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Preston LJ, Jungblut AD, Montgomery W, Ballard CJ, Wilbraham J. The Preservation and Spectral Detection of Historic Museum Specimen Microbial Mat Biosignatures Within Martian Dust: Lessons Learned for Mars Exploration and Sample Return. ASTROBIOLOGY 2024; 24:684-697. [PMID: 38979614 DOI: 10.1089/ast.2023.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The key building blocks for life on Mars could be preserved within potentially habitable paleo-depositional settings with their detection possible by utilizing mid-infrared spectroscopy; however, a definite identification and confirmation of organic or even biological origin will require the samples to be returned to Earth. In the present study, Fourier-transform infrared (FTIR) spectroscopic techniques were used to characterize both mineralogical and organic materials within Mars dust simulant JSC Mars-1 and ancient Antarctic cyanobacterial microbial mats from 1901 to 1904 Discovery Expedition. When FTIR spectroscopy is applied to cyanobacterial microbial mat communities, the resulting spectra will reflect the average biochemical composition of the mats rather than taxa-specific spectral patterns of the individual organisms and can thus be considered as a total chemical analysis of the mat colony. This study also highlights the potential difficulties in the detection of these communities on Mars and which spectral biosignatures will be most detectable within geological substrates. Through the creation and analysis of a suite of dried microbial mat material and Martian dust simulant mixtures, the spectral signatures and wavenumber positions of CHx aliphatic hydrocarbons and the C-O and O-H bands of polysaccharides remained detectable and may be detectable within sample mixtures obtained through Mars Sample Return activities.
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Affiliation(s)
- Louisa J Preston
- Department of Space & Climate Physics, Mullard Space Science Laboratory, University College London, Dorking, United Kingdom
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Wren Montgomery
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Connor J Ballard
- Department of Space & Climate Physics, Mullard Space Science Laboratory, University College London, Dorking, United Kingdom
| | - Jo Wilbraham
- Life Sciences Department, Natural History Museum, London, United Kingdom
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Medeiros W, Hidalgo K, Leão T, de Carvalho LM, Ziemert N, Oliveira V. Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients. Microbiol Spectr 2024; 12:e0024424. [PMID: 38747631 PMCID: PMC11237469 DOI: 10.1128/spectrum.00244-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.
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Affiliation(s)
- William Medeiros
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
- Interfaculty Institute of Microbiology, and Infection Medicine Institute for Bioinformatics and Medical Informatics, German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Kelly Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
| | - Tiago Leão
- Chemistry Institute, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Lucas Miguel de Carvalho
- Center for Computing in Engineering and Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology, and Infection Medicine Institute for Bioinformatics and Medical Informatics, German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Valeria Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
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Vipindas PV, Venkatachalam S, Jabir T, Yang EJ, Jung J, Jain A, Krishnan KP. Salinity-controlled distribution of prokaryotic communities in the Arctic sea-ice melt ponds. World J Microbiol Biotechnol 2023; 40:25. [PMID: 38057653 DOI: 10.1007/s11274-023-03850-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
The thawing of snow and sea ice produces distinctive melt ponds on the surface of the Arctic sea ice, which covers a significant portion of the surface sea ice during summer. Melt-pond salinity impacts heat transfer to the ice below and the melting rate. It is widely known that melt ponds play a significant role in heat fluxes, ice-albedo feedback, and sea-ice energy balance. However, not much attention has been given to the fact that melt ponds also serve as a unique microbial ecosystem where microbial production begins as soon as they are formed. Here, we investigated the role of melt pond salinity in controlling the diversity and distribution of prokaryotic communities using culture-dependent and -independent approaches. The 16 S rRNA gene amplicon based next generation sequencing analysis retrieved a total of 14 bacterial phyla, consisting of 146 genera, in addition to two archaeal phyla. Further, the culture-dependent approaches of the study allowed for the isolation and identification of twenty-four bacterial genera in pure culture. Flavobacterium, Candidatus_Aquiluna, SAR11 clade, Polaribacter, Glaciecola, and Nonlabens were the dominant genera observed in the amplicon analysis. Whereas Actimicrobium, Rhodoglobus, Flavobacterium, and Pseudomonas were dominated in the culturable fraction. Our results also demonstrated that salinity, chlorophyll a, and dissolved organic carbon were the significant environmental variables controlling the prokaryotic community distribution in melt ponds. A significant community shift was observed in melt ponds when the salinity changed with the progression of melting and deepening of ponds. Different communities were found to be dominant in melt ponds with different salinity ranges. It was also observed that melt pond prokaryotic communities significantly differed from the surface ocean microbial community. Our observations suggest that complex prokaryotic communities develop in melt ponds immediately after its formation using dissolved organic carbon generated through primary production in the oligotrophic water.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India.
