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Marois C, Girard C, Klanten Y, Vincent WF, Culley AI, Antoniades D. Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic. Front Microbiol 2022; 13:779505. [PMID: 35222324 PMCID: PMC8873593 DOI: 10.3389/fmicb.2022.779505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.
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Affiliation(s)
- Catherine Marois
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Catherine Girard
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Yohanna Klanten
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
| | - Warwick F. Vincent
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Dermot Antoniades
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
- *Correspondence: Dermot Antoniades,
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2
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Lipko IA, Belykh OI. Environmental Features of Freshwater Planktonic Actinobacteria. CONTEMP PROBL ECOL+ 2021. [DOI: 10.1134/s1995425521020074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Liu K, Yao T, Pearce DA, Jiao N, Zeng Y, Guo B, Liu Y. Bacteria in the lakes of the Tibetan Plateau and polar regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142248. [PMID: 33254884 DOI: 10.1016/j.scitotenv.2020.142248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 06/12/2023]
Abstract
The Tibetan Plateau, also termed 'the Third Pole' harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic.
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Affiliation(s)
- Keshao Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tandong Yao
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - David A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle, Newcastle-upon-Tyne NE1 8ST, UK; Natural Environment Research Council, British Antarctic Survey, Cambridge CB3 0ET, UK
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Yonghui Zeng
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
| | - Bixi Guo
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Møller TE, van der Bilt WGM, Roerdink DL, Jørgensen SL. Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions. Front Microbiol 2020; 11:1520. [PMID: 32903319 PMCID: PMC7396534 DOI: 10.3389/fmicb.2020.01520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.
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Affiliation(s)
- Tor Einar Møller
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Willem G M van der Bilt
- Department of Earth Science, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, Bergen, Norway
| | - Desiree L Roerdink
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Steffen L Jørgensen
- Department of Earth Science, University of Bergen, Bergen, Norway.,K.G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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5
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Aguilar P, Sommaruga R. The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time. Mol Ecol 2020; 29:3117-3130. [PMID: 32628343 PMCID: PMC7540538 DOI: 10.1111/mec.15538] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 06/21/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023]
Abstract
One major goal in microbial ecology is to establish the importance of deterministic and stochastic processes for community assembly. This is relevant to explain and predict how diversity changes at different temporal scales. However, understanding of the relative quantitative contribution of these processes and particularly of how they may change over time is limited. Here, we assessed the importance of deterministic and stochastic processes based on the analysis of the bacterial microbiome in one alpine oligotrophic and in one subalpine mesotrophic lake, which were sampled over two consecutive years at different time scales. We found that in both lakes, homogeneous selection (i.e., a deterministic process) was the main assembly process at the annual scale and explained 66.7% of the bacterial community turnover, despite differences in diversity and temporal variability patterns between ecosystems. However, in the alpine lake, homogenizing dispersal (i.e., a stochastic process) was the most important assembly process at the short‐term (daily and weekly) sampling scale and explained 55% of the community turnover. Alpha diversity differed between lakes, and seasonal stability of the bacterial community was more evident in the oligotrophic lake than in the mesotrophic one. Our results demonstrate how important forces that govern temporal changes in bacterial communities act at different time scales. Overall, our study validates on a quantitative basis, the importance and dominance of deterministic processes in structuring bacterial communities in freshwater environments over long time scales.
