1
|
Li F, Jia M, Chen H, Chen M, Su R, Usman S, Ding Z, Hao L, Franco M, Guo X. Responses of microbial community composition and CAZymes encoding gene enrichment in ensiled Elymus nutans to altitudinal gradients in alpine region. Appl Environ Microbiol 2024:e0098624. [PMID: 39324818 DOI: 10.1128/aem.00986-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 09/06/2024] [Indexed: 09/27/2024] Open
Abstract
High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc, Latilactobacillus, and Levilactobacillus. IMPORTANCE The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Fuhou Li
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mengya Jia
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hu Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mengyan Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rina Su
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Samaila Usman
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zitong Ding
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, Academy of Animal and Veterinary Sciences, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Marcia Franco
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Xusheng Guo
- School of Life Sciences, Lanzhou University, Lanzhou, China
| |
Collapse
|
2
|
Grettenberger CL, Abou‐Shanab R, Hamilton TL. Limiting factors in the operation of photosystems I and II in cyanobacteria. Microb Biotechnol 2024; 17:e14519. [PMID: 39101352 PMCID: PMC11298993 DOI: 10.1111/1751-7915.14519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/16/2024] [Indexed: 08/06/2024] Open
Abstract
Cyanobacteria are important targets for biotechnological applications due to their ability to grow in a wide variety of environments, rapid growth rates, and tractable genetic systems. They and their bioproducts can be used as bioplastics, biofertilizers, and in carbon capture and produce important secondary metabolites that can be used as pharmaceuticals. However, the photosynthetic process in cyanobacteria can be limited by a wide variety of environmental factors such as light intensity and wavelength, exposure to UV light, nutrient limitation, temperature, and salinity. Carefully considering these limitations, modifying the environment, and/or selecting cyanobacterial species will allow cyanobacteria to be used in biotechnological applications.
Collapse
Affiliation(s)
- Christen L. Grettenberger
- Department of Earth and Planetary SciencesUniversity of California DavisDavisCaliforniaUSA
- Department of Environmental ToxicologyUniversity of California DavisDavisCaliforniaUSA
| | - Reda Abou‐Shanab
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Trinity L. Hamilton
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
- The Biotechnology Institute, University of MinnesotaSt. PaulMinnesotaUSA
| |
Collapse
|
3
|
Gladkov GV, Kimeklis AK, Tembotov RK, Ivanov MN, Andronov EE, Abakumov EV. Linking the composition of cryoconite prokaryotic communities in the Arctic, Antarctic, and Central Caucasus with their chemical characteristics. Sci Rep 2024; 14:15838. [PMID: 38982048 PMCID: PMC11233692 DOI: 10.1038/s41598-024-64452-3] [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: 08/31/2023] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Cryoconites are the deposits on the surface of glaciers that create specific ecological niches for the development of microorganism communities. The sediment material can vary in origin, structure, and nutrient content, creating local variations in the growth conditions. An additional factor of variability is the location of the glaciers, as they are found in different climatic zones in the high mountain regions and closer to the poles. Here, using the analysis of amplicon sequencing of the 16S rRNA gene, we studied the taxonomic composition of the prokaryotic communities from glaciers from remote regions, including the Arctic (Mushketova on the Severnaya Zemlya, IGAN in Polar Ural), Antarctic (Pimpirev on the Livingstone Island) and Central Caucasus (Skhelda and Garabashi) and connected it with the variation of the physicochemical characteristics of the substrate: pH, carbon, nitrogen, macro- and microelements. The cryoconite microbiomes were comprised of specific for this environment phyla (mostly Pseudomonadota, Cyanobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota), but each glacier had a unique taxonomic imprint. The core microbiome between regions was composed of only a few ASVs, among which the most likely globally distributed ones attributed to Polaromonas sp., Rhodoferax sp., Cryobacterium sp., and Hymenobacter frigidus. The WGSNA defined clusters of co-occurring ASVs between microbiomes, that significantly change their abundance corresponding with the variation of chemical parameters of cryoconites, but do not fully coincide with their regional separation. Thus, our work demonstrates that the chemical characteristics of the sediment material can explain the variation in the cryoconite prokaryotic community which is not always linked to geographic isolation.
Collapse
Affiliation(s)
- Grigory V Gladkov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Anastasiia K Kimeklis
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Rustam Kh Tembotov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Tembotov Institute of Ecology of Mountain Territories, Russian Academy of Sciences, Nalchik, Russia, 360051
| | - Mikhail N Ivanov
- Department of Cryolithology and Glaciology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, Russia, 119991
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
- V.V. Dokuchaev Soil Science Institute, Moscow, Russia, 119017
| | - Evgeny V Abakumov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034.
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608.
| |
Collapse
|
4
|
Ugwuanyi IR, Steele A, Glamoclija M. Microbial Ecology of an Arctic Travertine Geothermal Spring: Implications for Biosignature Preservation and Astrobiology. ASTROBIOLOGY 2024; 24:734-753. [PMID: 38985714 DOI: 10.1089/ast.2023.0130] [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: 07/12/2024]
Abstract
Jotun springs in Svalbard, Norway, is a rare warm environment in the Arctic that actively forms travertine. In this study, we assessed the microbial ecology of Jotun's active (aquatic) spring and dry spring transects. We evaluated the microbial preservation potential and mode, as well as the astrobiological relevance of the travertines to marginal carbonates mapped at Jezero Crater on Mars (the Mars 2020 landing site). Our results revealed that microbial communities exhibited spatial dynamics controlled by temperature, fluid availability, and geochemistry. Amorphous carbonates and silica precipitated within biofilm and on the surface of filamentous microorganisms. The water discharged at the source is warm, with near neutral pH, and undersaturated in silica. Hence, silicification possibly occurred through cooling, dehydration, and partially by a microbial presence or activities that promote silica precipitation. CO2 degassing and possible microbial contributions induced calcite precipitation and travertine formation. Jotun revealed that warm systems that are not very productive in carbonate formation may still produce significant carbonate buildups and provide settings favorable for fossilization through silicification and calcification. Our findings suggest that the potential for amorphous silica precipitation may be essential for Jezero Crater's marginal carbonates because it significantly increases the preservation potential of putative martian organisms.
Collapse
Affiliation(s)
- Ifeoma R Ugwuanyi
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| | - Andrew Steele
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, District of Columbia, USA
| | - Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| |
Collapse
|
5
|
Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. JOURNAL OF PHYCOLOGY 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
Collapse
Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| |
Collapse
|
6
|
Chrismas N, Tindall-Jones B, Jenkins H, Harley J, Bird K, Cunliffe M. Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea. THE NEW PHYTOLOGIST 2024; 241:2243-2257. [PMID: 37840369 DOI: 10.1111/nph.19320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023]
Abstract
Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.
Collapse
Affiliation(s)
- Nathan Chrismas
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Beth Tindall-Jones
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Helen Jenkins
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Joanna Harley
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Kimberley Bird
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, Devon, PL1 2PB, UK
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| |
Collapse
|
7
|
Lumian J, Sumner DY, Grettenberger CL, Jungblut AD, Irber L, Pierce-Ward NT, Brown CT. Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater. Front Microbiol 2024; 15:1328083. [PMID: 38440141 PMCID: PMC10909832 DOI: 10.3389/fmicb.2024.1328083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones.
Collapse
Affiliation(s)
- Jessica Lumian
- Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
| | - Christen L. Grettenberger
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| | - Anne D. Jungblut
- Department of Science, The Natural History Museum, London, United Kingdom
| | - Luiz Irber
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
| | - N. Tessa Pierce-Ward
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
| | - C. Titus Brown
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
| |
Collapse
|
8
|
Lumian J, Grettenberger C, Jungblut AD, Mackey TJ, Hawes I, Alatorre-Acevedo E, Sumner DY. Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Front Microbiol 2024; 14:1330602. [PMID: 38282730 PMCID: PMC10812107 DOI: 10.3389/fmicb.2023.1330602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/29/2023] [Indexed: 01/30/2024] Open
Abstract
Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp - 6.07 Mbp, and the bin completion ranges from 74.2-92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.