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Polar Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama, Goa, 403 804, India
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Kollár J, Kopalová K, Kavan J, Vrbická K, Nývlt D, Nedbalová L, Stibal M, Kohler TJ. Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts. FEMS Microbiol Ecol 2023; 99:fiad087. [PMID: 37516444 PMCID: PMC10446143 DOI: 10.1093/femsec/fiad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023] Open
Abstract
Glacier recession is creating new water bodies in proglacial forelands worldwide, including Antarctica. Yet, it is unknown how microbial communities of recently formed "young" waterbodies (originating decades to a few centuries ago) compare with established "old" counterparts (millennia ago). Here, we compared benthic microbial communities of different lake types on James Ross Island, Antarctic Peninsula, using 16S rDNA metabarcoding and light microscopy to explore bacterial and diatom communities, respectively. We found that the older lakes host significantly more diverse bacterial and diatom communities compared to the young ones. To identify potential mechanisms for these differences, linear models and dbRDA analyses suggested combinations of water temperature, pH, and conductivity to be the most important factors for diversity and community structuring, while differences in geomorphological and hydrological stability, though more difficult to quantify, are likely also influential. These results, along with an indicator species analysis, suggest that physical and chemical constraints associated with individual lakes histories are likely more influential to the assembly of the benthic microbial communities than lake age alone. Collectively, these results improve our understanding of microbial community drivers in Antarctic freshwaters, and help predict how the microbial landscape may shift with future habitat creation within a changing environment.
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Affiliation(s)
- Jan Kollár
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Kateřina Kopalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Jan Kavan
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Alfred Jahn Cold Regions Research Centre, University of Wroclaw, pl. Uniwersytecki 1, Wroclaw 50-137, Poland
| | - Kristýna Vrbická
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Daniel Nývlt
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Linda Nedbalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Marek Stibal
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
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Wada T, Kudoh S, Koyama H, Iakovenko N, Elster J, Kvíderová J, Otani M, Shimada S, Imura S. Abundance and biomass of Bdelloid rotifers in the microbial mats from East Antarctica: The ecological relations between microscopic phototrophs and invertebrates. Ecol Res 2022. [DOI: 10.1111/1440-1703.12368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Tomotake Wada
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
| | - Sakae Kudoh
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
- National Institute of Polar Research Research Organization of Information and Systems Tokyo Japan
| | - Hiroshi Koyama
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
| | - Nataliia Iakovenko
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Prague Czechia
- Department of Biology and Ecology, Faculty of Science University of Ostrava Ostrava Czechia
- Department of Invertebrate Fauna and Systematics Schmalhausen Institute of Zoology NAS of Ukraine Kiev Ukraine
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics AS ČR Liběchov Czech Republic
| | - Josef Elster
- Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czechia
- Centre for Polar Ecology University of South Bohemia České Budějovice Czechia
| | - Jana Kvíderová
- Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czechia
- Centre for Polar Ecology University of South Bohemia České Budějovice Czechia
| | | | - Sho Shimada
- Department of Microbiology and Infectious Diseases Toho University School of Medicine Tokyo Japan
- Department of Respiratory Medicine Tokyo Medical and Dental University Tokyo Japan
| | - Satoshi Imura
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
- National Institute of Polar Research Research Organization of Information and Systems Tokyo Japan
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Akulava V, Miamin U, Akhremchuk K, Valentovich L, Dolgikh A, Shapaval V. Isolation, Physiological Characterization, and Antibiotic Susceptibility Testing of Fast-Growing Bacteria from the Sea-Affected Temporary Meltwater Ponds in the Thala Hills Oasis (Enderby Land, East Antarctica). BIOLOGY 2022; 11:biology11081143. [PMID: 36009770 PMCID: PMC9404859 DOI: 10.3390/biology11081143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022]
Abstract
Simple Summary The characterization of microbial communities from Antarctic temporary meltwater ponds is limited, while they could serve as a source of biotechnologically interesting microorganisms. In this study, we characterized a set of bacteria isolated from the sea-affected temporary meltwater ponds in the East Antarctica area of the Vecherny region of the Thala Hills Oasis, Enderby Land. The isolated meltwater bacteria were identified as Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, where Proteobacteria and Actinobacteria were predominant. The isolated bacteria were able to grow in a relatively wide temperature range between 4 °C and 37 °C, with an optimal temperature range of 18–25 °C. Further, most of the isolates showed an ability to secrete lipases and proteases, and several of them were pigmented. Bacterial isolates from the genera Pseudomonas and Acinetobacter exhibited multi-resistance against β-lactams, sulfonamide, macrolide, diaminopyrimidines, and chloramphenicol antibiotics. This study shows that bacterial communities from the temporary meltwater ponds in East Antarctica consist of metabolically versatile bacteria that might be defined by their location near the sea and the close presence of animals, penguins and skuas in particular. Abstract In this study, for the first time, we report the identification and characterization of culturable fast-growing bacteria isolated from the sea-affected temporary meltwater ponds (MPs) in the East Antarctica area of the Vecherny region (−67.656317, 46.175058) of the Thala Hills Oasis, Enderby Land. Water samples from the studied MPs showed alkaline pH (from 8.0 to 10.1) and highly varied total dissolved solids (86–94,000 mg/L). In total, twenty-nine bacterial isolates were retrieved from the studied MPs. The phylogenetic analysis based on 16S rRNA gene sequence similarities showed that the isolated bacteria belong to the phyla Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes and the twelve genera Pseudomonas, Shewanella, Acinetobacter, Sporosarcina, Facklamia, Carnobacterium, Arthrobacter, Brachybacterium, Micrococcus, Agrococcus, Leifsonia, and Flavobacterium. Most of the isolated bacteria were psychrotrophs and showed the production of one or more extracellular enzymes. Lipolytic and proteolytic activities were more prevalent among the isolates. Five isolates from the Actinobacteria phylum and one isolate from the Bacteroidetes phylum had strong pigmentation. Antibiotic susceptibility testing revealed that most of the isolates are resistant to at least one antibiotic, and seven isolates showed multi-resistance.