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Affiliation(s)
- Pablo Aguilar
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Ruben Sommaruga
- Lake and Glacier Ecology Research Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
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6
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Li Y, Cha QQ, Dang YR, Chen XL, Wang M, McMinn A, Espina G, Zhang YZ, Blamey JM, Qin QL. Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica. Front Microbiol 2019; 10:2408. [PMID: 31681251 PMCID: PMC6813960 DOI: 10.3389/fmicb.2019.02408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/07/2019] [Indexed: 11/17/2022] Open
Abstract
Antarctica is covered by multiple larger glaciers with diverse extreme conditions. Microorganisms in Antarctic regions are primarily responsible for diverse biogeochemical processes. The identity and functionality of microorganisms from polar glaciers are defined. However, little is known about microbial communities from the high elevation glaciers. The Union Glacier, located in the inland of West Antarctica at 79°S, is a challenging environment for life to survive due to the high irradiance and low temperatures. Here, soil and rock samples were obtained from three high mountains (Rossman Cove, Charles Peak, and Elephant Head) adjacent to the Union Glacier. Using metagenomic analyses, the functional microbial ecosystem was analyzed through the reconstruction of carbon, nitrogen and sulfur metabolic pathways. A low biomass but diverse microbial community was found. Although archaea were detected, bacteria were dominant. Taxa responsible for carbon fixation were comprised of photoautotrophs (Cyanobacteria) and chemoautotrophs (mainly Alphaproteobacterial clades: Bradyrhizobium, Sphingopyxis, and Nitrobacter). The main nitrogen fixation taxa were Halothece (Cyanobacteria), Methyloversatilis, and Leptothrix (Betaproteobacteria). Diverse sulfide-oxidizing and sulfate-reducing bacteria, fermenters, denitrifying microbes, methanogens, and methane oxidizers were also found. Putative producers provide organic carbon and nitrogen for the growth of other heterotrophic microbes. In the biogeochemical pathways, assimilation and mineralization of organic compounds were the dominant processes. Besides, a range of metabolic pathways and genes related to high irradiance, low temperature and other stress adaptations were detected, which indicate that the microbial communities had adapted to and could survive in this harsh environment. These results provide a detailed perspective of the microbial functional ecology of the Union Glacier area and improve our understanding of linkages between microbial communities and biogeochemical cycling in high Antarctic ecosystems.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Jenny M Blamey
- Fundación Científica y Cultural Biociencia, Santiago, Chile.,Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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7
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Haque MM, Mande SS. Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls. J Biosci 2019; 44:118. [PMID: 31719227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent studies have highlighted the potential of 'translational' microbiome research in addressing real-world challenges pertaining to human health, nutrition and disease. Additionally, outcomes of microbiome research have also positively impacted various aspects pertaining to agricultural productivity, fuel or energy requirements, and stability/preservation of various ecological habitats. Microbiome data is multi-dimensional with various types of data comprising nucleic and protein sequences, metabolites as well as various metadata related to host and or environment. This poses a major challenge for computational analysis and interpretation of data to reach meaningful, reproducible (and replicable) biological conclusions. In this review, we first describe various aspects of microbiomes that make them an attractive tool/target for developing various translational applications. The challenge of deciphering signatures from an information-rich resource like the microbiome is also discussed. Subsequently, we present three case-studies that exemplify the potential of microbiome- based solutions in solving real-world problems. The final part of the review attempts to familiarize readers with the importance of a robust study design and the diligence required during every stage of analysis for achieving solutions with potential translational value.
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Affiliation(s)
- Mohammed Monzoorul Haque
- Bio-Sciences R and D Division, TCS Research, Tata Consultancy Services Limited, Pune 411 013, India
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8
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Haque MM, Mande SS. Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls. J Biosci 2019. [DOI: 10.1007/s12038-019-9932-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Abstract
Mercury (Hg) is a global pollutant emitted primarily as gaseous Hg0 that is deposited in aquatic and terrestrial ecosystems following its oxidation to HgII. From that point, microbes play a key role in determining Hg’s fate in the environment by participating in sequestration, oxidation, reduction, and methylation reactions. A wide diversity of chemotrophic and phototrophic microbes occupying oxic and anoxic habitats are known to participate directly in Hg cycling. Over the last few years, new findings have come to light that have greatly improved our mechanistic understanding of microbe-mediated Hg cycling pathways in the environment. In this review, we summarize recent advances in microbially mediated Hg cycling and take the opportunity to compare the relatively well-studied chemotrophic pathways to poorly understood phototrophic pathways. We present how the use of genomic and analytical tools can be used to understand Hg transformations and the physiological context of recently discovered cometabolic Hg transformations supported in anaerobes and phototrophs. Finally, we propose a conceptual framework that emphasizes the role that phototrophs play in environmental Hg redox cycling and the importance of better characterizing such pathways in the face of the environmental changes currently underway.
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Affiliation(s)
- Daniel S. Grégoire
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Alexandre J. Poulain
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
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10
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Ruuskanen MO, St Pierre KA, St Louis VL, Aris-Brosou S, Poulain AJ. Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada. Front Microbiol 2018; 9:1138. [PMID: 29922252 PMCID: PMC5996194 DOI: 10.3389/fmicb.2018.01138] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.
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Affiliation(s)
| | - Kyra A St Pierre
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Vincent L St Louis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
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11
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Pessi IS, Lara Y, Durieu B, Maalouf PDC, Verleyen E, Wilmotte A. Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats. FEMS Microbiol Ecol 2018; 94:4935156. [DOI: 10.1093/femsec/fiy042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Igor S Pessi
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Yannick Lara
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Benoit Durieu
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Pedro de C Maalouf
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
| | - Elie Verleyen
- Research Group Protistology and Aquatic Ecology, Department of Biology, Ghent University, Campus Sterre, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Annick Wilmotte
- InBioS—Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000 Liège, Belgium
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