Collapse
Affiliation(s)
- Jessica Lumian
- Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States
| | - Christen Grettenberger
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| | - Anne D. Jungblut
- Department of Sciences, The Natural History Museum, London, United Kingdom
| | - Tyler J. Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Eduardo Alatorre-Acevedo
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
| |
Collapse
|
9
|
Kong L, Feng Y, Du W, Zheng R, Sun J, Rong K, Sun W, Liu S. Cross-Feeding between Filamentous Cyanobacteria and Symbiotic Bacteria Favors Rapid Photogranulation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16953-16963. [PMID: 37886803 DOI: 10.1021/acs.est.3c04867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Photogranules are dense algal-bacterial aggregates used in aeration-free and carbon-negative wastewater treatment, wherein filamentous cyanobacteria (FC) are essential components. However, little is known about the functional role of symbiotic bacteria in photogranulation. Herein, we combined cyanobacterial isolation, reactor operation, and multiomics analysis to investigate the cyanobacterial-bacterial interaction during photogranulation. The addition of FC to the inoculated sludge achieved a 1.4-fold higher granule size than the control, and the aggregation capacity of FC-dominant photogranules was closely related to the extracellular polysaccharide (PS) concentration (R = 0.86). Importantly, we found that cross-feeding between FC and symbiotic bacteria for macromolecular PS synthesis is at the heart of photogranulation and substantially enhanced the granular stability. Chloroflexi-affiliated bacteria intertwined with FC throughout the photogranules and promoted PS biosynthesis using the partial nucleotide sugars produced by FC. Proteobacteria-affiliated bacteria were spatially close to FC, and highly expressed genes for vitamin B1 and B12 synthesis, contributing the necessary cofactors to promote FC proliferation. In addition, Bacteroidetes-affiliated bacteria degraded FC-derived carbohydrates and influenced granules development. Our metabolic characterization identified the functional role of symbiotic bacteria of FC during photogranulation and shed light on the critical cyanobacterial-bacterial interactions in photogranules from the viewpoint of cross-feeding.
Collapse
Affiliation(s)
- Lingrui Kong
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Yiming Feng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Wenran Du
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ru Zheng
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Jingqi Sun
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Kaiyu Rong
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Weiling Sun
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| | - Sitong Liu
- Department of Environmental Engineering, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Peking University, Beijing 100871, China
| |
Collapse
|
10
|
Hay MC, Mitchell AC, Soares AR, Debbonaire AR, Mogrovejo DC, Els N, Edwards A. Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss. Microb Genom 2023; 9. [PMID: 37937832 DOI: 10.1099/mgen.0.001131] [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] [Indexed: 11/09/2023] Open
Abstract
The rapid warming of the Arctic is threatening the demise of its glaciers and their associated ecosystems. Therefore, there is an urgent need to explore and understand the diversity of genomes resident within glacial ecosystems endangered by human-induced climate change. In this study we use genome-resolved metagenomics to explore the taxonomic and functional diversity of different habitats within glacier-occupied catchments. Comparing different habitats within such catchments offers a natural experiment for understanding the effects of changing habitat extent or even loss upon Arctic microbiota. Through binning and annotation of metagenome-assembled genomes (MAGs) we describe the spatial differences in taxon distribution and their implications for glacier-associated biogeochemical cycling. Multiple taxa associated with carbon cycling included organisms with the potential for carbon monoxide oxidation. Meanwhile, nitrogen fixation was mediated by a single taxon, although diverse taxa contribute to other nitrogen conversions. Genes for sulphur oxidation were prevalent within MAGs implying the potential capacity for sulphur cycling. Finally, we focused on cyanobacterial MAGs, and those within cryoconite, a biodiverse microbe-mineral granular aggregate responsible for darkening glacier surfaces. Although the metagenome-assembled genome of Phormidesmis priestleyi, the cyanobacterium responsible for forming Arctic cryoconite was represented with high coverage, evidence for the biosynthesis of multiple vitamins and co-factors was absent from its MAG. Our results indicate the potential for cross-feeding to sustain P. priestleyi within granular cryoconite. Taken together, genome-resolved metagenomics reveals the vulnerability of glacier-associated microbiota to the deletion of glacial habitats through the rapid warming of the Arctic.
Collapse
Affiliation(s)
- Melanie C Hay
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
- Present address: Department of Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Andrew C Mitchell
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
| | - Andre R Soares
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Geography and Earth Sciences (DGES), Aberystwyth University, Wales, UK
- Present address: Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Aliyah R Debbonaire
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
| | - Diana C Mogrovejo
- Dr. Brill + Partner GmbH Institut für Hygiene und Mikrobiologie, Hamburg, Germany
| | - Nora Els
- Department of Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Arwyn Edwards
- Department of Life Sciences (DLS), Aberystwyth University, Wales, UK
- Interdisciplinary Centre for Environmental Microbiology (iCEM), Aberystwyth University, Wales, UK
- Department of Arctic Biology, University Centre in Svalbard (UNIS), Longyearbyen, Svalbard and Jan Mayen
| |
Collapse
|
11
|
Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-y] [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: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
Collapse
Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
12
|
Pessi IS, Popin RV, Durieu B, Lara Y, Tytgat B, Savaglia V, Roncero-Ramos B, Hultman J, Verleyen E, Vyverman W, Wilmotte A. Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics. Microb Genom 2023; 9:mgen001056. [PMID: 37417735 PMCID: PMC10438808 DOI: 10.1099/mgen.0.001056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.
Collapse
Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
| | - Rafael V. Popin
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Benoit Durieu
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- Early Life Traces & Evolution-Astrobiology, UR-Astrobiology, University of Liège, Liège, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Valentina Savaglia
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Beatriz Roncero-Ramos
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Helsinki, Finland
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS – Centre for Protein Engineering, University of Liège, Liège, Belgium
| |
Collapse
|
13
|
Ferheen I, Ahmed Z, Alonazi WB, Pessina A, Ibrahim M, Pucciarelli S, Bokhari H. Diverse Repertoire and Relationship of Exopolysaccharide Genes in Cold-Adapted Acinetobacter sp. CUI-P1 Revealed by Comparative Genome Analysis. Microorganisms 2023; 11:microorganisms11040885. [PMID: 37110308 PMCID: PMC10143279 DOI: 10.3390/microorganisms11040885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
This study focused on the exploration of microbial communities inhabiting extreme cold environments, such as the Passu and Pisan glaciers of Pakistan, and their potential utilization in industrial applications. Among the 25 initially screened strains, five were found to be suitable candidates for exopolysaccharide (EPS) production, with strain CUI-P1 displaying the highest yield of 7230.5 mg/L compared to the other four strains. The purified EPS from CUI-P1 was tested for its ability to protect probiotic bacteria and E. coli expressing green fluorescence protein (HriGFP) against extreme cold temperatures, and it exhibited excellent cryoprotectant and emulsification activity, highlighting its potential use in the biotechnological industry. Furthermore, the genome of Acinetobacter sp., CUI-P1 comprised 199 contigs, with a genome size of 10,493,143bp and a G + C content of 42%, and showed 98.197% nucleotide identity to the type genome of Acinetobacter baumannii ATCC 17978. These findings offer promising avenues for the application of EPS as a cryoprotectant, an essential tool in modern biotechnology.
