/young and large/old trees and coincided with the establishment of trees outside the forest range, reflecting a connection between the physiological performance of dominant species and shifts in forest distribution. Measurements of stable isotopes (carbon, oxygen, and nitrogen) in tree rings indicate that tree growth has been stimulated by the synergistic effect of rising atmospheric CO2 and a warming-induced increase in water and nutrient availability from thawing permafrost. These findings illustrate the importance of considering soil-plant-atmosphere interactions to understand current and anticipate future changes in productivity and distribution of forest ecosystems.
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Affiliation(s)
- Lucas C R Silva
- Environmental Studies Program and Department of Geography, University of Oregon, Eugene, OR 97403, USA
| | - Geng Sun
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, China
| | - Xia Zhu-Barker
- Department of Land, Air, and Water Resources, University of California, Davis, CA 95616, USA
| | - Qianlong Liang
- College of Life Science, Sichuan University, Sichuan 610041, China
| | - Ning Wu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, China
| | - William R Horwath
- Department of Land, Air, and Water Resources, University of California, Davis, CA 95616, USA
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150
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Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr 2016; 4:10.1128/microbiolspec.EMF-0006-2015. [PMID: 27726770 PMCID: PMC5287379 DOI: 10.1128/microbiolspec.emf-0006-2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
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