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Affiliation(s)
- Volha Akulava
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway;
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus; (U.M.); (L.V.)
- Correspondence:
| | - Uladzislau Miamin
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus; (U.M.); (L.V.)
- Scientific and Practical Center of the National Academy of Sciences of Belarus for Bioresources, 220072 Minsk, Belarus
| | - Katsiaryna Akhremchuk
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus;
| | - Leonid Valentovich
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus; (U.M.); (L.V.)
- Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus;
| | - Andrey Dolgikh
- Institute of Geography, Russian Academy of Sciences, 119017 Moscow, Russia;
| | - Volha Shapaval
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1432 Ås, Norway;
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Evans TW, Kalambokidis MJ, Jungblut AD, Millar JL, Bauersachs T, Grotheer H, Mackey TJ, Hawes I, Summons RE. Lipid Biomarkers From Microbial Mats on the McMurdo Ice Shelf, Antarctica: Signatures for Life in the Cryosphere. Front Microbiol 2022; 13:903621. [PMID: 35756013 PMCID: PMC9232131 DOI: 10.3389/fmicb.2022.903621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Persistent cold temperatures, a paucity of nutrients, freeze-thaw cycles, and the strongly seasonal light regime make Antarctica one of Earth's least hospitable surface environments for complex life. Cyanobacteria, however, are well-adapted to such conditions and are often the dominant primary producers in Antarctic inland water environments. In particular, the network of meltwater ponds on the 'dirty ice' of the McMurdo Ice Shelf is an ecosystem with extensive cyanobacteria-dominated microbial mat accumulations. This study investigated intact polar lipids (IPLs), heterocyte glycolipids (HGs), and bacteriohopanepolyols (BHPs) in combination with 16S and 18S rRNA gene diversity in microbial mats of twelve ponds in this unique polar ecosystem. To constrain the effects of nutrient availability, temperature and freeze-thaw cycles on the lipid membrane composition, lipids were compared to stromatolite-forming cyanobacterial mats from ice-covered lakes in the McMurdo Dry Valleys as well as from (sub)tropical regions and hot springs. The 16S rRNA gene compositions of the McMurdo Ice Shelf mats confirm the dominance of Cyanobacteria and Proteobacteria while the 18S rRNA gene composition indicates the presence of Ochrophyta, Chlorophyta, Ciliophora, and other microfauna. IPL analyses revealed a predominantly bacterial community in the meltwater ponds, with archaeal lipids being barely detectable. IPLs are dominated by glycolipids and phospholipids, followed by aminolipids. The high abundance of sugar-bound lipids accords with a predominance of cyanobacterial primary producers. The phosphate-limited samples from the (sub)tropical, hot spring, and Lake Vanda sites revealed a higher abundance of aminolipids compared to those of the nitrogen-limited meltwater ponds, affirming the direct affects that N and P availability have on IPL compositions. The high abundance of polyunsaturated IPLs in the Antarctic microbial mats suggests that these lipids provide an important mechanism to maintain membrane fluidity in cold environments. High abundances of HG keto-ols and HG keto-diols, produced by heterocytous cyanobacteria, further support these findings and reveal a unique distribution compared to those from warmer climates.