Collapse
Affiliation(s)
- Ifra Ferheen
- Department of Biosciences, COMSATS University Islamabad, Islamabad 44000, Pakistan
| | - Zaheer Ahmed
- Department of Nutritional Sciences and Environmental Design, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11587, Saudi Arabia
| | - Alex Pessina
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal 55000, Pakistan
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Habib Bokhari
- Department of Microbiology, Kohsar University Murree, Murree 47150, Pakistan
| |
Collapse
|
14
|
Čanković M, Dutour-Sikirić M, Radić ID, Ciglenečki I. Bacterioneuston and Bacterioplankton Structure and Abundance in Two Trophically Distinct Marine Environments - a Marine Lake and the Adjacent Coastal Site on the Adriatic Sea. MICROBIAL ECOLOGY 2022; 84:996-1010. [PMID: 34817641 DOI: 10.1007/s00248-021-01934-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Marine surface microlayer (SML) is a large and extreme marine environment with an important role in biogeochemical cycling and climate regulation. We explored the seasonal structure and abundance of bacterial assemblages in SML (bacterioneuston) and underlying water layer (ULW) (bacterioplankton) in eutrophic marine Rogoznica Lake and more oligotrophic coastal area of the adjacent Adriatic Sea. SML and ULW in each site were similar in pH, salinity, dissolved oxygen, oxygen saturation, and temperature. Rogoznica Lake was colder in winter and warmer in summer compared to the Adriatic Sea. Regarding nutrients, SML and ULW were notably different environments. SML was consistently enriched in nitrate, nitrite, orthophosphate, and total organic carbon than ULW in both investigated environments. Except in spring in Rogoznica Lake, bacterial abundance in SML was also significantly higher (p < 0.05) than in ULW. Both layers and sites show prominent seasonal variability. High-throughput 16S rRNA gene sequencing of DNA and cDNA revealed a considerable difference in bacterial assemblage structure, although study sites were < 200 m apart. Heterotrophs were predominant in both layers with pronounced spatial and temporal structural differences, except in autumn in Rogoznica Lake when, autotrophs became the dominant fraction under oxygen-deprived conditions. All these variations were driven by in situ conditions, the most important ones being total organic carbon and temperature (and additionally dissolved oxygen in Rogoznica Lake). This is especially important in terms of ongoing eutrophication, warming and deoxygenation, noticed not only in the Adriatic Sea and Rogoznica Lake but globally as well. Therefore, further structural and physiological changes in bacterioneuston and bacterioplankton assemblages can be expected.
Collapse
Affiliation(s)
- Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia.
| | - Mathieu Dutour-Sikirić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Iris Dupčić Radić
- Institute for Marine and Coastal Research, Ul. kneza Damjana Jude 12, 20 000, Dubrovnik, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| |
Collapse
|
15
|
Jensen LZ, Glasius M, Gryning SE, Massling A, Finster K, Šantl-Temkiv T. Seasonal Variation of the Atmospheric Bacterial Community in the Greenlandic High Arctic Is Influenced by Weather Events and Local and Distant Sources. Front Microbiol 2022; 13:909980. [PMID: 35879956 PMCID: PMC9307761 DOI: 10.3389/fmicb.2022.909980] [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: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Arctic is a hot spot for climate change with potentially large consequences on a global scale. Aerosols, including bioaerosols, are important players in regulating the heat balance through direct interaction with sunlight and indirectly, through inducing cloud formation. Airborne bacteria are the major bioaerosols with some species producing the most potent ice nucleating compounds known, which are implicated in the formation of ice in clouds. Little is known about the numbers and dynamics of airborne bacteria in the Arctic and even less about their seasonal variability. We collected aerosol samples and wet deposition samples in spring 2015 and summer 2016, at the Villum Research Station in Northeast Greenland. We used amplicon sequencing and qPCR targeting the 16S rRNA genes to assess the quantities and composition of the DNA and cDNA-level bacterial community. We found a clear seasonal variation in the atmospheric bacterial community, which is likely due to variable sources and meteorology. In early spring, the atmospheric bacterial community was dominated by taxa originating from temperate and Subarctic regions and arriving at the sampling site through long-range transport. We observed an efficient washout of the aerosolized bacterial cells during a snowstorm, which was followed by very low concentrations of bacteria in the atmosphere during the consecutive 4 weeks. We suggest that this is because in late spring, the long-range transport ceased, and the local sources which comprised only of ice and snow surfaces were weak resulting in low bacterial concentrations. This was supported by observed changes in the chemical composition of aerosols. In summer, the air bacterial community was confined to local sources such as soil, plant material and melting sea-ice. Aerosolized and deposited Cyanobacteria in spring had a high activity potential, implying their activity in the atmosphere or in surface snow. Overall, we show how the composition of bacterial aerosols in the high Arctic varies on a seasonal scale, identify their potential sources, demonstrate how their community sizes varies in time, investigate their diversity and determine their activity potential during and post Arctic haze.
Collapse
Affiliation(s)
- Lasse Z. Jensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
| | | | - Sven-Erik Gryning
- DTU Wind and Energy Systems, Technical University of Denmark, Roskilde, Denmark
| | - Andreas Massling
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Aarhus University, Aarhus, Denmark
- iCLIMATE Aarhus University Interdisciplinary Centre for Climate Change, Roskilde, Denmark
- Department of Physics and Astronomy, Stellar Astrophysics Centre, Aarhus University, Aarhus, Denmark
- *Correspondence: Tina Šantl-Temkiv,
| |
Collapse
|
16
|
Sheikh T, Hamid B, Baba Z, Iqbal S, Yatoo A, Fatima S, Nabi A, Kanth R, Dar K, Hussain N, Alturki AI, Sunita K, Sayyed R. Extracellular polymeric substances in psychrophilic cyanobacteria: A potential bioflocculant and carbon sink to mitigate cold stress. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
17
|
Murakami T, Takeuchi N, Mori H, Hirose Y, Edwards A, Irvine-Fynn T, Li Z, Ishii S, Segawa T. Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite. MICROBIOME 2022; 10:50. [PMID: 35317857 PMCID: PMC8941735 DOI: 10.1186/s40168-022-01238-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions. RESULTS Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation). CONCLUSIONS Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.
Collapse
Affiliation(s)
- Takumi Murakami
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Aichi, Japan
| | - Arwyn Edwards
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
| | - Tristram Irvine-Fynn
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences/Tien Shan Glaciological Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN USA
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
| |
Collapse
|
18
|
Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
Collapse
Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| |
Collapse
|
19
|
OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6551890. [DOI: 10.1093/femsec/fiac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 11/14/2022] Open
|
20
|
Park C, Takeuchi N. Unmasking photogranulation in decreasing glacial albedo and net autotrophic wastewater treatment. Environ Microbiol 2021; 23:6391-6404. [PMID: 34545673 PMCID: PMC9292683 DOI: 10.1111/1462-2920.15780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
In both natural and built environments, microbes on occasions manifest in spherical aggregates instead of substratum‐affixed biofilms. These microbial aggregates are conventionally referred to as granules. Cryoconites are mineral rich granules that appear on glacier surfaces and are linked with expanding surface darkening, thus decreasing albedo, and enhanced melt. The oxygenic photogranules (OPGs) are organic rich granules that grow in wastewater, which enables wastewater treatment with photosynthetically produced oxygen and which presents potential for net autotrophic wastewater treatment in a compact system. Despite obvious differences inherent in the two, cryoconite and OPG pose striking resemblance. In both, the order Oscillatoriales in Cyanobacteria envelope inner materials and develop dense spheroidal aggregates. We explore the mechanism of photogranulation on account of high similarity between cryoconites and OPGs. We contend that there is no universal external cause for photogranulation. However, cryoconites and OPGs, as well as their intravariations, which are all under different stress fields, are the outcome of universal physiological processes of the Oscillatoriales interfacing with goldilocks interactions of stresses. Finding the rules of photogranulation may enhance engineering of glacier and wastewater systems to manipulate their ecosystem impacts.
Collapse
Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| |
Collapse
|
21
|
Solon AJ, Mastrangelo C, Vimercati L, Sommers P, Darcy JL, Gendron EMS, Porazinska DL, Schmidt SK. Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica. Front Microbiol 2021; 12:654135. [PMID: 34177836 PMCID: PMC8222675 DOI: 10.3389/fmicb.2021.654135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.