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Affiliation(s)
- Thomas W. Evans
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Maria J. Kalambokidis
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Anne D. Jungblut
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Jasmin L. Millar
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Thorsten Bauersachs
- Institute of Geosciences, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Hendrik Grotheer
- Marine Geochemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Tyler J. Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Roger E. Summons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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Lezcano MÁ, Sánchez-García L, Quesada A, Carrizo D, Fernández-Martínez MÁ, Cavalcante-Silva E, Parro V. Comprehensive Metabolic and Taxonomic Reconstruction of an Ancient Microbial Mat From the McMurdo Ice Shelf (Antarctica) by Integrating Genetic, Metaproteomic and Lipid Biomarker Analyses. Front Microbiol 2022; 13:799360. [PMID: 35928160 PMCID: PMC9345047 DOI: 10.3389/fmicb.2022.799360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Paleobiological reconstructions based on molecular fossils may be limited by degradation processes causing differential preservation of biomolecules, the distinct taxonomic specificity of each biomolecule type, and analytical biases. Here, we combined the analysis of DNA, proteins and lipid biomarkers using 16S and 18S rRNA gene metabarcoding, metaproteomics and lipid analysis to reconstruct the taxonomic composition and metabolisms of a desiccated microbial mat from the McMurdo Ice Shelf (MIS) (Antarctica) dated ~1,000 years BP. The different lability, taxonomic resolution and analytical bias of each biomolecule type led to a distinct microbial community profile. DNA analysis showed selective preservation of DNA remnants from the most resistant taxa (e.g., spore-formers). In contrast, the proteins profile revealed microorganisms missed by DNA sequencing, such as Cyanobacteria, and showed a microbial composition similar to fresh microbial mats in the MIS. Lipid hydrocarbons also confirmed Cyanobacteria and suggested the presence of mosses or vascular plant remnants from a period in Antarctica when the climate was warmer (e.g., Mid-Miocene or Eocene). The combined analysis of the three biomolecule types also revealed diverse metabolisms that operated in the microbial mat before desiccation: oxygenic and anoxygenic photosynthesis, nitrogen fixation, nitrification, denitrification, sulfur reduction and oxidation, and methanogenesis. Therefore, the joint analysis of DNA, proteins and lipids resulted in a powerful approach that improved taxonomic and metabolic reconstructions overcoming information gaps derived from using individual biomolecules types.
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Affiliation(s)
- María Ángeles Lezcano
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- *Correspondence: María Ángeles Lezcano,
| | | | - Antonio Quesada
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
- Departamento de Biología, C. Darwin 2, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
| | | | | | - Víctor Parro
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir, Madrid, Spain
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Sivasankar P, Poongodi S, Sivakumar K, Al-Qahtani WH, Arokiyaraj S, Jothiramalingam R. Exogenous production of cold-active cellulase from polar Nocardiopsis sp. with increased cellulose hydrolysis efficiency. Arch Microbiol 2022; 204:218. [PMID: 35333982 DOI: 10.1007/s00203-022-02830-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/08/2022] [Indexed: 12/01/2022]
Abstract
The present work was designed to isolate and characterise the actinobacteria in the Polar Front region of the Southern Ocean waters and species of Nocardiopsis and Streptomyces were identified. Among those, the psychrophilic actinobacterium, Nocardiopsis dassonvillei PSY13 was found to have good cellulolytic activity and it was further studied for the production and characterisation of cold-active cellulase enzyme. The latter was found to have a specific activity of 6.36 U/mg and a molar mass of 48 kDa with a 22.9-fold purification and 5% recovery at an optimum pH of 7.5 and a temperature of 10 °C. Given the importance of psychrophilic actinobacteria, N. dassonvillei PSY13 can be further exploited for its benefits, meaning that the Southern Ocean harbours biotechnologically important microorganisms that can be further explored for versatile biotechnological and industrial applications.
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Affiliation(s)
- Palaniappan Sivasankar
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland. .,Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India.
| | - Subramaniam Poongodi
- Department of Microbiology, Shri Sakthikailassh Women's College, Salem, 636 003, Tamil Nadu, India
| | - Kannan Sivakumar
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | - Wahidah H Al-Qahtani
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Selvaraj Arokiyaraj
- Department of Food Science and Biotechnology, Sejong University, Seoul, South Korea
| | - R Jothiramalingam
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
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Krucon T, Dziewit L, Drewniak L. Insight Into Ecology, Metabolic Potential, and the Taxonomic Composition of Bacterial Communities in the Periodic Water Pond on King George Island (Antarctica). Front Microbiol 2021; 12:708607. [PMID: 34690951 PMCID: PMC8531505 DOI: 10.3389/fmicb.2021.708607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Polar regions contain a wide variety of lentic ecosystems. These include periodic ponds that have a significant impact on carbon and nitrogen cycling in polar environments. This study was conducted to assess the taxonomic and metabolic diversity of bacteria found in Antarctic pond affected by penguins and sea elephants and to define their role in ongoing processes. Metabolic assays showed that of the 168 tested heterotrophic bacteria present in the Antarctic periodic pond, 96% are able to degrade lipids, 30% cellulose, 26% proteins, and 26% starch. The taxonomic classification of the obtained isolates differs from that based on the composition of the 16S rRNA relative abundances in the studied pond. The dominant Actinobacteria constituting 45% of isolates represents a low proportion of the community, around 4%. With the addition of run-off, the proportions of inhabiting bacteria changed, including a significant decrease in the abundance of Cyanobacteria, from 2.38 to 0.33%, increase of Firmicutes from 9.32 to 19.18%, and a decreasing richness (Chao1 index from 1299 to 889) and diversity (Shannon index from 4.73 to 4.20). Comparative studies of communities found in different Antarctic environments indicate a great role for penguins in shaping bacterial populations.
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Affiliation(s)
- Tomasz Krucon
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Hawes I, Howard-Williams C, Gilbert N, Joy K. Towards an Environmental Classification of Lentic Aquatic Ecosystems in the McMurdo Dry Valleys, Antarctica. ENVIRONMENTAL MANAGEMENT 2021; 67:600-622. [PMID: 33559688 DOI: 10.1007/s00267-021-01438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The McMurdo Dry Valleys are the largest single ice-free area in Antarctica, and of considerable scientific and conservation value as an extreme polar desert. This is recognised through the McMurdo Dry Valleys Antarctic Specially Managed Area (ASMA), where management's goals focus on protection of its unique features, while facilitating science access. Using a mix of remote sensing and existing cartography, we have identified over 6000 lakes and ponds in the ASMA. This study develops a classification of those aquatic ecosystems to provide a framework for management. It uses a limited top-down, hierarchical classification to define 13 class separations based on physical attributes that could largely be ascribed from existing databases or remotely sensed information. The first hierarchical level was based on landscape position, separating coastal kettle holes (reflecting recent glacial history), from other "topographic" water bodies. The second level was based on endorheic vs exorheic drainage, the third on mid-summer ice condition (no-ice cap; ice capped; frozen to base) and the fourth on source of inflow (glacial or non-glacial). Kettles were sub-classed by mid-summer ice only. Classes were tested against a set of field observations and an expert workshop validation process considered management implications for the ASMA. This study shows how the classification assists our understanding of Dry Valley landscapes and addresses management issues faced by researchers, environmental managers and policy makers. The approach to classification, rather than the detailed classes that may be specific to the Dry Valleys, has potential for wider use in other polar landscapes.
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Affiliation(s)
- Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Sulphur Point, Tauranga, 3110, New Zealand.
| | - Clive Howard-Williams
- National Institute of Water and Atmospheric Research, Lt Box 8602, Christchurch, New Zealand
| | - Neil Gilbert
- Constantia Consulting Ltd, 310 Papanui Road, Christchurch, 8052, New Zealand
| | - Kurt Joy
- Department of Biological Science, University of Waikato, Hamilton, New Zealand
- Orbica Ltd, 128 Litchfield St., Christchurch, 8011, New Zealand
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12
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16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.
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The Impact of Air Pollution on Intestinal Microbiome of Asthmatic Children: A Panel Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5753427. [PMID: 33204702 PMCID: PMC7661118 DOI: 10.1155/2020/5753427] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/05/2020] [Accepted: 10/18/2020] [Indexed: 12/22/2022]
Abstract
Air pollution could impact on the alteration of intestinal microbiome. Maturation of intestinal microbiome in early life played an important role in the development of allergic diseases, including asthma. Recent studies presented an increase in the evidence of association between the shift of gut microbiota and asthma. This article is aimed at exploring whether the alteration in the intestinal microbiome triggered by a short wave of air pollution could influence the colonization of bacteria that have been related to the immunological mechanisms of the asthma attack. The impact of air pollution on intestinal microbiome was assessed by longitudinal comparison. Fecal samples were collected twice for twenty-one children in clean and smog days, respectively, including eleven asthmatic children and ten healthy children. Intestinal bacteria were discriminated by using the method of 16S rRNA gene sequence. The results showed that the composition of intestinal microbiome changed between clean and smog days among all children (PERMANOVA, P = 0.03). During smog days, Bifidobacteriaceae, Erysipelotrichaceae, and Clostridium sensu stricto 1 decreased, and Streptococcaceae, Porphyromonadaceae, Rikenellaceae, Bacteroidales S24-7 group, and Bacteroides increased in asthmatic children (Wilcoxon test, P < 0.05), while Fusicatenibacter decreased and Rikenellaceae and Terrisporobacter increased in healthy children (Wilcoxon test, P < 0.05). After controlling for food consumption, the relative abundance of some bacteria belonging to Firmicutes negatively associated with concentration of PM2.5, PM10, NO2, and SO2 (multiple linear regression, P < 0.05). This study demonstrated that short wave of air pollution had an impact on the intestinal microbiome of asthmatic children. Intestinal bacteria, which have been related to immunological mechanisms of asthma attack, were also found to be associated with air pollution. This finding suggested that a short wave of air pollution may trigger asthma by impacting on intestinal bacteria.