Collapse
Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Claire Mastrangelo
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado-Anschutz Medical Campus, Denver, CO, United States
| | - Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| |
Collapse
|
22
|
Jungblut AD, Raymond F, Dion MB, Moineau S, Mohit V, Nguyen GQ, Déraspe M, Francovic-Fontaine É, Lovejoy C, Culley AI, Corbeil J, Vincent WF. Genomic diversity and CRISPR-Cas systems in the cyanobacterium Nostoc in the High Arctic. Environ Microbiol 2021; 23:2955-2968. [PMID: 33760341 DOI: 10.1111/1462-2920.15481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 03/22/2021] [Indexed: 11/27/2022]
Abstract
Nostoc (Nostocales, Cyanobacteria) has a global distribution in the Polar Regions. However, the genomic diversity of Nostoc is little known and there are no genomes available for polar Nostoc. Here we carried out the first genomic analysis of the Nostoc commune morphotype with a recent sample from the High Arctic and a herbarium specimen collected during the British Arctic Expedition (1875-76). Comparisons of the polar genomes with 26 present-day non-polar members of the Nostocales family highlighted that there are pronounced genetic variations among Nostoc strains and species. Osmoprotection and other stress genes were found in all Nostoc strains, but the two Arctic strains had markedly higher numbers of biosynthetic gene clusters for uncharacterised non-ribosomal peptide synthetases, suggesting a high diversity of secondary metabolites. Since viral-host interactions contribute to microbial diversity, we analysed the CRISPR-Cas systems in the Arctic and two temperate Nostoc species. There were a large number of unique repeat-spacer arrays in each genome, indicating diverse histories of viral attack. All Nostoc strains had a subtype I-D system, but the polar specimens also showed evidence of a subtype I-B system that has not been previously reported in cyanobacteria, suggesting diverse cyanobacteria-virus interactions in the Arctic.
Collapse
Affiliation(s)
- Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Frédéric Raymond
- Department of Molecular Medicine and Big Data Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada.,School of Nutrition and Institute on Nutrition and Functional Foods, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Moïra B Dion
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Vani Mohit
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Takuvik Joint International Laboratory and Institute of Integrative Biology and Systems, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Guillaume Quang Nguyen
- School of Nutrition and Institute on Nutrition and Functional Foods, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Maxime Déraspe
- Department of Molecular Medicine and Big Data Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Élina Francovic-Fontaine
- Department of Molecular Medicine and Big Data Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Connie Lovejoy
- Takuvik Joint International Laboratory and Institute of Integrative Biology and Systems, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Québec-Océan, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Alexander I Culley
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Takuvik Joint International Laboratory and Institute of Integrative Biology and Systems, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Jacques Corbeil
- Department of Molecular Medicine and Big Data Research Centre, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Warwick F Vincent
- Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Takuvik Joint International Laboratory and Institute of Integrative Biology and Systems, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de Biologie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| |
Collapse
|
23
|
Lumian JE, Jungblut AD, Dillion ML, Hawes I, Doran PT, Mackey TJ, Dick GJ, Grettenberger CL, Sumner DY. Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. Genes (Basel) 2021; 12:genes12030426. [PMID: 33809699 PMCID: PMC8002359 DOI: 10.3390/genes12030426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/11/2023] Open
Abstract
Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1–2 mm thick layer of 50 µmol L−1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. A metagenome-assembled genome of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, the ability of the organism to reduce Photosystem I via sulfide quinone reductase while Photosystem II is sulfide-inhibited, thereby performing anoxygenic photosynthesis in the presence of sulfide, has yet to be demonstrated.
Collapse
Affiliation(s)
- Jessica E. Lumian
- Microbiology Graduate Group, University of California, Davis, CA 95616, USA;
| | - Anne D. Jungblut
- Life Sciences Department, The Natural History Museum, London SW7 5BD, UK;
| | - Megan L. Dillion
- Genomics and Bioinformatics, Novozymes, Inc., Davis, CA 95616, USA;
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga 3110, New Zealand;
| | - Peter T. Doran
- Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Tyler J. Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA;
| | | | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-5353
| |
Collapse
|
24
|
Boden JS, Grego M, Bolhuis H, Sánchez-Baracaldo P. Draft genome sequences of three filamentous cyanobacteria isolated from brackish habitats. J Genomics 2021; 9:20-25. [PMID: 33613774 PMCID: PMC7893532 DOI: 10.7150/jgen.53678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/27/2021] [Indexed: 11/20/2022] Open
Abstract
Brackish cyanobacterial genome sequences are relatively rare. Here, we report the 5.5 Mbp, 5.8 Mbp and 6.1 Mbp draft genomes of Spirulina sp. CCY15215, Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 isolated from coastal microbial mats on the North Sea beach of the island of Schiermonnikoog in the Netherlands. Large scale phylogenomic analyses reveal that Spirulina sp. CCY15215 is a large cell diameter cyanobacterium, whereas Leptolyngbya sp. CCY15150 and Halomicronema sp. CCY15110 are the first reported brackish genomes belonging to the LPP clade consisting primarily of Leptolyngbya, Plectonema and Phormidium spp. Further genome mining divulges that all new draft genomes contain, ggpS and ggpP, the genes responsible for synthesising glucosylglycerol (GG), a compatible solute found in moderately salt-tolerant cyanobacteria.
Collapse
Affiliation(s)
- Joanne Sarah Boden
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| | - Michele Grego
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, the Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, the Netherlands
| | - Patricia Sánchez-Baracaldo
- School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, BS8 1SS, United Kingdom
| |
Collapse
|
25
|
Wang W, Li H, Guénon R, Yang Y, Shu X, Cheng X, Zhang Q. Geographical Variability of Mineral Elements and Stability of Restrictive Mineral Elements in Terrestrial Cyanobacteria Across Gradients of Climate, Soil, and Atmospheric Wet Deposition Mineral Concentration. Front Microbiol 2021; 11:582655. [PMID: 33584560 PMCID: PMC7874062 DOI: 10.3389/fmicb.2020.582655] [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: 07/13/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
Terrestrial cyanobacteria Nostoc commune is an ideal species to study the geographical variation of mineral elements of soil cyanobacteria at the species level. Here, we first address the following questions: (1) from where are these mineral elements, (2) are there geographical variations for these mineral elements, and if so, (3) which environmental factors drive the geographical variation of these mineral elements? Second, we tested whether the soil cyanobacterial mineral elements followed the “restrictive element stability hypothesis” of higher plants. Finally, we explored the effect of mineral geographic variation on ecological adaptation of soil cyanobacteria. We collected N. commune samples across gradients of climate, soil, and atmospheric wet deposition mineral concentration in mainland China. We measured fifteen minerals, including five macroelements (N, Ca, K, Fe, P), five microelements (Mn, Zn, Cu, Co, Se), and five heavy metals (Pb, Cr, As, Cd, Hg). We found that five elements (P, Cu, Zn, Co, Pb) had significant geographical variation. They increased as the distance from the equator increased and decreased as the distance from the prime meridian increased. Mean annual precipitation and mean annual temperature explained most of the variation. We did not find any significant correlations between the mineral element contents in N. commune and the minerals in soil and rainfall, except for P. There was no significant correlation between the variation coefficients of different elements and their actual detected contents and their potential physiological required contents. The statistical results of our experiment did not support the “restrictive element stability hypothesis.” We speculated that net accumulation of mineral elements in cyanobacterial cells and extracellular polysaccharides (EPS) might play an important role for terrestrial cyanobacteria in the adaptation to dry and cold conditions.
Collapse
Affiliation(s)
- Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Yuyi Yang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xiao Shu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoli Cheng
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Quanfa Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
26
|
Athmika, Ghate SD, Arun AB, Rao SS, Kumar STA, Kandiyil MK, Saptami K, Rekha PD. Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29 T reveals its exopolysaccharide and pigment producing capabilities. Sci Rep 2021; 11:1749. [PMID: 33462335 PMCID: PMC7814019 DOI: 10.1038/s41598-021-81395-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/04/2021] [Indexed: 11/08/2022] Open
Abstract
Halomonas malpeensis strain YU-PRIM-29T is a yellow pigmented, exopolysaccharide (EPS) producing halophilic bacterium isolated from the coastal region. To understand the biosynthesis pathways involved in the EPS and pigment production, whole genome analysis was performed. The complete genome sequencing and the de novo assembly were carried out using Illumina sequencing and SPAdes genome assembler (ver 3.11.1) respectively followed by detailed genome annotation. The genome consists of 3,607,821 bp distributed in 18 contigs with 3337 protein coding genes and 53% of the annotated CDS are having putative functions. Gene annotation disclosed the presence of genes involved in ABC transporter-dependent pathway of EPS biosynthesis. As the ABC transporter-dependent pathway is also implicated in the capsular polysaccharide (CPS) biosynthesis, we employed extraction protocols for both EPS (from the culture supernatants) and CPS (from the cells) and found that the secreted polysaccharide i.e., EPS was predominant. The EPS showed good emulsifying activities against the petroleum hydrocarbons and its production was dependent on the carbon source supplied. The genome analysis also revealed genes involved in industrially important metabolites such as zeaxanthin pigment, ectoine and polyhydroxyalkanoate (PHA) biosynthesis. To confirm the genome data, we extracted these metabolites from the cultures and successfully identified them. The pigment extracted from the cells showed the distinct UV-Vis spectra having characteristic absorption peak of zeaxanthin (λmax 448 nm) with potent antioxidant activities. The ability of H. malpeensis strain YU-PRIM-29T to produce important biomolecules makes it an industrially important bacterium.
Collapse
Affiliation(s)
- Athmika
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Sudeep D Ghate
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - A B Arun
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Sneha S Rao
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - S T Arun Kumar
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Mrudula Kinarulla Kandiyil
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Kanekar Saptami
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| |
Collapse
|
27
|
Obi LU, Tekere M, Roopnarain A, Sanko T, Maguvu TE, Bezuidenhout CC, Adeleke RA. Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain. ACTA ACUST UNITED AC 2020; 28:e00542. [PMID: 33102161 PMCID: PMC7569290 DOI: 10.1016/j.btre.2020.e00542] [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: 05/21/2020] [Revised: 09/27/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass. Serratia marcescens 39_H1 is a plant growth promoting organism. Genome analysis showed diverse potential biotechnological application of organism. This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production.
Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.
Collapse
Affiliation(s)
- Linda U Obi
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa.,Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa
| | - Memory Tekere
- Department of Environmental Sciences, University of South Africa, Johannesburg, South Africa
| | - Ashira Roopnarain
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa
| | - Tomasz Sanko
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Tawanda E Maguvu
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Cornelius C Bezuidenhout
- Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Rasheed A Adeleke
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Arcadia, 0083, Pretoria, South Africa.,Unit for Environment Sciences and Management, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| |
Collapse
|
28
|
Conradi FD, Mullineaux CW, Wilde A. The Role of the Cyanobacterial Type IV Pilus Machinery in Finding and Maintaining a Favourable Environment. Life (Basel) 2020; 10:life10110252. [PMID: 33114175 PMCID: PMC7690835 DOI: 10.3390/life10110252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022] Open
Abstract
Type IV pili (T4P) are proteinaceous filaments found on the cell surface of many prokaryotic organisms and convey twitching motility through their extension/retraction cycles, moving cells across surfaces. In cyanobacteria, twitching motility is the sole mode of motility properly characterised to date and is the means by which cells perform phototaxis, the movement towards and away from directional light sources. The wavelength and intensity of the light source determine the direction of movement and, sometimes in concert with nutrient conditions, act as signals for some cyanobacteria to form mucoid multicellular assemblages. Formation of such aggregates or flocs represents an acclimation strategy to unfavourable environmental conditions and stresses, such as harmful light conditions or predation. T4P are also involved in natural transformation by exogenous DNA, secretion processes, and in cellular adaptation and survival strategies, further cementing the role of cell surface appendages. In this way, cyanobacteria are finely tuned by external stimuli to either escape unfavourable environmental conditions via phototaxis, exchange genetic material, and to modify their surroundings to fit their needs by forming multicellular assemblies.
Collapse
Affiliation(s)
- Fabian D. Conradi
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (F.D.C.); (C.W.M.)
| | - Conrad W. Mullineaux
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (F.D.C.); (C.W.M.)
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104 Freiburg; Germany
- Correspondence:
| |
Collapse
|
29
|
Uetake J, Nagatsuka N, Onuma Y, Takeuchi N, Motoyama H, Aoki T. Bacterial community changes with granule size in cryoconite and their susceptibility to exogenous nutrients on NW Greenland glaciers. FEMS Microbiol Ecol 2020; 95:5499017. [PMID: 31132102 DOI: 10.1093/femsec/fiz075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022] Open
Abstract
Cryoconite granules are dark-colored biological aggregates on glaciers. Bacterial community varies with granule size, however, community change in space and their susceptibility to environmental factors has not been described yet. Therefore, we focused on bacterial community from four different granule sizes (30-249 μm, 250-750 μm, 750-1599 μm, more than 1600 μm diameter) in 10 glaciers in northwestern Greenland and their susceptibility to exogenous nutrients in cryoconite hole. A filamentous cyanobacterium Phormidesmis priestleyi, which has been frequently reported from glaciers in Arctic was abundant (10%-26%) across any size of granules on most of glaciers. Bacterial community across glaciers became similar with size increase, and whence smallest size fractions contain more unique genera in each glacier. Multivariate analysis revealed that effect of nutrients to beta diversity is larger in smaller granules (30-249 μm and 250-750 μm diameter), suggesting that bacterial susceptibility to nutrients changes with growth of granule (i.e. P. priestleyi was affected by nitrate in early growth stage).
Collapse
Affiliation(s)
- Jun Uetake
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Naoko Nagatsuka
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Yukihiko Onuma
- The University of Tokyo, Institute of Industrial Science, Institute of Industrial Science, 4-6-1 Komaba, Meguro, Tokyo, 153-8505 Japan
| | - Nozomu Takeuchi
- Chiba University, Department of Earth Science, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba, 263-8522 Japan
| | - Hideaki Motoyama
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan
| | - Teruo Aoki
- National Institute of Polar Research, 10-3 Midoricho, Tachikawa, Tokyo, 190-8518 Japan.,Okayama University, Department of Earth Science, Department of Earth Science, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530 Japan
| |
Collapse
|
30
|
Edwards A, Cameron KA, Cook JM, Debbonaire AR, Furness E, Hay MC, Rassner SM. Microbial genomics amidst the Arctic crisis. Microb Genom 2020; 6:e000375. [PMID: 32392124 PMCID: PMC7371112 DOI: 10.1099/mgen.0.000375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.
Collapse
Affiliation(s)
- Arwyn Edwards
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Karen A. Cameron
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Joseph M. Cook
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Aliyah R. Debbonaire
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Eleanor Furness
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Melanie C. Hay
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| | - Sara M.E. Rassner
- Interdisciplinary Centre for Environmental Microbiology, Institute of Biological, Environmental and Rural Sciences, Cledwyn Building, Aberystwyth University, Cymru SY23 3DD, UK
| |
Collapse
|
31
|
Investigating Algal Communities in Lacustrine and Hydro-Terrestrial Environments of East Antarctica Using Deep Amplicon Sequencing. Microorganisms 2020; 8:microorganisms8040497. [PMID: 32244517 PMCID: PMC7232531 DOI: 10.3390/microorganisms8040497] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/24/2022] Open
Abstract
Antarctica has one of the most extreme environments on Earth, with low temperatures and low nutrient levels. Antarctica’s organisms live primarily in the coastal, ice-free areas which cover approximately 0.18% of the continent’s surface. Members of Cyanobacteria and eukaryotic algae are important primary producers in Antarctica since they can synthesize organic compounds from carbon dioxide and water using solar energy. However, community structures of photosynthetic algae in Antarctica have not yet been fully explored at molecular level. In this study, we collected diverse algal samples in lacustrine and hydro-terrestrial environments of Langhovde and Skarvsnes, which are two ice-free regions in East Antarctica. We performed deep amplicon sequencing of both 16S ribosomal ribonucleic acid (rRNA) and 18S rRNA genes, and we explored the distribution of sequence variants (SVs) of these genes at single nucleotide difference resolution. SVs of filamentous Cyanobacteria genera, including Leptolyngbya, Pseudanabaena, Phormidium, Nodosilinea, Geitlerinama, and Tychonema, were identified in most of the samples, whereas Phormidesmis SVs were distributed in fewer samples. We also detected unicellular, multicellular or heterocyst forming Cyanobacteria strains, but in relatively small abundance. For SVs of eukaryotic algae, Chlorophyta, Cryptophyta, and Ochrophyta were widely distributed among the collected samples. In addition, there was a red colored bloom of eukaryotic alga, Geminigera cryophile (Cryptophyta), in the Langhovde coastal area. Eukaryotic SVs of Acutuncus antarcticus and/or Diphascon pingue of Tardigrada were dominant among most of the samples. Our data revealed the detailed structures of the algal communities in Langhovde and Skarvsnes. This will contribute to our understanding of Antarctic ecosystems and support further research into this subject.