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14
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A glance at the gut microbiota of five experimental animal species through fecal samples. Sci Rep 2020; 10:16628. [PMID: 33024229 PMCID: PMC7538948 DOI: 10.1038/s41598-020-73985-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Experimental animals including the ferret, marmoset, woodchuck, mini pig, and tree shrew have been used in biomedical research. However, their gut microbiota have not been fully investigated. In this study, the gut microbiota of these five experimental animals were analyzed with 16S rRNA sequencing. The phyla Firmicutes, Bacteroidetes, and Fusobacteria were present in the gut microbiota of all the species. Specific phyla were present in different animals: Proteobacteria in the ferret, Tenericutes in the marmoset, and Spirochaetes in the mini pig. Fusobacterium and unidentified Clostridiales were the dominant genera in the ferret, whereas Libanicoccus, Lactobacillus, Porphyromonas, and Peptoclostridium were specific to marmoset, mini pig, woodchuck, and tree shrew, respectively. A clustering analysis showed that the overall distribution of microbial species in the guts of these species mirrored their mammalian phylogeny, and the microbiota of the marmoset and tree shrew showed the closest bray_curtis distances to that of humans. PICRUSt functional prediction separated the woodchuck from the other species, which may reflect its herbivorous diet. In conclusion, both the evolutionary phylogeny and daily diet affect the gut microbiota of these experimental animals, which should not be neglected for their usage in biomedical research.
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15
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Huang IS, Pinnell LJ, Turner JW, Abdulla H, Boyd L, Linton EW, Zimba PV. Preliminary Assessment of Microbial Community Structure of Wind-Tidal Flats in the Laguna Madre, Texas, USA. BIOLOGY 2020; 9:E183. [PMID: 32707990 PMCID: PMC7464120 DOI: 10.3390/biology9080183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022]
Abstract
Aside from two samples collected nearly 50 years ago, little is known about the microbial composition of wind tidal flats in the hypersaline Laguna Madre, Texas. These mats account for ~42% of the lagoon's area. These microbial communities were sampled at four locations that historically had mats in the Laguna Madre, including Laguna Madre Field Station (LMFS), Nighthawk Bay (NH), and two locations in Kenedy Ranch (KRN and KRS). Amplicon sequencing of 16S genes determined the presence of 51 prokaryotic phyla dominated by Bacteroidota, Chloroflexi, Cyanobacteria, Desulfobacteria, Firmicutes, Halobacteria, and Proteobacteria. The microbial community structure of NH and KR is significantly different to LMFS, in which Bacteroidota and Proteobacteria were most abundant. Twenty-three cyanobacterial taxa were identified via genomic analysis, whereas 45 cyanobacterial taxa were identified using morphological analysis, containing large filamentous forms on the surface, and smaller, motile filamentous and coccoid forms in subsurface mat layers. Sample sites were dominated by species in Oscillatoriaceae (i.e., Lyngbya) and Coleofasciculaceae (i.e., Coleofasciculus). Most cyanobacterial sequences (~35%) could not be assigned to any established taxa at the family/genus level, given the limited knowledge of hypersaline cyanobacteria. A total of 73 cyanobacterial bioactive metabolites were identified using ultra performance liquid chromatography-Orbitrap MS analysis from these commu nities. Laguna Madre seems unique compared to other sabkhas in terms of its microbiology.
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Affiliation(s)
- I.-Shuo Huang
- Center for Coastal Studies, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA;
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, USA
| | - Lee J. Pinnell
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA; (L.J.P.); (J.W.T.)
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Jeffrey W. Turner
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA; (L.J.P.); (J.W.T.)
| | - Hussain Abdulla
- Department of Physical and Environmental Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA;
| | - Lauren Boyd
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA; (L.B.); (E.W.L.)
| | - Eric W. Linton
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA; (L.B.); (E.W.L.)
| | - Paul V. Zimba
- Center for Coastal Studies, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA;
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16
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Shen N, Liang Z, Chen Y, Song H, Wan J. Enhancement of syntrophic acetate oxidation pathway via single walled carbon nanotubes addition under high acetate concentration and thermophilic condition. BIORESOURCE TECHNOLOGY 2020; 306:123182. [PMID: 32199400 DOI: 10.1016/j.biortech.2020.123182] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
The effect of single walled carbon nanotubes (SWCNT) on methane production under high acetate concentration and thermophilic condition was evaluated. An isotope labeling experiment verified that >85% of methane was generated from syntrophic acetate oxidation (SAO) at 50, 100 and 150 mM acetate and almost 100% at 200 mM. SWCNT addition had little effect on the methanogenesis pathway, whereas it accelerated methane production via decreasing lag phase times and increasing maximum methane production rates. Electrochemical impedance spectroscopy (EIS) results revealed the electrical resistivity of sludge in groups of SWCNT was distinctly smaller than CK groups, indicating higher sludge conductivity was achieved. Further, the results of communities described that Coprothermobacter and Thermacetogenium played the most important role in SAO under all conditions. Meanwhile, the enriched Thermacetogenium and direct interspecies electron transfer (DIET) pathway in SAO consortia contributed to the acceleration of methane production via SWCNT addition.