Collapse
|
32
|
Sánchez-Baracaldo P, Cardona T. On the origin of oxygenic photosynthesis and Cyanobacteria. THE NEW PHYTOLOGIST 2020; 225:1440-1446. [PMID: 31598981 DOI: 10.1111/nph.16249] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/25/2019] [Indexed: 05/14/2023]
Abstract
Oxygenic phototrophs have played a fundamental role in Earth's history by enabling the rise of atmospheric oxygen (O2 ) and paving the way for animal evolution. Understanding the origins of oxygenic photosynthesis and Cyanobacteria is key when piecing together the events around Earth's oxygenation. It is likely that photosynthesis evolved within bacterial lineages that are not extant, so it can be challenging when studying the early history of photosynthesis. Recent genomic and molecular evolution studies have transformed our understanding about the evolution of photosynthetic reaction centres and the evolution of Cyanobacteria. The evidence reviewed here highlights some of the most recent advances on the origin of photosynthesis both at the genomic and gene family levels.
Collapse
Affiliation(s)
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
33
|
Sharma Ghimire P, Tripathee L, Zhang Q, Guo J, Ram K, Huang J, Sharma CM, Kang S. Microbial mercury methylation in the cryosphere: Progress and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 697:134150. [PMID: 32380618 DOI: 10.1016/j.scitotenv.2019.134150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 06/11/2023]
Abstract
Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.
Collapse
Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal
| | - Lekhendra Tripathee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; Himalayan Environment Research Institute (HERI), Kathmandu, Nepal.
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China
| | - Junming Guo
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China
| | - Kirpa Ram
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Jie Huang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China; Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Chhatra Mani Sharma
- Himalayan Environment Research Institute (HERI), Kathmandu, Nepal; Central Department of Environmental Science, Tribhuvan University, Kathmandu, Nepal
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou 730000, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing 100085, China.
| |
Collapse
|
34
|
Conservation Genomics in a Changing Arctic. Trends Ecol Evol 2019; 35:149-162. [PMID: 31699414 DOI: 10.1016/j.tree.2019.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
Abstract
Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.
Collapse
|
35
|
Chrismas NAM, Williamson CJ, Yallop ML, Anesio AM, Sánchez-Baracaldo P. Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology. Mol Ecol 2019; 27:5279-5293. [PMID: 30565777 DOI: 10.1111/mec.14953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are important photoautotrophs in extreme environments such as the McMurdo Dry Valleys, Antarctica. Terrestrial Antarctic cyanobacteria experience constant darkness during the winter and constant light during the summer which influences the ability of these organisms to fix carbon over the course of an annual cycle. Here, we present a unique approach combining community structure, genomic and photophysiological analyses to understand adaptation to Antarctic light regimes in the cyanobacterium Leptolyngbya sp. BC1307. We show that Leptolyngbya sp. BC1307 belongs to a clade of cyanobacteria that inhabits near-surface environments in the McMurdo Dry Valleys. Genomic analyses reveal that, unlike close relatives, Leptolyngbya sp. BC1307 lacks the genes necessary for production of the pigment phycoerythrin and is incapable of complimentary chromatic acclimation, while containing several genes responsible for known photoprotective pigments. Photophysiology experiments confirmed Leptolyngbya sp. BC1307 to be tolerant of short-term exposure to high levels of photosynthetically active radiation, while sustained exposure reduced its capacity for photoprotection. As such, Leptolyngbya sp. BC1307 likely exploits low-light microenvironments within cyanobacterial mats in the McMurdo Dry Valleys.
Collapse
Affiliation(s)
- Nathan A M Chrismas
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Christopher J Williamson
- School of Geographical Sciences, University of Bristol, Bristol, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Marian L Yallop
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, University of Bristol, Bristol, UK.,Department of Environmental Sciences, Aarhus University, Roskilde, Denmark
| | | |
Collapse
|
36
|
Urrejola C, Alcorta J, Salas L, Vásquez M, Polz MF, Vicuña R, Díez B. Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054. Front Microbiol 2019; 10:950. [PMID: 31134010 PMCID: PMC6513891 DOI: 10.3389/fmicb.2019.00950] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 04/15/2019] [Indexed: 01/06/2023] Open
Abstract
For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.
Collapse
Affiliation(s)
- Catalina Urrejola
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jaime Alcorta
- Laboratorio de Ecología Microbiana de Sistemas Extremos, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto Salas
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mónica Vásquez
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rafael Vicuña
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Laboratorio de Ecología Microbiana de Sistemas Extremos, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
37
|
Parrilli E, Tedesco P, Fondi M, Tutino ML, Lo Giudice A, de Pascale D, Fani R. The art of adapting to extreme environments: The model system Pseudoalteromonas. Phys Life Rev 2019; 36:137-161. [PMID: 31072789 DOI: 10.1016/j.plrev.2019.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/10/2023]
Abstract
Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications. Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures. In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
Collapse
Affiliation(s)
- Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Pietro Tedesco
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077 Toulouse, France
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126 Napoli, Italy
| | | | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Napoli, Italy, Stazione Zoologica "Anthon Dorn", Villa Comunale, I-80121 Napoli, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, ViaMadonna del Piano 6, 50019 Sesto Fiorentino, FI, Italy.
| |
Collapse
|
38
|
Blanco Y, Rivas LA, González-Toril E, Ruiz-Bermejo M, Moreno-Paz M, Parro V, Palacín A, Aguilera Á, Puente-Sánchez F. Environmental parameters, and not phylogeny, determine the composition of extracellular polymeric substances in microbial mats from extreme environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:384-393. [PMID: 30199683 DOI: 10.1016/j.scitotenv.2018.08.440] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
The ability to establish biofilms is a key trait for microorganisms growing in extreme environments. The extracellular polymeric substances (EPS) present in biofilms provide not only surface attachment, but also protection against all kinds of environmental stressors, including desiccation, salinity, temperature or heavy metal pollution. The acquisition of suitable biofilm characteristics might thus be an important process mediating the adaptation of microorganisms to novel environmental conditions. In this work we have characterized the EPS of 20 phylogenetically diverse biofilms collected in situ from five contrasting extreme environments, including two geothermal areas (Copahue, Argentina; Seltun, Iceland), two cold areas (Pastoruri glacier, Peru; Byers Peninsula, Antarctica) and one extremely acidic river (Río Tinto, Spain). Biofilms were subjected to biochemical characterization, glycan profiling and immunoprofiling with an antibody microarray. Our results showed that environmental conditions strongly influence biofilm characteristics, with microorganisms from the same environment achieving similar EPS compositions regardless of the phylogeny of their main species. The concentration of some monosaccharides in the EPS could be related to environmental conditions such as temperature or heavy metal toxicity, suggesting that in some cases stress resistance can be mediated by specific sugars. Overall, our results highlight the existence of conserved EPS compositional patterns for each extreme environment, which could in turn be exploited to engineer ecological adaptations in genetically modified microorganisms.
Collapse
Affiliation(s)
- Yolanda Blanco
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Luis Alfonso Rivas
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Elena González-Toril
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Marta Ruiz-Bermejo
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Mercedes Moreno-Paz
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Víctor Parro
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Arantxa Palacín
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ángeles Aguilera
- Centro de Astrobiología (INTA-CSIC), Instituto Nacional de Técnica Aeroespacial, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología, C/Darwin n° 3, Campus de Cantoblanco, 28049 Madrid, Spain.
| |
Collapse
|
39
|
Extremophilic exopolysaccharides: A review and new perspectives on engineering strategies and applications. Carbohydr Polym 2019; 205:8-26. [DOI: 10.1016/j.carbpol.2018.10.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022]
|
40
|
Sánchez-Baracaldo P, Bianchini G, Di Cesare A, Callieri C, Chrismas NAM. Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes ( mpeBA and cpeBA). Front Microbiol 2019; 10:45. [PMID: 30761097 PMCID: PMC6363710 DOI: 10.3389/fmicb.2019.00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/11/2019] [Indexed: 11/13/2022] Open
Abstract
Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.