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Affiliation(s)
- Nan Shen
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Zhu Liang
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Yun Chen
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, People's Republic of China.
| | - Hailiang Song
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, People's Republic of China
| | - Junfeng Wan
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, Henan 450001, People's Republic of China
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17
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Airborne microbial transport limitation to isolated Antarctic soil habitats. Nat Microbiol 2019; 4:925-932. [DOI: 10.1038/s41564-019-0370-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/15/2019] [Indexed: 11/08/2022]
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18
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Sommers P, Darcy JL, Porazinska DL, Gendron EMS, Fountain AG, Zamora F, Vincent K, Cawley KM, Solon AJ, Vimercati L, Ryder J, Schmidt SK. Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica. Front Microbiol 2019; 10:65. [PMID: 30778338 PMCID: PMC6369369 DOI: 10.3389/fmicb.2019.00065] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We extracted DNA and chlorophyll a from the sediments and water of these samples to describe biodiversity and quantify proxies for biomass. Contrary to our expectation, we found that cryoconite holes with greater richness and biomass showed less partitioning of phylotypes by the sediments versus the water, perhaps indicating that the probability of sediment microbes being mixed into the water is higher from richer sediments. Another explanation may be that organisms from the water were compressed by freezing down to the sediment layer, leaving primarily relic DNA of dead cells to be detected higher in the frozen water. Further evidence of this explanation is that the dominant sequences unique to water closely matched organisms that do not live in cryoconite holes or the Dry Valleys (e.g., vertebrates); so this cryptic biodiversity could represent unknown microbial animals or DNA from atmospheric deposition of dead biomass in the otherwise low-biomass water. Although we cannot rule out spatial niche partitioning occurring at finer scales or in melted cryoconite holes, we found no evidence of partitioning between the sediments and water in frozen holes. Future work should include more sampling of cryoconite holes at a finer spatial scale, and characterizing the communities of the sediments and water when cryoconite holes are melted and active.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - John L Darcy
- Department of Botany, University of Hawai'i Mānoa, Honolulu, HI, United States
| | - Dorota L Porazinska
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States.,Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Eli M S Gendron
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Andrew G Fountain
- Geology Department, Portland State University, Portland, OR, United States
| | - Felix Zamora
- Geology Department, Portland State University, Portland, OR, United States
| | - Kim Vincent
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Kaelin M Cawley
- National Ecological Observatory Network Operated by Battelle, Boulder, CO, United States.,Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Adam J Solon
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Lara Vimercati
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Jenna Ryder
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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19
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Lee KC, Caruso T, Archer SD, Gillman LN, Lau MC, Cary SC, Lee CK, Pointing SB. Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica. Front Microbiol 2018; 9:2619. [PMID: 30450087 PMCID: PMC6225844 DOI: 10.3389/fmicb.2018.02619] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
Antarctic soil supports surface microbial communities that are dependent on ephemeral moisture. Understanding the response to availability of this resource is essential to predicting how the system will respond to climate change. The McMurdo Dry Valleys are the largest ice-free soil region in Antarctica. They are a hyper-arid polar desert with extremely limited moisture availability. Microbial colonization dominates this ecosystem but surprisingly little is known about how communities respond to changing moisture regimes. We utilized the natural model system provided by transiently wetted soil at lake margins in the Dry Valleys to interrogate microbial responses along a well-defined contiguous moisture gradient and disentangle responses between and within phyla. We identified a striking non-linear response among bacteria where at low moisture levels small changes resulted in a large impact on diversity. At higher moister levels community responses were less pronounced, resulting in diversity asymptotes. We postulate that whilst the main drivers of observed community diversity were deterministic, a switch in the major influence occurred from abiotic factors at low moisture levels to biotic interactions at higher moisture. Response between and within phyla was markedly different, highlighting the importance of taxonomic resolution in community analysis. Furthermore, we resolved apparent stochasticity at high taxonomic ranks as the result of deterministic interactions taking place at finer taxonomic and spatial scales. Overall the findings provide new insight on the response to moisture and this will be useful in advancing understanding of potential ecosystem responses in the threatened McMurdo Dry Valleys system.