Collapse
Affiliation(s)
| | - Giorgio Bianchini
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrea Di Cesare
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
- Department of Earth, Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Cristiana Callieri
- Institute of Ecosystem Study–Consiglio Nazionale delle Ricerche, Verbania, Italy
| | - Nathan A. M. Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, United Kingdom
- The Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| |
Collapse
|
41
|
Tang J, Du LM, Liang YM, Daroch M. Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat. Int J Mol Sci 2019; 20:E152. [PMID: 30609821 PMCID: PMC6337551 DOI: 10.3390/ijms20010152] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022] Open
Abstract
Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.
Collapse
Affiliation(s)
- Jie Tang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
- Shenzhen Aone Medical Laboratory Co Ltd, Shenzhen 518107, China.
| | - Lian-Ming Du
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China.
| | - Yuan-Mei Liang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| |
Collapse
|
42
|
Pessi IS, Pushkareva E, Lara Y, Borderie F, Wilmotte A, Elster J. Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic. MICROBIAL ECOLOGY 2019; 77:136-147. [PMID: 29796758 DOI: 10.1007/s00248-018-1203-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.
Collapse
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.
- Department of Microbiology, University of Helsinki, P.O. Box 56 (Viikinkaari 9), 00014, Helsinki, Finland.
| | - Ekaterina Pushkareva
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
| | - Yannick Lara
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- UR Geology - Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Allée du Six Août14, B18, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Fabien Borderie
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
- Laboratoire Chrono-environnement, UMR 6249 CNRS Université Bourgogne Franche-Comté UsC INRA, Campus La Bouloie, Route de Gray 16, 25030, Besançon, France
| | - Annick Wilmotte
- InBioS - Centre for Protein Engineering, University of Liège, Allée du Six Août 13, B6a, Quartier Agora, Sart-Tilman, 4000, Liège, Belgium
| | - Josef Elster
- Centre for Polar Ecology, University of South Bohemia, Na Zlaté Stoce 3, 37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 37982, Třeboň, Czech Republic
| |
Collapse
|
43
|
Di Cesare A, Cabello-Yeves PJ, Chrismas NAM, Sánchez-Baracaldo P, Salcher MM, Callieri C. Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization. BMC Genomics 2018; 19:259. [PMID: 29661139 PMCID: PMC5902973 DOI: 10.1186/s12864-018-4648-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus. sp. nov., isolated from the volcanic Lake Albano (Central Italy). RESULTS The novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium. CONCLUSIONS In this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.
Collapse
Affiliation(s)
- Andrea Di Cesare
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.,Department of Earth, Environmental, and Life Sciences, University of Genoa, 16132, Genoa, Italy
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Nathan A M Chrismas
- School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS, UK.,Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK
| | | | - Michaela M Salcher
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cristiana Callieri
- National Research Council CNR-ISE, Largo Tonolli 50, 28922, Verbania, Italy.
| |
Collapse
|
44
|
Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. The future of genomics in polar and alpine cyanobacteria. FEMS Microbiol Ecol 2018; 94:4904125. [PMID: 29506259 PMCID: PMC5939894 DOI: 10.1093/femsec/fiy032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/23/2018] [Indexed: 01/01/2023] Open
Abstract
In recent years, genomic analyses have arisen as an exciting way of investigating the functional capacity and environmental adaptations of numerous micro-organisms of global relevance, including cyanobacteria. In the extreme cold of Arctic, Antarctic and alpine environments, cyanobacteria are of fundamental ecological importance as primary producers and ecosystem engineers. While their role in biogeochemical cycles is well appreciated, little is known about the genomic makeup of polar and alpine cyanobacteria. In this article, we present ways that genomic techniques might be used to further our understanding of cyanobacteria in cold environments in terms of their evolution and ecology. Existing examples from other environments (e.g. marine/hot springs) are used to discuss how methods developed there might be used to investigate specific questions in the cryosphere. Phylogenomics, comparative genomics and population genomics are identified as methods for understanding the evolution and biogeography of polar and alpine cyanobacteria. Transcriptomics will allow us to investigate gene expression under extreme environmental conditions, and metagenomics can be used to complement tradition amplicon-based methods of community profiling. Finally, new techniques such as single cell genomics and metagenome assembled genomes will also help to expand our understanding of polar and alpine cyanobacteria that cannot readily be cultured.
Collapse
Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| | - Patricia Sánchez-Baracaldo
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| |
Collapse
|
45
|
Temraleeva AD. Cyanobacterial Diversity in the Soils of Russian Dry Steppes and Semideserts. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
46
|
Hoffman PF, Abbot DS, Ashkenazy Y, Benn DI, Brocks JJ, Cohen PA, Cox GM, Creveling JR, Donnadieu Y, Erwin DH, Fairchild IJ, Ferreira D, Goodman JC, Halverson GP, Jansen MF, Le Hir G, Love GD, Macdonald FA, Maloof AC, Partin CA, Ramstein G, Rose BEJ, Rose CV, Sadler PM, Tziperman E, Voigt A, Warren SG. Snowball Earth climate dynamics and Cryogenian geology-geobiology. SCIENCE ADVANCES 2017; 3:e1600983. [PMID: 29134193 PMCID: PMC5677351 DOI: 10.1126/sciadv.1600983] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/21/2017] [Indexed: 05/02/2023]
Abstract
Geological evidence indicates that grounded ice sheets reached sea level at all latitudes during two long-lived Cryogenian (58 and ≥5 My) glaciations. Combined uranium-lead and rhenium-osmium dating suggests that the older (Sturtian) glacial onset and both terminations were globally synchronous. Geochemical data imply that CO2 was 102 PAL (present atmospheric level) at the younger termination, consistent with a global ice cover. Sturtian glaciation followed breakup of a tropical supercontinent, and its onset coincided with the equatorial emplacement of a large igneous province. Modeling shows that the small thermal inertia of a globally frozen surface reverses the annual mean tropical atmospheric circulation, producing an equatorial desert and net snow and frost accumulation elsewhere. Oceanic ice thickens, forming a sea glacier that flows gravitationally toward the equator, sustained by the hydrologic cycle and by basal freezing and melting. Tropical ice sheets flow faster as CO2 rises but lose mass and become sensitive to orbital changes. Equatorial dust accumulation engenders supraglacial oligotrophic meltwater ecosystems, favorable for cyanobacteria and certain eukaryotes. Meltwater flushing through cracks enables organic burial and submarine deposition of airborne volcanic ash. The subglacial ocean is turbulent and well mixed, in response to geothermal heating and heat loss through the ice cover, increasing with latitude. Terminal carbonate deposits, unique to Cryogenian glaciations, are products of intense weathering and ocean stratification. Whole-ocean warming and collapsing peripheral bulges allow marine coastal flooding to continue long after ice-sheet disappearance. The evolutionary legacy of Snowball Earth is perceptible in fossils and living organisms.