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Affiliation(s)
- Kevin C. Lee
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Stephen D.J. Archer
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Len N. Gillman
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Maggie C.Y. Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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20
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Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Sci Rep 2017; 7:6094. [PMID: 28733608 PMCID: PMC5522477 DOI: 10.1038/s41598-017-06687-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022] Open
Abstract
An increasing number of studies are showing that Antarctic mega- and macrofauna are highly diverse, however, little is known about meiofaunal biodiversity in sediment communities, which are a vital part of a healthy and functional ecosystem. This is the first study to analyse community DNA (targeting meiofauna) using metabarcoding to investigate biodiversity levels in sediment communities of the Antarctic Peninsula. The results show that almost all of the meiofaunal biodiversity in the benthic habitat has yet to be characterised, levels of biodiversity were higher than expected and similar to temperate regions, albeit with the existence of potentially new and locally adapted species never described before at the molecular level. The Rothera meiofaunal sample sites showed four dominant eukaryotic groups, the nematodes, arthropods, platyhelminthes, and the annelids; some of which could comprise species complexes. Comparisons with deep-sea data from the same region suggest little exchange of Operational Taxonomic Units (OTUs) between depths with the nematodes prevalent at all depths, but sharing the shallow water benthos with the copepods. This study provides a preliminary analysis of benthic Antarctic Peninsula meiofauna using high throughput sequencing which substantiates how little is known on the biodiversity of one of the most diverse, yet underexplored communities of the Antarctic: the benthos.
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21
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Yun Y, Wang H, Man B, Xiang X, Zhou J, Qiu X, Duan Y, Engel AS. The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification. Front Microbiol 2016; 7:1955. [PMID: 28018299 PMCID: PMC5159436 DOI: 10.3389/fmicb.2016.01955] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023] Open
Abstract
Enhanced monsoon duration and soil acidification from acid rain are expected to impact the distribution of microbial communities in surface and subsurface environments, although these impacts are poorly understood for most systems. In central China, soluble carbonate bedrock forms extensive karst landscapes. Current predictions are that the amount of monsoonal precipitation and acid rainfall in central China will increase, which is expected to lead to changes in the pH balance of karst ecosystems. To evaluate the role of pH, total organic carbon, and other geochemical parameters (e.g., Ca2+, Mg2+, NH4+, NOx, SO42-) in shaping bacterial communities within a single karst system in central China, samples were collected from the thin surface soils overlying Heshang Cave, cave sediments, and weathered cave passage rocks from the entrance, twilight, and dark zones, as well as from epikarstic drip waters inside the cave. Illumina sequencing of 16S rRNA genes and multivariate statistical analyses revealed that each tested community was distinct and the community variability was significantly correlated with pH, total organic carbon, and potassium concentrations. Specifically, surface soils were dominated by Acidobacteria, Verrucomicrobia and Planctomycetes, and diversity significantly decreased with acidic pH values. Nitrospirae, Gemmatimonadetes, Firmicutes, and Chloroflexi were unique to cave sediments, while Actinobacteria and Proteobacteria dominated weathered rocks and drip waters, respectively. The results reveal important implications regarding the effects of acidification on bacterial communities in karst areas, and on the control of pH in shaping bacterial communities throughout a karst system. Increased water flux into and through karst habitats due to monsoonal precipitation may result in deeper penetration of acidic solutions into karst and shift the bacterial communities inside the cave in the future.
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Affiliation(s)
- Yuan Yun
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Hongmei Wang
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of GeosciencesWuhan, China; Laboratory of Basin Hydrology and Wetland Eco-restoration, China University of GeosciencesWuhan, China
| | - Baiying Man
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Xing Xiang
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Jianping Zhou
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Xuan Qiu
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Yong Duan
- Geomicrobiology Group, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan, China
| | - Annette S Engel
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville TN, USA
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22
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Nie Y, Xu L, Liu X, Emslie SD. Radionuclides in ornithogenic sediments as evidence for recent warming in the Ross Sea region, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 557-558:248-256. [PMID: 26999368 DOI: 10.1016/j.scitotenv.2016.03.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/05/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
Radionuclides including (210)Pb, (226)Ra and (137)Cs were analyzed in eight ornithogenic sediment profiles from McMurdo Sound, Ross Sea region, East Antarctica. Equilibration between (210)Pb and (226)Ra were reached in all eight profiles, enabling the determination of chronology within the past two centuries through the Constant Rate of Supply (CRS) model. Calculated fluxes of both (210)Pb and (137)Cs varied drastically among four of the profiles (MB4, MB6, CC and CL2), probably due to differences in their sedimentary environments. In addition, we found the flux data exhibiting a clear decreasing gradient in accordance with their average deposition rate, which was in turn related to the specific location of the profiles. We believe this phenomenon may correspond to global warming of the last century, since warming-induced surface runoff would bring more inflow water and detritus to the coring sites, thus enhancing the difference among the profiles. To verify this hypothesis, the deposition rate against age of the sediments was calculated based on their determined chronology, which showed ascending trends in all four profiles. The significant increase in deposition rates over the last century is probably attributable to recent warming, implying a potential utilization of radionuclides as environmental indicators in this region.
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Affiliation(s)
- Yaguang Nie
- Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China; Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui 230031, China
| | - Liqiang Xu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xiaodong Liu
- Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Steven D Emslie
- Department of Biology and Marine Biology, University of North Carolina Wilmington, 601 S. College Road, Wilmington, NC 28403, USA
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