Collapse
Affiliation(s)
- Paul F. Hoffman
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
- School of Earth and Ocean Sciences, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Dorian S. Abbot
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Yosef Ashkenazy
- Department of Solar Energy and Environmental Physics, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Douglas I. Benn
- School of Geography and Sustainable Development, University of St Andrews, St Andrews, Fife KY16 8YA, UK
| | - Jochen J. Brocks
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | | | - Grant M. Cox
- Centre for Tectonics, Resources and Exploration (TRaX), Department of Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Department of Applied Geology, Curtin University, Bentley, Western Australia 6845, Australia
| | - Jessica R. Creveling
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331–5503, USA
| | - Yannick Donnadieu
- Laboratoire des Sciences du Climat et de l’Environnement (LSCE), Institut Pierre Simon Laplace (IPSL), CEA-CNRS-UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- Aix-Marseille Université, CNRS, L’Institut de recherche pour le développement (IRD), Centre Européen de Recherche et D’enseignement de Géosciences de L’environnement (CEREGE), 13545 Aix-en-Provence, France
| | - Douglas H. Erwin
- Department of Paleobiology, Smithsonian Institution, P.O. Box 37012, MRC 121, Washington, DC 20013–7012, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Ian J. Fairchild
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David Ferreira
- Department of Meteorology, University of Reading, Reading, RG6 6BB, UK
| | - Jason C. Goodman
- Department of Environmental Science, Wheaton College, Norton, MA 02766, USA
| | - Galen P. Halverson
- Department of Earth and Planetary Sciences, McGill University, Montréal, Québec H3A 0E8, Canada
| | - Malte F. Jansen
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Guillaume Le Hir
- Institut de Physique du Globe de Paris, 1, rue Jussieu, 75005 Paris, France
| | - Gordon D. Love
- Department of Earth Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Francis A. Macdonald
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Adam C. Maloof
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Camille A. Partin
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Gilles Ramstein
- Laboratoire des Sciences du Climat et de l’Environnement (LSCE), Institut Pierre Simon Laplace (IPSL), CEA-CNRS-UVSQ, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Brian E. J. Rose
- Department of Atmospheric and Environmental Sciences, University at Albany, Albany, NY 12222, USA
| | | | - Peter M. Sadler
- Department of Earth Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Eli Tziperman
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Aiko Voigt
- Institute of Meteorology and Climate Research, Department of Troposphere Research, Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
- Lamont-Doherty Earth Observatory, Columbia University, P.O. Box 1000, Palisades, NY 10964–1000, USA
| | - Stephen G. Warren
- Department of Atmospheric Sciences, University of Washington, Seattle, WA 98195–1640, USA
| |
Collapse
|
47
|
Santander RD, Biosca EG. Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures. PeerJ 2017; 5:e3931. [PMID: 29085749 PMCID: PMC5660878 DOI: 10.7717/peerj.3931] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022] Open
Abstract
The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent at 4 °C). This work reveals E. amylovora as a highly adaptable pathogen that retains its pathogenic potential even at the minimal growth temperatures, with an improved exopolysaccharide synthesis, biofilm formation or oxidative stress resistance at 14 °C, with respect to the optimal growth temperature (28 °C). Finally, our results also demonstrate the thermal modulation of starvation responses in E. amylovora, suggesting that the starvation-survival and the VBNC states are part of its life cycle. These results confirm the particular psychrotrophic adaptations of E. amylovora, revealing its pathogenic potential and survival at temperate and low environmental temperatures, which have probably contributed to its successful spread to countries with different climates. This knowledge might improve integrated control measures against fire blight.
Collapse
Affiliation(s)
- Ricardo D. Santander
- Department of Microbiology and Ecology, Universitat de València, Burjassot, Spain
| | - Elena G. Biosca
- Department of Microbiology and Ecology, Universitat de València, Burjassot, Spain
| |
Collapse
|
48
|
Raven JA, Beardall J, Sánchez-Baracaldo P. The possible evolution and future of CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3701-3716. [PMID: 28505361 DOI: 10.1093/jxb/erx110] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
CO2-concentrating mechanisms (CCMs), based either on active transport of inorganic carbon (biophysical CCMs) or on biochemistry involving supplementary carbon fixation into C4 acids (C4 and CAM), play a major role in global primary productivity. However, the ubiquitous CO2-fixing enzyme in autotrophs, Rubisco, evolved at a time when atmospheric CO2 levels were very much higher than today and O2 was very low and, as CO2 and O2 approached (by no means monotonically), today's levels, at some time subsequently many organisms evolved a CCM that increased the supply of CO2 and decreased Rubisco oxygenase activity. Given that CO2 levels and other environmental factors have altered considerably between when autotrophs evolved and the present day, and are predicted to continue to change into the future, we here examine the drivers for, and possible timing of, evolution of CCMs. CCMs probably evolved when CO2 fell to 2-16 times the present atmospheric level, depending on Rubisco kinetics. We also assess the effects of other key environmental factors such as temperature and nutrient levels on CCM activity and examine the evidence for evolutionary changes in CCM activity and related cellular processes as well as limitations on continuity of CCMs through environmental variations.
Collapse
Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Functional Plant Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - John Beardall
- School of Biological Sciences, Monash University, Building 18, Clayton Campus, Vic 3800, Australia
| | | |
Collapse
|
49
|
Anesio AM, Lutz S, Chrismas NAM, Benning LG. The microbiome of glaciers and ice sheets. NPJ Biofilms Microbiomes 2017; 3:10. [PMID: 28649411 PMCID: PMC5460203 DOI: 10.1038/s41522-017-0019-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 01/09/2023] Open
Abstract
Glaciers and ice sheets, like other biomes, occupy a significant area of the planet and harbour biological communities with distinct interactions and feedbacks with their physical and chemical environment. In the case of the glacial biome, the biological processes are dominated almost exclusively by microbial communities. Habitats on glaciers and ice sheets with enough liquid water to sustain microbial activity include snow, surface ice, cryoconite holes, englacial systems and the interface between ice and overridden rock/soil. There is a remarkable similarity between the different specific glacial habitats across glaciers and ice sheets worldwide, particularly regarding their main primary producers and ecosystem engineers. At the surface, cyanobacteria dominate the carbon production in aquatic/sediment systems such as cryoconite holes, while eukaryotic Zygnematales and Chlamydomonadales dominate ice surfaces and snow dynamics, respectively. Microbially driven chemolithotrophic processes associated with sulphur and iron cycle and C transformations in subglacial ecosystems provide the basis for chemical transformations at the rock interface under the ice that underpin an important mechanism for the delivery of nutrients to downstream ecosystems. In this review, we focus on the main ecosystem engineers of glaciers and ice sheets and how they interact with their chemical and physical environment. We then discuss the implications of this microbial activity on the icy microbiome to the biogeochemistry of downstream ecosystems.
Collapse
Affiliation(s)
- Alexandre M. Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS UK
| | - Stefanie Lutz
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
| | - Nathan A. M. Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, Bristol, BS8 1SS UK
| | - Liane G. Benning
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
- Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany
| |
Collapse
|
50
|
Cameron KA, Stibal M, Chrismas N, Box J, Jacobsen CS. Nitrate addition has minimal short-term impacts on greenland ice sheet supraglacial prokaryotes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:144-150. [PMID: 27943630 DOI: 10.1111/1758-2229.12510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Tropospheric nitrate levels are predicted to increase throughout the 21st century, with potential effects on terrestrial ecosystems, including the Greenland ice sheet (GrIS). This study considers the impacts of elevated nitrate concentrations on the abundance and composition of dominant bulk and active prokaryotic communities sampled from in situ nitrate fertilization plots on the GrIS surface. Nitrate concentrations were successfully elevated within sediment-filled meltwater pools, known as cryoconite holes; however, nitrate additions applied to surface ice did not persist. Estimated bulk and active cryoconite community cell abundance was unaltered by nitrate additions when compared to control holes using a quantitative PCR approach, and nitrate was found to have a minimal affect on the dominant 16S rRNA gene-based community composition. Together, these results indicate that sampled cryoconite communities were not nitrate limited at the time of sampling. Instead, temporal changes in biomass and community composition were more pronounced. As these in situ incubations were short (6 weeks), and the community composition across GrIS surface ice is highly variable, we suggest that further efforts should be considered to investigate the potential long-term impacts of increased nitrate across the GrIS.
Collapse
Affiliation(s)
- Karen A Cameron
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FL, UK
| | - Marek Stibal
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
- Department of Ecology Faculty of Science, Charles University, Viničná 7, Prague, 128 43, Czech Republic
| | - Nathan Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
| | - Jason Box
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, Copenhagen, DK-1350, Denmark
| | - Carsten S Jacobsen
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, DK-1350, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, DK-4000, Denmark
| |
Collapse
|